WO2008024227A2 - Marqueurs génétiques et procédés permettant d'améliorer la génétique des porcs - Google Patents

Marqueurs génétiques et procédés permettant d'améliorer la génétique des porcs Download PDF

Info

Publication number
WO2008024227A2
WO2008024227A2 PCT/US2007/017949 US2007017949W WO2008024227A2 WO 2008024227 A2 WO2008024227 A2 WO 2008024227A2 US 2007017949 W US2007017949 W US 2007017949W WO 2008024227 A2 WO2008024227 A2 WO 2008024227A2
Authority
WO
WIPO (PCT)
Prior art keywords
snps
tables
animal
genotype
snp
Prior art date
Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
Ceased
Application number
PCT/US2007/017949
Other languages
English (en)
Other versions
WO2008024227A3 (fr
Inventor
Archie C. Clutter
Fengxing Du
Laura Grapes
Michael D. Grosz
Nengbing Tao
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
Monsanto Technology LLC
Original Assignee
Monsanto Technology LLC
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by Monsanto Technology LLC filed Critical Monsanto Technology LLC
Publication of WO2008024227A2 publication Critical patent/WO2008024227A2/fr
Publication of WO2008024227A3 publication Critical patent/WO2008024227A3/fr
Anticipated expiration legal-status Critical
Ceased legal-status Critical Current

Links

Classifications

    • 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
    • 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
    • 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
    • C12Q2600/172—Haplotypes

Definitions

  • the invention relates to the enhancement of desirable characteristics in swine. More specifically, it relates to genetic markers and methods for improving swine genetics.
  • Genomics offers the potential for greater improvement in traits of pork production and quality through the discovery of genes, or genetic markers linked to genes, that account for genetic variation and can be used for more direct and accurate selection. Although some markers with associations with pork production and quality traits have been reported (see Rothschild and Plastow, 1999, AgBioTechNet 10: 1-8 for a review), each of these traits is extremely complex and it is likely that a large number of genes per trait must be discovered to create significant value in selection. Only through comprehensive and powerful scans of the entire porcine genome can this goal be achieved.
  • the pigs harvested for pork around the world are typically produced by crossing closed breeding populations with distinct characteristics for maternal productivity, growth efficiency and meat quality. These closed populations typically have low levels of inbreeding and genome scans yielding markers that can be used across the population for selection require densely-spaced genetic markers on each of the porcine chromosomes.
  • the application of such a marker map to discover and Finely-map genes contributing to variation in growth, body composition and pork quality traits is described herein.
  • the large number of resulting linked markers can be used in several methods of marker or marker-assisted selection, including whole-genome selection (Meu Giveaway et al., Genetics 2001) to improve the genetic merit of the population for these traits and the value created in the pork production chain.
  • Various embodiments of the invention provide isolated nucleic acids having the sequence of alleles comprising single nucleotide polymorphisms (SNPs) that are provided by the present invention. Aspects of these embodiments of the invention provide for isolated nucleic acids identical to all or a portion of the genomic sequences surrounding the SNPs (described in Tables 1 and 2), or identical to all or portion of the complementary strands of the genomic sequences surrounding the SNPs (described in Tables 1 and 2). For example the sequence may be 100% identical or greater than 99%, 98%, 97%, 96%, 95%, or 90% with all or a portion of the sequences described by Tables 1 and 2 and the SEQUENCE LISTING.
  • the isolated nucleic acid sequence may be 100% , greater than 99%, greater than 98%, greater than 97%, greater than 96%, greater than 95%, or greater than 90% identical with a contiguous segment of 17 or more nucleotides, 25 or more, 50 or more, or 100 or more nucleotides.
  • inventions of the invention provide methods for evaluating an animal's genotype at one or more positions in the animal's genome.
  • the animal's genotype is evaluated at a position within a segment of DNA (an allele) that contains at least one SNP selected from the SNPs described in the Tables and Sequence Listing of the present application.
  • Other embodiments of the invention provide methods for allocating animals for use based on their genotype (e.g. allocating for use as a breeding animal or to be sold for finishing and/or slaughter).
  • Various aspects of this embodiment of the invention provide methods that comprise: a) analyzing the animal's genomic sequence at one or more alleles (where the alleles analyzed each comprise at least one SNP) to determine the animal's genotype at each of those alleles; b) analyzing the genotype determined for each allele to determine which allele of the SNP is present; c) allocating the animal for use based on its genotype at one or more of the alleles analyzed.
  • a) analyzing the animal's genomic sequence at one or more alleles where the alleles analyzed each comprise at least one SNP to determine the animal's genotype at each of those alleles
  • embodiment of the invention provide methods for allocating animals for use based on a favorable association between the animal's genotype, at one or more SNP alleles disclosed in the present application, and a desired phenotype.
  • the methods provide for not allocating an animal for a certain use because it has one or more SNP alleles that are either associated with undesirable phenotypes or are not associated with desirable phenotypes.
  • Other embodiments of the invention provide methods for selecting animals for use in breeding to produce progeny.
  • Various aspects of these methods comprise: A) determining the genotype of at least one potential parent animal at one or more locus/loci, where at least one of the loci analyzed contains an allele of a SNP selected from the group of SNPs described in Tables 1 and 2. B) Analyzing the determined genotype at one or more positions for at least one animal to determine which of the SNP alleles is present. C) Correlating the analyzed allele(s) with one or more phenotypes. D) Allocating at least one animal for use to produce progeny. [0012] Other embodiments of the invention provide methods for producing offspring animals (progeny animals).
  • aspects of this embodiment of the invention provide methods that comprise: breeding an animal that has been selected for breeding by methods described herein to produce offspring.
  • the offspring may be produced by purely natural methods or through the use of any appropriate technical means, including but not limited to: artificial insemination; embryo transfer (ET), multiple ovulation embryo transfer (MOET), in vitro fertilization (IVF), or any combination thereof.
  • databases or groups of databases each database comprising lists of the nucleic acid sequences, which lists include a plurality of the SNPs described in Tables 1 and 2.
  • Preferred aspects of this embodiment of the invention provide for databases comprising the sequences for 50 or more SNPs.
  • Other aspects of these embodiments comprise methods for using a computer algorithm or algorithms that use one or more database(s), each database comprising a plurality of the SNPs described in Tables 1 and 2 to identify phenotypic traits associated with the inheritance of one or more alleles of the SNPs, and/or using such a database to aid in animal allocation.
  • Still other embodiments of the invention provide diagnostic kits and/or arrays for detecting one or more of the SNPs described in Tables 1 and 2.
  • Further embodiments of the invention provide methods for identifying associations between one or more of the SNPs described in Tables 1 and 2 and one or more phenotypic traits.
  • Additional embodiments of the invention provide methods for identifying other genetic markers that are in allelic association with one or more of the SNPs described in Tables 1 and 2.
  • allocating animals for use and “allocation for use” preferably mean deciding how an animal will be used within a herd or that it will be removed from the herd to achieve desired herd management goals.
  • an animal might be allocated for use as a breeding animal or allocated for sale as a non- breeding animal (e.g. allocated to animals intended to be sold for meat).
  • animals may be allocated for use in sub-groups within the breeding programs that have very specific goals (e.g. to improve meat color or carcass composition). Accordingly, even within the group of animals allocated for breeding purposes, there may be more specific allocation for use to achieve more specific and/or specialized breeding goals.
  • animal or “animals” preferably refer to pigs/swine.
  • composition and “body composition” preferably refer to measurements of the physical characteristics of the animal/pig and/or its carcass or to the characteristics themselves.
  • growth refers to the measurement of various parameters associated with an increase in an animal's size/weight.
  • linkage disequilibrium preferably means allelic association wherein Ai and Bi (as used in the above definition of allelic association) are present on the same chromosome.
  • the term “meat color” refers to measurements of color of meat obtained from a slaughtered animal.
  • the term “meat quality” refers measurements of the palatability and/or eating qualities (e.g. marbling, texture, and tenderness) of meat from a slaughtered animal.
  • natural breeding preferably refers to mating animals without human intervention in the fertilization process. That is, without the use of mechanical or technical methods such as artificial insemination or embryo transfer. The term does not refer to selection of the parent animals.
  • quantitative trait is used to denote a trait that is controlled by multiple (two or more, and often many) genes each of which contributes small to moderate effect on the trait. The observations on quantitative traits often follow a normal distribution.
  • QTL quantitative trait locus
  • reproductive material includes, but is not limited to semen, spermatozoa, ova, and zygote(s).
  • single nucleotide polymorphism refers to a location in an animal's genome that is polymorphic within the population. That is, within the population some individual animals have one type of base at that position, while others have a different base.
  • SNP single nucleotide polymorphism
  • a SNP might refer to a location in the genome where some animals have a "G" in their DNA sequence, while others have a llrpy*
  • hybridization under stringent conditions and “stringent hybridization conditions” preferably mean conditions under which a "probe” will hybridize to its target sequence to a detectably greater degree than to other sequences (e.g., at least 5-fold over background).
  • Stringent conditions are target- sequence-dependent and will differ depending on the structure of the polynucleotide. By controlling the stringency of the hybridization and/or washing conditions, target sequences that are 100% complementary to the probe can be identified (homologous probing). Alternatively, stringency conditions can be adjusted to allow some mismatching in sequences so that lower degrees of similarity are detected (heterologous probing).
  • stringent conditions will be those in which the salt concentration is less than about 1.5 M Na ion, typically about 0.01 to 1.0 M Na ion concentration (or other salts) at pH 7.0 to 8.3 and the temperature is at least about 30 0 C for short probes (e.g., 10 to 50 nucleotides) and at least about 60 0 C for long probes (e.g., greater than 50 nucleotides). Stringency may also be adjusted with the addition of destabilizing agents such as formamide.
  • Exemplary moderate stringency conditions include hybridization in 40 to 45% formamide, 1 M NaCl, 1% SDS at 37 0 C, and a wash in 0.5X to IX SSC at 55 to 60 0 C.
  • Exemplary high stringency conditions include hybridization in 50% formamide, 1 M NaCl, 1% SDS at 37°C, and a wash in 0.1 X SSC at 60 to 65 0 C.
  • the duration of hybridization is generally less than about 24 hours, usually about 4 to about 12 hours.
  • T m the thermal melting point
  • % GQ-0.61 (% form)-500/L the thermal melting point
  • M the molarity of monovalent cations
  • % GC the percentage of guanine and cytosine nucleotides in the DNA
  • % form is the percentage of formamide in the hybridization solution
  • L the length of the hybrid in base pairs.
  • the T m is the temperature (under defined ionic strength and pH) at which 50% of a complementary target sequence hybridizes to a perfectly matched probe.
  • T n is reduced by about 1 0 C for each 1% of mismatching; thus, T m , hybridization, and/or wash conditions can be adjusted to hybridize to sequences of the desired identity. For example, if sequences with 90% identity are sought, the T n , can be decreased 10 0 C.
  • stringent conditions are selected to be about 5°C lower than the T n , for the specific sequence and its complement at a defined ionic strength and pH.
  • highly stringent conditions can utilize a hybridization and/or wash at 1 , 2, 3, or 4°C lower than the thermal melting point (T m ); moderately stringent conditions can utilize a hybridization and/or wash at 6, 7, 8, 9, or 10 0 C lower than the thermal melting point (T n ,); low stringency conditions can utilize a hybridization and/or wash at I I, 12, 13, 14, 15, or 20 0 C lower than the thermal melting point (T n ,).
  • T n a temperature at which the desired degree of mismatching results in a T n , of less than 45 C C (aqueous solution) or 32°C (formamide solution).
  • SSC concentration a temperature at which a higher temperature can be used.
  • An extensive guide to the hybridization of nucleic acids is found in Tijssen (1993) Laboratory Techniques in Biochemistry and Molecular Biology— Hybridization with Nucleic Acid Probes, Part I, Chapter 2 (Elsevier, N. Y.); and Ausubel et al., eds. (1995) Current Protocols in Molecular Biology, Chapter 2 (Greene Publishing and Wiley-Interscience, New York). See also Sambrook et al. (1989) Molecular Cloning: A Laboratory Manual (2d ed., Cold Spring Harbor Laboratory Press, Plainview, N. Y.).
  • Various embodiments of the present invention provide methods for evaluating an animal's (especially a pig's) genotype at one or more positions in the animal's genome. Aspects of these embodiments of the invention provide methods that comprise determining the animal's genomic sequence at one or more locations (loci) that contain single nucleotide polymorphisms (SNPs). Specifically, the invention provides methods for evaluating an animal's genotype by determining which of two or more alleles for the SNP are present for one or more SNPs selected from the group consisting of the SNPs described in Tables 1 and 2 of the instant application.
  • the animal's genotype is evaluated to determine which allele is present for 10 or more SNPs selected from the group of SNPs described in Tables 1 and 2. More, preferably the animal's genotype is determined for positions corresponding with 25, 50, 100, 200, 500, or 1000, or more of the SNPs described in Tables 1 and 2.
  • the animal's genotype is analyzed with respect to at least 1, 10, 25, 50, 100, 200, 500, or more SNPs that have been shown to be associated with growth, composition, meat color, or meat quality, or any combination thereof (see Table 1 for a list of the SNPs associated with these traits).
  • embodiments of the invention provides a method for genotyping for a single SNP or for genotyping 10 or more, 25 or more, 50 or more, 100 or more, 200 or more, or 500 or more SNPs that have been determined to be significantly associated with growth.
  • the genomic sequence at the SNP locus may be determined by any means compatible with the present invention.
  • Suitable means are well known to those skilled in the art and include, but are not limited to direct sequencing, sequencing by synthesis, primer extension, Matrix Assisted Laser Desorption /Ionization-Time Of Flight (MALDI-TOF) mass spectrometry, polymerase chain reaction-restriction fragment length polymorphism, microarray/multiplex array systems (e.g. those available from Affimetrix, Santa Clara, California), and allele- specific hybridization.
  • MALDI-TOF Matrix Assisted Laser Desorption /Ionization-Time Of Flight
  • Other embodiments of the invention provide methods for allocating animals for subsequent use (e.g. to be used as sire/dams or to be sold for immediate slaughter or to be sold for finishing or any other use).
  • Various aspects of this embodiment of the invention comprise determining at least one animal's genotype for at least one SNP selected from the group of SNPs described in Tables 1 and 2 (methods for determining animals' genotypes for one or more SNPs are described supra).
  • the animal's allocation for use may be determined based on its genotype at one or more, 10 or more, 25 or more, 50 or more, 100 or more, 300 or more, or 500 or more of the SNPs described in Tables 1 and 2.
  • the instant invention provides embodiments where analysis of the genotypes of the SNPs described in Tables 1 and 2 is the only analysis done.
  • Other embodiments provide methods where analysis of the SNPs disclosed herein is combined with any other desired type of genomic or phenotypic analysis (e.g. analysis of any genetic markers beyond those disclosed in the instant invention).
  • the SNPs analyzed may be selected from those SNPs only associated with growth, only composition, only meat color, only meat quality, or the analysis may be done for SNPs selected from any desired combination of traits. SNPs associated with various traits are listed in Table 1.
  • the animal's genetic sequence for the selected SNP(s) are evaluated to determine which allele of the SNP is present for at least one of the selected SNPs.
  • the animal's allelic complement for all of the determined SNPs is evaluated.
  • the animal is allocated for use based on its genotype for one or more of the SNP positions evaluated.
  • the allocation is made taking into account the animal's genotype at each of the SNPs evaluated, but its allocation may be based on any subset or subsets of the SNPs evaluated. [0040] The allocation may be made based on any suitable criteria.
  • Phenotypic traits that may be associated with the SNPs of the current invention include, but are not limited to: growth traits, body and/or carcass composition, meat quality, meat color, health traits (resistance to disease and injury and stress tolerance), breeding traits such as litter size, survival of young, breeding efficiency, and length of reproductive life of the female.
  • allocation for use of the animal may entail either positive selection for the animals having the desired genotype(s) (e.g. the animals with the desired genotypes are selected for breeding purposes), negative selection of animals having undesirable genotypes (e.g. animals with an undesirable genotypes are culled from the herd), or any combination of these methods.
  • animals identified as having SNP alleles associated with desirable phenotypes are allocated for use consistent with that phenotype (e.g. allocated for breeding based on phenotypes positively associated with improved growth).
  • animals that do not have SNP genotypes that are positively correlated with the desired phenotype (or possess SNP alleles that are negatively correlated with that phenotype) are not allocated for the same use as those with a positive correlation for the trait.
  • Other embodiments of the invention provide methods for selecting potential parent animals ⁇ i.e., allocation for breeding).
  • Various aspects of this embodiment of the invention comprise determining at least one animal's genotype for at least one SNP selected from the group of SNPs described in Tables 1 and 2.
  • determination of whether and how an animal will be used as a potential parent animal may be based on its genotype at one or more, 10 or more, 25 or more, 50 or more, 100 or more, 300 or more, or 500 or more of the SNPs described in Tables 1 and 2.
  • various aspects of these embodiments of the invention provide methods where the only analysis done is to genotype the animal for one or more of the SNPs described in Tables 1 and 2.
  • SNPs are analyzed using any other desired genomic or phenotypic analysis (e.g. analysis of any genetic markers beyond those disclosed in the instant invention).
  • the SNP(s) analyzed may all be selected from those associated only with growth, or only with composition, or only meat color, or only meat quality. Conversely, the analysis may be done for SNPs selected from any desired combination of these or other traits.
  • the animal's genetic sequence at the site of the selected SNP(s) have been determined, this information is evaluated to determine which allele of the SNP is present for at least one of the selected SNPs.
  • the animal's allelic complement for all of the sequenced SNPs is evaluated.
  • the animal's allelic complement is analyzed and correlated with the probability that the animal's progeny will express one or more phenotypic traits.
  • the animal is allocated for breeding use based on its genotype for one or more of the SNP positions evaluated and the probability that it will pass the desired genotype(s)/allele(s) to its progeny.
  • the breeding allocation is made taking into account the animal's genotype at each of the SNPs evaluated. However, its breeding allocation may be based on any subset or subsets of the SNPs evaluated.
  • breeding allocation may be made based on any suitable criteria. For example, breeding allocation may be made so as to increase the probability of enhancing a single certain desirable characteristic in a population (in preference to other characteristics); alternatively, the selection may be made so as to generally maximize overall production based on a combination of traits. The allocations chosen are dependent on the breeding goals.
  • the animals used to produce the progeny are those that have been allocated for breeding according to any of the embodiments of the current invention. Those using the animals to produce progeny may perform the necessary analysis or, alternatively, those producing the progeny may obtain animals that have been analyzed by another.
  • the progeny may be produced by any appropriate means, including, but not limited to using: (i) natural breeding, (ii) artificial insemination, (iii) in vitro fertilization (FVF) or (iv) collecting semen/spermatozoa and/or at least one ovum from the animal and contacting it, respectively with ova/ovum or semen/spermatozoa from a second animal to produce a conceptus by any means.
  • FVF in vitro fertilization
  • the progeny are produced by a process comprising natural breeding.
  • the progeny are produced through a process comprising the use of standard artificial insemination (AI), in vitro fertilization, multiple ovulation embryo transfer (MOET), deep intrauterine insemination (DIUI), or any combination thereof.
  • AI artificial insemination
  • MOET multiple ovulation embryo transfer
  • DIUI deep intrauterine insemination
  • inventions provide for methods that comprise allocating an animal for breeding purposes and collecting/isolating genetic material from that animal: wherein genetic material includes but is not limited to: semen, spermatozoa, ovum, zygotes, blood, tissue, serum, DNA, and RNA.
  • the various embodiments of the instant invention provide for databases comprising all or a portion of the sequences corresponding to at least 10 SNPs described in Tables 1 and 2.
  • the databases comprise sequences for 25 or more, 50 or more, 100 or more, 200 or more, 500 or more, 1000 or more, or substantially all of the SNPs described in Tables 1 and 2.
  • inventions provide methods wherein one or more of the SNP sequence databases described herein are accessed by one or more computer- executable programs. Such methods include, but are not limited to, use of the databases by programs to analyze for an association between the SNP and a phenotypic trait, or other user-defined trait (e.g. traits measured using one or more metrics such as gene expression levels, protein expression levels, or chemical profiles), and programs used to allocate animals for breeding or market.
  • a phenotypic trait e.g. traits measured using one or more metrics such as gene expression levels, protein expression levels, or chemical profiles
  • Other embodiments of the invention provide methods comprising collecting genetic material from an animal that has been allocated for breeding. Wherein the animal has been allocated for breeding by any of the methods disclosed as part of the instant invention.
  • inventions are drawn to isolated nucleic acids comprising 17 or more contiguous nucleotides corresponding to any one of the SNP sequences described in Tables 1 and 2 (i.e. any of SEQ ID NO: 1—521 1 and the Tables).
  • the isolated nucleic acid comprises a nucleotide corresponding with the polymorphic site in the sequence (i.e. it contains the site that defines the SNP's polymorphism as described in Tables 1 and 2).
  • isolated nucleic acid molecules comprising 100 or more contiguous nucleotides which are at least 90 percent identical with any of SEQ ID NO: 1-5211.
  • the isolated nucleic comprises the polymorphic site for one or more SNPs selected from the group of SNPs described in Tables 1 and 2.
  • kits or other diagnostic devices for determining which allele of a SNP is present in a sample; wherein the SNP(s) are selected from the group of SNPs described in Tables 1 and 2.
  • the kit or device provides reagents/instruments to facilitate a determination as to whether nucleic acid corresponding to the SNP is present. Such kit/or device may further facilitate a determination as to which allele of the SNP is present.
  • the kit or device comprises at least one nucleic acid oligonucleotide suitable for DNA amplification (e.g. through polymerase chain reaction).
  • the kit or device comprises a purified nucleic acid fragment capable of specifically hybridizing, under stringent conditions, with at least one allele of at least one SNP described in Tables 1 and 2.
  • the kit or device comprises at least one nucleic acid array (e.g. DNA micro-arrays) capable of determining which allele of one or more of the SNPs described in Tables 1 and 2 is present in a sample.
  • nucleic acid array e.g. DNA micro-arrays
  • Preferred aspects of this embodiment of the invention provide DNA micro-arrays capable of simultaneously determining which allele is present in a sample for 10 or more SNPs.
  • the DNA micro-array is capable of determining which SNP allele is present in a sample for 25 or more, 50 or more, 100 or more, 200 or more, 500 or more, or 1000 or more SNPs. Methods for making such arrays are known to those skilled in the art and such arrays are commercially available (e.g. from Affimetrix, Santa Clara, California).
  • Other embodiments of the present invention provide methods for identifying, within a plurality of animals, an association between one or more of the SNPs described in Tables 1 and 2 and at least one phenotypic trait.
  • the method comprises: (a) measuring one or more phenotypic traits in a plurality of animals; (b) determining the genotype for at least one SNP for a plurality of animals, wherein at least one SNP genotype determined is selected from the group of SNPs described in Tables 1 and 2; and (c) statistically correlating the presence of at least one phenotypic trait with the presence of an allele of at least one SNP selected from the group of SNPs described in Tables 1 and 2; wherein the presence of different alleles for that SNP is associated with different phenotypic attributes or with distinguishable phenotypic variation.
  • the presence of different alleles, for at least one SNP is associated with a statistically distinct phenotypic difference in the animals possessing them.
  • the distinct phenotype may be detectable either between individual animals or it may be detectable when pluralities of the animals having different genotypes are compared as groups.
  • the method comprises: (a) identifying a marker, Bi, that is suspected of being in allelic association with at least one marker, Aj, wherein Ai is selected from the group of SNPs described in Tables 1 and 2; (b) determining whether A
  • represents an allele at one locus (A SNP described by Tables 1 and 2); Bi represents a genetic marker at another locus; f(AiB
  • Bi is a SNP. Even more preferred aspects of this embodiment of the invention provide methods for identifying genetic markers in linkage disequilibrium with one or more SNPs selected from the group of SNPs described in Tables 1 and 2. In other aspects of these embodiments of the invention the value of r 2 is greater than 0.5, greater than 0.7, or greater than 0.9.
  • Additional embodiments of the invention provide for genetic markers that are in allelic association with one or more of the SNPs described in Tables 1 and 2. Markers provided as part of this embodiment of the invention may be identified by any suitable means known to those of ordinary skill in the art. A marker falls within this embodiment of the invention if it is determined to be in allelic association with one or more of the SNPs described in Tables 1 and 2 as defined by Equation 1 , supra, where r 2 is greater than 0.2, greater than 0.5, greater than 0.7, or greater than 0.9. In preferred aspects of these embodiments of the invention the markers are in linkage disequilibrium with one or more of the SNPs described in Tables 1 and 2.
  • Genetic markers that are in allelic association with any of the SNPs described in the Tables may be identified by any suitable means known to those skilled in the art. For example, a genomic library may be screened using a probe specific for any of the sequences of the SNPs described in the Tables. In this way clones comprising at least a portion of that sequence can be identified and then up to 300 kilobases of 3' and/or 5' flanking chromosomal sequence can be determined. By this means, genetic markers in allelic association with the SNPs described in the Tables will be identified.
  • chromosomal location of a SNP associated with a particular phenotypic variation can be determined, by means well known to those skilled in the art. Once the chromosomal location is determined genes suspected to be involved with determination of the phenotype can be analyzed. Such genes may be identified by sequencing adjacent portions of the chromosome or by comparison with analogous section of the human genetic map (or known genetic maps for other species).
  • Other embodiments of the invention provide methods for identifying causal mutations that underlie one or more quantitative trait loci (QTL).
  • QTL quantitative trait loci
  • Various aspects of this embodiment of the invention provide for the identification QTL that are in allelic association with one or more of the SNPs described in Tables I and 2. Once these SNPs are identified, it is within the ability of skilled artisans to identify mutations located proximal to such SNP(s). Further, one skilled in the art can identify genes located proximate to the identified SNP(s) and evaluate these genes to select those likely to contain the causal mutation. Once identified these genes and the surrounding sequence can be analyzed for the presence of mutations, in order to identify the causal mutation.
  • the new linkage mapping tools build on the basic mapping principles programmed in CRIMAP to improve efficiency through partitioning of large pedigrees, automation of chromosomal assignment and two-point linkage analysis, and merging of sub-maps into complete chromosomes.
  • the resulting whole-genome discovery map included -5,926 markers and a map length of 2,373.6 cM for an average map density of 2.41 markers/cM. The average gap between markers was 0.44 cM and the largest gap was 1 1.1 cM. This map provided the basis for whole-genome discovery and fine-mapping of QTL contributing to variation in pig growth, efficiency, carcass composition and meat quality.
  • Systems for discovery and mapping populations can take many forms.
  • the most effective strategies for determining population-wide marker/QTL associations include a large and genetically diverse sample of individuals with phenotypic measurements of interest collected in a design that allows accounting for non-genetic effects and includes information regarding the pedigree of the individuals measured.
  • three populations were used to discovery and map QTL: a population derived from the Pietrain breed, a population derived from the Duroc breed, and a composite of the other two populations produced by crossing followed by several generations of inter se mating.
  • DNA samples were collected from approximately 1,000 to 2,000 progeny per population; representing multiple sire and grandsire families. DNA samples were also collected from the sire of each progeny, and in some cases from additional members of the pedigree.
  • the progeny sampled from these populations had been measured for several phenotypic traits including average daily gain in weight, ultrasonically-measured fat thickness and loin muscle area, fat and muscle depth at slaughter, pH and water-holding capacity of the meat, color of the meat, intra-muscular fat or marbling in the meat, and tenderness of the meat.
  • DNA samples collected from the progeny and members of the pedigree were genotyped for approximately 4,600 SNP markers that are approximately evenly distributed across the WGDM and that were previously determined to be informative for mapping purposes in these populations. For each animal, and each SNP marker, a genotype is generated reflecting the alleles present on the chromosome pair at that locus (e.g., AA, AB or BB) and is used in subsequent marker/trait association analyses.
  • Measurements of periodic growth rate can be adjusted for the beginning age of the animal and the number of days measured.
  • Body composition measurements e.g., lean percentage
  • Data collected after slaughter are typically adjusted for the effect of day of slaughter.
  • Meat quality data can be adjusted for other relevant information (e.g., extended time to reach the cooler or excessive skinning). After adjustments for these non-genetic factors, the data can again be examined for outliers and values with a residual standard deviation of 4.0 or more excluded from analyses.
  • mapping the location of QTL through associations between marker genotypes and phenotypic traits can be approached in several ways, including simple regressions of each trait on the genotype for each SNP marker (e.g., trait regressed on number of "A" alleles: 0, 1, or 2) or analyses of families within the population to detect linkage between markers and QTL.
  • the marker/trait associations most useful as animal selection tools are those of markers tightly linked to a QTL and based on marker/QTL allele configurations that are present in most individuals across the population.
  • marker haplotypes with known parental origin By using ordered marker genotypes along the chromosome (marker haplotypes with known parental origin) to determine the probabilities at each locus that individuals with phenotypic data are EBD, marker alleles in population-wide linkage with valuable QTL alleles can be identified.
  • LD mapping was performed in the aforementioned discovery population using statistical analyses that require knowledge of ordered genotypes. Ordered genotypes of an individual can be inferred partially or with certainty conditional on pedigree information and observed genotype data (Du and Hoeschele, 2000). With simple pedigrees such as a nuclear family and small numbers of linked markers, exact calculation of the probabilities of linkage phases is achievable, by evaluating all possible genotype configurations. The exact calculation quickly becomes infeasible as the size and complexity of the pedigree and number of linked markers increases. For example, there are totally 2 k l linkage phases when a parent has k linked heterozygous loci.
  • Windig and Meu Giveaway (2004) provide a computationally efficiency method for phase construction. They start with a likely phase derived with a simple rule based method, calculate the parental origin of the two alleles at a marker, and perform a switch if the probability of the switch is greater than 0.5. The process is repeated until the probability of a switch is less than 0.5 for all linked markers.
  • probabilities of parental linkage phases for the entire set of linked loci were determined by choosing small subsets of markers (e.g., 5 to 10) and considering all possible phases for these markers by calculating their probability conditional on the observed genotypes for all markers under evaluation. Only phases with likelihood ratio greater than some pre-specified threshold are retained, and the iteration of the method over the entire marker set produces a collection of likely phases and their probabilities conditional on the observed data.
  • haplotypes of neighboring (and/or non-neighboring) markers across each chromosome were defined by setting the maximum length of a chromosomal interval and minimum and maximum number of markers to be included.
  • haplotype evaluation The association between pre-adjusted trait phenotypes and haplotype was evaluated via a regression approach with the following model:
  • Y k is the preadjusted phenotype of one of the traits described above for individual k, and e* is the residual;
  • P(H s i k ) and P(Hdi k ) are the probability of paternal and maternal haplotype of individual k being haplotype i;
  • P(H S i k , H ⁇ ⁇ k ) is the probability of individual k has paternal haplotype i and maternal haplotype j; all ⁇ are corresponding regression coefficients.
  • one or more of the markers with significant association to that trait can be used in selection of breeding animals.
  • use of animals possessing a marker allele (or a haplotype of multiple marker alleles) in population-wide LD with a favorable QTL allele will increase the breeding value of animals used in breeding, increase the frequency of that QTL allele in the population over time and thereby increase the average genetic merit of the population for that trait. This increased genetic merit can be disseminated to commercial populations for full realization of value.
  • a closed genetic nucleus (GN) population of pigs may be maintained to produce boars for use in commercial production of market hogs.
  • a GN herd of 200 sows would be expected to produce approximately 4,000 offspring per year (2,000 boar offspring per year), typically according to a weekly breeding and farrowing schedule.
  • a commercial sow herd of 300,000 would be expected to produce more than 6,000,000 market pigs per year and might maintain a boar stud with inventory of 1 ,500 boars to service the 300,000 sows.
  • the GN herd of 200 sows could support boar replacements for the 300,000 sows of commercial production by shipping 500 boars every six months to the commercial boar stud (assumes inventory in the commercial boar stud is turned over every 1.5 years and the top half of boar candidates from the GN are selected for commercial breeding).
  • the first step in using a SNP for estimation of breeding value and selection in the GN is collection of DNA from all offspring that will be candidates for selection as breeders in the GN or as breeders in other commercial populations (in the present example, the 4,000 offspring produced in the GN each year).
  • One method is to capture shortly after farrowing a small bit of tail tissue from each piglet into a labeled (bar- coded) tube. The DNA extracted from this tissue can be used to assay an essentially unlimited number of SNP markers and the results can be included in selection decisions before the animal reaches breeding age.
  • One method for incorporating into selection decisions the markers (or marker haplotypes) determined to be in population-wide LD with valuable QTL alleles is based on classical quantitative genetics and selection index theory (Falconer and Mackay, 1996; Dekkers and Chakraborty, 2001 ).
  • a random sample of animals with phenotypic measurements for the trait of interest can be analyzed with a mixed animal model with the marker fitted as a fixed effect or as a covariate (regression of phenotype on number of allele copies).
  • Results from either method of fitting marker effects can be used to derive the allele substitution effects, and in turn the breeding value of the marker:
  • g ⁇ 2A2 are the (marker) breeding values for animals with marker genotypes AlAl,
  • the total trait breeding value for an animal is the sum of breeding values for each marker (or haplotype) considered and the residual polygenic breeding value:
  • EBVj j is the Estimated Trait Breeding Value for the i th animal
  • n is the total number of markers (haplotypes) under consideration
  • Ui is the polygenic breeding value for the i' h animal after fitting the marker genotype(s).
  • a nucleic acid sequence contains a SNP of the present invention if it comprises at least 20 consecutive nucleotides that include and/or are adjacent to a polymorphism described in Tables 1 and 2 and the Sequence Listing.
  • a SNP of the present invention may be identified by a shorter stretch of consecutive nucleotides which include or are adjacent to a polymorphism which is described in Tables 1 and 2 and the Sequence Listing in instances where the shorter sequence of consecutive nucleotides is unique in the pig genome.
  • a SNP site is usually characterized by the consensus sequence in which the polymorphic site is contained, the position of the polymorphic site, and the various alleles at the polymorphic site.
  • Consensus sequence means DNA sequence constructed as the consensus at each nucleotide position of a cluster of aligned sequences. Such clusters are often used to identify SNP and Indel (insertion/deletion) polymorphisms in alleles at a locus.
  • Consensus sequence can be based on either strand of DNA at the locus, and states the nucleotide base of either one of each SNP allele in the locus and the nucleotide bases of all Indels in the locus, or both SNP alleles using degenerate code (IUPAC code: M for A or C; R for A or G; W for A or T; S for C or G; Y for C or T; K for G or T; V for A or C or G; H for A or C or T; D for A or G or T; B for C or G or T; N for A or C or G or T; Additional code that we use include I for "-"or A; O for "-” or C; E for "-” or G; L for "-” or T; where "-” means a deletion).
  • IUPAC code M for A or C; R for A or G; W for A or T; S for C or G; Y for C or T; K for G or T; V for A or C or G
  • Such SNP have a nucleic acid sequence having at least 90% sequence identity, more preferably at least 95% or even more preferably for some alleles at least 98% and in many cases at least 99% sequence identity, to the sequence of the same number of nucleotides in either strand of a segment of pig DNA which includes or is adjacent to the polymorphism.
  • the nucleotide sequence of one strand of such a segment of pig DNA may be found in a sequence in the group consisting of SEQ ID NO:1 through SEQ DD NO:521 1. It is understood by the very nature of polymorphisms that for at least some alleles there will be no identity at the polymorphic site itself. Thus, sequence identity can be determined for sequence that is exclusive of the polymorphism sequence.
  • the polymorphisms in each locus are described in Tables 1 and 2.
  • ssl6337002 gcaacctacaccacagctcayggcaaggcccaatccttaac
  • Quantifying an animal's body and/or carcass composition can be accomplished by measuring a number of phenotypes including, but not limited to: average backfat thickness (e.g. in inches or centimeters) measured on the carcass or on the live animal using ultrasound; loin muscle (eye) area (e.g. in 2 ) measured on the carcass or on the live animal using ultrasound; fat depth, loin depth (millimeters) and carcass weight (pounds) measured on-line after slaughter using industry standard equipment (e.g., Fat-O-Meater); predicted lean percentage (%) calculated from backfat thickness, loin muscle depth or area, and body or carcass weight; carcass length (e.g.
  • NPPC National Pork Producers Council
  • Quantifying an animal's growth can be accomplished by measuring phenotypes including, but not limited to: average daily weight gain (e.g. lbs/day); average daily feed intake (lbs/day); feed conversion ratio (lbs feed per Ib gain); growth from birth to any desired age (Ib); and growth during a specified test period (e.g. from 21 to 165 days of age).
  • average daily weight gain e.g. lbs/day
  • average daily feed intake lbs/day
  • feed conversion ratio lbs feed per Ib gain
  • growth during a specified test period e.g. from 21 to 165 days of age.
  • Quantifying meat color can be accomplished by measuring phenotypes including, but not limited to: Hunter colorimeter scores; change in Hunter colorimeter score over a 24 hour period; Japanese color score (1—5); and NPPC color quality score (1-5).
  • Quantifying meat quality can be accomplished by measuring phenotypes including, but not limited to: Drip loss (%); purge loss (%); pH of loin or ham; moisture content in the loin (%); NPPC firmness quality score (1-5); Werner-Bratzler shear force (kg); and cooking loss (%).
  • Ciobanu DC, Bastiaansen, JWM, Longergan, SM, Thomsen, H, Dekkers, JCM, Plastow, GS, and Rothschild, MF, (2004) J. Anim. ScL 82:2829-39.
  • Table 1 provides a list of phenotypic traits and the assigned identification numbers of SNPs found to be associated with each trait.
  • the left column provides a counter to allow easier reading of the table.
  • the 'Trait” column lists the following traits: “COLOR” (meat color), rows 1-4139; “COMPOSITION” (body composition) rows 4140-8687; “GROWTH”, rows 8787-13083; and “MEAT QUALITY”, rows 13084- 16695.
  • Table 2 provides the SEQ ID NO of the sequence associated with each of the SNPs listed in Table 1.
  • the "SNP POSITION” column provides the position (nucleotide number) of the SNP within the associated sequence (SEQ ID NO) and the "SNP ALLELE 1" and “SNP ALLELE 2" columns provide the identity of the two nucleotides that occur most frequently at the SNP POSITION within the population analyzed.

Landscapes

  • Chemical & Material Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Organic Chemistry (AREA)
  • Analytical Chemistry (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • Health & Medical Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Microbiology (AREA)
  • Immunology (AREA)
  • Molecular Biology (AREA)
  • Biotechnology (AREA)
  • Biophysics (AREA)
  • Physics & Mathematics (AREA)
  • Biochemistry (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • General Engineering & Computer Science (AREA)
  • General Health & Medical Sciences (AREA)
  • Genetics & Genomics (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)

Abstract

L'invention porte sur des compositions et des procédés qui permettent de déterminer le génotype d'un animal et de sélectionner des animaux possédant un génotype désiré. Des modes de réalisation de l'invention concernent aussi des molécules d'acide nucléiques isolées et des trousses d'analyse permettant de déterminer le génotype d'un animal. En outre, l'invention se rapporte à des procédés qui permettent d'améliorer des traits désirables chez les animaux, tels qu' une croissance augmentée, une composition corporelle enrichie, une couleur de viande plus appétissante et une qualité de viande supérieure. L'invention concerne également des procédés qui permettent d'attribuer des animaux à des usages prédéterminés, de désigner des animaux parents potentiels pour l'élevage et de produire une descendance animale à partir de ces derniers. L'invention porte aussi sur des procédés qui permettent d'identifier des associations entre des polymorphismes mononucléotidiques ('single nucleotide polymorphisms' ou SNP) et des traits phénotypiques. L'invention concerne aussi des procédés qui permettent d'identifier des marqueurs génétiques en association allélique avec les SNP précités et d'identifier les génotypes d'une mutation causale sous-jacente à un locus de trait quantitatif ('quantitative trait locus' ou QTL)
PCT/US2007/017949 2006-08-22 2007-08-13 Marqueurs génétiques et procédés permettant d'améliorer la génétique des porcs Ceased WO2008024227A2 (fr)

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US83940406P 2006-08-22 2006-08-22
US60/839,404 2006-08-22

Publications (2)

Publication Number Publication Date
WO2008024227A2 true WO2008024227A2 (fr) 2008-02-28
WO2008024227A3 WO2008024227A3 (fr) 2008-12-04

Family

ID=39107294

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2007/017949 Ceased WO2008024227A2 (fr) 2006-08-22 2007-08-13 Marqueurs génétiques et procédés permettant d'améliorer la génétique des porcs

Country Status (1)

Country Link
WO (1) WO2008024227A2 (fr)

Cited By (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN104982387A (zh) * 2015-05-25 2015-10-21 广东温氏食品集团股份有限公司 一种muc13和fut1基因的分子标记辅助选择方法
CN105028260A (zh) * 2015-06-11 2015-11-11 王卫军 一种贝类肉质性状新品系的选育方法
CN110144414A (zh) * 2019-06-27 2019-08-20 广西扬翔农牧有限责任公司 与公猪精子畸形率相关的分子遗传标记及其应用和获取方法

Non-Patent Citations (2)

* Cited by examiner, † Cited by third party
Title
DATABASE GENBANK [Online] 10 July 2008 Retrieved from NCBI Database accession no. (NW_001886119) *
ROTHSCHILD M.F.: 'US Pig Genome Coordination Program Activities' SWINE SEQUENCING NEWSLETTER 12 January 2008, page 2 *

Cited By (4)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN104982387A (zh) * 2015-05-25 2015-10-21 广东温氏食品集团股份有限公司 一种muc13和fut1基因的分子标记辅助选择方法
CN105028260A (zh) * 2015-06-11 2015-11-11 王卫军 一种贝类肉质性状新品系的选育方法
CN110144414A (zh) * 2019-06-27 2019-08-20 广西扬翔农牧有限责任公司 与公猪精子畸形率相关的分子遗传标记及其应用和获取方法
CN110144414B (zh) * 2019-06-27 2022-11-18 广西贵港秀博基因科技股份有限公司 与公猪精子畸形率相关的分子遗传标记及其应用和获取方法

Also Published As

Publication number Publication date
WO2008024227A3 (fr) 2008-12-04

Similar Documents

Publication Publication Date Title
US20110123983A1 (en) Methods of Using Genetic Markers and Related Epistatic Interactions
US20110262909A1 (en) Genetic Markers for Horned and Polled Cattle and Related Methods
US20100324356A1 (en) Methods for improving genetic profiles of dairy animals and products
CA2543786A1 (fr) Methodes et systemes presentant d'inferer des traits en vue de la gestion de cheptels non bovins
KR102235340B1 (ko) 토종닭의 성장 형질을 예측하기 위한 snp 마커 세트 및 이의 용도
JP2015526099A (ja) 乳房炎抵抗性の遺伝子マーカ
US20110054246A1 (en) Whole genome scan to discover quantitative trai loci (qtl) affecting growth, body composition, and reproduction in maternal pig lines
CA2554517A1 (fr) Adaptations logicielles ma-blup (marker assisted best linear unbiased predicted) destinees a des applications pratiques pour des populations importantes d'especes d'elevage
JP2020074781A (ja) 乳生産量を改善するための雌牛の育種方法
CN116590433B (zh) 大白母猪繁殖性能的分子标记、引物、试剂盒、鉴定方法及应用
WO2009055805A2 (fr) Marqueurs génétiques et procédés permettant d'améliorer la génétique porcine
WO2008140467A2 (fr) Marqueurs génétiques et procédés permettant d'améliorer les caractères de productivité et d'adaptation chez les animaux laitiers
US20100304353A1 (en) Methods of improving a genomic marker index of dairy animals and products
WO2008024227A2 (fr) Marqueurs génétiques et procédés permettant d'améliorer la génétique des porcs
RU2754039C2 (ru) Способ прогнозирования резистентности
Shihabi Inbreeding and selection on the X chromosome in domestic animal populations
Pienaar Genetic diversity in the Afrikaner cattle breed
Tinarelli Innovative exploitation of pig genetic resources
CN120624662A (zh) 与白羽肉种鸡蛋重性状相关的snp标记及其应用
CN120624663A (zh) 与白羽肉种鸡开产日龄性状相关的snp标记及其应用
CN111154893A (zh) 猪生长速度相关的snp标记及其应用
Mishra et al. Application of advanced molecular marker technique for improvement of animal: A critical
Mousel et al. Breeding and Genetics: Swine
AU2013204384A1 (en) Genetic markers for horned and polled cattle and related methods

Legal Events

Date Code Title Description
121 Ep: the epo has been informed by wipo that ep was designated in this application

Ref document number: 07811306

Country of ref document: EP

Kind code of ref document: A2

NENP Non-entry into the national phase in:

Ref country code: DE

NENP Non-entry into the national phase in:

Ref country code: RU

122 Ep: pct application non-entry in european phase

Ref document number: 07811306

Country of ref document: EP

Kind code of ref document: A2