Genome-wide association study for longevity with whole-genome sequencing in 3 cattle breeds

Abstract

Longevity is an important economic trait in dairy production. Improvements in longevity could increase the average number of lactations per cow, thereby affecting the profitability of the dairy cattle industry. Improved longevity for cows reduces the replacement cost of stock and enables animals to achieve the highest production period. Moreover, longevity is an indirect indicator of animal welfare. Using whole-genome sequencing variants in 3 dairy cattle breeds, we carried out an association study and identified 7 genomic regions in Holstein and 5 regions in Red Dairy Cattle that were associated with longevity. Meta-analyses of 3 breeds revealed 2 significant genomic regions, located on chromosomes 6 (META-CHR6-88MB) and 18 (META-CHR18-58MB). META-CHR6-88MB overlaps with 2 known genes: neuropeptide G-protein coupled receptor (NPFFR2; 89,052,210-89,059,348 bp) and vitamin D-binding protein precursor (GC; 88,695,940-88,739,180 bp). The NPFFR2 gene was previously identified as a candidate gene for mastitis resistance. META-CHR18-58MB overlaps with zinc finger protein 717 (ZNF717; 58,130,465-58,141,877 bp) and zinc finger protein 613 (ZNF613; 58,115,782-58,117,110 bp), which have been associated with calving difficulties. Information on longevity-associated genomic regions could be used to find causal genes/variants influencing longevity and exploited to improve the reliability of genomic prediction.

GWAS using 2b-RAD sequencing identified three mastitis important SNPs via two-stage association analysis in Chinese Holstein cows

“…Thus, Screening and identifying susceptibility or resistance genes associated with mastitis traits will improve the properties of dairy cow populations and is worthwhile to reduce the incidence of mastitis (SAHANA et al 2014;KADRI et al 2015;WANG et al 2015). Different research strategies successfully used to identify significant genes associated with the mastitis traits, including SNP in a candidate gene, quantitative trait loci (QTL) and GWAS (BRONDUM et al 2015;POKORSKA et al 2016;ZHANG et al 2016).…”

“…Sahana and his colleagues reported two clinical mastitis candidate genes (vitamin D-binding protein precursor, GC and neuropeptide FF receptor 2, NPFFR2) using high-density single nucleotide polymorphic array and WGAS (SAHANA et al 2014). These two candidate genes detected to associate with mastitis traits in dairy cows through genomic sequencing in 2016 (ZHANG et al 2016). In 2015, Wang et al identified another two mastitis susceptibility genes (TRAPPC9 and ARHGAP39) in Chinese Holstein .…”

Contribution of rare and low-frequency whole-genome sequence variants to complex traits variation in dairy cattle

“…Associations of common genetic variants with complex diseases and quantitative traits have been successfully identified in humans and livestock [ 1 – 3 ]. However, these loci explain only a small fraction of the total genetic variance of a trait.…”

Genetic correlation and genome-wide association study (GWAS) of the length of productive life, days open, and 305-days milk yield in crossbred Holstein dairy cattle

“…It can identify the quantitative trait loci (QTL) regions and candidate genes that affect the traits of interest. In dairy cattle, the GWAS of production traits, such as milk yield, fat yield, and protein yield, (Maxa et al, 2012;Minozzi et al, 2013;Nayeri et al, 2016;van den Berg et al, 2016); functional or fertility traits, such as calving to the first service interval, days open, non-return rate, and conception rate (Olsen et al, 2011;Minozzi et al, 2013;Nayeri et al, 2016;Parker Gaddis et al, 2016); health traits, such as clinical mastitis and udder type (Flury et al, 2014;Sahana et al, 2014); and longevity (Zhang et al, 2016), have been reported. A previous GWAS showed that the DGAT1 gene on bovine chromosome BTA14 was associated with milk production and the FAM1818 gene on BTA21 was associated with days open (Minozzi et al, 2013;Nayeri et al, 2016).…”