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WO2007070965A1 - Locus quantitatifs pour ration nette bovine - Google Patents

Locus quantitatifs pour ration nette bovine Download PDF

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Publication number
WO2007070965A1
WO2007070965A1 PCT/AU2006/001970 AU2006001970W WO2007070965A1 WO 2007070965 A1 WO2007070965 A1 WO 2007070965A1 AU 2006001970 W AU2006001970 W AU 2006001970W WO 2007070965 A1 WO2007070965 A1 WO 2007070965A1
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WIPO (PCT)
Prior art keywords
feed intake
bovine
qtl
gene
autosome
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PCT/AU2006/001970
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Inventor
Wayne Pitchford
Cynthia Bottema
Madan Naik
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Commonwealth Scientific and Industrial Research Organization CSIRO
University of New England
Agriculture Victoria Services Pty Ltd
Department of Primary Industries and Regional Development
Adelaide Research and Innovation Pty Ltd
Meat and Livestock Autralia Ltd
Queensland Department of Primary Industries and Fisheries
Original Assignee
Commonwealth Scientific and Industrial Research Organization CSIRO
University of New England
Agriculture Victoria Services Pty Ltd
Department of Primary Industries and Regional Development
Adelaide Research and Innovation Pty Ltd
Department of Agriculture and Fisheries
Meat and Livestock Autralia Ltd
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Publication of WO2007070965A1 publication Critical patent/WO2007070965A1/fr
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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6888—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms
    • A—HUMAN NECESSITIES
    • A01—AGRICULTURE; FORESTRY; ANIMAL HUSBANDRY; HUNTING; TRAPPING; FISHING
    • A01K—ANIMAL HUSBANDRY; AVICULTURE; APICULTURE; PISCICULTURE; FISHING; REARING OR BREEDING ANIMALS, NOT OTHERWISE PROVIDED FOR; NEW BREEDS OF ANIMALS
    • A01K2227/00—Animals characterised by species
    • A01K2227/10—Mammal
    • A01K2227/101—Bovine
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/158—Expression markers

Definitions

  • the present invention relates generally to quantitative trait loci (QTL) in animals. More particularly, the present invention relates to QTL for improved feed efficiency, measured as net feed intake, in bovine animals.
  • QTL quantitative trait loci
  • the breeding herd accounts for 65- 85% of the total feed requirements and 65-75% of this is used for maintenance.
  • this maintenance requirement is because cattle are a large, slowly maturing species with a low annual reproductive rate.
  • only a single product is harvested (meat).
  • the 'machinery' of production represented by the breeding cow requires a proportionately higher level of raw 'inputs' to maintain itself than is required to produce the actual 'product', represented by the cow's offspring.
  • the large maintenance requirement is in contrast to other production systems such as pigs or poultry, where the breeding animal has a small intake relative to the total intake of all progeny.
  • Net feed efficiency is opposite in sign but equal in magnitude to net feed intake such that animals with low net feed intake are said to have high net feed efficiency. It would also be desirable to have a means for selecting animals for meat production on the basis of feed conversion (feed/weight gain) or gross efficiency as well as selecting breeding animals for net feed intake.
  • QTL quantitative trait loci
  • the present invention is predicated, in part, on the identification of quantitative trait loci, or QTL, on bovine autosomes 1 , 8, 1 1 and 20, which are associated with feed intake and/or net feed intake in bovine animals.
  • the QTL identified in accordance with the present invention represent regions of the bovine genome where genetic variation is correlated with the level of feed intake and/or net feed intake in bovine animals.
  • the present invention provides a method for identifying a genomic nucleotide sequence associated with a particular level of feed intake and/or net feed intake in a bovine animal, the method comprising: selecting a bovine animal having a known level of feed intake and/or net feed intake; and determining a genomic nucleotide sequence of the animal at a QTL on one or more of bovine autosomes 1 , 8, 1 1 and 20; wherein the genomic nucleotide sequence at the QTL is associated with the level of feed intake and/or net feed intake of the bovine animal.
  • the first aspect of the invention provides a method for identifying a genomic nucleotide sequence that is associated with low feed intake and/or low net feed intake in a bovine animal.
  • the present invention also provides a genomic nucleotide sequence that is associated with a particular level of feed intake and/or net feed intake in a bovine animal, wherein the genomic nucleotide sequence is identified in accordance with the first aspect of the invention.
  • genomic nucleotide sequences at the QTL have been identified as being associated with a particular level of feed intake and/or net feed intake, it is then possible, for example, to screen for one or more of these genomic nucleotide sequences in animals of unknown feed intake and/or net feed intake in order to predict the level of feed intake and/or net feed intake of the animal.
  • the present invention also provides a method for predicting the feed intake and/or net feed intake of a bovine animal, the method comprising determining a genomic nucleotide sequence of one or more cells of the bovine animal at a QTL on one or more of bovine autosomes 1 , 8, 1 1 or 20, wherein the genomic nucleotide sequence at the QTL is indicative of the feed intake and/or net feed intake of the bovine animal.
  • the QTL, and/or genomic nucleotide sequences at the QTL, identified in accordance with the present invention can also be used for the development of marker-assisted breeding or rapid assessment techniques to identify and select for animals having a desired level of feed intake and/or net feed intake.
  • the present invention provides a method of producing a bovine animal with a desired level of feed intake and/or net feed intake, the method comprising the steps of: selecting a first bovine animal comprising a genomic nucleotide sequence that is associated with a desired level of feed intake and/or net feed intake at a QTL on one or more of bovine autosomes 1 , 8, 1 1 or 20; sexually or asexually reproducing the animal; and selecting progeny arising from the sexual or asexual reproduction which comprise the genomic nucleotide sequence associated with the desired level of feed intake and/or net feed intake at the QTL.
  • the present invention provides a bovine animal, the bovine animal being a progeny of the breeding method of the fourth aspect of the invention.
  • the present invention also contemplates the use of the bovine animal of the fifth aspect of the invention, or reproductive material therefrom, for breeding.
  • the present invention also provides a method for modulating the overall feed intake and/or overall net feed intake of a herd of bovine animals, the method comprising: selecting bovine animals for breeding within the herd, wherein the bovine animals selected for breeding comprise a genomic nucleotide sequence that is associated with a desired level of feed intake and/or net feed intake at a QTL on one or more of bovine autosomes 1 , 8, 1 1 or 20; and breeding the herd from those selected animals which comprise the genomic nucleotide sequence associated with the desired level of feed intake and/or net feed intake at the one or more QTL.
  • the present invention provides a herd of bovine animals wherein the herd has altered overall feed intake and/or altered overall net feed intake, wherein the herd is produced according to the method of the seventh aspect of the invention.
  • the present invention is predicated, in part, on the identification of quantitative trait loci, or QTL, that are associated with feed intake and/or net feed intake in bovine animals.
  • a bovine animal includes at least all species within the genus Bos, including Bos taurus, Bos indicus, Bos frontalis, Bos grunniens, Bos javanic ⁇ s, Bos m ⁇ t ⁇ s and Bos sauveli, as well as hybrids of any of these species.
  • a bovine animal refers to a member of the species Bos taurus or Bos indicus or a hybrid of these species.
  • feed intake should be understood as the actual feed intake of an animal per unit time (eg. per day, week, month, year etc.). In one embodiment, feed intake may be measured as average daily feed intake.
  • Net Feed Intake or “NFI” should be understood as the difference between the actual feed intake of an animal and the predicted feed intake of the animal, wherein the predicted feed intake of the animal is determined on the basis of the body weight of the animal and/or the average daily gain of the animal. Accordingly, a relatively low net feed intake (high feed efficiency) is considered an actual feed intake that is lower than the predicted feed intake, whereas a relatively high net feed intake (low feed efficiency) is a feed intake that is higher than the predicted feed intake.
  • intake may be modelled (eg. the multiple regression model below) as a function of average weight and weight gain during a test period.
  • intake data may be modelled as a regression of weight as below:
  • Y is the animal's feed intake
  • ⁇ is the mean intake of the test group
  • ⁇ i is the regression coefficient of intake on average weight
  • ⁇ 2 is the regression coefficient of intake on weight gain
  • R is the residual (net) feed intake.
  • the present invention utilises genetic marker technology to statistically correlate the presence or absence of particular genetic markers in bovine animal populations with the magnitude of a particular physiological trait, eg. feed intake and/or net feed intake.
  • This statistical association is based on the technique of multiple simultaneous linear regressions of trait data with genetic marker allele data using computer software.
  • the cattle genome was "scanned” for groups of markers that exhibited covariance with the trait of interest, ie. feed intake and/or net feed intake. These groups of markers were then classified as bounding a QTL at least partially controlling that trait.
  • the degree of association between the markers and the trait can then be used to estimate the "strength" of the QTL, i.e., the percentage of the trait variance that the particular QTL can account for.
  • the QTL identified in accordance with the present invention may include, but are not necessarily limited to, the particular gene or genes involved in the control of feed intake and/or net feed intake in bovine animals. Rather, the QTL of the present invention represent regions of the bovine genome that include genes, transcriptional control sequences (such as promoters, enhancers, repressors and the like) or other genomic nucleotide sequences that are potentially involved in the control of feed intake and/or net feed intake in bovine animals, and/or include genetic markers linked to these traits.
  • transcriptional control sequences such as promoters, enhancers, repressors and the like
  • other genomic nucleotide sequences that are potentially involved in the control of feed intake and/or net feed intake in bovine animals, and/or include genetic markers linked to these traits.
  • a "quantitative trait locus” or “QTL” should be understood to refer to a genetic locus or region of genomic DNA in an organism wherein genetic variation at the locus is associated with variation in a phenotypic trait. Therefore, the QTL of the present invention comprise genetic loci in the bovine genome where genetic variation is associated with variation in the feed intake and/or net feed intake of the bovine animal.
  • the identification of the QTL in accordance with the present invention identifies regions of the cattle genome that are associated with feed intake and/or net feed intake. These genomic regions may include, for example: a genomic nucleotide sequence which is directly or indirectly involved in determining the feed intake and/or net feed intake of a bovine animal; and/or a genomic nucleotide sequence which may not be involved in determining the feed intake and/or net feed intake of a bovine animal, but which nonetheless exhibits linkage with this trait.
  • the present invention provides a method for identifying a genomic nucleotide sequence associated with a particular level of feed intake and/or net feed intake in a bovine animal, the method comprising: selecting a bovine animal having a known level of feed intake and/or net feed intake; and determining a genomic nucleotide sequence of the animal at a QTL on one or more of bovine autosomes 1 , 8, 1 1 and 20; wherein the genomic nucleotide sequence at the QTL is associated with the level of feed intake and/or net feed intake of the bovine animal.
  • the QTL of the present invention may be further defined, for example, with reference to the genetic markers that delimit the region of genomic DNA which defines the QTL and/or the genetic markers that are encompassed by the QTL.
  • the QTL is on bovine autosome 1.
  • the QTL is a region of bovine autosome 1 that is delimited by microsatellite marker CSSM032 and microsatellite marker
  • BMS2263 and/or is between BTA1 Flanking marker 1 and BTA1 Flanking marker 2 as defined in Table 3.
  • the QTL is a genomic region proximal to microsatellite marker BM1824 on bovine autosome 1 ; and/or proximal to the BTA1 peak marker as defined in Table 3.
  • the QTL on bovine autosome 1 comprises one or more of: the alpha-HS-glycoprotein gene (ASHG), the glucose transporter 2 gene (SLC2A2), the growth hormone factor 1 /pituitary specific positive transcription factor 1 gene (P0LJ1 F1 ), the interleukin 12A gene (IL12A), the uridine monophosphate synthetase gene (UMPS), or the NADH dehydrogenase (ubiquinone) 1 -alpha subcomplex, 10, 75kDa gene (Tables 1-2).
  • ASHG alpha-HS-glycoprotein gene
  • SLC2A2A2 glucose transporter 2 gene
  • P0LJ1 F1 the growth hormone factor 1 /pituitary specific positive transcription factor 1 gene
  • IL12A interleukin
  • the QTL is on bovine autosome 8.
  • the QTL is a region of bovine autosome 8 that is delimited by microsatellite marker BMS1341 and microsatellite marker BMS836; and/or is between BTA8 Flanking marker 1 and BTA8 Flanking marker 2 as defined in Table 3.
  • the QTL is a genomic region proximal to the LPL gene and/or microsatellite marker BMS71 1 on bovine autosome 8; and/or proximal to the BTA8 peak marker as defined in Table 3.
  • the QTL on bovine autosome 8 comprises one or more of: the cathepsin B gene (CTSB), the lipoprotein lipase gene (LPL) and the endothelial tyrosine kinase gene (TEK) (Tables 1-2).
  • CTSB cathepsin B gene
  • LPL lipoprotein lipase gene
  • TEK endothelial tyrosine kinase gene
  • the QTL is on bovine autosome 1 1.
  • the QTL is a region of bovine autosome 1 1 that is delimited by microsatellite marker RM096 and microsatellite marker RM363; and/or is between BTA1 1 Flanking marker 1 and BTA1 1 Flanking marker 2 as defined in Table 3.
  • the QTL is a genomic region proximal to microsatellite marker BM1048 on bovine autosome 1 1 ; and/or proximal to the BTA1 1 peak marker as defined in Table 3.
  • the QTL on bovine autosome 1 1 comprise one or more of: the argininosuccinate gene (ASS), the follicle stimulating hormone receptor gene (FSHR) and the proopiomelanocortin (POMC) gene, the lnterleukin 1 ⁇ (IL1 B) gene, the or the NADH dehydrogenase (ubiquinone) 1- alpha subcomplex, 10, 19kDa gene or the ATPase, V1 subunit G2 gene (Tables 1 -2).
  • the QTL is on bovine autosome 20.
  • the QTL is a region of bovine autosome 20 that is delimited by microsatellite marker TGLA126 and microsatellite marker BM5004; and/or is between BTA20 Flanking marker 1 and BTA20 Flanking marker 2 as defined in Table 3.
  • the QTL is a genomic region proximal to microsatellite marker BMS703 on bovine autosome 20; and/or proximal to the
  • the QTL on bovine autosome 20 comprise one or more of: the 5'-AMP-activated protein kinase, catalytic alpha-1 chain gene (PRKAA1 ) gene, the follistatin precursor gene (FST), the growth hormone receptor (GHR) gene, the microtubule-associated protein 1 B (MAPI B) gene, the phosphatidylinositol 3-kinase P-85-alpha subunit (PI3KR1 ) gene, or the prolactin receptor gene (PRLR) (Tables 1-2).
  • PRKAA1 catalytic alpha-1 chain gene
  • FST follistatin precursor gene
  • GHR growth hormone receptor
  • MAI B microtubule-associated protein 1 B
  • PI3KR1 phosphatidylinositol 3-kinase P-85-alpha subunit
  • PRLR prolactin receptor gene
  • a QTL comprising a region which is "proximal" to a particular marker refers to genomic sequence within about 5OcM, 2OcM, 1 OcM or 5cM of the marker, as determined by genetic linkage analysis.
  • the region may be genomic sequence within 2cM, within 1 cM or within 0.5 cM, 0.2 cM or 0.1 cM of the marker.
  • MMC Meat Animal Research Centre
  • NCBI National Center for Biotechnology Information
  • Methods for identifying and amplifying microsatellite markers, such as those referred to above, as well as methods for the determination of polymorphisms thereof are known in the art. For example, suitable methods are described by Casas ef a/. ⁇ Anim. Genet. 35: 2, 2003) and lhara et al. ⁇ Genome Res.
  • the genomic nucleotide sequence associated with a particular level of feed intake and/or net feed intake in a bovine animal at the one or more QTL may comprise any nucleotide sequence present in the genomic region defined by the QTL.
  • the determined genomic nucleotide sequence may be the entire genomic sequence in the region defined by the QTL or, more typically, the determined genomic sequence may be a part of the genomic sequence in the region defined by the QTL.
  • the genomic nucleotide sequence may include one or more of: a protein encoding nucleotide sequence, a 5' or 3' UTR region, a transcriptional control sequence, a non-transcribed RNA encoding genomic sequence, or a non-transcribed genomic nucleotide sequence within the QTL.
  • the genomic nucleotide sequence associated with a particular level of feed intake and/or net feed intake in a bovine animal at the one or more QTL comprises a mutation, sequence variant or SNP.
  • the genomic nucleotide sequence at the QTL may comprise a genomic nucleotide sequence that directly or indirectly influences the net feed intake of a bovine animal, for example a sequence, sequence variant, mutation or SNP which is in a gene or associated regulatory sequence that influences the feed intake and/or net feed intake of the bovine animal.
  • the genomic nucleotide sequence at the QTL may comprise a genomic nucleotide sequence that does not influence the feed intake and/or net feed intake of the animal, but rather is in linkage disequilibrium with a sequence that does influence the feed intake and/or net feed intake of the bovine animal.
  • Linkage disequilibrium refers to the non-random association of alleles at two or more loci.
  • the loci in linkage disequilibrium may be on the same chromosome, but are not necessarily on the same chromosome.
  • LD describes a situation in which some combinations of alleles or genetic markers occur more or less frequently in a population than would be expected from a random formation of haplotypes from alleles based on their frequencies.
  • Methods for identifying a genomic nucleotide sequence at a QTL include, for example, the methods of positional cloning, the candidate gene approach and combinations thereof (for examples see Coppieters et ai, Archiv fur Tierzucht - Archives of Animal Breeding 42: 86-92, 1999; and Goddard, Animal Science 76: 353-365, 2003).
  • a DNA sample is generally first collected from the test animal.
  • the DNA sample may be derived from any suitable material such as a hair, blood, semen or other tissue or cell sample derived from the test animal. Once a sample has been collected, DNA may be extracted from the sample using any suitable method known in the art. For example, the method of Miller et al. ⁇ Nucl. Acids Res. 16: 1215, 1988) may be used to isolate a DNA sample from the blood of a test animal.
  • the first aspect of the invention provides a method for identifying a genomic nucleotide sequence, at the one or more QTL of the present invention, which is associated with low feed intake and/or low net feed intake in a bovine animal.
  • the method of the first aspect of the invention was applied to identify a number of exemplary 'candidate genes' and specific SNPs in these candidate genes which are associated (either directly or via linkage disequilibrium) with the level of feed intake and/or net feed intake in bovine animals.
  • Table 4 in the Examples identifies a number of exemplary SNPs in genes within the QTL of the present invention which are associated with the level of feed intake and/or net feed intake in bovine animals.
  • the present invention also provides a genomic nucleotide sequence that is associated with a particular level of feed intake and/or net feed intake in a bovine animal, wherein the genomic nucleotide sequence is identified in accordance with the first aspect of the invention.
  • the genomic nucleotide sequence of the second aspect of the invention comprises a genomic nucleotide sequence associated with low feed intake and/or low net feed intake. In an alternate preferred embodiment, the genomic nucleotide sequence of the second aspect of the invention comprises a genomic nucleotide sequence associated with high feed intake and/or high net feed intake.
  • genomic nucleotide sequences at the QTL have been identified as being associated with a particular level of feed intake and/or net feed intake, it is then possible, for example, to screen for one or more of these genomic nucleotide sequences in animals of unknown feed intake and/or net feed intake in order to predict the level of feed intake and/or net feed intake of the animal.
  • the present invention also provides a method for predicting the feed intake and/or net feed intake of a bovine animal, the method comprising determining a genomic nucleotide sequence of one or more cells of the bovine animal at a QTL on one or more of bovine autosomes 1 , 8, 1 1 or 20, wherein the genomic nucleotide sequence at the QTL is indicative of the feed intake and/or net feed intake of the bovine animal.
  • the one or more cells used to determine a genomic nucleotide sequence at the QTL may be any cell from the animal, including, for example, somatic cells, blood cells, sperm cells, egg cells and the like.
  • the genomic nucleotide sequence at the QTL which is indicative of the feed intake and/or net feed intake of the animal, comprises a genomic nucleotide sequence identified in accordance with the method of the first aspect of the invention.
  • the genomic nucleotide sequence at the QTL which is indicative of the feed intake and/or net feed intake of the animal, comprises may comprise a SNP as set out in Table 4 of the Examples.
  • the method of the third aspect of the invention may be used, for example, to identify animals having a relatively low feed intake and/or low net feed intake or a relatively high feed intake and/or high net feed intake by screening for genomic nucleotide sequences at the QTL that are associated with relatively low- or relatively high feed intake and/or net feed intake, respectively.
  • the method of the third aspect of the invention may further comprise the step of identifying a bovine animal having a feed intake level and/or net feed intake level of interest on the basis of the genomic nucleotide sequence of the animal at a QTL defined by the present invention.
  • Genetic identification of animals having a relatively low feed intake and/or low net feed intake in accordance with the third aspect of the invention provides, among other things, a significantly more economical method for identifying animals having these traits than current feeding-trial based tests.
  • the QTL, and/or genomic nucleotide sequences at the QTL, identified in accordance with the present invention can also be used for the development of marker-assisted breeding or rapid assessment techniques to identify and select animals having a desired level of feed intake and/or net feed intake.
  • the genetic variation at each of the QTL on chromosomes 1 , 8, 11 and 20 identified in accordance with the present invention accounts for approximately 8% of the variance observed in net feed intake in cattle. Therefore, in combination, the genetic variation at these QTL could account for up to about 30% of the variance in net feed intake observed in bovine animals.
  • the method of the third aspect of the invention may be used to identify and select animals having a desired level of feed intake and/or net feed intake for any purpose.
  • the selected animals may be used in breeding programs, may be selected for use in a feedlot, or the like.
  • the present invention also provides methods for producing bovine animals to produce progeny having low feed intake and/or low net feed intake.
  • the present invention provides A method of producing a bovine animal with a desired level of feed intake and/or net feed intake, the method comprising the steps of: selecting a first bovine animal comprising a genomic nucleotide sequence that is associated with a desired level of feed intake and/or net feed intake at a QTL on one or more of bovine autosomes 1 , 8, 1 1 or 20; sexually or asexually reproducing the animal; and selecting progeny arising from the sexual or asexual reproduction which comprise the genomic nucleotide sequence associated with the desired level of feed intake and/or net feed intake at the QTL.
  • selecting a first bovine animal comprising a genomic nucleotide sequence that is associated with a desired level of feed intake and/or net feed intake at a QTL on one or more of bovine autosomes 1 , 8, 11 or 20 may include selecting an animal on the basis of the animal including a particular genomic nucleotide sequence at the QTL which is associated with a desired level of feed intake and/or net feed intake. For example, an animal may be selected on the basis of it having a genomic nucleotide sequence at the QTL which is known to be associated with low feed intake and/or low net feed intake.
  • selecting a first bovine animal comprising a genomic nucleotide sequence that is associated with a desired level of feed intake and/or net feed intake at a QTL on one or more of bovine autosomes 1 , 8, 1 1 or 20 may include selecting an animal on the basis that it does not contain a genomic nucleotide sequence at the QTL which is known to be associated with a non-desired level of feed intake and/or net feed intake. For example an animal may be selected on the basis of it not having a genomic nucleotide sequence at the QTL which is known to be associated with high feed intake and/or net feed intake.
  • the selected bovine animal is identified in accordance with the third aspect of the invention. In another embodiment, the selected bovine animal has low feed intake and/or low net feed intake.
  • “Sexually or asexually reproducing the animal” contemplates any means by which a selected bovine animal may be reproduced.
  • this term includes natural service mating, in-vitro fertilisation (including intracytoplasmic sperm injection techniques), cloning (including nuclear transfer cloning) and the like.
  • the present invention provides a bovine animal, the bovine animal being a progeny of the breeding method of the fourth aspect of the invention.
  • the present invention also contemplates the use of the bovine animal of the fifth aspect of the invention, or reproductive material therefrom, for breeding.
  • the term “reproductive material” includes a gamete from a bovine animal including a sperm or egg.
  • the term “reproductive material” may include a somatic cell, or the nucleus thereof, if such a cell or nucleus is used to clone a bovine animal using methods such as nuclear transfer.
  • nuclear-transfer mediated cloning see Wilmut ef a/. ⁇ Nature 385: 810-813, 1997), Westhusin ef a/. ⁇ Nature 415: 859, 2002) and Hochedlinger and Jaenisch (Nature 415: 1035-1038, 2002).
  • the present invention also provides methods for decreasing the overall feed intake and/or net feed intake of a herd of bovine animals by selecting animals comprising genomic nucleotide sequences associated with low feed intake and/or low net feed intake at one or more of the QTL defined herein for breeding within the herd.
  • the present invention also provides a method for modulating the overall feed intake and/or overall net feed intake of a herd of bovine animals, the method comprising: selecting bovine animals for breeding within the herd, wherein the bovine animals selected for breeding comprise a genomic nucleotide sequence that is associated with a desired level of feed intake and/or net feed intake at a QTL on one or more of bovine autosomes 1 , 8, 1 1 or 20; and breeding the herd from those selected animals which comprise the genomic nucleotide sequence associated with the desired level of feed intake and/or net feed intake at the one or more QTL.
  • the animals selected for breeding may on the basis of the animal(s) including a particular genomic nucleotide sequence at the QTL that is associated with a desired level of feed intake and/or net feed intake. For example, animals may be selected on the basis of having a genomic nucleotide sequence at the QTL which is known to be associated with low feed intake and/or low net feed intake. However, in another embodiment animals may be selected on the basis that they do not contain a genomic nucleotide sequence at the QTL that is known to be associated with a non-desired level of feed intake and/or net feed intake. For example animals may be selected on the basis of not having a genomic nucleotide sequence at the QTL which is known to be associated with high feed intake and/or net feed intake.
  • a decrease in the overall feed intake and/or net feed intake of a herd of includes, for example, a decrease in the mean or median feed intake and/or net feed intake of one or more of the bovine animals in the herd. Furthermore, a decrease in the overall feed intake of the animals in the herd includes, for example, an overall decrease in the amount of feed eaten by the herd.
  • one or more of the selected bovine animal(s) are identified in accordance with the third aspect of the invention. In another embodiment, one or more of the selected bovine animal(s) have low feed intake and/or low net feed intake.
  • the present invention provides a herd of bovine animals wherein the herd has altered overall feed intake and/or altered overall net feed intake, wherein the herd is produced according to the method of the seventh aspect of the invention.
  • Figure 1 shows the results of QTL mapping for NFI on bovine autosomes 1 , 8, 1 1 and 20 in the Trangie Angus selection lines. Log ratio of greater than 3.84 is considered significant.
  • Panels A to D show the results for BTA1 , BTA8, BTA1 1 and BTA20, respectively, “fcr” is feed conversion ratio (feed intake / weight gain during the 70 day test period), “sdfi70” is standardised (to 10MJ/kg DM) daily feed intake during the 70 test period, “nfi70” is net feed intake during the 70 day test period, and “adg” is average daily weight gain during the 70 day test period.
  • Figure 2 is a graphical representation of the QTL significance for net feed intake with and without SNPs in the analysis and also comparing results with those in Angus cattle.
  • Panels A to D show the results for BTA1 , BTA8, BTA1 1 and BTA20, respectively.
  • Figure 3 is a graphical representation showing AMPK enzyme activity in liver cells of high and low efficiency animals.
  • Figure 4 is a graphical representation showing the activity of oxidative phosphorylation complexes in liver mitochondria of high and low efficiency animals.
  • C. Complex IV. Bar indicates the mean.
  • Figure 5 shows a 2D electrophoresis gel of liver mitochondrial proteins from high and low efficiency animals.
  • Panel A shows an example of a gel run with Cy3 and Cy5 fluorescently labelled proteins.
  • Panel B shows an example of a protein spot that varies in concentration by more than 1.5-fold, as measured by the difference in signal intensity.
  • the trial design involved two of the more extreme Bos taurus dam breeds, Jersey (J) and Limousin (L), mated to first cross (JxL or LxJ) sires to produce back-cross calves. A total of about 400 heifer and steer progeny were generated in three calf crops (born 1996-98) with a total of 323 records available for analysis.
  • Calves were weaned at approximately 8 months of age, and raised on pasture for a further 12 months. The animals were then transported to an intensive feeding facility where feed intake was measured using Ruddweigh electronic feeders. Cattle in a feeding pen (8-10 per pen) were tagged with electronic ear tags that produce a signal with a unique number. When an animal enters the feeding box, an infra-red beam is broken recording of feed intake and body weight (1996 born cattle were weighed weekly in separate system). When the animal leaves the feeding box, the infra-red beam is reset. The weight of food that an animal has eaten is then calculated as the weight of the food bin after feeding has finished subtracted from the weight of the feed bin before feeding commenced.
  • Feed intake data was processed by calculating least-squares means for each animal over a test period. Day was included in the model to allow for weather, personnel, time of feeding and any other factors that could affect the intake. Metabolic mid-weight (MMWT) was calculated as the average weight over the test period raised by the power 0.73. Average daily weight gain (ADG) was calculated as the regression coefficient of weight against day of test. Net feed intake (NFI) was calculated after modelling daily feed intake for MMWT and ADG while on the feed intake test. The initial equation used to calculate NFI included the main effect of cohort (6 combinations of year of birth and sex of calf) and interactions between MMWT and ADG. Thus, a model comprising MMWT, ADG and cohort was used.
  • CRI-MAP Green et al., Documentation for CRI-MAP, version 2.4, Washington University School of Medicine, St. Louis MO, 1990
  • CRI-MAP analyses pedigree and genomic nucleotide sequence data file ( * .gen file).
  • Error rate is less than the true error rate
  • Chrompic finds the maximum likelihood estimates of the recombination fractions of the specified locus order; these estimates are then used to find the particular phase for each sire family and the grand-parental and grand-maternal phases (Green et al., 1990, supra). Chrompic also gives the number of recombination events. Any individuals with double or triple recombination events were carefully examined for genotyping or pedigree errors, as double recombinations are unlikely when markers are spaced at 2OcM intervals.
  • progeny inherited either an "A” or “B” allele from their sire.
  • the genomic nucleotide sequences of the progeny were coded AA, AB, BB, AC or BC with the "C” representing any other allele.
  • 43 SNP markers in 22 candidate genes were sequenced by primer extension.
  • the MARC2004 marker locations were used for the linkage analysis and for candidate genes not on the MARC map, locations were based on CRIMAP analyses.
  • Genomic nucleotide sequence probabilities were calculated using QTL Express (Seaton et ai, Bioinformatics 18: 339-340, 2002; http://qtl.cap.ed.ac.uk ; accessed November 2002 then regularly during 2004-5) for every 1cM on each chromosome. Animals were assigned a value of either 0 (which represents the "A" allele) or 1 ("B" allele) or 0.5 if uninformative. The genomic nucleotide sequence probability was then calculated between 0.5 and 1 , depending on the level of confidence.
  • Phenotypes were regressed against the genomic nucleotide sequence probabilities for every chromosome using "Haley and Knott regression" (Haley and Knott, Heredity 69: 312-324, 1992). Cohort (combination of sex and breed) and breed of dam (Jersey or Limousin) were included as factors in the model and the regression was nested within sire. Additional models that included two QTL or QTL by breed of dam interactions were also tested for a number of traits. Experiment-wise threshold values were calculated according to Lander and Kruglyak (Nature Genetics 1 1 : 241-247, 1995) and results reported are at least suggestive of linkage.
  • the QTL were identified as regions of relatively high F-ratios in the offspring of one or more of the sires (F-ratio (361 ), F-ratio (368) or F-ratio (398)) or a relatively high F-ratio across the offspring of the three different sires.
  • the data shown in table 1 indicates:
  • Table 2 sets out the size of effect (in kg feed/day) of the QTL associated with each of the markers and Table 3 documents the comparative map locations of the flanking markers for each QTL.
  • NFI net feed intake
  • a pre-test adjustment period of at least 21 days was allowed for the animals to adapt to the feeding system and diet, followed by a 70-day test.
  • the average age at the start of test was 268 days.
  • animals had ad libitum access to a pelleted ration of approximately 10.5 MJ/kg dry matter and 16% crude protein. Records taken during the test were used to calculate NFI for each animal.
  • the growth of each animal during the test was modelled by linear regression of weight on time (days), and the regression coefficient represented average daily gain (ADG).
  • the mean weight (MWT) of an animal during the test was computed as the average of the start and end of test weights.
  • Metabolic body weight (MMWT) was calculated as MWT 0 73 .
  • Feed intake (Fl) was standardised to a concentration of 10 MJ ME/kg dry matter. Feed conversion ratio was calculated as Fl divided by ADG.
  • a linear regression model of Fl on MMWT and ADG for each animal, with test group and sex included as class variables, was fitted to the data. The regression coefficients from this model were used to obtain expected feed intake of all animals based on ADG and MMWT.
  • NFI was calculated as the actual (measured) feed intake minus that predicted using the regression equation.
  • chromosomes 1 , 8, 1 1 , 20 There were between 4 to 7 microsatellite markers per chromosome. The markers were selected to be evenly spaced along the chromosome.
  • the sire families that were genotyped were selected across the Trangie pedigree, with the main criterion being sufficient numbers of progeny per sire to provide adequate power to detect QTL of moderate to large effect. Of the progeny, 1600 animals were genotyped for each marker.
  • the microsatellite data and the NFI phenotypes were analysed in a two-step approach.
  • the inheritance of the markers is traced through the complex pedigree that connects all the animals using a Gibbs sampling method.
  • This computer program calculates the probability that any two animals inherited QTL alleles, at a specific point on the chromosome, that are identical by descent.
  • the second step uses these probabilities in a linear model that includes the QTL, polygenic inheritance and fixed effects.
  • a likelihood ratio test was performed to evaluate if the QTL was significant at each point along the chromosome. Let L 0 be the likelihood value for the model under H 0 , where the QTL is not included in the model. Then Li is the likelihood value for the alternative model, that is, the QTL are included in the model.
  • the test statistic was defined as - 2(lnL 0 - InL 1 ) . This statistic is significant at P ⁇ 0.05 when it exceeds 3.84.
  • the corresponding region of the bovine genome is aligned with the human and/or mouse genomes. Based on this comparative mapping, the human and/or mouse genome databases are examined for genes within the aligned regions that potentially affect net feed intake (for example see O'Brien et al., Science 286: 458).
  • Genes identified as potential candidates for controlling net feed intake are then sequenced from the genomic DNA of the three mapping sires. Sequence variants observed among the candidate genes in the three sires are analysed to determine whether they could potentially be functional, that is, whether the sequence variation is likely to affect gene expression or activity.
  • Potential functional sequence variants are then genotyped in the progeny of the sires and statistical analyses are performed to determine if the sequence variant is associated with high or low net feed intake.
  • a SNP marker in the GHR gene which effects an amino acid substitution, addition or deletion in the growth hormone receptor, may lead to altered net feed intake in animals which carry the SNP marker.
  • QTL mapping was also conducted in mouse net feed intake selection lines.
  • the QTL for net feed efficiency that mapped to homeologous or equivalent regions in cattle and mouse were examined for candidate genes by comparative mapping.
  • comparative chromosomal maps for human and mouse from the 4 cattle QTL map locations were prepared (e.g. Table 3). Genes within the homeologous human and mouse genomic regions were selected as candidate genes based on their known function.
  • primers were designed to amplify the coding regions of the gene and the PCR conditions were optimised to obtain a single genomic product from the primers.
  • the genomic DNA from the 3 F1 mapping sires was amplified and sequenced. Sequence from the three sires were aligned using Sequencher software and any sequence variant (single nucleotide polymorphisms, in/del, etc) was noted. Sequence variants were confirmed by 1 ) sequencing the sire PCR products in the opposite direction and 2) sequencing PCR products amplified using genomic DNA from the grandparents to verify Mendelian inheritance.
  • SNPs single nucleotide polymorphisms
  • K G/T
  • M A/C
  • R A/G
  • S C/G
  • W A/T
  • Y C/T
  • the SNP genotype information may be used to estimate breeding values.
  • the genotypes can be coded as covariates with values -1 , 0 or 1 representing aa, ab and bb, respectively. Fitting the SNPs in this form either saves a degree of freedom for each SNP (if fixed) or minimizes bias (if random). Results from this analysis are presented in Table 8.
  • SNPs were selected as markers for additional linkage analysis in the QTL regions.
  • the SNPs markers were chosen such that 3 haplotypes/gene were present and, generally, 3 - 4 genes were informative in the sire of interest for that QTL (Table 9).
  • SNPs per gene were chosen for both linkage analysis and association testing on BTA 1 , 8, 1 1 and 20.
  • the lack of genes mapped on BTA11 resulted in fewer informative genes for this chromosome.
  • SNPs were likely to be functional variants. That is, the change in the DNA sequence would be likely to affect the expression or activity of the gene product. All functional SNPs were also genotyped in the gene mapping progeny. The SNP markers were placed on linkage maps using CRIMAP and positions verified where possible from other sources (eg USDA MARC 2004 map). TABLE 9 - Number of genes containing SNPs included in linkage analysis
  • AMPK Differential enzyme
  • Biochemical and proteomic experiments were conducted to determine if high and low efficiency animals differ in these pathways, and thereby, validating candidate genes in these pathways.
  • the initial experiments focused on two of these pathways, oxidative phosphorylation and malonyl coenzyme A / long chain fatty acid synthesis.
  • AMPK AMP-activated protein kinase
  • PRKAA 1 The AMPK gene, PRKAA 1, is located within the net feed efficiency QTL on BTA20 in cattle.
  • PRKAA 1 may be a gene involved in determining the feed intake and/or net feed intake in bovine animals. Therefore, in addition to investigating the association between net feed efficiency and SNPs within the PRKAA 1 gene, the activity of the enzyme was measured in liver samples from high and low efficiency animals
  • Muscle and liver samples were collected from Angus animals at the abattoir and frozen immediately in liquid nitrogen. The samples were stored at -80 0 C until analysed. The samples came from animals in the Angus Elite Progeny Testing Program, a joint venture between Angus Australia and Meat and Livestock Australia (MLA). The animals were derived from the Trangie Angus net feed intake selection lines and measured for net feed efficiency at Tullimba. The animals differed in net feed efficiency by up to 6 kg feed/day. Samples from the 20 most extreme high and low efficiency animals were used in the assays to ensure the maximum physiological difference.
  • cytosol and mitochondria Frozen muscle and liver samples from these animals were used to prepare the cytosol and mitochondria.
  • the cytosol for the AMP-activated protein kinase assay
  • mitochondria for the complex I, complex Il and complex IV assays
  • the mitochondrial preparations also were used in the proteomic experiments.
  • acetyl-CoA carboxylase and other proteins are phosphorylated by AMPK.
  • a synthetic peptide SAMS
  • SAMS synthetic peptide
  • AMPK enzyme activity was determined as the level of phosphorylation measured by using 32 P-ATP to label SAMS in the presence and absence of AMP.
  • the activity of the AMPK enzyme is increased in the highly efficient animals (p ⁇ 0.05, Figure 3). None of the SNPs discovered in the PRKAA1 gene are likely to be functional DNA variants that could explain this difference observed in activity. Nevertheless, the analysis of the SNP data from the PRKAA1 gene did indicate an association between AMPK and net feed intake.
  • complex I complex I
  • NADH-ubiquinone oxidoreductase/NADH dehydrogenase was measured spectrophotometrically by following the reduction of 2,6-dichlorophenolindophenol (DCIP) by NADH at 600nm absorbance. The sensitivity of the assay was verified by using the complex I inhibitor rotenone.
  • the activity of the succinate-ubiquinone oxidoreductase/succinate dehydrogenase was measured spectrophotometrically by following the reduction of 2,6- dichlorophenolindophenol (DCIP) by decylubiquinone (ubiquinone analogue) at 600nm absorbance.
  • DCIP 2,6- dichlorophenolindophenol
  • decylubiquinone ubiquinone analogue
  • the activity of the ferrocytochrome c oxygen oxidoreductase/cytochrome c oxidase was measured spectrophotometrically by following the oxidation of reduced cytochrome c at 550nm.
  • the sensitivity of the assay was verified by using the complex IV inhibitor potassium cyanide.
  • complex I complex I
  • complex Il complex IV
  • Figure 5 The activity of these three respiratory enzyme complexes involved in oxidative phosphorylation (complex I, complex Il and complex IV) were examined in the liver and muscle mitochondria of these low and high intake animals. The data indicated that although there is no difference in the activity of complexes Il and IV, the activity of the rate-limiting complex I does differ by 1.5-fold between liver mitochondria of low and high intake animals (p ⁇ 0.02) ( Figure 5).
  • proteomic approach was also taken.
  • Proteomics involves using 2D gel electrophoresis to separate proteins based on charge and mass by iso-electrical focusing.
  • DIGE differential gel electrophoresis
  • the proteins are then separated in an electrical field according to their isoelectric points (pi values) using pre-cast immobilised-pH-gradient (IPG) gel strips and carrier ampholytes.
  • IPG immobilised-pH-gradient
  • the proteins migrated to a position where their net charge is 0.
  • the focusing range was wide (pH 3-1 1 ), so resolution was approximately 0.5 pH units.
  • the gels are then scanned by densitometry to detect differences in quantity of specific proteins between the samples based on the spot intensity.
  • the spots representing proteins that varied by more than 1.5-fold concentration between the samples from high and low efficiency animals were located.
  • the Cy3 and Cy5 intensities of the protein spots were measured to determine the relative quantity of each protein in the high versus low efficiency animals (Figure 5).
  • sequence variant for example a sequence variant of a growth hormone receptor gene
  • a population screen is conducted. In this screen, a large number of animals representing many breeds are genotyped and the magnitude of effect of the sequence variation is determined. When a large magnitude of effect is observed, then the sequence variant may be used as a marker for marker assisted selection, for example as described by Georges ⁇ Theriogenology 55(1 ): 15-21 , 2001 ) or Dekkers and Hospital (Nature Reviews Genetics 3(1 ): 22-32, 2002). Animals selected by genotyping markers for net feed intake may be used for breeding or managed to enhance production (for example in a feedlot).
  • a quantitative trait locus or "a QTL” refers to a single quantitative trait locus or QTL or two or more quantitative trait loci or QTL; similarly reference to “a SNP marker” refers to a single SNP or two or more SNPs; and so forth.

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Abstract

La présente invention concerne de manière générale des locus quantitatifs (QTL) chez des animaux. Plus particulièrement, la présente invention concerne des QTL pour un rendement alimentaire amélioré, mesuré comme une ration nette, chez des bovins. Les QTL identifiés selon la présente invention représentent des régions du génome bovin où une variation génétique est liée au niveau de ration et/ou de ration nette chez des bovins.
PCT/AU2006/001970 2005-12-22 2006-12-22 Locus quantitatifs pour ration nette bovine Ceased WO2007070965A1 (fr)

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WO2015060732A1 (fr) * 2013-10-25 2015-04-30 Livestock Improvement Corporation Limited Marqueurs génétiques et leurs utilisations
WO2015187564A1 (fr) * 2014-06-02 2015-12-10 The Texas A&M University System Marqueurs d'adn pour l'efficacité alimentaire chez le bétail
CN115992249A (zh) * 2022-07-22 2023-04-21 中国水产科学研究院黄海水产研究所 一个大菱鲆饲料转化率相关的微卫星标记引物及其应用

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Cited By (6)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN102080126A (zh) * 2010-06-01 2011-06-01 山东农业大学 鸡fshr基因5′调控区两个突变位点的分子标记方法及其在鸡育种中的应用
CN102080126B (zh) * 2010-06-01 2012-10-24 山东农业大学 鸡fshr基因5′调控区两个突变位点的分子标记方法及其在鸡育种中的应用
WO2015060732A1 (fr) * 2013-10-25 2015-04-30 Livestock Improvement Corporation Limited Marqueurs génétiques et leurs utilisations
US10779518B2 (en) 2013-10-25 2020-09-22 Livestock Improvement Corporation Limited Genetic markers and uses therefor
WO2015187564A1 (fr) * 2014-06-02 2015-12-10 The Texas A&M University System Marqueurs d'adn pour l'efficacité alimentaire chez le bétail
CN115992249A (zh) * 2022-07-22 2023-04-21 中国水产科学研究院黄海水产研究所 一个大菱鲆饲料转化率相关的微卫星标记引物及其应用

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