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

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Journal of Animal Science and Biotechnology 2020年第4期11卷 937-949页

作者： Megan Scholtens Andrew Jiang Ashley Smith Mathew Littlejohn klaus lehnert Russell Snell Nicolas Lopez-Villalobos Dorian Garrick Hugh Blair AL Rae Centre for Genetics and Breeding School of AgricultureMassey UniversityPalmerston NorthNew Zealand Applied Translational Genetics Group School of Biological SciencesThe University of AucklandAucklandNew Zealand Research and Development Livestock Improvement CorporationRuakura RoadHamiltonNew Zealand.

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

关键词： Dairy goat GWAS Milk production New Zealand QTL

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A Capra hircus chromosome 19 locus linked to milk production influences mammary conformation

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Journal of Animal Science and Biotechnology 2022年第3期13卷 697-706页

作者： Andrew Jiang Alex Ankersmit-Udy Sally-Anne Turner Megan Scholtens Mathew D.Littlejohn Nicolas Lopez-Villalobos Colin G.Proser Russell G.Snell klaus lehnert Applied Translational Genetics Group School of Biological SciencesThe University of AucklandAucklandNew Zealand Dairy Goat Co-operative HamiltonNew Zealand Cawthron Institute NelsonNew Zealand AL Rae Centre of Genetics and Breeding Massey UniversityHamiltonNew Zealand Dairy Cattle Breeding and Genetics School of Agriculture&EnvironmentMassey UniversityHamiltonNew Zealand

Background:Economically important milk production traits including milk volume,milk fat and protein yield vary considerably across dairy goats in New Zealand.A significant portion of the variation is attributable to genetic *** of genetic markers linked to milk production traits can be utilised to drive selection of highperformance animals.A previously reported genome wide association study across dairy goats in New Zealand identified a quantitative trait locus(QTL)located on chromosome *** most significantly associated single nucleotide polymorphism(SNP)marker for this locus is located at position 26,610,610(SNP marker rs268292132).This locus is associated with multiple milk production traits including fat,protein and *** predicted effect of selection for the beneficial haplotype would result in an average production increase of 2.2 kg fat,1.9 kg protein and 73.6 kg milk *** outstanding question was whether selection for the beneficial allele would co-select for any negative pleiotropic *** adverse relationship between milk production and udder health traits has been reported at this ***,a genome wide association study was undertaken looking for loci associated with udder ***:The QTL and production associated marker rs268292132 was identified in this study to also be associated with several goat udder traits including udder depth(UD),fore udder attachment(FUA)and rear udder attachment(RUA).Our study replicates the negative relationship between production and udder traits with the high production allele at position 19:26,610,610(SNP marker rs268292132)associated with an adverse change in UD,FUA and ***:Our study has confirmed the negative relationship between udder traits and production traits in the NZ goat *** have found that the frequency of the high production allele is relatively high in the NZ goat population,indicating that its effect on udder conformation is not significantly

关键词： Capra hircus Milk production Pleiotropic effects Quantitaive trait loci Udder conformation

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