Genome-wide association studies of lactation yields of milk, fat, protein and somatic cell score in New Zealand dairy goats

作     者：Megan Scholtens Andrew Jiang Ashley Smith Mathew Littlejohn Klaus Lehnert Russell Snell Nicolas Lopez-Villalobos Dorian Garrick Hugh Blair Megan Scholtens;Andrew Jiang;Ashley Smith;Mathew Littlejohn;Klaus Lehnert;Russell Snell;Nicolas Lopez-Villalobos;Dorian Garrick;Hugh Blair

作者机构：AL Rae Centre for Genetics and BreedingSchool of AgricultureMassey UniversityPalmerston NorthNew Zealand Applied Translational Genetics GroupSchool of Biological SciencesThe University of AucklandAucklandNew Zealand Research and DevelopmentLivestock Improvement CorporationRuakura RoadHamiltonNew Zealand. 

出 版 物：《Journal of Animal Science and Biotechnology》 (畜牧与生物技术杂志（英文版）)

年 卷 期：2020年第11卷第4期

页      面：937-949页

核心收录：

学科分类：0905[农学-畜牧学] 09[农学] 

基　　金：funded by the Dairy Goat Co-operative New Zealand 

主　　题：Dairy goat GWAS Milk production New Zealand QTL 

摘      要：Background: Identifying associations between genetic markers and traits of economic importance will provide practical benefits for the dairy goat industry, enabling genomic prediction of the breeding value of individuals, and facilitating discovery of the underlying genes and mutations. Genome-wide association studies were implemented to detect genetic regions that are significantly associated with effects on lactation yields of milk(MY), fat(FY),protein(PY) and somatic cell score(SCS) in New Zealand dairy ***: A total of 4,840 goats were genotyped with the Caprine 50 K SNP chip(Illumina Inc., San Diego, CA).After quality filtering, 3,732 animals and 41,989 SNPs were analysed assuming an additive linear model. Four GWAS models were performed, a single-SNP additive linear model and three multi-SNP Bayes C models. For the single-SNP GWAS, SNPs were fitted individually as fixed covariates, while the Bayes C models fit all SNPs simultaneously as random effects. A cluster of significant SNPs were used to define a haplotype block whose alleles were fitted as covariates in a Bayesian model. The corresponding diplotypes of the haplotype block were then fit as class variables in another Bayesian ***: Across all four traits, a total of 43 genome-wide significant SNPs were detected from the SNP GWAS. At a genome-wide significance level, the single-SNP analysis identified a cluster of variants on chromosome 19 associated with MY, FY, PY, and another cluster on chromosome 29 associated with SCS. Significant SNPs mapped in introns of candidate genes(45%), in intergenic regions(36%), were 0–5 kb upstream or downstream of the closest gene(14%) or were synonymous substitutions(5%). The most significant genomic window was located on chromosome 19 explaining up to 9.6% of the phenotypic variation for MY, 8.1% for FY, 9.1% for PY and 1% for ***: The quantitative trait loci for yield traits on chromosome 19 confirms reported findings in other dairy goat p