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

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 genome-wide 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 [-log(P-value) > 5.95] SNP for milk yield was identified on chromosome 19, with additional chromosome-wise significant (-log(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.

Detection of quantitative trait loci and putative causal variants affecting somatic cell score in dairy sheep by using a 50K SNP chip and whole-genome sequencing

“…Polymorphisms affecting these genes should be assessed as potential genetic markers in relation to increased SCS in dairy sheep. Comparing with results reported in goats, we did not find a relevant coincidence, as the sheep genomic regions on OAR11 orthologous to the intervals harboring recently reported QTL on goat chromosome 19 for SCS and udder traits (Martin et al, 2018;Mucha et al, 2018;26-28 Mb and 40-42 Mb) are not coincident with the significant LDLA association reported here on OAR11 (56.8-56.9 Mb). The scarce number of goat studies on this topic may explain the lack of coincidences.…”

Analyzing the genomic and transcriptomic architecture of milk traits in Murciano-Granadina goats

“…Such work enabled the identification of 109 significant associations and further uncovered two polymorphisms in the DGAT1 gene that have major effects on fat content by modifying the activity of this enzyme [1]. In another recent study, Mucha et al [2] detected a single nucleotide polymorphism (SNP) on goat chromosome 19 displaying a genome-wide significant association with milk yield as well as a number of chromosome-wide significant associations with dairy traits on chromosomes 4, 8, 14, and 29. Although these two studies represent a valuable step towards elucidating the genomic architecture of milk yield and composition traits in goats, analyzing a broader array of goat populations, as has been done in cattle [3], would provide a more comprehensive view of the genetic determinism of caprine dairy phenotypes.…”

Accuracy of genomic evaluation with weighted single-step genomic best linear unbiased prediction for milk production traits, udder type traits, and somatic cell scores in French dairy goats

“…In another study, GWAS analyses were performed in dairy goats (French Alpine and Saanen, or mixedbreed goats) to identify QTL that affect traits under selection. Martin et al (2018) and Mucha et al (2018) investigated the genetic architecture of different traits. These authors observed a large QTL associated with milk yield, fat yield, protein yield, udder floor position, rear udder attachment, and SCS on chromosome 19.…”