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WO2009048344A2 - Marqueurs génétiques et procédés servant d'indicateurs prévisionnels de caractéristiques de production chez des animaux, en particulier des bovins - Google Patents

Marqueurs génétiques et procédés servant d'indicateurs prévisionnels de caractéristiques de production chez des animaux, en particulier des bovins Download PDF

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Publication number
WO2009048344A2
WO2009048344A2 PCT/NZ2008/000344 NZ2008000344W WO2009048344A2 WO 2009048344 A2 WO2009048344 A2 WO 2009048344A2 NZ 2008000344 W NZ2008000344 W NZ 2008000344W WO 2009048344 A2 WO2009048344 A2 WO 2009048344A2
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tables
set out
indicative
polymorphism
polymorphism set
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WO2009048344A3 (fr
WO2009048344A8 (fr
Inventor
Richard John Spelman
Bevin Lyal Harris
Michael Dominic Keehan
Renae Sandra Bennett
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LIVESTOCK IMPROVEMENT Corp Ltd
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LIVESTOCK IMPROVEMENT Corp Ltd
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Publication of WO2009048344A3 publication Critical patent/WO2009048344A3/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
    • C12Q1/6881—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for tissue or cell typing, e.g. human leukocyte antigen [HLA] probes
    • 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
    • C12Q2600/124—Animal traits, i.e. production traits, including athletic performance or the like
    • 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
    • C12Q2600/156—Polymorphic or mutational markers

Definitions

  • the present invention relates to genetic markers and to methods which are of use as predictive indicators for production traits in animals, particularly bovine animals, and which are of use in estimating or determining Breeding Worth and the like.
  • EBVs are an estimate of a dairy bull or cow's genetic merit for any given trait. Such genetic merit may also reflect somatic cell and/or germ cell characteristics, depending on the trait(s) being examined. EBVs can therefore not only predict phenotype performance and herd lifetime productivity (that is, provide a genetic diagnostic of phenotype) but also provide predictive insight into the ability of an animal to pass on superior genetic material (such as increased protein yield) to its offspring. Breeding values are calculated/estimated for production traits (expressed in units of measurements, that is, litres of milk and kilograms of fat and protein), fertility traits, conformation traits as well as other health, management and survival traits.
  • EBVs are calculated using Best Linear Unbiased Prediction (BLUP), and provide the best estimate of a bull's genetic merit, given the information available.
  • the current rate of genetic gain for the New Zealand dairy cow population is approximately 1% per annum which equates to approximately $10 per cow per year.
  • Factors that influence the rate of genetic gains are intensity of selection, accuracy of selection and generation interval.
  • intensity of selection can be influenced at the level of progeny testing of bull candidates in breeding programs (using only top bulls), and at the dairy farm level. The accuracy of testing is reflected by the results of progeny testing programmes.
  • the invention provides a method for predicting the phenotype of an animal wherein the method comprises at least the step of analysing a nucleic acid sample from said animal for a polymorphism in at least one genetic marker selected from the group set out in any one of tables 2 to 161 wherein the polymorphism is predictive of one or more phenotype listed in table A.
  • the invention provides a method for estimating the breeding value of an animal wherein the method comprises at least the step of analysing a nucleic acid sample from said animal for one or more polymorphism in at least one genetic marker selected from the group set out in any one of tables 2 to 161.
  • the invention provides a method for estimating the worth of an animal wherein the method comprising at least the step of analysing a nucleic acid sample from said animal for one or more polymorphism in at least one genetic marker from the group set out in tables 2 to 161.
  • the invention provides a method for selecting an animal for one or more of the traits listed in table A wherein the method comprises at least the step of analysing a nucleic acid sample from said animal for one or more polymorphism in at least one genetic marker from the group set out in tables 2 to 161, wherein: One or more polymorphism set out in tables 25, 65, 105 and 145 are indicative of protein yield;
  • One or more polymorphism set out in tables 2, 42, 82, and 122 are indicative of adaptability to milking
  • One or more polymorphism set out in tables 3, 43, 83, and 123 are indicative of body score condition;
  • One or more polymorphism set out in tables 4, 44, 84, and 124 are indicative of Breeding Worth;
  • One or more polymorphism set out in tables 5, 45, 85, and 125 are indicative of calving difficulty
  • One or more polymorphism set out in tables 6, 46, 86, and 126 are indicative of capacity
  • One or more polymorphism set out in tables 7, 47, 87 and 127 are indicative of dairy conformation
  • One or more polymorphism set out in tables 8, 48, 88, and 128 are indicative of fat percentage;
  • One or more polymorphism set out in tables 9, 49, 89 and 129 are indicative of fat yield;
  • One or more polymorphism set out in tables 10, 50, 90 and 130 are indicative of fat persistency
  • One or more polymorphism set out in tables 11, 51, 91, and 131 are indicative of fertility
  • One or more polymorphism set out in tables 12, 52, 92 and 132 are indicative of fore udder;
  • One or more polymorphism set out in tables 13, 53, 93, and 133 are indicative of front teat;
  • One or more polymorphism set out in tables 14, 54, 94 and 134 are indicative of gestation length
  • One or more polymorphism set out in tables 15, 55, 95 and 135 are indicative of high input index
  • One or more polymorphism set out in tables 16, 56, 96, and 136 are indicative of legs;
  • One or more polymorphism set out in tables 17, 57, 97, and 137 are indicative of liveweight;
  • One or more polymorphism set out in tables 18, 58, 98 and 138 are indicative of milk volume
  • One or more polymorphism set out in tables 19, 59, 99 and 139 are indicative of milk persistency
  • One or more polymorphism set out in tables 20, 60, 100 and 140 are indicative of milking speed
  • One or more polymorphism set out in tables 22, 62, 102 and 142 are indicative of overall opinion
  • One or more polymorphism set out in tables 23, 63, 103 and 143 are indicative of PM21;
  • One or more polymorphism set out in tables 24, 64, 104 and 144 are indicative of protein percentage;
  • One or more polymorphism set out in tables 26, 66, 106 and 146 are indicative of protein persistency;
  • One or more polymorphism set out in tables 27, 67, 107 and 147 are indicative of rear teat;
  • One or more polymorphism set out in tables 28, 68, 108 and 148 are indicative of rear udder;
  • One or more polymorphism set out in tables 29, 69, 109 and 149 are indicative of residual survival;
  • One or more polymorphism set out in tables 30, 70, 110 and 150 are indicative of rump angle;
  • One or more polymorphism set out in tables 31, 71, 111 and 151 are indicative of rump width
  • One or more polymorphism set out in tables 32, 72, 112 and 152 are indicative of somatic cell
  • One or more polymorphism set out in tables 33, 73, 113 and 153 are indicative of stature
  • One or more polymorphism set out in tables 34, 74, 114 and 154 are indicative of temperament;
  • One or more polymorphism set out in tables 35, 75, 115 and 155 are indicative of total longevity;
  • One or more polymorphism set out in tables 36, 76, 116 and 156 are indicative of udder overall;
  • One or more polymorphism set out in tables 37, 77, 117 and 157 are indicative of udder support
  • One or more polymorphism set out in tables 38, 78, 118 and 158 are indicative of OAD milk volume;
  • One or more polymorphism set out in tables 39, 79, 119 and 159 are indicative of OAD fat yield;
  • One or more polymorphism set out in tables 40, 80, 120,and 160 are indicative of OAD protein yield;
  • One or more polymorphism set out in tables 41, 81, 121 and 161 are indicative of OAD somatic cell count.
  • the method further comprises the step of selecting the animal based on the one or more polymorphism which is indicative of one or more desirable traits.
  • the invention provides a method for estimating the worth of an animal, estimating the breeding value of an animal, or selecting an animal on the basis of one or more the traits as defined in table A by analysing a nucleic acid sample from said animal for a polymorphism in at least one genetic marker selected from the group set out in any one of tables 2 to 161.
  • the invention may also be said broadly to consist in the parts, elements and features referred to or indicated in the specification of the application, individually or collectively, in any or all combinations of two or more of said parts, elements or features, and where specific integers are mentioned herein which have known equivalents in the art to which the invention relates, such known equivalents are deemed to be incorporated herein as if individually set forth.
  • Table 1 describes the SNPs used in this invention with respect to their genomic location, the nucleotide sequence that they reside in and their allelic nucleotide variation.
  • the parameters identified in this table are as follows:
  • the SNPJLD is used in Tables 2-161
  • Genome Build The Genome build that was used to physically map the SNP location
  • Tables 2 to 161 identify single nucleotide polymorphisms (SNPs) that the inventors have identified through statistical analysis to be associated with the relevant economic index or production trait as identified.
  • SNPs single nucleotide polymorphisms
  • Delta mean breeding values of bulls homozygous for minor allele - mean of breeding values of bulls homozygous for major allele.
  • the Sequence Listing provides the forward sequences provided in Table 1.
  • the SEQ ID No. provided in the sequence listing aligns with the SNP ID used in Table 1; ie, the forward sequence in which SNP ID 1 is contained is sequence SEQ ID No. 1 in the sequence listing, the forward sequence in which SNP ID 2 is contained is sequence SEQ ID No. 2 in the sequence listing, and so on.
  • animal refers to an individual at any stage of life, or after death, including an entity prior to birth such as a fertilised ovum, either before fusion of the male and female pro-nucleus or after the pronuclei have fused to form a zygote, an embryo (created by any means including somatic cell nuclear transfer) or an individual cell (N, 2N or greater); for the avoidance of doubt, this also includes a cell or a cluster of cells including stem cells and stem cell-like cells, cell line, haploid gametes and their progenitor cell lines. Also products resulting from the gametes, including embryos.
  • primer means a single-stranded oligonucleotide capable of acting as a point of initiation of template-directed DNA synthesis.
  • An "oligonucleotide” is a single-stranded nucleic acid typically ranging in length from 2 to about 500 bases. The precise length of a primer will vary according to the particular application, but typically ranges from 15 to 30 nucleotides. A primer need not reflect the exact sequence of the template but must be sufficiently complementary to hybridize to the template.
  • BW Billing Worth
  • BW is the sum of the Estimated Breeding Values for milkfat, protein, milk volume, liveweight, fertility, milk somatic cells and residual survival each weighted by an economic value.
  • the BW economic values for each trait represent the expected net income per unit of genetic change (per unit of feed) from breeding replacements.
  • “Breeding Worth” is referred to herein as an example of an index used to evaluate an animal to which the invention may be applied. It should be appreciated that there are a number of alternative indexes which may be used to evaluate the worth of an animal and the invention is also applicable to these. Skilled persons will be aware of such alternative indexes and methods.
  • GBV Genetic Breeding Value
  • genotyp means the genetic constitution of an organism. This may be considered in total, or as in the present application, with respect to the alleles of a single gene (that is, at a given genetic locus). Accordingly, the term “homozygote” refers to an organism that has identical alleles at a given locus on homologous chromosomes, whereas the term “heterozygote” refers to an organism in which different alleles are found on homologous chromosomes for a given locus.
  • genetic marker refers to nucleic acids that are polymorphic in a population, the alleles of which can be detected and distinguished by one or more analytic methods.
  • the term “genetic marker” further includes within its scope a plurality of genetic markers cosegregating, in the form of a "haplotype".
  • haplotype refers to a plurality of genetic markers that are generally inherited together, and in this group may be represented as a single "tag genetic marker”. Typically, genetic markers within a haplotype are in linkage disequilibrium.
  • tag genetic marker refers to a genetic marker located within a haplotype and which is in linkage disequilibrium with at least one other marker in the haplotype. Accordingly, a “tag marker” may act as proxy for all markers either known or unknown, within the haplotype.
  • phenotype means the observable physical or biochemical characteristics of an organism, as determined by both genetic makeup and environmental influences and may also mean the expression of a specific trait, such as milk volume, based on genetic and environmental influences.
  • homozygote refers to an organism that has identical alleles at a given locus on homologous chromosomes.
  • heterozygote refers to an organism in which different alleles are found on homologous chromosomes for a given locus.
  • single nucleotide polymorphism refers to nucleic acid sequence variations that occur when a single nucleotide in the genome sequence is altered.
  • a single nucleotide polymorphism may also be a single nucleotide insertion or deletion.
  • the nucleotides involved in SNPs are called alleles.
  • base pair means a pair of nitrogenous bases, each in a separate nucleotide, in which each base is present on a separate strand of DNA and the bonding of these bases joins the component DNA strands.
  • a DNA molecule contains four bases; A (adenine), G (guanine), C (cytosine), and T (thymidine).
  • a and G are purine bases, typically designated by the letter “R”
  • C and T are pyrimidine bases, typically designated by the letter "Y”. Where A or T may occupy a single position it is typically designated by the letter W. Where G or C may occupy a single position it is typically designated by the letter S.
  • a or C may occupy a single position it is typically designated by the letter M.
  • G or T may occupy a single position it is typically designated by the letter K.
  • A, T or C may occupy a single position it is typically designated by the letter H.
  • G, C or T may occupy a single position it is typically designated by the letter B.
  • G, A or T may occupy a single position it is typically designated by the letter D.
  • G, C or A may occupy a single position it is typically designated by the letter V.
  • G, C, A or T may occupy a single position it is typically designated by the letter N.
  • base pair is abbreviated to "bp”
  • kilobase pair is abbreviated to kb.
  • restriction enzyme as used herein means an endonuclease enzyme that recognises and cleaves a specific sequence of DNA (recognition sequence).
  • the methods of the invention involve the analysis of one or a combination of the SNPs identified in tables 2 to 161.
  • the presence or absence of one or more of those SNPs can be used to predict or assess whether or not a particular animal will have one or more desirable phenotypes or traits. This information can be used to select animals for breeding programmes, estimate breeding values, estimate or evaluate the worth of an animal including estimating Breeding Worth and the like indexes as will be appreciated by those of skill in the art to which the invention relates having regard to the description provided herein.
  • the methods of the invention may be combined with one or more other known methods for assessing genotype, predicting phenotype, estimating breeding values or estimating worth for example.
  • the methods of the invention may include, in addition to detection and analysis of the SNPs identified herein, detection and analysis of SNPs previously known to be associated with a particular trait.
  • the methods of the invention may broaden selection options available and/or provide improvements in selection accuracy by assessing the association of polymorphisms in proven bull sires with breeding value records of the daughters from those bulls. Based on the relationships established, the use of pedigree and assessment of polymorphisms predict genetic merit for Breeding Worth (BW) up to 50% above and beyond pedigree alone.
  • the methods of the invention may be used for the selection of breeding animals and for the selection of animals for milk production and other desirable traits.
  • the invention is therefore also concerned with animals selected by the methods of the invention, their progeny and the use of both selected animals and their progeny for breeding, as well as products derived from these animals.
  • the invention may also be used to predict bull or cow phenotype performance and as such can be used in production management systems known as Marker Assisted management. Animals more or less suitable for a particular production system can be screened early at birth or as embryo's to predict life time performance and segregated or managed to suit their genotype and therefore predicted phenotype. Typically combinations of markers may account for up to 50% of the phenorypic differences between individuals. Examples include high and low milk or milk components, disease resistance, lactation persistency, semen quality, temperament, fertility, or any of the other traits described herein.
  • Genotype - Trait Associations Tables 2 to 161 identify single nucleotide polymorphisms (SNPs) that the inventors have identified through statistical analysis to be associated with the relevant economic index or production trait as identified.
  • SNPs single nucleotide polymorphisms
  • the nature and location of SNPs of the invention is provided in the bovine sequence assembly Btau 4 (ftp ://ftp.hgsc.bcm.tmc.edu/pub/data/Btaurus/fasta/Btau2Qg70913 -freeze/) and/or table 1.
  • Table 1 includes the nucleotide sequence in the region of the SNP and the polymorphism of interest. .
  • the information provided in the tables and database will allow a skilled person to develop a genotyping test for any SNP of interest identified hi Tables 2 to 161.
  • the method of the invention will broadly comprise selecting animals to be tested, taking a sample containing nucleic acid from the animal, determining the presence or absence of one or more SNP of the invention in said sample, and analysing the results to predict phenotype and/or genetic merit, estimate breeding value, or estimate Breeding Worth or any other indicator of the animal's worth. Skilled persons will readily appreciate appropriate methodology for practising the methods of the invention. However, specific examples of appropriate methodology are described herein below.
  • Any animal may be selected for testing. However, by way of example an animal identified as a potential breeding animal or an animal that is a potential candidate for retention in the herd is selected.
  • DNA from a subject animal to be assessed may be extracted by a number of suitable methods known to those skilled in the art. Most typically, DNA is extracted from a blood or semen sample, and in particular from peripheral blood leucocytes.
  • the polymorphisms may be detected by any means capable of resolving single nucleotide polymorphisms. Such methods will be known to those of skill in the art to which the invention relates and include for example one or a combination of PCR, LCR, nucleic acid sequencing, RFLP, hybridisation with appropriate nucleic acid probes, Southern Blotting, electrophoretic separation including SSCP electrophoresis.
  • the presence or absence of a polymorphism may be detected and analysed through the use of nucleic acid sequences flanking the polymorphism, wherein the nucleic acid sequences flanking the polymorphism may be PCR primers or sites for enzyme restriction digests, or sites for location for unambiguous assignment of probe to target sites in a polymorphism detection method.
  • the nucleic acid sequences flanking the polymorphism may be PCR primers or sites for enzyme restriction digests, or sites for location for unambiguous assignment of probe to target sites in a polymorphism detection method.
  • amplification products are separated by agarose, agarose-acrylamide or polyacrylamide gel electrophoresis using standard methods. Amplification products isolated in this way may be eluted from an excised portion of the gel for further manipulation.
  • the nucleic acid may be removed from the excised portion of an agarose gel by heating the gel in a chaotropic solution, followed by extraction of the nucleic acid.
  • Separation and isolation of nucleic acids may also be performed by chromatographic techniques known in art. Numerous kinds of chromatography may be used in the present invention, including adsorption, partition, ion-exchange, hydroxylapatite, gel-filtration (molecular sieve), and reverse-phase. These may be performed in a number of formats including, column, paper, thin-layer, and gas chromatography as well as by batch HPLC or FPLC. The range of techniques also includes polymorphism detection by Single strand conformational polymorphism (SCCP) or similar based DNA denaturation and conformational detection systems.
  • SCCP Single strand conformational polymorphism
  • the amplification products are visualized.
  • a typical visualization method involves staining of a gel with ethidium bromide and visualization of bands under UV light.
  • the amplification products are integrally labeled with radio- or fiuorometrically-labeled nucleotides, the separated amplification products can be exposed to x-ray film or visualized under light of the appropriate excitatory wavelength.
  • a labeled nucleic acid probe is brought into contact with the amplified marker sequence.
  • the probe preferably is conjugated to a chromophore but may be radiolabeled or otherwise labeled to facilitate detection.
  • the probe is conjugated to a molecule, such as an antibody or biotin, or another molecule carrying a moiety to facilitate detection.
  • Some embodiments of the present invention encompass methods involving marker assisted selection wherein oligonucleotides are used as primers to detect polymorphisms in genetic markers, wherein the presence or absence of the polymorphism in the genetic marker is indicative of the presence or absence of the genetic trait, or vice versa.
  • the use of oligonucleotides as primers may involve attachment, binding or tethering of an oligonucleotide to an insoluble support, wherein the insoluble support is in the form of a "chip", otherwise known as an array or microarray.
  • the oligonucleotides are substrates, wherein typically a plurality of substrates is coupled, tethered or otherwise attached to the chip.
  • a plurality of oligonucleotides may be positioned upon a chip by any suitable method known in the art, for example, by pipette, ink-jet printing, contact printing or photolithography.
  • the chip may be comprised of at least one element, with each element comprising at least one oligonucleotide.
  • the at least one element may be comprised of a plurality of oligonucleotides of the same sequence.
  • the number of elements comprising a chip may be any number, and where a plurality of elements is positioned on a chip, the elements may be spaced apart at a uniform or a variable distance, or a combination thereof. In some embodiments, the elements may be positioned randomly, with the respective location of each element then determined.
  • the size and shape of the elements will depend upon the particular application of the present invention, and different sized and shaped elements may be combined into a single chip.
  • the surface of the chip may be substantially planar or may have features such as depressions or protuberances, and the elements may be positioned either into the depressions or onto the protuberances. Such depressions may provide a reservoir for solutions into which the elements are immersed, or such protuberances may facilitate drying of the elements.
  • elements may be placed in each well of a 96 well plate.
  • the chip may include unique identifiers such as indicia, radio frequency tags, integrated devices such as microprocessors, barcodes or other markings in order to identify each of the elements.
  • the unique identifiers may additionally or alternatively comprise the depressions or protuberances on the surface of the array. Furthermore, the unique identifiers can provide for correct orientation or identification of the chip. The unique identifiers may be read directly by a data capture device or by an optical scanner or detector.
  • each of the genotyped SNPs there is a phenotypic effect for each allele or for each of the 3 ⁇ genotypic states (heterozygous, homozygous minor allele, homozygous major allele).
  • the appropriate phenotypic effect based on the animal's allelic or genotypic state. This process can be repeated for each of the assayed SNPs and the appropriate phenotypic effects for each SNP summed to give, for example, a Genomic Breeding Value for the animal. This would be repeated for each trait for which a Genomic Breeding Value is to be estimated.
  • Breeding values can be calculated/estimated by combining the Genomic Breeding Value with other sources of information such as phenotypic information on the animal itself and/or phenotypic information on genetically related animals for example but not limited to progeny, parents and siblings. In combining the different data sources appropriate weightings should be used that reflect the reliability of each information source.
  • Breeding Worth An economic index such as Breeding Worth can be calculated by summing the estimated breeding values for milk fat, protein, milk volume, liveweight, fertility, mild somatic cells and residual survival each weighted by an economic value.
  • the phenotype of a particular animal for a particular trait can be predicted on the basis of the presence or absence of one or more SKP correlated with the particular trait, as outlined in the tables 2 to 161 herein. Further, phenotypic performance for the animals can be calculated by combining the Genomic Breeding Value with other sources of information such as phenotypic information on the animal itself and/or phenotypic information on genetically related animals for example but not limited to progeny, parents and siblings. In combining the different data sources appropriate weightings should be used that reflect the reliability of each information source.
  • kits may comprise a probe or pairs of primers designed to hybridize specifically to individual genetic markers of interest in the practice of the present invention. Also included may be enzymes, cofactors and other reagents suitable for amplifying nucleic acids, including various polymerases, deoxynucleotides, metal salts and buffers to provide the necessary reaction mixture for amplification. Such kits also may include enzymes and other reagents required for detection of specific nucleic acids or amplification products. Such kits may comprise, in suitable means, distinct containers- for each individual reagent or enzyme as well as for each probe or primer pair.
  • kits may contain a primer pair comprising a nucleotide sequence for the amplification of a region of the genetic marker containing one of the polymorphisms described herein.
  • the following evaluation information describes the calculation of phenotypes that have been used in the analysis by the inventors to identify SNPs that are correlated and affect the phenotype.
  • the BVs reported from these models are calculated as the simple average of the four 270-day lactation BVs.
  • genetic groups are assigned by breed, sex of missing parent, birth year and country of origin. Four breed classes are assigned genetic grouping, namely, Holstein-Friesian, Jersey, Ayrshire-Red, and other breeds. Genetic groups are assigned in five year intervals from 1960 to 1980 then yearly, with the first birth year group being prior to 1960. Country of origin was defined as New Zealand, North American and Other. Missing male parents of New Zealand origin had two categories: (i) unknown male but known from mating records to be an artificial insemination proven sire, or ( ⁇ ) completely unknown male.
  • Liveweight The statistical model for liveweight is a repeated record, single trait, additive effects repeatability model. It includes effects for herd-year-season-age contemporary group, age at calving in months (nested within breed), stage of lactation when weighed (nested within age), heterosis, genetic merit of the animal, and random non-additive genetic and permanent environment effects.
  • Cow Fertility The objective for herd reproductive performance in most New Zealand herds is to achieve high pregnancy rates in a short time period following the planned start of mating, and to maintain calving intervals very close to 365 days. In this system successful reproduction depends on two factors which display genetic variation.
  • the first factor is the ability of the cow to resume cycling soon after calving, and to be mated early in the herd's mating period.
  • the second factor is the cow's ability to conceive, sustain a pregnancy and calve early in the herd's subsequent calving period.
  • Animal Evaluation has developed a genetic evaluation of cow fertility that incorporates both these aspects of successful reproductive performance in seasonal dairying. Mating records - Being presented for mating in the first 21 days of the herd's mating period (PM21) is scored 1 for the cows that are mated in this period, and 0 for cows which fail to be mated.
  • CR42 standing for Calving Rate in the first 42 days of the herd's calving period.
  • CR42 is scored 1 for cows that successfully re-calve in the first 42 days, and 0 for cows that fail to re-calve in this period.
  • CR42 is coded "missing" for cows which leave the herd prior to the re-calving period for reasons other than low fertility, or which have not yet had the opportunity to re-calve to the recorded mating.
  • Somatic Cells in milk - Test day records for somatic cell counts are transformed into somatic cell scores (SCS) by taking the log (base 2) of test day SCC/1000.
  • SCS is analysed in a multiple trait random regression animal model.
  • the two traits are first lactation SCS — and second and third lactation SCS analysed as repeated observations of a single trait.
  • the statistical model for analysis of a cow with SCS records includes effects for herdyear-season-age-testday contemporary groups, induced lactation, heterosis, age at calving (in months nested within breed class), stage of lactation, genetic group, genetic merit of the animal, random non- additive genetic and permanent environment effects, and random residual effects. Results for breeding values averaged over the two traits are reported.
  • Herd-life - Herd-life is defined as the interval from the date a cow has her first calf to the date when she has her last herd test, and is recorded in days. It is evaluated using a single-trait animal model.
  • the multiple- trait (MT) animal model used for the national genetic evaluation of survival contains 4 survival traits (SV12, SV13, SV14, SV15) and 9 predictor traits. The model can cope with missing data on any combination of traits.
  • SV15 is the trait reported by the AE system (converted into days of herd life). Each individual trait record was modelled as:
  • y, j i c i is the record for ith trait
  • hysjj is the jth herd-year-season fixed effect for a cow' s first lactation for trait i, with season referring to spring or autumn calving period
  • hti S is the linear regression coefficient for the sth heterosis effect for trait i
  • V ⁇ ns is the sth heterosis covariate for animal n
  • a ⁇ is the random additive genetic effect of animal k for trait i
  • ey H is the random residual associated with record yijkl.
  • Residual Survival has been defined in a way that ensures that herd-life is counted only once in the index.
  • Residual Survival is defined as "Herd-life after accounting for the genetic effects of production, liveweight, fertility and milk somatic cells on herd life.”
  • the Residual Survival trait included in BW is calculated from the following equation, where EBV stands for Estimated Breeding Value.
  • EBV(Total Long'ty) 5.434*EBV(Milkfat) + 4.408*EBV(Protein) + 0.03815*EBV(Milk) -
  • the estimated Residual Survival Breeding Values calculated by this method are uncorrelated .with the production, liveweight and fertility traits included in the BW index. This property is important in order to ensure that effects on herd life are counted only once in the BW index.
  • Management and Conformation Traits The models for the linear management and conformation traits (apart from Udder overall) are single record, multiple trait, additive genetic effects models.
  • the statistical model for analysis of a cow with linear type scores includes effects for herd-year-season contemporary group, stage of lactation class when scored and age at first calving class (in months nested within breed), heterosis, genetic group, animal genetic merit and the random residual.
  • the four farmer-scored management traits (Adaptability to milking, Shed temperament, Milking speed, Overall opinion) are evaluated together in a multiple trait evaluation that takes the genetic correlations amongst the four traits into account.
  • the inspector-scored traits associated with body conformation (Stature, Capacity, Rump angle, Rump width, Legs, Dairy conformation) are evaluated together in a multiple trait evaluation that takes the genetic correlations amongst these six traits into account.
  • the inspector-scored traits associated with udder conformation (but excluding Udder overall) are analysed together in a multiple trait evaluation. These traits are Udder support, Front udder, Rear udder, Front teat placement, and Rear teat placement. They are evaluated together in a multiple trait evaluation that takes the genetic correlations amongst the five traits into account.
  • Udder overall is evaluated in a single trait model. Breeding Values for individual traits are expressed in the units in which the trait is measured.
  • Calving Difficulty - Calving Difficulty Breeding Values are supplied to help Artificial Breeding organisations assess the suitability of bulls for mating with yearling heifers; and to give farmers knowledge about bulls which cause higher than usual rates of calving assistance when mated to their cows and heifers.
  • a sire's Calving Difficulty Breeding Value predicts the percentage of assisted carvings expected when he is mated to yearling heifers. The higher the BV, the higher the expected percentage of assisted calvings. The average BV of sires born in 1985 is set to zero. All breeds have been evaluated together for the calculation of Calving Difficulty BVs.
  • the Calving Difficulty BV is expressed in terms of assisted births in first- calving heifers, the BV can also be used to identify bulls that are expected to increase rates of calving assistance for cows carrying the bulls' calves.
  • the records used for the analysis comprise over 5 million records of calving assistance collected from New Zealand herds since 1994. The records were extracted in January 2006.
  • the BV for Calving Difficulty was estimated with a multiple-trait sire model using BLUP methodology (best linear unbiased prediction). The two traits were: - assistance for calves born to heifers, and - assistance for calves born to cows.
  • the statistical model used in the estimation was:
  • Body Condition Score Breeding Values - Body condition score (BCS) is commonly used as a method to assess body energy reserves.
  • BCS Body Condition Score
  • breeders are interested in knowing about sires that transmit lower or higher BCS for their daughters in early lactation when cows' body reserves are being mobilised for lactation at the same time as the cows are expected to get back in calf. Consequently Estimated Breeding Values for day 60 of first lactation heifers have been calculated for all AE Enrolled Sires.
  • Persistency Breeding Values have been calculated for milkfat, protein, and volume.
  • the Persistency BVs are estimates of the genetic ability of cows to maintain production subsequent to peak of lactation. They are reported on a scale where higher values correspond to greater persistency of lactation after the peak. Describing the mathematical technique used is beyond the scope of this Introduction. Two explanatory points are relevant. Cows with persistent lactation curves can have high total lactation yields, average total lactation yields or low total lactation yields.
  • the persistency measure is designed to be independent of total yield - so farmers ought not to use high Persistency Breeding Values in an attempt to select for higher yields.
  • Persistency Breeding Values are reported in the same units as the dairy production traits - kilograms of milkfat, kilograms of protein, and litres of volume.
  • a Persistency BV of +5 kg can be interpreted as the genetic predisposition to yield 5 kg more in the lactation period after the 115th day of lactation compared to the earlier lactation period.
  • a Persistency BV of -5 kg can be interpreted as the genetic pre-disposition to yield 5 kg less in the lactation period after the 115th day of lactation compared to the earlier lactation period.
  • the total lactation period used for the evaluation is 270 days.
  • Gestation length Gestation length is the number of days from date of insemination to the date of parturition.
  • the average number of days for Gestation length in dairy bovine is 282 days.
  • a breeding value of -10 can be interpreted as an animal that will leave progeny on average 5 days shorter than the dairy bovine average.
  • Once a dayCOAD) index A number of farmers are milking their cows once a day. To breed cows that are more suited to OAD milking an index has been developed.
  • the index includes information for Fat, Protein, Milk and Somatic Cells where conversion equations have been developed to estimate OAD BVs for these traits from Twice-a-day (TAD) BVs. For the traits Liveweight, Fertility and Residual Survival TAD BVs for these traits are used.
  • the OAD Index uses the same economic weightings for each trait as used in BW.
  • High input index To give high input farmers more help to breed the animals suited to their systems, a High Input Index has been developed.
  • the High Input index uses information and economic weights appropriate for the average high input system.
  • the High Input index considers all of the traits in BW plus udder overalL
  • the High Input index places more emphasis on the somatic cell score, and weights almost one-tenth of the index on the udder than BW.
  • the BW is the sum of the Breeding Values for milkfat, protein, milk volume, liveweight, fertility, milk somatic cells and residual survival each weighted by an economic value.
  • the BW economic values for each trait represent the expected net income per unit of genetic change (per unit of feed) from breeding replacements.
  • the economic values are calculated using a bio ⁇ economic devised to value technological change.
  • the model includes income streams from milk production, cull cows and bobby calf sales and cost streams associated with maintaining and growing cows and replacements, the feed required for production and dairy cash expenses. Predictions of future milk component prices are taken into account. The prices and costs used in the farm model are reviewed annually.
  • the unit of feed adopted for reporting economic values is 4.5 tonnes of dry matter of feed containing 10.5 megajoules of metabolisable energy per kilogram.
  • the economic values used in the BW are given in the following table.
  • Breeding Worth BW () - The expected ability of an animal to breed replacements which are efficient converters of feed into profit.
  • a Breeding Worth of 206 indicates the bull is expected to generate an extra $206 profit per year per unit of feed, through breeding replacements, compared with using a bull with a BW of zero.
  • the reliability figure is the amount of confidence we can place in the figure. The more information included in the evaluation, the greater the reliability and less likely it is to change with additional records. Reliability ranges from 0%, meaning we know nothing about the animal or any of its ancestors, to 99%. If a sire has a Milkfat Breeding Value of +25 with 80% reliability it is expected that his future Milkfat Breeding Value would be in the interval of +15 to +35 in the great majority of cases. If a sire has a Milkfat Breeding Value of +25 with 95% reliability it is expected that his future Milkfat Breeding Value would be in the interval of +20 to +30 in the great majority of cases. The reliability reflects the amount of information used in the calculation of the Breeding Value.
  • Breeding Value The genetic merit of an animal for individual traits relative to a base zero (1985 born cow). A Breeding Value of +10 kg protein indicates the bull will produce daughters, which on average are genetically superior by 5kg protein per lactation above the base cow (a bull can pass 1/2 of its genetic merit on average onto offspring).
  • Fat %, Protein % - The Fat % and Protein % are Breeding Value estimates for the sire.
  • the Traits Other than Production (TOP) Evaluation System is a national scheme for assessment of non-productive characteristics of dairy cattle (bulls and cows) based on linear assessment. Its main objective is to provide bull and herd owners with accurate and easy-to-use information for decision making.
  • Daughters are evaluated for 16 traits using a linear assessment on a scale from 1 to 9 where 1 and 9 represent the biological extremes. The traits are scored across breed and are defined as follows:
  • Adaptability to milking - describes how soon the animal settled into the milking routine after calving.
  • Shed Temperament describes the temperament of the animal in the shed while being handled and milked. It is a different trait to adaptability to milking and should be assessed once animals have settled into the milking routine. Vicious 1 5 9 Placid
  • Milking Speed - describes the milking speed of the animal, i.e. the time from putting cups on to the time milk flow stops or the cups are taken off.
  • Stature - describes the height at the shoulders of the animal. Each score represents 5 cm height at the withers. Under 105cm 1 5 9 Over 140cm
  • Capacity - describes the capacity of the animal as a combination of strength and depth of chest and body as viewed from side, rear and front in relation to the physical size of the animal.
  • Rump Angle - describes the angle of a line between the centre of the hips and the top of the pins. Pins high 1 5 9 Pins low/Sloping
  • Rump Width - describes the width of the pins, hips and thurls relative to the size of the animal.
  • Legs - describes the straightness or curvature of the back legs from an imaginary line between the thurls and the mid hoof while the animal is walking.
  • Udder Support - describes the strength of the suspensory ligament as viewed from the rear. It also includes udder depth relative to the hocks.
  • Front Udder - describes how well the front udder is attached to the body wall. Loose 1 5 9 Strong
  • Rear Udder - describes the height and width of the rear udder attachment, as distinct from udder support.
  • Rear Teat Placement - describes the placement of the rear teats (at the point of attachment to the udder) relative to the centre of the quarter as viewed from the rear. Wide 1 5 9 Close
  • Dairy Conformation All traits pertaining to dairy conformation including those body traits that have been linearly scored, but excluding all the udder traits.
  • Genomic BVs Table A below provides the correlation between the Genomic BVs calculated for each animal based on their SKP profiles and their estimated breeding values from the New Zealand Animal Evaluation Unit as at 19/12/2007.
  • the Genomic BVs for each trait were constructed from i) all SNPs that had a P-value ⁇ 0.05 and from ⁇ ) all SNPs evaluated regardless of the statistical significance.
  • the genomic value was calculated with the heterozygote being centred at zero and the minor allele homozygote have the value of Delta/2 and the major allele homozygote having the value of -Delta/2,.
  • Delta is the Difference between the means of two homozygotes (AA and aa) more specifically mean breeding values of bulls homozygous for minor allele - mean of breeding values of bulls homozygous for major allele.
  • AA and aa more specifically mean breeding values of bulls homozygous for minor allele - mean of breeding values of bulls homozygous for major allele.
  • the appropriate genotypic value was assigned to based on the given genotype for the locus. This was undertaken over all the appropriate loci and genomic value was calculated as the sum of all appropriate genotypic values.
  • Table A outlines the predictive ability of the SNPs.
  • the correlation for protein yield is 0.80 when all SNP effects from the across breed estimation are used and 0.80 for the SNP effects that had a P-value ⁇ 0.05.
  • the correlation for protein yield for the Holstein-Friesian breed is 0.69 when all SNP effects from the Holstein-Friesian breed estimation are used and 0.69 for the SNP effects that had a P-value ⁇ 0.05,
  • the correlation for protein yield for the Jersey breed is 0.67 when all SNP effects from the Jersey breed estimation are used and 0.67 for the SNP effects that had a P-value ⁇ 0.05,
  • the correlation for protein yield for the KiwiCross breed is 0.75 when all SNP effects from the KiwiCross breed estimation are used and 0.76 for the SNP effects that had a P-value ⁇ 0.05.
  • Body condition score 0.57 0.57 0.73 0.73 0.63 0.63 0.75 0.76
  • the inventors used statistical methods to identify SNPs associated with the relevant profit ranking or production trait. Analysis was undertaken across and within the 3 breeds in the dataset.
  • the units attached to the numerical values vary between traits, and include, for example, standard metric units such as weight, length and time, currency units such as dollars, percentages , and specifically designed unit ranges, for example, a range of 1 to 9 to describe differences in a particular trait.
  • the bulls are from the main bovine dairy breeds in New Zealand; Holstein-Friesian (1907), Jersey (1257), KiwiCross (265) and Ayrshire (1).
  • the KiwiCross breed is where the animals have a combination of the more than one breed in their genetic makeup and thus are crossbred animals. All the animals included in the study were considered unrelated, though the animals were related in a complex pedigree and therefore there is a moderate amount of relatedness and inbreeding. Genotyping was undertaken on a fee for service contract by Illumina ( " www.illnmina.com1. 54001
  • SNPs were genotyped on the Illumina Infinium Whole Genome Genotyping Standard Panel.
  • SNPs The locations of the SNPs were determined on the bovine sequence assembly Btau 4 (ftp://ftp.hgsc.bcm.tmc.edu/pub/data/Btaurus/fasta/Btau20070913-freeze/). Positions for 52329 out of 54001 SNPs were identified where the sequence has been allocated to a real chromosome. In this analysis 48365 SNPs were used as described in Table 1.
  • KiwiCross (KX) only including animals that are KiwiCross in the t-test analysis.
  • Tables 2 to 161 identify the SNPs that the inventors have identified to be associated with the relevant profit ranking or production trait as identified.
  • the invention has been described herein with reference to certain preferred embodiments, in order to enable the reader to practice the invention without undue experimentation. Those skilled in the art will appreciate that the invention is susceptible to variations and modifications other than those specifically described. It is to be understood that the invention includes all such variations and modifications. Furthermore, titles, headings, or the like are provided to enhance the reader's comprehension of this document, and should not be read as limiting the scope of the present invention.

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Abstract

L'invention concerne des marqueurs génétiques et des procédés servant d'indicateurs prévisionnels de caractéristiques de production chez des animaux, en particulier des bovins et permettant d'évaluer ou de déterminer, par exemple, la valeur d'élevage (Breeding Worth). Ces marqueurs génétiques peuvent indiquer une ou plusieurs caractéristiques, telles que la production de protéines, la capacité de lactation, l'état physiologique, la valeur d'élevage (Breeding Worth), la difficulté de vêlage ou sa capacité, la conformité à la production laitière, le pourcentage de graisses, la production de graisses, la persistance des graisses, la fertilité, l'état des pis et mamelles avant, la longueur de gestation, le niveau d'indice de production, les membres, le poids vivant, le volume laitier, la constance et la vitesse de la production laitière, la valeur d'élevage (Breeding Worth) journalière (OAD), l'opinion générale, PM21, le pourcentage de protéines, la constance des protéines, l'état des pis et mamelles arrière, la survie résiduelle, l'inclinaison et la largeur de la croupe, les cellules somatiques, la stature, le tempérament, la longévité totale, l'état général et l'entretien des pis, le volume de lactation journalière (OAD), la production de graisses journalière (OAD), la production de protéines journalière (OAD) et le nombre journalier de cellules somatiques (OAD).
PCT/NZ2008/000344 2007-12-21 2008-12-19 Marqueurs génétiques et procédés servant d'indicateurs prévisionnels de caractéristiques de production chez des animaux, en particulier des bovins Ceased WO2009048344A2 (fr)

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Cited By (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2014193247A1 (fr) * 2013-05-31 2014-12-04 Livestock Improvement Corporation Limited Marqueurs génétiques du nanisme et leur utilisation
CN115281145A (zh) * 2022-07-08 2022-11-04 河南省种牛遗传性能测定中心 一种基于测定日模型和动物模型blup筛选优质高产奶牛的育种方法
CN117852824A (zh) * 2024-01-09 2024-04-09 内蒙古盛健农牧业工程技术研究有限公司 一种基于智能化的奶山羊育种情况监控管理系统

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* Cited by examiner, † Cited by third party
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WO2007050735A2 (fr) * 2005-10-25 2007-05-03 Innovative Dairy Products Pty Ltd As Trustee For The Participants Of The Cooperative Research Centre For Innovative Dairy Products Marqueurs de traits de production

Cited By (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2014193247A1 (fr) * 2013-05-31 2014-12-04 Livestock Improvement Corporation Limited Marqueurs génétiques du nanisme et leur utilisation
CN115281145A (zh) * 2022-07-08 2022-11-04 河南省种牛遗传性能测定中心 一种基于测定日模型和动物模型blup筛选优质高产奶牛的育种方法
CN117852824A (zh) * 2024-01-09 2024-04-09 内蒙古盛健农牧业工程技术研究有限公司 一种基于智能化的奶山羊育种情况监控管理系统

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