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

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    11 Citations (Scopus)
    14 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

    Bibliographical note

    1029813

    Keywords

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

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