Abstract
Fertility is an economically important trait in livestock. Poor fertility in dairy cattle can be due to loss-of-function variants affecting any essential gene that causes early embryonic mortality in homozygotes. To identify fertility-associated quantitative trait loci, we performed single-marker association analyses for 8 fertility traits in Holstein, Jersey, and Nordic Red Dairy cattle using imputed whole-genome sequence variants including SNPs, indels, and large deletion. We then performed stepwise selection of independent markers from GWAS loci using conditional and joint association analyses. From single-marker analyses for fertility traits, we reported genome-wide significant associations of 30,384 SNPs, 178 indels, and 3 deletions in Holstein; 23,481 SNPs, 189 indels, and 13 deletions in Nordic Red; and 17 SNPs in Jersey cattle. Conditional and joint association analyses identified 37 and 23 independent associations in Holstein and Nordic Red Dairy cattle, respectively. Fertility-associated GWAS loci were enriched for developmental and cellular processes (Gene Ontology enrichment, false discovery rate < 0.05). For these quantitative trait loci regions (top marker and 500 kb of surrounding regions), we proposed several candidate genes with functional annotations corresponding to embryonic lethality and various fertility-related phenotypes in mouse and cattle. The inclusion of these top markers in future releases of the custom SNP chip used for genomic evaluations will enable their validation in independent populations and improve the accuracy of genomic predictions.
Highlights
Over the years, GWAS have provided a better understanding of underlying genetic architectures for many economical traits in dairy cattle
We hypothesized that inclusion of indels and large deletions in addition to whole-genome single nucleotide variants could identify candidate genes for female fertility traits in dairy cattle
The genomic inflation seen in this study despite the correction for population stratification and relatedness could be explained by the nature of polygenic inheritance of the fertility traits we analyzed
Summary
GWAS have provided a better understanding of underlying genetic architectures for many economical traits in dairy cattle. Mesbah-Uddin et al.: GENOME-WIDE ASSOCIATION STUDY FOR FEMALE FERTILITY IN DAIRY CATTLE To include deletions in addition to SNPs and indels in gene mapping and prediction of breeding values in cattle, we previously performed genome-wide mapping of deletions in 175 whole-genome sequence (WGS) animals, 67 Holstein (HOL), 81 Nordic Red (RDC), and 27 Jersey (JER) cattle, and identified ~8,500 variants ranging from 199 bp to 773 kb in size (Mesbah-Uddin et al, 2018).
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