Genome-wide association study of conformation and milk yield in mixed-breed dairy goats

S Mucha, R Mrode, MP Coffey, M Kizilaslan, S Desire, JE Conington

Research output: Contribution to journalArticle

3 Citations (Scopus)
8 Downloads (Pure)

Abstract

Identification of genetic markers that affect economically important traits is of high value from a biological point of view, enabling the targeting of candidate genes and providing practical benefits for the industry such as wide-scale genomic selection. This study is one of the first to investigate the genetic background of economically important traits in dairy goats using the caprine 50K single nucleotide polymorphism (SNP) chip. The aim of the project was to perform a genomewide association study for milk yield and conformation of udder, teat, and feet and legs. A total of 137,235 milk yield records on 4,563 goats each scored for 10 conformation traits were available. Out of these, 2,381 goats were genotyped with the Illumina Caprine 50K BeadChip (Illumina Inc., San Diego, CA). A range of pseudo-phenotypes were used including deregressed breeding values and pseudo-estimated breeding values. Genome-wide association studies were performed using the multi-locus mixed model (MLMM) algorithm implemented in SNP & Variation Suite v7.7.8 (Golden Helix Inc., Bozeman, MT). A genome-wise significant [−log10(P-value) > 5.95] SNP for milk yield was identified on chromosome 19, with additional chromosomewise significant (−log10(P-value) > 4.46] SNP on chromosomes 4, 8, 14, and 29. Three genome-wise significant SNP for conformation of udder attachment, udder depth, and front legs were identified on chromosome 19, and chromosome-wise SNP were found on chromosomes 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 23, and 27. The proportion of variance explained by the significant SNP was between 0.4 and 7.0% for milk yield and between 0.1 and 13.8% for conformation traits. This study is the first attempt to identify SNP associated with milk yield and conformation in dairy goats. Two genome-wise significant SNP for milk yield and 3 SNP for conformation of udder attachment, udder depth, and front legs were found. Our results suggest that conformation traits have a polygenic background because, for most of them, we did not identify any quantitative trait loci with major effect.
Original languageEnglish
Pages (from-to)2213 - 2225
Number of pages13
JournalJournal of Dairy Science
Volume101
Issue number3
Early online date28 Dec 2017
DOIs
Publication statusFirst published - 28 Dec 2017

Fingerprint

dairy goats
single nucleotide polymorphism
milk yield
udders
legs
chromosomes
goats
loci
genome
teats
mixed breeds
genome-wide association study
breeding value
marker-assisted selection
genetic background
phenotype
genetic markers

Bibliographical note

1029813

Keywords

  • Conformation
  • Dairy goat
  • Genome-wide association study (GWAS)
  • Quantitative trait loci (QTL)

Cite this

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abstract = "Identification of genetic markers that affect economically important traits is of high value from a biological point of view, enabling the targeting of candidate genes and providing practical benefits for the industry such as wide-scale genomic selection. This study is one of the first to investigate the genetic background of economically important traits in dairy goats using the caprine 50K single nucleotide polymorphism (SNP) chip. The aim of the project was to perform a genomewide association study for milk yield and conformation of udder, teat, and feet and legs. A total of 137,235 milk yield records on 4,563 goats each scored for 10 conformation traits were available. Out of these, 2,381 goats were genotyped with the Illumina Caprine 50K BeadChip (Illumina Inc., San Diego, CA). A range of pseudo-phenotypes were used including deregressed breeding values and pseudo-estimated breeding values. Genome-wide association studies were performed using the multi-locus mixed model (MLMM) algorithm implemented in SNP & Variation Suite v7.7.8 (Golden Helix Inc., Bozeman, MT). A genome-wise significant [−log10(P-value) > 5.95] SNP for milk yield was identified on chromosome 19, with additional chromosomewise significant (−log10(P-value) > 4.46] SNP on chromosomes 4, 8, 14, and 29. Three genome-wise significant SNP for conformation of udder attachment, udder depth, and front legs were identified on chromosome 19, and chromosome-wise SNP were found on chromosomes 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 23, and 27. The proportion of variance explained by the significant SNP was between 0.4 and 7.0{\%} for milk yield and between 0.1 and 13.8{\%} for conformation traits. This study is the first attempt to identify SNP associated with milk yield and conformation in dairy goats. Two genome-wise significant SNP for milk yield and 3 SNP for conformation of udder attachment, udder depth, and front legs were found. Our results suggest that conformation traits have a polygenic background because, for most of them, we did not identify any quantitative trait loci with major effect.",
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Genome-wide association study of conformation and milk yield in mixed-breed dairy goats. / Mucha, S; Mrode, R; Coffey, MP; Kizilaslan, M; Desire, S; Conington, JE.

In: Journal of Dairy Science, Vol. 101, No. 3, 28.12.2017, p. 2213 - 2225.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Genome-wide association study of conformation and milk yield in mixed-breed dairy goats

AU - Mucha, S

AU - Mrode, R

AU - Coffey, MP

AU - Kizilaslan, M

AU - Desire, S

AU - Conington, JE

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AB - Identification of genetic markers that affect economically important traits is of high value from a biological point of view, enabling the targeting of candidate genes and providing practical benefits for the industry such as wide-scale genomic selection. This study is one of the first to investigate the genetic background of economically important traits in dairy goats using the caprine 50K single nucleotide polymorphism (SNP) chip. The aim of the project was to perform a genomewide association study for milk yield and conformation of udder, teat, and feet and legs. A total of 137,235 milk yield records on 4,563 goats each scored for 10 conformation traits were available. Out of these, 2,381 goats were genotyped with the Illumina Caprine 50K BeadChip (Illumina Inc., San Diego, CA). A range of pseudo-phenotypes were used including deregressed breeding values and pseudo-estimated breeding values. Genome-wide association studies were performed using the multi-locus mixed model (MLMM) algorithm implemented in SNP & Variation Suite v7.7.8 (Golden Helix Inc., Bozeman, MT). A genome-wise significant [−log10(P-value) > 5.95] SNP for milk yield was identified on chromosome 19, with additional chromosomewise significant (−log10(P-value) > 4.46] SNP on chromosomes 4, 8, 14, and 29. Three genome-wise significant SNP for conformation of udder attachment, udder depth, and front legs were identified on chromosome 19, and chromosome-wise SNP were found on chromosomes 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 23, and 27. The proportion of variance explained by the significant SNP was between 0.4 and 7.0% for milk yield and between 0.1 and 13.8% for conformation traits. This study is the first attempt to identify SNP associated with milk yield and conformation in dairy goats. Two genome-wise significant SNP for milk yield and 3 SNP for conformation of udder attachment, udder depth, and front legs were found. Our results suggest that conformation traits have a polygenic background because, for most of them, we did not identify any quantitative trait loci with major effect.

KW - Conformation

KW - Dairy goat

KW - Genome-wide association study (GWAS)

KW - Quantitative trait loci (QTL)

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DO - 10.3168/jds.2017-12919

M3 - Article

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