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WO2014081730A1 - Mutations dans des solanacées modulant l'architecture de la pousse et améliorant les phénotypes associés au rendement - Google Patents

Mutations dans des solanacées modulant l'architecture de la pousse et améliorant les phénotypes associés au rendement Download PDF

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Publication number
WO2014081730A1
WO2014081730A1 PCT/US2013/070825 US2013070825W WO2014081730A1 WO 2014081730 A1 WO2014081730 A1 WO 2014081730A1 US 2013070825 W US2013070825 W US 2013070825W WO 2014081730 A1 WO2014081730 A1 WO 2014081730A1
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Prior art keywords
mutant
altered
genetically
gene
seq
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English (en)
Inventor
Zachary Lippman
Soon-Ju PARK
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Cold Spring Harbor Laboratory
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Cold Spring Harbor Laboratory
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Priority claimed from US13/799,831 external-priority patent/US9732352B2/en
Application filed by Cold Spring Harbor Laboratory filed Critical Cold Spring Harbor Laboratory
Priority to CA2892012A priority Critical patent/CA2892012A1/fr
Priority to US14/443,357 priority patent/US11624074B2/en
Priority to EP13857579.0A priority patent/EP2922960A4/fr
Publication of WO2014081730A1 publication Critical patent/WO2014081730A1/fr
Anticipated expiration legal-status Critical
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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/63—Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
    • C12N15/79—Vectors or expression systems specially adapted for eukaryotic hosts
    • C12N15/82—Vectors or expression systems specially adapted for eukaryotic hosts for plant cells, e.g. plant artificial chromosomes (PACs)
    • C12N15/8241—Phenotypically and genetically modified plants via recombinant DNA technology
    • C12N15/8261—Phenotypically and genetically modified plants via recombinant DNA technology with agronomic (input) traits, e.g. crop yield
    • C12N15/8262—Phenotypically and genetically modified plants via recombinant DNA technology with agronomic (input) traits, e.g. crop yield involving plant development
    • C12N15/827—Flower development or morphology, e.g. flowering promoting factor [FPF]
    • A—HUMAN NECESSITIES
    • A01—AGRICULTURE; FORESTRY; ANIMAL HUSBANDRY; HUNTING; TRAPPING; FISHING
    • A01H—NEW PLANTS OR NON-TRANSGENIC PROCESSES FOR OBTAINING THEM; PLANT REPRODUCTION BY TISSUE CULTURE TECHNIQUES
    • A01H5/00—Angiosperms, i.e. flowering plants, characterised by their plant parts; Angiosperms characterised otherwise than by their botanic taxonomy
    • A01H5/08—Fruits
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/415—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from plants

Definitions

  • Solanaceae plants e.g., tomato plants, that (a) exhibit modified flowering time and shoot architecture; (b) exhibit higher yield, higher quality products (e.g., fruits); (c) produce products (e.g., fruits) with different compositions, (e.g., brix, also known as enhanced soluble solids or sugar concentration in the fruits,); or (d) any combination of (a) to (c), compared to corresponding "wild-type (WT)" 0 Solanaceae plants (Solanaceae plants that have not been genetically altered).
  • WT wild-type
  • a genetically- altered plant such as a genetically-altered semi- determinate or semi-indeterminate Solanaceae plant, comprises a mutant suppressor ofspl (sspl) gene and a mutant single flower truss (sft) gene.
  • sspl suppressor ofspl
  • sft single flower truss
  • Such Solanaceae plants are heterozygous or homozygous for mutant genes (e.g., heterozygous or homozygous for a mutant suppressor ofspl (sspl) gene or heterozygous or homozygous for a mutant single flower truss (sft) gene) or heterozygous or homozygous for both a mutant suppressor ofspl (sspl) gene and a mutant single flower truss (sft) gene (double heterozygotes or double homozygotes).
  • Such plants may further comprise a mutant self pruning (sp) gene.
  • Such plants may be heterozygous or homozygous for a mutant self pruning (sp) gene.
  • Such plants can also be in the wild type SELF PRUNING (SP) background.
  • Solanaceae plants comprise a mutant self pruning (sp) gene and a mutant single flower truss (sft) gene.
  • Such Solanaceae plants are heterozygous or homozygous for mutant genes (e.g., for a mutant self pruning (sp) gene or for a mutant single flower truss (sft) gene) or heterozygous or homozygous for both a mutant self pruning (sp) gene and a mutant single flower truss (sft) gene (double heterozygotes or double
  • Solanaceae plants comprise a mutant self pruning (sp) gene and a mutant suppressor ofspl (sspl) gene.
  • Such Solanaceae plants are heterozygous or homozygous for mutant genes (e.g., for a mutant self pruning (sp) gene or for a mutant suppressor ofspl (sspl) gene) or heterozygous or homozygous for both a mutant self pruning (sp) gene and a mutant suppressor ofspl (sspl) gene (double heterozygotes or double homozygotes).
  • Solanaceae plants comprise a mutant suppressor ofspl (sspl) gene or a mutant single flower truss (sft) gene. Such Solanaceae plants are
  • Such plants may further comprise a mutant self pruning (sp) gene.
  • Such plants may be heterozygous or homozygous for a mutant self pruning (sp) gene.
  • Such plants can also be in the wild type SELF PRUNING (SP) background.
  • the mutant sspl gene comprises a nucleic acid sequence that encodes a mutant sspl protein that comprises a mutant SAP motif. In some embodiments, the mutant sspl gene comprises a nucleic acid sequence that encodes a mutant sspl protein that comprises a mutant SAP motif with a sequence of SEQ ID NO: 14 or SEQ ID NO: 15. In some embodiments, the mutant sspl gene encodes a mutant sspl polypeptide comprising the sequence of SEQ ID NO: 5 or SEQ ID NO: 6.
  • the mutant sspl gene comprises a C to T mutation at position 641 of SEQ ID NO: 1, a C to T mutation at position 647 of SEQ ID NO: 1, or a C to T mutation at position 641 and 647 of SEQ ID NO: 1.
  • the mutant sspl gene comprises a coding sequence that comprises the nucleic acid sequence of SEQ ID NO: 2 or SEQ ID NO: 3.
  • the mutant sspl gene comprises the nucleic acid sequence of SEQ ID NO: 2 or SEQ ID NO: 3.
  • the mutant sspl gene comprises the nucleic acid sequence of SEQ ID NO: 25 or SEQ ID NO: 26.
  • the mutant sspl gene is ssp-2129 or ssp- 610. In some embodiments, the mutant sp gene comprises a coding sequence that comprises the nucleic acid sequence of SEQ ID NO: 8. In some embodiments, the mutant sp gene comprises the nucleic acid sequence of SEQ ID NO: 8. In some embodiments, the mutant sp gene comprises the nucleic acid sequence of SEQ ID NO: 23. In some embodiments, the mutant sp gene comprises a nucleic acid that encodes the amino acid sequence of mutant sp protein (e.g., SEQ ID NO: 10).
  • SEQ ID NO: 2 is the nucleotide sequence of the coding sequence of ssp-2129
  • a mutant allele of SSPL SEQ ID NO: 3 is the nucleotide sequence of the coding sequence of ssp-610
  • a mutant allele of SSPL SEQ ID NO: 5 is the amino acid sequence of ssp-2129 mutant protein.
  • SEQ ID NO: 6 is the amino acid sequence of ssp-610 mutant protein.
  • the mutant sft gene comprises a coding sequence that comprises the nucleic acid sequence of SEQ ID NO: 20.
  • the mutant sft gene comprises SEQ ID NO: 20.
  • the mutant sft gene comprises the nucleic acid sequence of SEQ ID NO: 17. In some embodiments, the mutant sft gene encodes a mutant sft polypeptide comprising the sequence of SEQ ID NO: 21. In some embodiments, the mutant sft gene comprises a nucleotide sequence that encodes a mutant sft polypeptide comprising a Val to Met mutation at position 132 of SEQ ID NO: 19. In some embodiments, the mutant sft gene is sft-1906.
  • the genetically- altered Solanaceae plant is a genetically altered semi-determinate or semi-indeterminate Solanaceae plant, such as a tomato (Solanum lycopersicum) plant.
  • the genetically-altered semi-determinate or semi-indeterminate Solanaceae plant is isogenic.
  • the genetically- altered semi-determinate or semi-indeterminate Solanaceae plant is inbred.
  • the genetically- altered semi-determinate or semi-indeterminate Solanaceae plant is a hybrid.
  • the disclosure relates to a seed for producing a genetically- altered Solanaceae plant, such as a semi-determinate or semi-indeterminate genetically- altered Solanaceae plant, as described herein, e.g., a genetically- altered semi-determinate or semi- indeterminate Solanaceae plant comprising (e.g., heterozygous or homozygous for) a mutant single flower truss (sfl) gene and a mutant suppressor ofspl (sspl) gene, a genetically- altered semi-determinate or semi-indeterminate Solanaceae plant comprising (e.g., heterozygous or homozygous for) a mutant single flower truss (sfl) gene and a mutant self pruning (sp) gene, a genetically-altered semi-determinate or semi-indeterminate Solanaceae plant comprising (e.g., heterozygous or homozygous for) a mutant suppressor ofsp
  • the mutant sspl gene comprises a nucleic acid sequence that encodes a mutant sspl protein that comprises a mutant SAP motif. In some embodiments, the mutant sspl gene comprises a nucleic acid sequence that encodes a mutant sspl protein that comprises a mutant SAP motif comprising SEQ ID NO: 14 or SEQ ID NO: 15. In some embodiments, the mutant sspl gene encodes a mutant sspl polypeptide comprising the sequence of SEQ ID NO: 5 or SEQ ID NO: 6.
  • the mutant sspl gene comprises a C to T mutation at position 641 of SEQ ID NO: 1, a C to T mutation at position 647 of SEQ ID NO: 1, or a C to T mutation at position 641 and 647 of SEQ ID NO: 1.
  • the mutant sspl gene comprises a coding sequence that comprises the nucleic acid sequence of SEQ ID NO: 2 or SEQ ID NO: 3.
  • the mutant sspl gene comprises the nucleic acid sequence of SEQ ID NO: 2 or SEQ ID NO: 3.
  • the mutant sspl gene comprises the nucleic acid sequence of SEQ ID NO: 25 or SEQ ID NO: 26.
  • the mutant sp gene comprises a coding sequence that comprises the nucleic acid sequence of SEQ ID NO: 8.
  • the mutant sp gene comprises the nucleic acid sequence of SEQ ID NO: 8. In some embodiments,
  • the mutant sp gene comprises the nucleic acid sequence of SEQ ID NO: 23. In some embodiments, the mutant sp gene comprises a nucleic acid that encodes the amino acid sequence of mutant sp protein (e.g., SEQ ID NO: 10).
  • the disclosure relates to methods of producing a genetically- altered Solanaceae plant, such as a semi-determinate or semi-indeterminate Solanaceae plant.
  • the method comprises:
  • (b) self-crossing the genetically- altered Solanaceae plant produced in (a) or crossing two genetically- altered Solanaceae plants produced in (a) under conditions appropriate for producing a genetically-altered Solanaceae plant heterozygous or homozygous for the mutant sft gene and heterozygous or homozygous for the mutant sspl gene.
  • the plant produced in (b) is heterozygous for the mutant sft gene and heterozygous for the mutant sspl gene.
  • the plant produced in (b) further comprises a mutant sp gene (e.g., is heterozygous or homozygous for a mutant sp gene).
  • the method of producing a genetically-altered Solanaceae plant comprises:
  • the plant produced in (c) is heterozygous for the mutant sft gene and heterozygous for the mutant sspl gene. In some embodiments, the plant produced in (c) further comprises a mutant sp gene (e.g., is heterozygous or homozygous for a mutant sp gene).
  • the mutant sspl gene comprises a nucleic acid sequence that 5 encodes a mutant sspl protein that comprises a mutant SAP motif. In some embodiments, the mutant sspl gene comprises a nucleic acid sequence that encodes a mutant sspl protein that comprises a mutant SAP motif with a sequence of SEQ ID NO: 14 or SEQ ID NO: 15. In some embodiments, the mutant sspl gene encodes a mutant sspl polypeptide comprising the sequence of SEQ ID NO: 5 or SEQ ID NO: 6.
  • the mutant sspl o gene comprises a C to T mutation at position 641 of SEQ ID NO: 1, a C to T mutation at position 647 of SEQ ID NO: 1, or a C to T mutation at position 641 and 647 of SEQ ID NO: 1.
  • the mutant sspl gene comprises a coding sequence that comprises the nucleic acid sequence of SEQ ID NO: 2 or SEQ ID NO: 3.
  • the mutant sspl gene comprises the nucleic acid sequence of SEQ ID NO: 2 or SEQ ID NO: 3.5
  • the mutant sspl gene comprises the nucleic acid sequence of SEQ ID NO: 25 or SEQ ID NO: 26.
  • the mutant sp gene comprises a coding sequence that comprises the nucleic acid sequence of SEQ ID NO: 8. In some embodiments, the mutant sp gene comprises the nucleic acid sequence of SEQ ID NO: 8. In some embodiments, the mutant sp gene comprises the nucleic acid sequence of SEQ ID NO: 23. In o some embodiments, the mutant sp gene comprises a nucleic acid that encodes the amino acid sequence of mutant sp protein (e.g., SEQ ID NO: 10). In some embodiments, the mutant sft gene comprises a coding sequence that comprises SEQ ID NO: 20. In some embodiments, the mutant sft gene comprises SEQ ID NO: 20. In some embodiments, the mutant sft gene comprises SEQ ID NO: 17. In some embodiments, the mutant sft gene comprises a nucleic 5 acid sequence that encodes a mutant sft polypeptide comprising the sequence of SEQ ID NO:
  • the mutant sft gene and/or mutant sspl gene is introduced into a plant or a plant part by a method selected from the group consisting of: Agrobacterium- mediated recombination, viral-vector mediated recombination, microinjection, gene gun bombardment/biolistic particle delivery, nuclease mediated recombination, and
  • the Solanaceae plant is a tomato (Solanum
  • the genetically-altered Solanaceae plant is a plant that suppresses sp imposed determinate growth and exhibits a sympodial index of less than three and either terminates (is semi-determinate), or continues to produce sympodial shoots (is semi-indeterminate). Accordingly, in some embodiments, the Solanaceae plant is semi-determinate or semi-indeterminate. In some embodiments, the Solanaceae plant is a semi-determinate or semi-indeterminate plant with a sympodial index of less than 3, less than 2.5, less than 2, or less than 1.5.
  • the Solanaceae plant is a semi- determinate or semi-indeterminate tomato plant. In some embodiments, the Solanaceae plant is a semi-determinate or semi-indeterminate tomato plant with a sympodial index of less than 3, less than 2.5, less than 2, or less than 1.5
  • the Solanaceae plant is inbred. In some embodiments, the genetically-altered semi-determinate Solanaceae plant is a hybrid. In another aspect, the disclosure relates to a genetically- altered Solanaceae plant produced by or producible by the methods described herein.
  • the disclosure relates to a genetically- altered Solanaceae plant, e.g., a semi-determinate or semi-indeterminate Solanaceae plant, homozygous for a mutant suppressor ofspl (sspl) gene and homozygous for a self pruning (sp) gene.
  • the mutant sspl gene comprises a nucleic acid sequence that encodes a mutant sspl protein that comprises a mutant SAP motif.
  • the mutant sspl gene comprises a nucleic acid sequence that encodes a mutant sspl protein that comprises a mutant SAP motif with a sequence of SEQ ID NO: 14 or SEQ ID NO: 15.
  • the mutant sspl gene encodes a mutant sspl polypeptide comprising the sequence of SEQ ID NO: 5 or SEQ ID NO: 6.
  • the mutant sspl gene comprises a C to T mutation at position 641 of SEQ ID NO: 1, a C to T mutation at 647 of SEQ ID NO: 1, or a C to T mutation at position 641 and 647 of SEQ ID NO: 1.
  • the mutant sspl gene comprises a coding sequence that comprises the nucleic acid sequence of SEQ ID NO: 2 or SEQ ID NO: 3.
  • the mutant sspl gene comprises the nucleic acid sequence of SEQ ID NO: 2 or SEQ ID NO: 3.
  • the mutant sspl gene comprises the nucleic acid sequence of SEQ ID NO: 25 or SEQ ID NO: 26. In some embodiments, the mutant sp gene comprises a coding sequence that comprises the nucleic acid sequence of SEQ ID NO: 8. In some embodiments, the mutant sp gene comprises the nucleic acid sequence of SEQ ID NO: 8. In some embodiments, the mutant sp gene comprises the nucleic acid sequence of SEQ ID NO: 23. In some embodiments, the mutant sp gene comprises a nucleic acid that encodes the amino acid sequence of mutant sp protein (e.g., SEQ ID NO: 10).
  • the genetically- altered Solanaceae plant e.g., a semi- determinate or semi-indeterminate Solanaceae plant
  • the genetically- altered Solanaceae plant e.g., a semi- determinate or semi-indeterminate Solanaceae plant
  • the genetically-altered Solanaceae plant e.g., a semi-determinate or semi-indeterminate
  • Solanaceae plant is inbred.
  • the genetically- altered Solanaceae plant e.g., a semi-determinate or semi-indeterminate Solanaceae plant, is a hybrid.
  • the disclosure relates to a genetically- altered Solanaceae plant heterozygous for a mutant suppressor ofspl (sspl) gene and homozygous for a mutant self pruning (sp) gene.
  • the mutant sspl gene comprises a nucleic acid sequence that encodes a mutant sspl protein that comprises a mutant SAP motif.
  • the mutant sspl gene comprises a nucleic acid sequence that encodes a mutant sspl protein that comprises a mutant SAP motif with a sequence of SEQ ID NO: 14 or SEQ ID NO: 15.
  • the mutant sspl gene encodes a mutant sspl polypeptide comprising the sequence of SEQ ID NO: 5 or SEQ ID NO: 6.
  • the mutant sspl gene comprises a C to T mutation at position 641 of SEQ ID NO: 1, a C to T mutation at 647 of SEQ ID NO: 1, or a C to T mutation at position 641 and 647 of SEQ ID NO: 1.
  • the mutant sspl gene comprises a coding sequence that comprises the nucleic acid sequence of SEQ ID NO: 2 or SEQ ID NO: 3.
  • the mutant sspl gene comprises the nucleic acid sequence of SEQ ID NO: 2 or SEQ ID NO: 3.
  • the mutant sspl gene comprises the nucleic acid sequence of SEQ ID NO: 25 or SEQ ID NO: 26. In some embodiments, the mutant sp gene comprises a coding sequence that comprises the nucleic acid sequence of SEQ ID NO: 8. In some embodiments, the mutant sp gene comprises the nucleic acid sequence of SEQ ID NO: 8. In some embodiments, the mutant sp gene comprises the nucleic acid sequence of SEQ ID NO: 23. In some embodiments, the mutant sp gene comprises a nucleic acid that encodes the amino acid sequence of mutant sp protein (e.g., SEQ ID NO: 10).
  • the genetically-altered Solanaceae plant is a tomato (Solanum lycopersicum) plant. In some embodiments, the genetically- altered Solanaceae plant is isogenic. In some embodiments, the genetically-altered Solanaceae plant is inbred. In some embodiments, the genetically-altered semi-determinate Solanaceae plant is a hybrid.
  • the disclosure relates to a genetically- altered Solanaceae plant homozygous for a mutant suppressor ofspl (sspl) gene.
  • the mutant sspl gene comprises a nucleic acid sequence that encodes a mutant sspl protein that comprises a mutant SAP motif.
  • the mutant sspl gene comprises a nucleic acid sequence that encodes a mutant sspl protein that comprises a mutant SAP motif with a sequence of SEQ ID NO: 14 or SEQ ID NO: 15.
  • the mutant sspl gene encodes a mutant sspl polypeptide comprising the sequence of SEQ ID NO: 5 or SEQ ID NO: 6.
  • the mutant sspl gene comprises a C to T mutation at position 641 of SEQ ID NO: 1, a C to T mutation at 647 of SEQ ID NO: 1, or a C to T mutation at position 641 and 647 of SEQ ID NO: 1.
  • the mutant sspl gene comprises a coding sequence that comprises the nucleic acid sequence of SEQ ID NO: 2 or SEQ ID NO: 3.
  • the mutant sspl gene comprises the nucleic acid sequence of SEQ ID NO: 2 or SEQ ID NO: 3.
  • the mutant sspl gene comprises the nucleic acid sequence of SEQ ID NO: 25 or SEQ ID NO: 26.
  • the mutant sp gene comprises a coding sequence that comprises the nucleic acid sequence of SEQ ID NO: 8. In some embodiments, the mutant sp gene comprises the nucleic acid sequence of SEQ ID NO: 8. In some embodiments, the mutant sp gene comprises the nucleic acid sequence of SEQ ID NO: 23. In some embodiments, the mutant sp gene comprises a nucleic acid that encodes the amino acid sequence of mutant sp protein (e.g., SEQ ID NO: 10). In some embodiments, the genetically-altered Solanaceae plant is a tomato (Solanum lycopersicum) plant. In some embodiments, the genetically-altered
  • Solanaceae plant is isogenic. In some embodiments, the genetically- altered Solanaceae plant is inbred. In some embodiments, the genetically- altered semi-determinate Solanaceae plant is a hybrid. In some embodiments, the genetically-altered Solanaceae plant is homozygous for a wild-type SELF PRUNING (SP) gene.
  • SP SELF PRUNING
  • the disclosure relates to a seed for producing a genetically- altered semi-determinate or semi-indeterminate Solanaceae plant as described herein, e.g. a genetically-altered semi-determinate or semi-indeterminate Solanaceae plant homozygous for a mutant suppressor ofspl (sspl) gene and homozygous for a mutant self pruning (sp) gene.
  • the mutant sspl gene comprises a nucleic acid sequence that encodes a mutant sspl protein that comprises a mutant SAP motif.
  • the mutant sspl gene comprises a nucleic acid sequence that encodes a mutant sspl protein that comprises a mutant SAP motif with a sequence of SEQ ID NO: 14 or SEQ ID NO: 15.
  • the mutant sspl gene encodes a mutant sspl polypeptide comprising the sequence of SEQ ID NO: 5 or SEQ ID NO: 6.
  • the mutant sspl gene comprises a C to T mutation at position 641 of SEQ ID NO: 1, a C to T mutation at 647 of SEQ ID NO: 1, or a C to T mutation at position 641 and 647 of SEQ ID NO: 1.
  • the mutant sspl gene comprises a coding sequence that comprises the nucleic acid sequence of SEQ ID NO: 2 or SEQ ID NO: 3. In some embodiments, the mutant sspl gene comprises the nucleic acid sequence of SEQ ID NO: 2 or SEQ ID NO: 3. In some embodiments, the mutant sspl gene comprises the nucleic acid sequence of SEQ ID NO: 25 or SEQ ID NO: 26. In some embodiments, the mutant sp gene comprises a coding sequence that comprises the nucleic acid sequence of SEQ ID NO: 8. In some embodiments, the mutant sp gene comprises the nucleic acid sequence of SEQ ID NO: 8. In some embodiments,
  • the mutant sp gene comprises the nucleic acid sequence of SEQ ID NO: 23. In some embodiments, the mutant sp gene comprises a nucleic acid that encodes the amino acid sequence of mutant sp protein (e.g., SEQ ID NO: 10).
  • the disclosure relates to methods of producing a genetically- altered semi-determinate or semi-indeterminate Solanaceae plant.
  • the method comprises:
  • the method of producing a genetically-altered semi-determinate or semi-indeterminate Solanaceae plant comprises: (a) introducing a mutant sspl gene into a Solanaceae plant part containing a mutant sp gene, thereby producing a genetically-altered Solanaceae plant part containing the mutant sspl gene and the mutant sp gene;
  • the mutant sspl gene comprises a nucleic acid sequence that encodes a mutant sspl protein that comprises a mutant5 SAP motif.
  • the mutant sspl gene comprises a nucleic acid sequence that encodes a mutant sspl protein that comprises a mutant SAP motif with a sequence of SEQ ID NO: 14 or SEQ ID NO: 15.
  • the mutant sspl gene encodes a mutant sspl polypeptide comprising the sequence of SEQ ID NO: 5 or SEQ ID NO: 6.
  • the mutant sspl gene comprises a C to T mutation at position 641 of o SEQ ID NO: 1, a C to T mutation at position 647 of SEQ ID NO: 1, or a C to T mutation at position 641 and 647 of SEQ ID NO: 1.
  • the mutant sspl gene comprises a coding sequence that comprises the nucleic acid sequence of SEQ ID NO: 2 or SEQ ID NO: 3.
  • the mutant sspl gene comprises the nucleic acid sequence of SEQ ID NO: 2 or SEQ ID NO: 3.
  • the mutant sspl gene 5 comprises the nucleic acid sequence of SEQ ID NO: 25 or SEQ ID NO: 26.
  • the mutant sp gene comprises a coding sequence that comprises the nucleic acid sequence of SEQ ID NO: 8. In some embodiments, the mutant sp gene comprises the nucleic acid sequence of SEQ ID NO: 8. In some embodiments, the mutant sp gene comprises the nucleic acid sequence of SEQ ID NO: 23. In some embodiments, the mutant 0 sp gene comprises a nucleic acid that encodes the amino acid sequence of mutant sp protein
  • the mutant sspl gene is introduced into a plant or a plant part by a method selected from the group consisting of: Agrobacterium- mediated recombination, viral-vector mediated recombination, microinjection, gene gun bombardment/biolistic particle delivery, nuclease mediated recombination, and
  • the Solanaceae plant is a tomato (Solanum lycopersicum) plant. In some embodiments, the Solanaceae plant is inbred. In some embodiments, the genetically- altered semi-determinate Solanaceae plant is a hybrid. In another aspect, the disclosure relates to a genetically- altered semi-determinate Solanaceae plant produced by or producible by the methods herein.
  • the isolated polynucleotide encodes a mutant sspl protein having the amino acid sequence of SEQ ID NO: 5 or SEQ ID NO: 6.
  • the isolated polynucleotide comprises the nucleic acid sequence of SEQ ID NO: 2 or SEQ ID NO: 3.
  • the isolated polynucleotide encodes a mutant sft protein having the amino acid sequence of SEQ ID NO: 21.
  • the isolated polynucleotide comprises the nucleic acid sequence of SEQ ID NO: 20.
  • Figure 1 shows the SSPl protein and SFT protein.
  • the bZIP domain and SAP motif are indicated and the two mutations (ssp-2129 and ssp-610) in the SAP motif of the SSPl protein are indicated: Proline to Leucine (P216L) and Threonine to Isoleucine (T214I), respectively.
  • Two putative ligand binding sites are indicated and the mutation in the external loop region of the SFT protein is indicated (se).
  • Figure 2 shows graphical representations of the suppression of sp mutant imposed sympodial shoot termination with the sspl and sft mutants in the sp mutant background.
  • Left depicts a sp "Determinate” (D) mutant plant.
  • Right depicts the wild-type “Indeterminate” (ID) plant with fully functional SP, SSPl and SFT genes.
  • ID wild-type "Indeterminate”
  • the second diagram from left depicts the "Semi- determinate” (SD) single heterozygote plants of ssp-2129, ssp610 or sftl906, and double heterozygote plants of ssp-2129, ssp610 or sftl906 in the sp mutant background. Note that shoot growth ends after a few more units of vegetative shoot (SYM) production compared to 5 the sp determinate plants. Right middle depicts the "semi-indeterminate" ssp-2129; sp
  • Figure 3 shows internode length between inflorescences in sympodial units in determinate (cultivar M82D), indeterminate (cultivar M82ID and sftl906; sp) and semi- indeterminate (ssp-2129; sp and, ssp-610; sp) plants. Note the intermediate internode length for the semi-indeterminate ssp-2129; sp and ssp-610; sp double mutant plants, which reflects5 a reduced sympodial index to an average of two leaves. ** P ⁇ 0.01, student t-test against M82D, and against M82ID indicated with lines.
  • Figure 4 is a series of graphs showing shoot determinacy of the primary shoot, the inflorescence, and the sympodial shoot in M82 indeterminate (M82ID), M82 determinate (M82D), two sspl mutant alleles (ssp-2129 and ssp-610), the sft-1906 mutant allele, and all o genotypic combinations among mutant alleles.
  • Figure 4A shows the numbers of leaves
  • Figure 4B shows the numbers of flowers per inflorescence.
  • Figure 4C shows the total number of inflorescences generated from each genotype.
  • Figure 4D shows numbers of leaves within each sympodial shoot (i.e.; sympodial index) in M82ID, M82D, ssp-2129 and ssp-610 and sftl906.
  • the primary and sympodial shoot architectures 5 from all genotypic combinations are shown in Figure 4E. Note the quantitative range of sympodial indices created by different homozygous and heterozygous mutant combinations. ID, indeterminate SYM growth; D, determinate SYM growth; SD, semi-determinate SYM growth.
  • Figure 5 is a schematic of the map-based cloning procedure used to identify the SSP1 gene. The highlighted region is the mapping interval identified using map-based cloning. Arrows indicate single nucleotide polymorphisms (SNPs). The coding region of SSP1 is shown. The C to T mutations in the protein C-terminus of ssp-2129 and ssp-610 are indicated.
  • Figure 6A and 6B is a ClustalW analysis of the nucleotide sequence of the coding sequence of the wild- type SSP1 gene and the coding sequences of the two mutant alleles e610 and e2129 (SEQ ID NOs: 1, 3 and 2, respectively).
  • Figure 7 is a ClustalW analysis of the amino acid sequence of the wild- type SSP1 gene and the two mutant alleles e610 and e2129 (SEQ ID NOs: 4, 6 and 5, respectively).
  • Figure 8A-8D are graphic representations of results of assessment of characteristics of plants of the genotypes indicated.
  • Figure 8A shows brix-yield (brix x yield) of plants of the genotypes indicated.
  • Figure 8B shows (soluble solids, sugar concentration in the fruits) of plants of the genotypes indicated.
  • Figure 8C shows yield of red fruit for plants of the genotypes indicated.
  • Figure 8D shows total yield of fruit for plants of the genotypes indicated. Yield was measured by taking 15 plants from each genotype in a completely randomized design with 1 plant/meter squared. * P ⁇ 0.05, ** P ⁇ 0.01, students t-test against M82D. Error bars are standard error.
  • Figure 9 is a ClustalW analysis of the nucleotide sequence of the wild-type SFT coding sequence and the mutant allele sft-1906 coding sequence (SEQ ID NOs: 18 and 20, respectively).
  • Figure 10 is a ClustalW analysis of the amino acid sequence of the wild- type SFT gene and the mutant allele sft-1906 (SEQ ID NOs: 19 and 21, respectively).
  • SEQ ID NO: 1 is the nucleotide sequence of the coding sequence of wild-type tomato SSP1.
  • SEQ ID NO: 2 is the nucleotide sequence of the coding sequence of ssp-2129, a mutant allele of SSP1.
  • SEQ ID NO: 3 is the nucleotide sequence of the coding sequence of ssp-610, a mutant allele of SSP1.
  • SEQ ID NO: 4 is the amino acid sequence of wild-type tomato SSP1 protein.
  • SEQ ID NO: 5 is the amino acid sequence of ssp-2129 mutant protein.
  • SEQ ID NO: 6 is the amino acid sequence of ssp-610 mutant protein.
  • SEQ ID NO: 7 is the nucleotide sequence of the coding sequence of wild-type tomato SP gene.
  • SEQ ID NO: 8 is the nucleotide sequence of the coding sequence of a mutant sp gene.
  • SEQ ID NO: 9 is the amino acid sequence of wild-type SP protein.
  • SEQ ID NO: 10 is the amino acid sequence of mutant sp protein.
  • SEQ ID NO: 11 is the amino acid sequence of the SAP motif of the tomato SSP1 protein.
  • SEQ ID NO: 12 is the nucleotide sequence of ssp-2129 that encodes the mutant SAP motif of ssp-2129 protein.
  • SEQ ID NO: 13 is the nucleotide sequence of ssp-610 that encodes the mutant SAP motif of ssp-610 protein.
  • SEQ ID NO: 14 is the amino acid sequence of the mutant SAP motif of ssp-2129 protein.
  • SEQ ID NO: 15 is the amino acid sequence of the mutant SAP motif of ssp-610 protein.
  • SEQ ID NO: 16 is the nucleic acid sequence of SFT wild- type genomic region.
  • SEQ ID NO: 17 is the nucleic acid sequence of sft-1906, a mutant allele of SFT, genomic region.
  • SEQ ID NO: 18 is the nucleic acid sequence of the coding sequence of wild-type S DNA.
  • SEQ ID NO: 19 is the amino acid sequence of wild- type SFT protein.
  • SEQ ID NO: 20 is the nucleic acid sequence of the coding sequence of sft-1906, a mutant of
  • SEQ ID NO: 21 is the amino acid sequence of mutant sft protein.
  • SEQ ID NO: 22 is the nucleic acid sequence of SP wild-type genomic region.
  • SEQ ID NO: 23 is the nucleic acid sequence of sp mutant genomic region.
  • SEQ ID NO: 24 is the nucleic acid sequence of SSP wild-type genomic region.
  • SEQ ID NO: 25 is the nucleic acid sequence of ssp-2129 mutant genomic region.
  • SEQ ID NO: 26 is the nucleic acid sequence of ssp-610 mutant genomic region. DETAILED DESCRIPTION
  • Tomato yield on both a per plant basis and in the context of tons per acre, depends partly on fruit size, but is mainly driven by the production of dozens of multi-flowered inflorescences and resulting fruit clusters that develop according to the "sympodial" growth 5 habit.
  • the defining feature of sympodial plants is that the shoot apical meristem (SAM) ends growth by differentiating into a terminal flower after producing a set number of leaves, and growth then renews from a specialized axillary (sympodial) meristem (SYM) that, in tomato, produces just three leaves before undergoing its own flowering transition and termination.
  • SAM shoot apical meristem
  • SYM specialized axillary meristem
  • SI serotodial index
  • Tomato breeding goals are multifaceted and shift according to the needs and desires of growers (e.g. improved pest resistances) and consumers (e.g. better quality), but one unwavering aim is to improve yield.
  • Indeterminate cultivars are grown commercially to5 enable continuous market delivery of "round”, “roma”, “cocktail”, “grape”, and “cherry” tomato types that are eaten fresh and command a premium price.
  • Indeterminate tomatoes are primarily grown in greenhouses where successively ripening clusters are harvested by hand multiple times over an extended period, in some cases up to a year, to maximize yield on plants that must be pruned to one or two main shoots to enable efficient greenhouse growth o and maintain fresh market quality.
  • SFT SINGLE FLOWER TRUSS
  • FT the tomato ortholog of the Arabidopsis thaliana gene FLOWERING LOCUS T
  • SSP1 SUPPRESSOR OF SP1
  • Arabidopsis thaliana gene FLOWERING LOCUS D FD
  • ssp-2129 ssp-610.
  • each homozygous sft and sspl mutant transforms determinate tomato plants into indeterminate tomato plants with a SI of less than three.
  • SSP1 and SFT mutations were introduced into the classic mutant self-pruning (sp) determinate background (sp-classic, coding sequence is SEQ ID NO: 8), which is a prerequisite genotype for generating indeterminate plants with a SI of less than 3.
  • SP is the tomato ortholog of the Arabidopsis thaliana gene TERMINAL FLOWER1 (TFLl).
  • TR is the tomato ortholog of the Arabidopsis thaliana gene TERMINAL FLOWER1 (TFLl).
  • Data from the roma cultivar 'M82' (which is homozygous for sp-classic) showed that homozygosity for ssp-2129 or ssp-610 in the sp-classic background results in semi-indeterminate plants with an average SI of 2.
  • pimpinelUfolium showed that homozygosity for sft-1906 or either of the sspl mutations created a SI of 2.
  • Double heterozygotes of sft-1906 and ssp-2129 or ssp-610 in hybrids resulted in an average SI less than 2, illustrating that combining mutations in either homozygous or heterozygous states can lead to subtle quantitative manipulation of sympodial shoot architecture and yield potential.
  • all three mutants increase the number of flowers per inflorescence, with sft-1906 exhibiting the strongest effect.
  • Described herein are genetically- altered Solanaceae plants, such as genetically- altered semi-determinate (SD) or semi-indeterminate (SID) Solanaceae plants, e.g., a tomato plant (Solarium lycopersicum), that comprise a mutant gene or mutant genes and exhibit characteristics different from those of the corresponding plant that has not been genetically altered.
  • SD genetically- altered semi-determinate
  • SID semi-indeterminate
  • the characteristics include any combination of the following: modified flowering time and shoot architecture; higher yield; higher quality products (e.g., fruits); and products (e.g., fruits) with different compositions (e.g., brix, also known as enhanced soluble solids or sugar concentration in the fruits,), compared to corresponding "wild-type (WT)" Solanaceae plants that have not been genetically altered.
  • WT wild-type
  • the genetically- altered Solanaceae plant has a sympodial index of less than 3, less than 2.5, less than 2, or less than 1.5.
  • the genetically- altered Solanaceae plant has a sympodial index of between 1 and 3 or between 1.5 and 2.5.
  • genetically- altered heterozygous or homozygous Solanaceae plants e.g., tomato plants (Solarium lycopersicum), comprise a mutant flowering gene SSP1
  • the genetically-altered heterozygous plants are semi-determinate (SD) or semi-indeterminate (SID). Such plants have increased yield; higher quality products (e.g., fruits); and products (e.g., fruits) with different compositions (e.g., brix, also known as enhanced soluble solids or sugar concentration in the fruits,) relative to these characteristics of corresponding plants that do not comprise such mutant genes.
  • SD semi-determinate
  • SID semi-indeterminate
  • Such plants have increased yield; higher quality products (e.g., fruits); and products (e.g., fruits) with different compositions (e.g., brix, also known as enhanced soluble solids or sugar concentration in the fruits,) relative to these characteristics of corresponding plants that do not comprise such mutant genes.
  • the plants comprise a variety of combinations of the different mutant alleles, such as mutant sspl (e.g., ssp-2129, ssp-610) with sft mutations (e.g., sft-1906).
  • mutant sspl e.g., ssp-2129, ssp-610
  • sft mutations e.g., sft-1906
  • the genetically-altered plants are heterozygotes or homozygotes and, in some cases, are double heterozygotes or double homozygotes.
  • such plants comprise ssp-2 ⁇ 29, described herein, and mutant SFT, such as sft-1906.
  • the plants comprise ssp-6 ⁇ 0, described herein, and mutant SFT, such as sft-
  • mutant SFT such as sft-
  • genetically-altered Solanaceae plants such as tomato plants designated herein as sft-1906 x M82 Fl, exhibited greater yield than the corresponding wild type tomato plants. See, for example, Figure 8D.
  • other genetically-engineered tomato plants produced greater yields (total fruit, red fruit, for example) than the
  • FIG. 8C and 8D graphic representations of yield of fruit by heterozygous tomato plants described herein (e.g., double heterozygotes ssp2 ⁇ 29 x sfil906 and ssp6l0 x sftl906, as well as the three heterozygotes indicated: sftl906 x M82F1; ssf610 x M82F1; ssp2129 x M82F1).
  • SD semi-determinate
  • SID semi-indeterminate
  • Solanaceae plants e.g., a tomato plant (Solarium lycopersicum), that comprise a mutant of SUPPRESSOR OF SP1 (SSP1).
  • the SSP1 gene encodes a bZIP transcription factor that physically interacts with the florigen hormone, SFT, to induce the flowering transition and flower production.
  • SSP1 has two domains, the bZIP domain and the SAP motif ( Figure 1).
  • the bZIP domain contains a basic leucine zipper capable of interacting with DNA.
  • the SAP motif, "RTSTAPF” (SEQ ID NO: 11), is found in the C-terminus of SSP1 from amino acid position 211 to 217 in SEQ ID NO: 4.
  • the SAP motif is similar to a conventional 14-3-3 recognition motif. Mutant sspl genes, such as ssp-2129 and ssp-610
  • the mutant sspl gene comprises, for example, a coding sequence comprising a nucleic acid (e.g., DNA) having the sequence of SEQ ID NO: 2; a coding sequence comprising a portion of SEQ ID NO: 2 that exhibits substantially the same activity (e.g., encoding the same polypeptide or substantially the same polypeptide that has the same activity) as a nucleic acid (e.g., DNA) having the sequence of SEQ ID NO: 2; a coding sequence comprising a nucleic acid (e.g., DNA) having at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity with the sequence of SEQ ID NO: 2; a nucleic acid (e.g., DNA) having the sequence of positions 631 to 651of SEQ ID NO: 2 (CGGACGTCAACTGCTCTATTT, SEQ ID NO: 12); a coding sequence comprising an ortho
  • nucleic acid e.g., DNA having the sequence of SEQ ID NO: 3; a coding sequence comprising a portion of SEQ ID NO: 3 that exhibits substantially the same activity (e.g., encoding the same polypeptide or substantially the same polypeptide that has the same activity) as a nucleic acid (e.g., DNA) having the 5 sequence of SEQ ID NO: 3; a coding sequence comprising a nucleic acid (e.g., DNA) having at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity with the sequence of SEQ ID NO: 3; a nucleic acid (e.g., DNA) having the sequence of positions 631 to 651of SEQ ID NO: 3 (CGGACGTCAATTGCTCCATTT, SEQ ID NO: 3 (CGGACGTCAATTGCTCCATTT, SEQ ID NO: 3 (CGGACGTCAATTGCTCCATTT, SEQ ID NO: 3 (
  • the mutant sspl gene comprises a C to T mutation at position 641 of SEQ ID NO: 1, a C to T mutation at position 647 of SEQ ID NO: 1, or a C to T mutation at position 641 and position 647 of SEQ ID NO: 1.
  • the mutant sspl gene comprises a nucleotide sequence that5 encodes a polypeptide of SEQ ID NOs: 5 or 6 or a nucleotide sequence that encodes a
  • the mutant sspl gene comprises a nucleic acid sequence that encodes a mutant sspl protein that comprises at least one mutation in a SAP motif, wherein the at least one mutation alters flowering time and shoot architecture of the Solanaceae plant, e.g., by conferring semi-determinacy.
  • the SAP motif with the at least one mutation has the amino acid sequence SEQ ID NOs: 14 or 15.
  • the mutant sspl gene comprises a nucleic acid sequence that encodes a mutant sspl protein that comprises at least one mutation in a SAP motif or in the two amino acids flanking the N-terminal position of the SAP motif and the one amino acid flanking the C-terminal position of the SAP motif, which includes the 5 phosphorylation site for Ca-dependent protein kinases (CDPKs), wherein the at least one mutation alters flowering time and shoot architecture of the Solanaceae plant, e.g., by conferring semi-determinacy.
  • CDPKs Ca-dependent protein kinases
  • the mutant sspl gene comprises, for example, a nucleic acid (e.g., DNA) having the sequence of SEQ ID NO: 25; a portion of SEQ ID NO: 25 that exhibits substantially the same activity (e.g., encoding the same
  • nucleic acid 0 polypeptide or substantially the same polypeptide that has the same activity
  • nucleic acid having the sequence of SEQ ID NO: 25; a nucleic acid (e.g., DNA) having at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity with the sequence of SEQ ID NO: 25; an orthologue or homologue of the nucleic acid having the sequence of SEQ ID NO: 25; a nucleic acid (e.g., DNA) having the sequence of SEQ ID NO: 26; a portion of SEQ ID NO: 26 that exhibits substantially the same activity (e.g., encoding the same polypeptide or substantially the same polypeptide that has the same activity) as a nucleic acid (e.g., DNA) having the sequence of SEQ ID NO: 26; a nucleic acid (e.g., DNA) having at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity with the sequence of SEQ ID NO: 25
  • the semi-determinate (SD) or semi-indeterminate (SID) are semi-determinate (SD) or semi-indeterminate (SID)
  • Solanaceae plant e.g., a tomato plant, comprises a mutant sspl polypeptide (e.g., a mutant sspl protein) encoded by a mutant sspl gene.
  • the mutant sspl polypeptide comprises the sequence of SEQ ID NO: 5; a portion of SEQ ID NO: 5 that exhibits substantially the same activity as a polypeptide (e.g., a protein) having the sequence of SEQ ID NO: 5; an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity with the sequence of SEQ ID NO: 5; the amino acid sequence of positions 211 to 217 in SEQ ID NO: 5 (RTSTALF, SEQ ID NO: 14); an orthologue or homologue of the polypeptide having the sequence of SEQ ID NO: 5; an orthologue or homologue of the amino acid sequence of positions 211 to 217 in SEQ ID NO: 14
  • the polypeptide comprises a Thr to He mutation at position 214 of SEQ ID NO: 4 or a Pro to Leu mutation at position 216 of SEQ ID NO: 4, or a Thr to He mutation at position 214 and a Pro to Leu mutation at position 216 of SEQ ID NO:
  • the mutant sspl polypeptide comprises an amino acid sequence with at least one mutation in a SAP motif, wherein the at least one mutation alters flowering time and shoot architecture of the Solanaceae plant, e.g., by conferring semi- determinacy or semi-indeterminacy.
  • the SAP motif with the at least one mutation has the amino acid sequence SEQ ID NO: 14 or SEQ ID NO: 15.
  • the mutant sspl polypeptide comprises an amino acid sequence with at least one mutation in a SAP motif or in the two amino acids flanking the N-terminal position of the SAP motif and the one amino acid flanking the C-terminal position of the SAP motif, which includes the phosphorylation site for Ca-dependent protein kinases (CDPKs), wherein the at least one mutation alters flowering time and shoot architecture of the Solanaceae plant, e.g., by conferring semi-determinacy or semi-indeterminacy.
  • CDPKs Ca-dependent protein kinases
  • Mutant sft gene such as s t-1906
  • the mutant sft gene comprises, for example, a coding sequence comprising a nucleic acid (e.g., DNA) having the sequence of SEQ ID NO: 20; a coding sequence comprising a portion of SEQ ID NO: 20 that exhibits substantially the same activity (e.g., encoding the same polypeptide or substantially the same polypeptide that has the same activity) as a nucleic acid (e.g., DNA) having the sequence of SEQ ID NO: 20; a coding sequence comprising a nucleic acid (e.g., DNA) having at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity with the sequence of SEQ ID NO: 20; a coding sequence comprising an orthologue or homologue of the nucleic acid having the sequence of SEQ ID NO:20.
  • the mutant sft gene comprises a G to A mutation at position 394 of SEQ ID NO: 20.
  • the mutant sft gene comprises, for example, a nucleic acid (e.g., DNA) having the sequence of SEQ ID NO: 17; a portion of SEQ ID NO: 17 that exhibits substantially the same activity (e.g., encoding the same polypeptide or substantially the same polypeptide that has the same activity) as a nucleic acid (e.g., DNA) having the sequence of SEQ ID NO: 17; a nucleic acid (e.g., DNA) having at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity with the sequence of SEQ ID NO: 17; or an orthologue or homologue of the nucleic acid having the sequence of SEQ ID NO: 17.
  • a nucleic acid e.g., DNA having the sequence of SEQ ID NO: 17
  • the mutant sft gene comprises a nucleotide sequence that encodes a mutant sft polypeptide of SEQ ID NO: 21. In some embodiments, the mutant sft gene comprises a nucleotide sequence that encodes a mutant sft polypeptide that comprises a Val to Met mutation at position 132 of SEQ ID NO: 19.
  • Solanaceae plants comprising mutant genes
  • the mutant sspl gene can comprise, for example, any of the sspl nucleic acids described herein.
  • the mutant sft gene can comprise, for example, any of the sft nucleic acids described herein.
  • the mutant sp gene can comprise, for example, any of the sp nucleic acids described herein.
  • the mutant sspl gene and/or the mutant sft gene is present along with a mutant self-pruning (sp) gene in a double mutant background and the mutant sp gene (Pnueli et al. Development.
  • a coding sequence comprising a nucleic acid (e.g., DNA) having the sequence of SEQ ID NO: 8; a coding sequence comprising a portion of SEQ ID NO: 8 that exhibits substantially the same o activity (e.g., encoding the same polypeptide or substantially the same polypeptide that has the same activity) as a nucleic acid (e.g., DNA) having the sequence of SEQ ID NO: 8; a coding sequence comprising a nucleic acid (e.g., DNA) having at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity with the sequence of SEQ ID NO: 8; or a coding sequence comprising an orthologue or homologue of the
  • the mutant sp gene comprises, for example, a nucleic acid (e.g., DNA) having the sequence of SEQ ID NO: 23; a portion of SEQ ID NO: 23 that exhibits substantially the same activity (e.g., encoding the same polypeptide or substantially the same polypeptide that has the same activity) as a nucleic acid (e.g., DNA) having the sequence of SEQ ID NO: 23; a nucleic acid (e.g., DNA) 0 having at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity with the sequence of SEQ ID NO: 23; or an orthologue or homologue of the nucleic acid having the sequence of SEQ ID NO: 23.
  • the mutant sp gene comprises a C to T mutation at position 227 of SEQ ID NO: 7.
  • the mutant sp gene comprises a nucleotide sequence with at least one mutation that reduces the activity of a sp protein encoded by the mutant sp gene.
  • the mutant sp gene comprises a nucleotide sequence that encodes a
  • the SD or SID Solanaceae plant comprises a mutant sp polypeptide (e.g., a protein) encoded by a mutant sp gene.
  • the mutant sp polypeptide comprises, for example, the sequence of SEQ ID NO: 10; a portion of SEQ ID NO: 10 that exhibits substantially the same activity as a polypeptide (e.g., a protein) having the sequence of SEQ ID NO: 10; an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity with the sequence of SEQ ID NO: 10; or an orthologue or homologue of the polypeptide having the sequence of SEQ ID NO: 10.
  • the mutant sp polypeptide comprises a Pro to Leu mutation at position 76 of SEQ ID NO: 9.
  • the mutant sp polypeptide comprises at least one mutation that reduces
  • the mutant sp polypeptide comprises at least one mutation that reduces the activity of the sp polypeptide, wherein the reduced (partially or completely) activity of the sp polypeptide can confer determinacy.
  • the Solanaceae plant can be, for example, inbred, isogenic or hybrid, as long as the plant comprises a mutant sspl gene, a mutant sft gene, a mutant sspl gene, and a mutant sft gene, a mutant sft gene and a mutant sp gene, a mutant sspl gene and a mutant sp gene, or a mutant ssplgene, a mutant sft gene, and a mutant sp gene.
  • Plants in the Solanaceae family include, e.g., tomato, potato, eggplant, petunia, tobacco, and pepper.
  • the Solanaceae plant is a tomato plant.
  • the Solanaceae plant, e.g. tomato plant is not a variety.
  • the Solanaceae plant comprises one wild-type copy of the SSP1 gene and one mutant copy of the sspl gene as described herein (is heterozygous for the mutant sspl gene). In some embodiments, the Solanaceae plant comprises two copies of a mutant sspl gene as described herein (is homozygous for the mutant sspl gene).
  • the Solanaceae plant comprises a first mutant sspl gene as described herein and a second mutant sspl gene as described herein, wherein the first mutant sspl gene and the second mutant sspl gene are different (e.g., the first mutant sspl gene comprises a coding sequence comprising SEQ ID NO: 2 and the second mutant sspl gene comprises a coding sequence comprising SEQ ID NO: 3).
  • the Solanaceae plant comprises 5 one copy of a mutant sspl gene as described herein and one copy of a mutant sp gene as described herein (is heterozygous for the mutant sspl gene and heterozygous for the mutant sp gene). In some embodiments, the Solanaceae plant comprises one copy of a mutant sspl gene as described herein and two copies of a mutant sp gene as described herein (is heterozygous for the mutant sspl gene and homozygous for the mutant sp gene).
  • the Solanaceae plant comprises two copies of a mutant sspl gene as described herein and two copies of a mutant sp gene as described herein (is homozygous for the mutant sspl gene and homozygous for the mutant sp gene).
  • the Solanaceae plant comprises one wild-type copy of a SFT gene and one mutant copy of a sft gene as described herein (is heterozygous for the mutant sft5 gene). In some embodiments, the Solanaceae plant comprises two copies of a mutant sft gene as described herein (is homozygous for the mutant sft gene). In some embodiments, the Solanaceae plant comprises one copy of a mutant sft gene as described herein and one copy of a mutant sp gene as described herein (is heterozygous for the mutant sft gene and heterozygous for the mutant sp gene). In some embodiments, the Solanaceae plant comprises o one copy of a mutant sft gene as described herein and two copies of a mutant sp gene as
  • the Solanaceae plant comprises two copies of a mutant sft gene as described herein and two copies of a mutant sp gene as described herein (is homozygous for the mutant sft gene and homozygous for the mutant sp gene).
  • the Solanaceae plant comprises one wild-type copy of a SFT gene and one mutant copy of a sft gene as described herein (is heterozygous for the mutant sft gene) and comprises one wild-type copy of the SSP1 gene and one mutant copy of the sspl gene as described herein (is heterozygous for the mutant sspl gene).
  • the Solanaceae plant comprises two copies of a mutant sft gene as described herein (is
  • mutant sft gene 0 homozygous for the mutant sft gene
  • the Solanaceae plant comprising a mutant sft gene (one or two copies) as described herein and a mutant sspl gene (one or two copies) further comprises one copy of a mutant sp gene as described herein (is heterozygous or homozygous for the mutant sft gene and the mutant sspigene and heterozygous for the mutant sp gene).
  • the Solanaceae plant further comprises two copies of a mutant sp gene as described herein (is homozygous for the mutant sp gene).
  • Exemplary, non-limiting genotype combinations include:
  • a genetically- altered Solanaceae plant (e.g., a tomato plant) provided herein is semi-determinate or semi-indeterminate.
  • a Solanaceae plant that is "semi-determinate” is a plant that (1) has a sympodial index that is less than 3 and (2) undergoes termination of the sympodial meristem.
  • a Solanaceae plant that is "semi-indeterminate” is a plant that (1) has a sympodial index that is less than 3 and (2) continuously produces sympodial shoots (the sympodial meristem does not undergo termination).
  • the genetically- altered Solanaceae plant has a sympodial index of less than 3, less than 2.9, less than 2.8, less than 2.7, less than 2.6, less than 2.5, less than 2.4, less than 2.3, less than 2.2, less than 2.1, less than 2, less than 1.9, less than 1.8, less than 1.7, less than 1.6, or less than 1.5.
  • the genetically-altered Solanaceae plant has a 5 sympodial index of between 1 and 3, 1.5 and 3, 1 and 2.5, 1.5 and 2.5, 1 and 2, or 1.5 and 2.
  • Solanaceae plant cells are also contemplated herein.
  • a Solanaceae plant cell may comprise any genotype described herein in the context of the Solanaceae plant (e.g., a Solanaceae plant cell heterozygous for a mutant sft gene and a mutant sspl gene or a
  • Solanaceae plant cell homozygous for a mutant sspl gene and a mutant sp gene). In some o embodiments, the Solanaceae plant cell is isolated. In some embodiments, the Solanaceae plant cell is a non-replicating plant cell.
  • any of the Solanaceae plants described above have an altered flowering time and shoot architecture compared to a wild-type Solanaceae plant (e.g., a Solanaceae plant comprising two copies of a wild-type SP gene), to a determinate Solanaceae5 plant (e.g., a Solanaceae plant comprising a mutant sp gene), or to both a wild-type Solanaceae plant (e.g., a Solanaceae plant comprising two copies of a wild-type SP gene), to a determinate Solanaceae5 plant (e.g., a Solanaceae plant comprising a mutant sp gene), or to both a wild-type
  • a wild-type Solanaceae plant e.g., a Solanaceae plant comprising two copies of a wild-type SP gene
  • a determinate Solanaceae5 plant e.g., a Solanaceae plant comprising
  • Solanaceae plant and a determinate Solanaceae plant have a higher yield than a corresponding wild-type Solanaceae plant.
  • a Solanaceae plant comprising two copies of a mutant sspl gene as described herein and two copies of a wild-type SP gene as described o herein has altered flowering time compared to a wild-type Solanaceae plant.
  • a Solanaceae plant comprising one copy of a mutant sspl gene as described herein and two copies of a mutant sp gene as described herein is semi-determinate or semi- indeterminate. In some embodiments, a Solanaceae plant comprising two copies of a mutant sspl gene as described herein and two copies of a mutant sp gene as described herein is semi- 5 determinate or semi-indeterminate.
  • Food products are also contemplated herein.
  • Such food products comprise a Solanaceae plant part, such as a fruit (e.g., a tomato fruit).
  • Non-limiting examples of food products include sauces (e.g., tomato sauce or ketchup), purees, pastes, juices, canned fruits, and soups.
  • Food products may be produced or producible by using methods known in the art.
  • 0 Isolated polynucleotides are also described herein, including wild-type and mutant alleles of the SSP1 gene, and specifically, two mutant alleles designated herein as ssp-2129 and ssp-610.
  • Isolated polynucleotides including wild-type and mutant alleles of the S FT gene are also contemplated, e.g., sft-1906.
  • Isolated polynucleotides can comprise, for example, a nucleic acid (e.g., DNA) having the sequence of SEQ ID NO: 2; a portion of SEQ ID NO: 2 that exhibits substantially the same activity as a nucleic acid (e.g., DNA) having the sequence of SEQ ID NO: 2; a nucleic acid (e.g., DNA) having at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity with the sequence of SEQ ID NO: 2; a nucleic acid (e.g., DNA) having the sequence of positions 631 to 651of SEQ ID NO: 2 (CGGACGTCAACTGCTCTATTT, SEQ ID NO: 12); an orthologue or homologue of the nucleic acid having
  • the isolated polynucleotide comprises a mutant sspl gene that includes a C to T mutation at position 641 of SEQ ID NO: 1, a C to T mutation at position 647 of SEQ ID NO: 1, or a C to T mutation at position 641 and position 647 of SEQ ID NO: 1.
  • the isolated polynucleotide comprises a nucleotide sequence that encodes the polypeptide of SEQ ID NOs: 5 or 6 or a nucleotide sequence that encodes a polypeptide that comprises SEQ ID NOs: 14 or 15.
  • the isolated polynucleotide comprises a nucleic acid sequence that encodes a mutant sspl protein that comprises at least one mutation in a SAP motif, wherein the at least one mutation alters flowering time and shoot architecture of the Solanaceae plant, e.g., by conferring semi-determinacy.
  • the SAP motif with the at least one mutation has the amino acid sequence SEQ ID NO: 14 or SEQ ID NO: 15.
  • the isolated polynucleotide comprises a nucleic acid sequence that encodes a mutant sspl protein that comprises at least one mutation in the SAP motif or in the two amino acids flanking the N-terminal position of the SAP motif and the one amino acid flanking the C-terminal position of the SAP motif, which includes the phosphorylation site for Ca-dependent protein kinases (CDPKs), wherein the at least one mutation alters flowering time and shoot architecture of the Solanaceae plant, e.g., by conferring semi-determinacy.
  • CDPKs Ca-dependent protein kinases
  • isolated polynucleotides can comprise, for example, a nucleic acid (e.g., DNA) having the sequence of SEQ ID NO: 20;_a portion of SEQ ID NO: 20 that exhibits substantially the same activity as a nucleic acid (e.g., DNA) having the sequence of SEQ ID NO: 20; a nucleic acid (e.g., DNA) having at least 70%, at least 80%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity with the sequence of SEQ ID NO: 20; or an orthologue or homologue of the nucleic acid having the sequence of SEQ ID NO: 20.
  • the isolated nucleic acid e.g., DNA having the sequence of SEQ ID NO: 20
  • a nucleic acid e.g., DNA having the sequence of SEQ ID NO: 20
  • a nucleic acid e.g., DNA having at least 70%, at least 80%, at least 90%, at least 95%
  • polynucleotide comprises a mutant sft gene comprising a G to A mutation at position 394 of SEQ ID NO: 20.
  • the isolated polynucleotide comprising a mutant sft gene comprises a nucleotide sequence that encodes a polypeptide of SEQ ID NO: 21.
  • the isolated polynucleotide comprises a mutant sft gene comprising a nucleotide sequence that encodes a mutant sft polypeptide that comprises a Val to Met mutation at position 132 of SEQ ID NO: 19.
  • the isolated polynucleotide comprises a mutant sft gene comprising a G to A mutation at position 394 of SEQ ID NO: 20.
  • the isolated polynucleotide comprising a mutant sft gene comprises a nucleotide sequence that encodes a polypeptide of SEQ ID NO: 21.
  • the isolated polynucleotide comprises a mutant sft gene comprising a
  • polynucleotide is a cDNA.
  • isolated polynucleotides can be used, for example, in methods of producing genetically- altered plants, such as genetically- altered semi-determinate or semi-indeterminate plants.
  • Isolated polypeptides e.g., proteins
  • proteins are also described herein, including wild- type and mutant sspl polypeptides, and specifically, the polypeptides encoded by the two mutant alleles ssp-2129 and ssp-610.
  • Isolated polypeptides also include wild-type and mutant sft polypeptides, such as those encoded by the mutant allele sft-1906.
  • the isolated polypeptide comprises, for example, the sequence of SEQ ID NO: 5; a portion of SEQ ID NO: 5 that exhibits substantially the same activity as a polypeptide (e.g., a protein) having the sequence of SEQ ID NO: 5; an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity with the sequence of SEQ ID NO: 5; the amino acid sequence of positions 211 to 217 in SEQ ID NO: 5 (RTSTALF, SEQ ID NO: 14); an orthologue or homologue of the polypeptide having the sequence of SEQ ID NO: 5; an orthologue or homologue of the amino acid sequence of positions 211 to 217 in SEQ ID NO: 5 (RTSTALF, SEQ ID NO: 14); a polypeptide (e.g., a protein) having the sequence of SEQ ID NO: 6; a portion of SEQ ID NO: 6 that exhibits substantially the same activity as
  • the isolated polypeptide comprises a Thr to He mutation at position 214 of SEQ ID NO: 4 or a Pro to Leu mutation at position 216 of SEQ ID NO: 4, or a Thr to He mutation at position 214 and a Pro to Leu mutation at position 216 of SEQ ID NO: 4.
  • the isolated polypeptide comprises a mutant sspl protein comprising an amino acid sequence with at least one mutation in a SAP motif, wherein the at least one mutation alters flowering time and shoot architecture of the Solanaceae plant, e.g., by conferring semi-determinacy.
  • the SAP motif with the at least one mutation has the amino acid sequence SEQ ID NO: 14 or SEQ ID NO: 15.
  • the isolated polypeptide comprises a mutant sspl protein comprising an amino acid sequence with at least one mutation in a SAP motif or in the two amino acids flanking the N-terminal position of the SAP motif and the one amino acid flanking the C-terminal position of the SAP motif, which includes the phosphorylation site for Ca-dependent protein kinases (CDPKs), wherein the at least one mutation alters flowering time and shoot architecture of the Solanaceae plant, e.g., by conferring semi-determinacy.
  • CDPKs Ca-dependent protein kinases
  • An isolated polypeptide may also comprise the sequence of SEQ ID NO: 21; a portion of SEQ ID NO: 21 that exhibits substantially the same activity as a polypeptide (e.g., a protein) having the sequence of SEQ ID NO: 21; an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity with the sequence of SEQ ID NO: 21; an orthologue or homologue of the polypeptide having the sequence of SEQ ID NO: 21.
  • Such isolated polypeptides can be used, for example, in methods of producing genetically- altered plants, such as genetically- altered semi-determinate or semi-indeterminate plants.
  • Methods described are methods of producing a genetically- altered Solanaceae plant, such as a semi-determinate (SD) or semi-indeterminate (SID) plant; and/or a Solanaceae plant with an altered flowering time and shoot architecture, increased yield, higher quality products (e.g., fruits), and/or products (e.g., fruits) with different compositions (e.g., brix, also known as enhanced soluble solids or sugar concentration in the fruits,) compared to a wild-type o Solanaceae plant.
  • SD semi-determinate
  • SID semi-indeterminate
  • a method of producing a genetically- altered semi- determinate or semi-indeterminate Solanaceae plant comprises: (a) introducing a mutant sspl gene into a Solanaceae plant that comprises a mutant sp gene or producing a mutant sspl gene in a Solanaceae plant that comprises a mutant sp gene, thereby producing a genetically- altered plant that comprises the mutant sspl gene and the mutant sp gene; (b) self-crossing5 the genetically- altered Solanaceae plant produced in (a) or crossing two genetically- altered Solanaceae plants produced in (a) under conditions appropriate for producing a genetically- altered Solanaceae plant homozygous for the mutant sspl gene and homozygous for the mutant sp gene, thereby producing a genetically-altered Solanaceae plant that is homozygous for the mutant sspl gene and the mutant sp gene and is semi-determinate or semi
  • Solanaceae plant with an altered flowering time and shoot architecture compared to a wild- type Solanaceae plant comprises: (a) introducing a mutant sspl gene into a Solanaceae plant that comprises a mutant sp gene or producing a mutant sspl gene in a Solanaceae plant that comprises a mutant sp gene, thereby producing a genetically-altered plant that comprises the 5 mutant sspl gene and the mutant sp gene; (b) self-crossing the genetically-altered Solanaceae plant produced in (a) or crossing two genetically- altered Solanaceae plants produced in (a) under conditions appropriate for producing a genetically- altered Solanaceae plant
  • the method comprises:
  • (b) self-crossing the genetically- altered Solanaceae plant produced in (a) or crossing two genetically- altered Solanaceae plants produced in (a) under conditions appropriate for producing a genetically-altered Solanaceae plant heterozygous or homozygous for the mutant sft gene and heterozygous or homozygous for the mutant sspl gene.
  • the plant produced in (b) is heterozygous for the mutant sft gene and heterozygous for the mutant sspl gene.
  • the mutant sspl gene comprises, for example, a coding sequence comprising a nucleic acid (e.g., DNA) having the sequence of SEQ ID NO: 2; a coding sequence comprising a portion of SEQ ID NO: 2 that exhibits substantially the same activity (e.g., encoding the same polypeptide or substantially the same polypeptide that has the same activity) as a nucleic acid (e.g., DNA) having the sequence of SEQ ID NO: 2; a coding sequence comprising a nucleic acid (e.g., DNA) having at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity with the sequence of SEQ ID NO: 2; a nucleic acid (e.g., DNA) having the sequence of positions 631 to 65 lof SEQ ID NO: 2 (CGGACGTCAACTGCTCTATTT, SEQ ID NO: 12); a coding sequence
  • the mutant sspl gene comprises, for example, a nucleic acid (e.g., DNA) having the sequence of SEQ ID NO: 25; a portion of SEQ ID NO: 25 that exhibits substantially the same activity (e.g., encoding the same polypeptide or substantially the same polypeptide that has the same activity) as a nucleic acid (e.g., DNA) having the sequence of SEQ ID NO: 25; a nucleic acid (e.g., DNA) having at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity with the sequence of SEQ ID NO: 25; an orthologue or homologue of the nucleic acid having the sequence of SEQ
  • the mutant sspl gene comprises a C to T mutation at position 641 of SEQ ID NO: 1, a C to T mutation at position 647 of SEQ ID NO: 1, or a C to T mutation at position 641 and position 647 of SEQ ID NO: 1.
  • the mutant sspl gene comprises a nucleotide sequence that encodes a polypeptide of SEQ ID NOs: 5 or 6 or a nucleotide sequence that encodes a polypeptide that comprises SEQ ID NOs: 14 or 15.
  • the mutant sspl gene comprises a nucleic acid sequence that encodes a mutant sspl protein that comprises at least one mutation in a SAP motif, wherein the at least one mutation alters flowering time and shoot architecture of the Solanaceae plant, e.g., by conferring semi-determinacy.
  • the SAP motif with the at least one mutation has the amino acid sequence SEQ ID NO: 14 or SEQ ID NO: 15.
  • the mutant sspl gene comprises a nucleic acid sequence that encodes a mutant sspl protein that comprises at least one mutation in a SAP motif or in the two amino acids flanking the N-terminal position of the SAP motif and the one amino acid flanking the C- terminal position of the SAP motif, which includes the phosphorylation site for Ca-dependent protein kinases (CDPKs), wherein the at least one mutation alters flowering time and shoot architecture of the Solanaceae plant, e.g., by conferring semi-determinacy.
  • CDPKs Ca-dependent protein kinases
  • the mutant sft gene comprises, for example, a coding sequence comprising a nucleic acid (e.g., DNA) having the sequence of SEQ ID NO: 20;_a coding sequence comprising a portion of SEQ ID NO: 20 that exhibits substantially the same activity (e.g., encoding the same polypeptide or substantially the same polypeptide that has the same 5 activity) as a nucleic acid (e.g., DNA) having the sequence of SEQ ID NO: 20; a coding sequence comprising a nucleic acid (e.g., DNA) having the sequence of SEQ ID NO: 20;_a coding sequence comprising a nucleic acid (e.g., DNA) having the sequence of SEQ ID NO: 20;_a coding sequence comprising a nucleic acid (e.g., DNA) having the sequence of SEQ ID NO: 20;_a coding sequence comprising a nucleic acid (e.g., DNA) having the sequence of SEQ ID NO: 20;_a coding
  • the mutant sft gene o comprises a G to A mutation at position 394 of SEQ ID NO: 20.
  • the mutant sft gene comprises a nucleotide sequence that encodes a polypeptide of SEQ ID NO: 21.
  • the mutant sft gene comprises a nucleotide sequence that encodes a mutant sft polypeptide comprising a Val to Met mutation at position 132 of SEQ ID NO: 19.
  • the mutant sft gene comprises, for example, a nucleic acid (e.g., 5 DNA) having the sequence of SEQ ID NO: 17; a portion of SEQ ID NO: 17 that exhibits substantially the same activity (e.g., encoding the same polypeptide or substantially the same polypeptide that has the same activity) as a nucleic acid (e.g., DNA) having the sequence of SEQ ID NO: 17; a nucleic acid (e.g., DNA) having at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity with the sequence of SEQ ID o NO: 17; or an orthologue or homologue of the nucleic acid having the sequence of SEQ ID
  • the sp mutant gene comprises, for example, a coding sequence comprising a nucleic acid (e.g., DNA) having the sequence of SEQ ID NO: 8; a coding sequence comprising a portion of SEQ ID NO: 8 that exhibits substantially the same 5 activity (e.g., encoding the same polypeptide or substantially the same polypeptide that has the same activity) as a nucleic acid (e.g., DNA) having the sequence of SEQ ID NO: 8; a coding sequence comprising a nucleic acid (e.g., DNA) having at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity with the sequence of SEQ ID NO: 8; or a coding sequence comprising an orthologue or homologue of the 0 nucleic acid having the sequence of SEQ ID NO: 8.
  • the mutant sp gene comprises a C to T mutation at position 227 of SEQ ID NO: 7. In some embodiments, the mutant sp gene comprises at least one mutation that reduces the activity of a sp protein encoded by the mutant sp gene. In some embodiments, the mutant sp gene comprises at least one mutation that reduces (partially or completely) the activity of a sp protein encoded by the mutant sp gene, wherein the reduced activity can confer determinacy. In some
  • the mutant sp gene comprises a nucleotide sequence that encodes a
  • the mutant sp gene comprises, for example, a nucleic acid (e.g., DNA) having the sequence of SEQ ID NO: 23; a portion of SEQ ID NO: 23 that exhibits substantially the same activity (e.g., encoding the same polypeptide or substantially the same polypeptide that has the same activity) as a nucleic acid (e.g., DNA) having the sequence of SEQ ID NO: 23; a nucleic acid (e.g., DNA) having at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity with the sequence of SEQ ID NO: 23; or an orthologue or homologue of the nucleic acid having the sequence of SEQ ID NO: 23.
  • a nucleic acid e.g., DNA having the sequence of SEQ ID NO: 23
  • a portion of SEQ ID NO: 23 that exhibits substantially the same activity e.g., encoding the same polypeptide or substantially the same poly
  • a method of producing a genetically- altered Solanaceae plant comprises: (a) introducing a mutant sspl gene into a Solanaceae plant part (e.g., a cell, a leaf or seed) that comprises a mutant sp gene or producing a mutant sspl gene in a Solanaceae plant part (e.g., a cell, a leaf or seed) that comprises a mutant sp gene, thereby producing a genetically-altered Solanaceae plant part that contains the mutant sspl gene and the mutant sp gene; (b) maintaining the genetically-altered Solanaceae plant part containing the mutant sspl gene produced in (a) under conditions and for sufficient time for production of a genetically- altered Solanaceae plant containing the mutant sspl gene and the mutant sp gene from the plant part,
  • a method of producing a genetically-altered Solanaceae plant with an altered flowering time and shoot architecture compared to a wild-type Solanaceae plant comprises: (a) introducing a mutant sspl gene into a Solanaceae plant part (e.g., a cell, a leaf or seed) that comprises a mutant sp gene or producing a mutant sspl gene in a Solanaceae plant part (e.g., a cell, a leaf or seed) that comprises a mutant sp gene, thereby producing a genetically-altered Solanaceae plant part that contains the mutant sspl gene and the mutant sp gene; (b) maintaining the genetically- 5 altered Solanaceae plant part containing the mutant sspl gene produced in (a) under
  • the mutant sspl gene and the mutant sp gene can be as described above.
  • the method of producing a genetically-altered Solanaceae plant comprises:
  • the plant produced in (c) is heterozygous for the mutant sft gene and heterozygous for the mutant sspl gene.
  • the mutant sspl gene or the mutant sft gene can be introduced into a Solanaceae plant or a plant part or produced in a Solanaceae plant or plant part by a method known to those of skill in the art, such as Agrobacterium-mediated recombination, viral-vector mediated recombination, microinjection, gene gun
  • mutagenesis e.g., by ethyl methanesulfonate or fast neutron irradiation
  • TILLING Targeting Induced Local Lesions in Genomes
  • nuclease mediated recombination e.g., use of custom-made restriction enzymes for targeting mutagenesis by gene replacement, see, e.g., CRISPR-Cas9: Genome engineering using the CRISPR-Cas9 system.
  • CRISPR-Cas9 Genome engineering using the CRISPR-Cas9 system.
  • TALEN endonucleases Nucleic Acids Res. 2011 Jul;39(12):e82. Efficient design and assembly of custom TALEN and other TAL effector-based constructs for DNA targeting. Cermak T, Doyle EL, Christian M, Wang L, Zhang Y, Schmidt C, Bailer JA, Somia NV, Bogdanove AJ, Voytas DF and Plant Biotechnol J. 2012 May;10(4):373-89. Genome modifications in plant cells by custom-made restriction enzymes. Tzfira T, Weinthal D, Marton I, Zeevi V, Zuker A, Vainstein A.). Genetically- altered Solanaceae plants, such as genetically-altered semi-determinate or semi-indeterminate Solanaceae plants, produced by or producible by a method described herein are also claimed.
  • a method of producing a semi-determinate or semi-indeterminate Solanaceae plant or a Solanaceae plant having one or more other characteristics described herein comprises: (a) reducing (partially or completely) function of a wild-type SSP1 gene comprising SEQ ID NO: 1 in a Solanaceae plant homozygous for a mutant sp gene, thereby producing a semi-determinate or semi-indeterminate Solanaceae plant.
  • reducing the function of the wild-type SSP1 gene comprising SEQ ID NO: 1 comprises performing any of the following methods of RNA-interference (e.g., administering to the Solanaceae plant a micro-RNA or a small interfering (si)-RNA or hairpin RNA) or translational blocking (e.g., administering to the Solanaceae plant a morpholino).
  • RNA-interference e.g., administering to the Solanaceae plant a micro-RNA or a small interfering (si)-RNA or hairpin RNA
  • translational blocking e.g., administering to the Solanaceae plant a morpholino.
  • Methods of RNA-interference and translational blocking are well-known in the art.
  • Methods of producing micro-RNAs, si-RNAs, and morpholinos are well-known in the art and can involve use of the nucleotides sequences provided herein, e.g., SEQ ID NO:
  • the mutant sp gene can be any mutant sp gene described herein.
  • the method further comprises (b) reducing (partially or completely) function of a wild-type SFT gene comprising SEQ ID NO: 16 or a coding sequence comprising SEQ ID NO: 18.
  • reducing the function of the wild-type SFT gene comprises performing any of the above methods of RNA-interference or translational blocking.
  • the disclosure provides a genetically-altered Solanaceae plant o comprising a mutant suppressor ofspl (sspl) gene and a mutant self pruning (sp) gene.
  • the mutant sspl gene comprises a nucleic acid sequence that encodes a mutant sspl protein that comprises a mutant SAP motif.
  • the mutant sspl gene comprises a nucleic acid sequence that encodes a mutant sspl protein that comprises a mutant SAP motif with a sequence of SEQ ID NO: 14 or SEQ ID NO: 15.
  • the mutant sspl gene encodes a mutant sspl polypeptide comprising the sequence of SEQ ID NO: 5 or SEQ ID NO: 6.
  • the mutant sspl gene comprises a C to T mutation at position 641 of SEQ ID NO: 1, a C to T mutation at 647 of SEQ ID NO: 1, or a C to T mutation at position 641 and 647 of SEQ ID NO: 1.
  • the mutant sspl gene comprises a coding sequence having the nucleic acid o sequence of SEQ ID NO: 2 or SEQ ID NO: 3.
  • the mutant sp gene encodes a mutant sp polypeptide comprising the sequence of SEQ ID NO: 10.
  • the mutant sp gene comprises a coding sequence having the nucleic acid sequence of SEQ ID NO: 8.
  • the genetically- altered Solanaceae plant is a tomato (Solanum lycopersicum) plant.
  • the genetically- altered 5 Solanaceae plant is isogenic.
  • the genetically- altered Solanaceae plant is inbred.
  • the genetically- altered Solanaceae plant is homozygous for the mutant sspl gene and homozygous for the mutant sp gene.
  • the genetically-altered Solanaceae plant is semi-determinate.
  • aspects relate to a seed for producing a genetically- altered Solanaceae plant as 0 described in any of the embodiments provided in the preceding paragraph. Yet other aspects relate to a method of producing a genetically- altered Solanaceae plant comprising:
  • genetically-altered Solanaceae plant comprises:
  • the 5 genetically-altered Solanaceae plant is homozygous for the mutant sspl gene and
  • the mutant sspl gene comprises a nucleic acid sequence that encodes a mutant sspl protein that comprises a mutant SAP motif. In some embodiments, the mutant sspl gene comprises a nucleic acid sequence that encodes a mutant sspl protein that comprises a mutant SAP motif with a sequence of SEQ ID 0 NO: 14 or SEQ ID NO: 15 In some embodiments, the mutant sspl gene encodes a mutant sspl polypeptide comprising the sequence of SEQ ID NO: 5 or SEQ ID NO: 6.
  • the mutant sspl gene comprises a C to T mutation at position 641 of SEQ ID NO: 1, a C to T mutation at 647 of SEQ ID NO: 1, or a C to T mutation at position 641 and 647 of SEQ ID NO: 1.
  • the mutant sspl gene comprises a coding sequence having the nucleic acid sequence of SEQ ID NO: 2 or SEQ ID NO: 3.
  • the mutant sp gene encodes a mutant sp polypeptide comprising the sequence of SEQ ID NO: 10.
  • the mutant sp gene comprises a coding sequence having the nucleic acid sequence of SEQ ID NO: 8.
  • the mutant sspl gene is introduced into a plant or a plant part by a method selected from the group consisting of: Agrobacterium-mediated recombination, viral- vector mediated recombination, o microinjection, gene gun bombardment/biolistic particle delivery, nuclease mediated
  • the mutant sspl gene is introduced into a plant or a plant part by nuclease mediated recombination.
  • the genetically- altered Solanaceae plant is a tomato (Solanum lycopersicum) plant.
  • the genetically- altered Solanaceae plant is inbred.
  • the genetically- altered Solanaceae plant is semi-determinate.
  • Another aspect relates to a genetically-altered Solanaceae plant produced by the method of any of the embodiments provided in the preceding paragraph.
  • sspl suppressor ofspl
  • sft single flower truss
  • the genetically- altered Solanaceae plant comprises a mutant suppressor ofspl
  • the sft gene comprises a coding sequence having the nucleic acid sequence of SEQ ID NO: 20. In some embodiments, the sft gene comprises SEQ ID NO: 20. In some embodiments, the mutant sspl gene comprises a coding sequence 5 having a nucleic acid sequence of SEQ ID NO: 2 or SEQ ID NO: 3 or encodes a mutant sspl protein that comprises SEQ ID NO: 5 or SEQ ID NO: 6.
  • the mutant sspl gene comprises a nucleic acid sequence that comprises SEQ ID NO: 2 or SEQ ID NO: 3 or encodes a mutant sspl protein that comprises SEQ ID NO: 5 or SEQ ID NO: 6.
  • the mutant sspl gene encodes a mutant sspl polypeptide that comprises a 0 mutant SAP motif with a sequence of SEQ ID NO: 14 or SEQ ID NO: 15.
  • the mutant sspl gene comprises a C to T mutation at position 641 of SEQ ID NO: 1, a C to T mutation at position 647 of SEQ ID NO: 1, or a C to T mutation at position 641 and 647 of SEQ ID NO: 1.
  • the mutant sspl gene comprises a coding sequence having the nucleic acid sequence of SEQ ID NO: 2 or SEQ ID NO: 3.
  • the mutant sspl gene comprises the nucleic acid sequence of SEQ ID 5 NO: 2 or SEQ ID NO: 3.
  • the genetically- altered Solanaceae plant is semi-determinate. In some embodiments, the genetically- altered semi-determinate
  • Solanaceae plant is a tomato (Solanum lycopersicum) plant.
  • the genetically-altered semi-determinate Solanaceae plant is inbred.
  • the mutant sft gene is sft-1906.
  • Yet another aspect relates to a seed for producing a genetically-altered Solanaceae plant as provided in any of the embodiments in the proceeding paragraph.
  • mutant self- pruning (sp) gene that comprises a coding sequence having the nucleic acid sequence of SEQ ID NO: 8. and a mutant single flower truss (sft) gene that comprises SEQ ID NO: 20.
  • the mutant self-pruning (sp) gene is heterozygous and the mutant single flower truss (sft) gene is heterozygous.
  • a genetically- altered Solanaceae plant comprising a mutant self-pruning (sp) gene that comprises the nucleic acid sequence of SEQ ID NO: 8. and a mutant single flower truss (sft) gene that comprises SEQ ID NO: 20, wherein the mutant o genes are heterozygous.
  • sp self-pruning
  • sft single flower truss
  • Another aspect relates to a method of producing a genetically- altered Solanaceae plant comprising:
  • the method of producing a genetically- altered Solanaceae plant comprises: (a) introducing a mutant sft gene into a Solanaceae plant part containing a mutant sspl gene, thereby producing a genetically- altered Solanaceae plant part containing the mutant sspl gene and the mutant sft gene;
  • Solanaceae plant heterozygous for a mutant suppressor ofspl (sspl) gene and homozygous for a mutant single flower truss (sft) gene, wherein the genetically- altered Solanaceae plant has an altered yield compared to the yield of a wild-type Solanaceae plant.
  • sspl suppressor ofspl
  • sft single flower truss
  • the mutant sspl gene comprises a nucleic acid sequence that encodes a mutant sspl protein that comprises a mutant SAP motif.
  • the mutant sspl gene comprises a nucleic acid sequence that encodes a mutant sspl protein that comprises a mutant SAP motif with a sequence of SEQ ID NO: 14 or SEQ ID NO: 15.
  • the mutant sspl gene encodes a mutant sspl polypeptide comprising the sequence of SEQ ID NO: 5 or SEQ ID NO: 6.
  • the mutant sspl gene comprises a C to T mutation at position 641 of SEQ ID NO: 1, a C to T 0 mutation at 647 of SEQ ID NO: 1, or a C to T mutation at position 641 and 647 of SEQ ID NO:
  • the mutant sspl gene comprises a coding sequence having the nucleic acid sequence of SEQ ID NO: 2 or SEQ ID NO: 3. In some embodiments, the mutant sspl gene comprises the nucleic acid sequence of SEQ ID NO: 2 or SEQ ID NO: 3. In some embodiments, the mutant sp gene comprises a coding sequence having the nucleic acid sequence of SEQ ID NO: 8. In some embodiments, the mutant sp gene comprises the nucleic 5 acid sequence of SEQ ID NO: 8. In some embodiments, the genetically- altered semi- determinate Solanaceae plant is a tomato (Solanum lycopersicum) plant. In some embodiments, the mutant sspl gene comprises a coding sequence having the nucleic acid sequence of SEQ ID NO: 2 or SEQ ID NO: 3. In some embodiments, the mutant sp gene comprises a coding sequence having the nucleic acid sequence of SEQ ID NO: 8. In some embodiments, the mutant sp gene comprises the nucleic 5 acid sequence
  • the genetically- altered semi-determinate Solanaceae plant is isogenic. In some embodiments, the genetically- altered semi-determinate Solanaceae plant is inbred.
  • Another aspect relates to a method of producing a genetically- altered semi- determinate Solanaceae plant comprising:
  • the method of producing a genetically- altered semi- determinate Solanaceae plant comprises:
  • the mutant sspl gene comprises a nucleic acid sequence that encodes a mutant sspl protein that comprises a mutant SAP motif. In some embodiments, the mutant sspl gene comprises a nucleic acid sequence that encodes a mutant sspl protein that comprises a mutant SAP motif with a sequence of SEQ ID NO: 14 or SEQ ID NO: 15. In some embodiments, the mutant sspl gene encodes a mutant sspl polypeptide comprising the sequence of SEQ ID NO: 5 or SEQ ID NO: 6.
  • the mutant sspl gene comprises a C to T mutation at position 641 of SEQ ID NO: 1, a C to T mutation at 647 of SEQ ID NO: 1, or a C to T mutation at position 641 and 647 of SEQ ID NO: 1.
  • the mutant sspl gene comprises a coding sequence having the nucleic acid sequence of SEQ ID NO: 2 or SEQ ID NO: 3.
  • the mutant sspl gene comprises the nucleic acid sequence of SEQ ID NO: 2 or SEQ ID NO: 3.
  • the mutant sp gene comprises a coding sequence having the nucleic acid sequence of SEQ ID NO: 8.
  • the mutant sp gene comprises the nucleic acid sequence of SEQ ID NO: 8.
  • the mutant sspl gene in (a), is introduced into a plant or a plant part by a method selected from the group consisting of: Agrobacterium-mediated recombination, viral- vector mediated recombination, microinjection, gene gun bombardment/biolistic particle delivery, nuclease mediated recombination, and electroporation.
  • the Solanaceae plant is a tomato (Solanum lycopersicum) plant. In some embodiments, the Solanaceae plant is inbred.
  • Another aspect relates to a genetically-altered semi-determinate Solanaceae plant produced by a method provided in the preceding paragraph.
  • aspects relate to a isolated polynucleotide encoding a mutant sspl protein having the amino acid sequence of SEQ ID NO: 5 or SEQ ID NO: 6.
  • the isolated polynucleotide comprises the nucleic acid sequence of SEQ ID NO: 2 or SEQ ID NO: 3.
  • Yet another aspect relates to a genetically- altered Solanaceae plant heterozygous for a mutant suppressor ofspl (sspl) gene and homozygous for a mutant self pruning (sp) gene, wherein the genetically- altered Solanaceae plant has an altered flowering time and shoot architecture compared to a wild-type Solanaceae plant.
  • the mutant sspl gene comprises a nucleic acid sequence that encodes a mutant sspl protein that comprises a mutant SAP motif. In some embodiments, the mutant sspl gene comprises a nucleic acid sequence that encodes a mutant sspl protein that comprises a mutant SAP motif with a sequence of SEQ ID NO: 14 or SEQ ID NO: 15. In some embodiments, the mutant sspl gene encodes a mutant sspl polypeptide comprising the sequence of SEQ ID NO: 5 or SEQ ID NO: 6.
  • the mutant sspl gene comprises a C to T mutation at position 641 of SEQ ID NO: 1, a C to T mutation at 647 of SEQ ID NO: 1, or a C to T mutation at position 641 and 647 of SEQ ID NO: 1.
  • the mutant sspl gene comprises a coding sequence having the nucleic acid sequence of SEQ ID NO: 2 or SEQ ID NO: 3.
  • the mutant sspl gene comprises the nucleic acid sequence of SEQ ID NO: 2 or SEQ ID NO: 3.
  • the mutant sp gene comprises a coding sequence having the nucleic acid sequence of SEQ ID NO: 8.
  • the mutant sp gene comprises the nucleic acid sequence of SEQ ID NO: 8.
  • the genetically-altered Solanaceae plant is a tomato (Solanum)
  • the genetically-altered Solanaceae plant is isogenic. In some embodiments, the genetically- altered Solanaceae plant is inbred. In some embodiments, the genetically- altered Solanaceae plant is semi-determinate.
  • Yet another aspect relates to a genetically- altered Solanaceae plant homozygous for a mutant suppressor ofspl (sspl) gene, wherein the genetically-altered Solanaceae plant has an altered flowering time compared to a wild-type Solanaceae plant.
  • the mutant sspl gene comprises a nucleic acid sequence that encodes a mutant sspl protein that comprises a mutant SAP motif.
  • the mutant sspl gene comprises a nucleic acid sequence that encodes a mutant sspl protein that comprises a mutant SAP motif with a sequence of SEQ ID NO: 14 or SEQ ID NO: 15.
  • mutant sspl gene encodes a mutant sspl polypeptide comprising the sequence of SEQ ID NO: 5 or SEQ ID NO: 6.
  • the mutant sspl gene comprises a C to T mutation at position 641 of SEQ ID NO: 1, a C to T mutation at 647 of SEQ ID NO: 1, or a C to T mutation at position 641 and 647 of SEQ ID NO: 1.
  • the mutant sspl gene comprises a coding sequence having the nucleic acid sequence of SEQ ID NO: 2 or 5 SEQ ID NO: 3.
  • the mutant sspl gene comprises the nucleic acid
  • the mutant sp gene comprises a coding sequence having the nucleic acid sequence of SEQ ID NO: 8. In some embodiments, the mutant sp gene comprises the nucleic acid sequence of SEQ ID NO: 8. In some embodiments, the genetically-altered Solanaceae plant is a tomato (Solanum
  • the genetically-altered Solanaceae plant is
  • the genetically- altered Solanaceae plant is inbred. In some embodiments, the genetically- altered Solanaceae plant is homozygous for a wild-type SELF PRUNING (SP) gene.
  • SP SELF PRUNING
  • Example 1 Identifying mutant plants providing semi-determinate or semi- indeterminate shoot architecture phenotypes
  • the crop plant tomato (Solanum lycopersicum) was used to identify mutant plants with a semi-determinate phenotype.
  • the previously generated tomato EMS mutation library in the determinate M82 background was used in the methods described below (Menda N Y et al. 2004. Plant J 38.861-72).
  • the mutation library was previously generated by treating seeds with ethyl methanesulfonate (0.5 percent EMS for 12 h; LD15), producing an Ml generation. These seeds were self-crossed to produce 13,000 M2 families with random mutations in unknown locations.
  • M82D The M82 determinate (M82D) isogenic background is known to contain a mutation in the SELF PRUNING (SP) gene (Pnueli, et al. Development 1989), resulting in a tomato plant with a determinate (D) growth habit.
  • SP SELF PRUNING
  • D determinate
  • the sympodial shoots produce progressively fewer leaves until the plant terminates growth in two successive inflorescences.
  • ID indeterminate tomato plants generate successive sympodial units (SYM) that produce three leaves each, and SYMs continue to reiterate to generate an ID shoot.
  • the M2 EMS mutation library described above was generated in an M82D background and self- crossed to produce approximately six thousand independent mutant tomato plants and many fertile mutants which contained mutations at unidentified locations which were carried over into the M3 inbred generation. These lines were screened in both the M2 and M3 generations for homozygous recessive mutant phenotypes that partially suppressed the determinate growth phenotype of the M82D background, resulting in a semi-determinate shoot architecture phenotype. In particular, flowering time, flower production per inflorescence, and shoot architecture were examined. Single lines were identified that contained at least one
  • M3 plant with a semi-determinate phenotype M3 plant with a semi-determinate phenotype.
  • FIG. 2 shows that homozygosity for the e2129 mutant (designated ssp-2129) in the sp ⁇ ' ⁇ M82 mutant background suppressed sympodial shoot termination compared to the sp ⁇ ' ⁇ mutant alone.
  • Figure 2 left, depicts a sp ⁇ ' ⁇ determinate plant where leaf number in each sympodial shoot gradually decreases, leading to shoot termination in two successive inflorescences.
  • Figure 2 depicts an indeterminate wild-type plant where each sympodial unit produces three leaves and this process continues indefinitely.
  • Figure 2, center depicts an ssp-2129; sp ⁇ ' ⁇ double mutant with semi-determinate sympodial shoot development, such that each sympodial shoot unit now produces two leaves, instead of the typical three leaves produced in wild- type indeterminate tomato plants.
  • Figure 3 shows quantification of internode length among 4 inflorescences in determinate sp ⁇ ' ⁇ mutants (M82D), semi-determinate ssp-2129; sp ⁇ ' ⁇ double mutants and ssp-610; sp ⁇ ' ⁇ double mutants (ssp-2129 and ssp-610, respectively), and wild-type plants (M82ID).
  • M82D determinate sp ⁇ ' ⁇ mutants
  • sp ⁇ ' ⁇ double mutants and ssp-610 respectively
  • wild-type plants M82ID
  • FIG. 4 shows quantification of leaf numbers produced by the primary shoot meristem (PSM) indicating flowering time and sympodial units in both sp ⁇ ' ⁇ and ssp-2129;sp ⁇ ' ⁇ backgrounds.
  • PSM primary shoot meristem
  • ssp-2129;sp ⁇ ' ⁇ double mutant plants displayed a delayed flowering time as indicated by the increased leaf numbers in the PSM compared to sp ⁇ ' ⁇ single mutant plants, ssp-2129; sp ⁇ " plants also displayed more leaves within sympodial units compared to sp ⁇ ' ⁇ plants, but fewer leaves within sympodial units compared to wild-type indeterminate plants. This semi-determinacy was observed for a second mutant allele, ssp- ⁇ 5i0 in the sp mutant background.
  • one family, e2129 was further analyzed using previously reported map-based cloning procedures (Lippman et al, PLoS Biology 2008).
  • a single M3 ssp-2129 mutant plant was crossed to a wild-type species, S. piminellifolium, with known polymorphisms throughout the genome (The Tomato Genome sequence, Nature, 2012).
  • the Fl hybrid was then self-crossed to produce an F2 generation of progeny plants segregating for both the ssp-2129 mutation and the DNA polymorphisms between M82 and S.
  • pimpinellifolium Approximately 200 F2 plants were scored for altered flowering time and semi-determinate shoot architecture phenotypes, reflecting homozygosity of the ssp-2129 mutation.
  • the homozygous mutant F2 plants (those with the altered flowering time and shoot architecture) were then genotyped with evenly spaced polymorphic DNA markers spanning all 12 tomato chromosomes using the bulk segregant mapping technique. DNA was isolated from at least 20 mutant plants (those with the altered flowering time and shoot architecture phenotype) and from 20 wild-type plants. DNA from the mutant plants was pooled to form pool 1 and DNA from the wild- type plants was pooled to form pool 2. A 10 centiM organ
  • RNA was extracted from wild- type and mutant plants. This RNA was converted to cDNA and sequenced using Illumina sequencing. The sequencing reads were then mapped to the known gene annotations and only those within the 2 Mb region described above were analyzed. A large number of C to T mutations were observed at a single location, position 647 according to SEQ ID NO: 2 which corresponds to amino acid position 216 according to SEQ ID NO: 5, within the C-terminus of the tomato orthologue of the Arabidopsis FLOWERING LOCUS D (FD) gene. The tomato orthologue is referred herein as SUPPRESSOR OF SP1 (SSP1).
  • SSP1 SUPPRESSOR OF SP1
  • the e610 mutant Following identification of the mutation present in the e2129 family, the e610 mutant, a confirmed allele in the SSP1 gene by complementation test with the ssp-2129 mutant as 5 described below, was examined to see if the unknown mutation in that family also occurred in the SSP1 gene. Heterozygous plants with one copy of ssp-2129 and one copy of ssp-610 phenocopied the ssp-2129 homozygous mutant and the ssp-610 homozygous mutant plant, indicating that these two mutations were in the same gene. Following the complementation test, DNA was extracted from e610 mutant plants and Sanger sequencing was performed to o determine if the SSP1 gene locus contained a mutation. A 'C to ' mutation was identified in SSP1 at position 641 according to SEQ ID NO: 3 which corresponds to amino acid position 214 according to SEQ ID NO: 6.
  • Figure 5 summarizes the map-based cloning of the SSP1 gene discussed above.
  • Figure 5A shows the SSP1 map position on chromosome 2 localized to a 2.1M interval between 5 markers indel4029 (4029x 1 Ok) and indel4230 (4230 x20k) was defined by bulk segragant analysis.
  • An F2 mapping population segregating for the recessive sspl mutant was generated by self-pollinating an S. pimpinellifolium sp- x sspl sp- (cv. M82) Fl plant.
  • At least four insertion-deletion (indel) PCR markers were used for each of the 12 tomato chromosomes on a pool of DNA composed of 20 sspl mutant individuals compared to a pool of DNA o composed of 20 wild-type individuals. Deconvolution of the mutant pool revealed a
  • FIG. 5B depicts Illumina RN A- sequencing (RNA-seq), which was performed on RNA isolated from reproductive meristems and used to identify and reconstruct DNA protein coding sequences from expressed genes in the mapping interval.
  • RNA-seq reads revealed eight genes (positions 5 indicated by arrows) expressed in meristems.
  • Single nucleotide polymorphisms (SNP) were identified relative to the reference annotation for the eight expressed genes, which revealed a C-to-T DNA change in the coding sequence of Solyc02g083520 of the ssp-2129 mutant allele.
  • FLOWERING LOCUS D (FD), encoding a bZIP transcription factor.
  • FD FLOWERING LOCUS D
  • Figures 6 and 7 depict ClustalW analyses of the nucleotide and amino acid sequences, respectively.
  • the nucleotide and amino acid sequences for wild-type SSP1, mutant ssp-2129, mutant ssp-610, wild-type SP, and mutant sp 5 are also listed after Example 2. Mutations present in the nucleotide and amino acid
  • sequences of each mutant nucleic acid or protein are indicated as underlined and bolded nucleotides or amino acids.
  • Example 2 Identifying mutant plants providing desirable plant traits such as brix, brix o yield, red fruit yield, and total yield
  • SFT SINGLE FLOWER TRUSS
  • nucleotide and amino acid sequences for the wild-type SFT gene and the mutant allele, sft-1906, are also listed below. Mutations present in the nucleotide and amino acid sequences of each mutant nucleic acid or protein are indicated as underlined and bolded nucleotides or amino acids.
  • Tomato plants doubly heterozygous for both an sspl mutation and a sft mutation had the highest improvement in Brix Yield, Brix, Red Fruit Yield, and Total Yield (FIG. 8).
  • Tomato plants were grown under wide (1 plant per m2) spacing using drip irrigation for field trials. When 0 all plants have 80% or more red fruits, total fruits and total red fruits were measured by

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Abstract

L'invention concerne des solanacées génétiquement modifiées, des compositions associées aux solanacées,et des procédés d'élaboration de ces solanacées.
PCT/US2013/070825 2012-11-20 2013-11-19 Mutations dans des solanacées modulant l'architecture de la pousse et améliorant les phénotypes associés au rendement Ceased WO2014081730A1 (fr)

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