CNV discovery for milk composition traits in dairy cattle using whole genome resequencing

Abstract

BackgroundCopy number variations (CNVs) are important and widely distributed in the genome. CNV detection opens a new avenue for exploring genes associated with complex traits in humans, animals and plants. Herein, we present a genome-wide assessment of CNVs that are potentially associated with milk composition traits in dairy cattle.ResultsIn this study, CNVs were detected based on whole genome re-sequencing data of eight Holstein bulls from four half- and/or full-sib families, with extremely high and low estimated breeding values (EBVs) of milk protein percentage and fat percentage. The range of coverage depth per individual was 8.2–11.9×. Using CNVnator, we identified a total of 14,821 CNVs, including 5025 duplications and 9796 deletions. Among them, 487 differential CNV regions (CNVRs) comprising ~8.23 Mb of the cattle genome were observed between the high and low groups. Annotation of these differential CNVRs were performed based on the cattle genome reference assembly (UMD3.1) and totally 235 functional genes were found within the CNVRs. By Gene Ontology and KEGG pathway analyses, we found that genes were significantly enriched for specific biological functions related to protein and lipid metabolism, insulin/IGF pathway-protein kinase B signaling cascade, prolactin signaling pathway and AMPK signaling pathways. These genes included INS, IGF2, FOXO3, TH, SCD5, GALNT18, GALNT16, ART3, SNCA and WNT7A, implying their potential association with milk protein and fat traits. In addition, 95 CNVRs were overlapped with 75 known QTLs that are associated with milk protein and fat traits of dairy cattle (Cattle QTLdb).ConclusionsIn conclusion, based on NGS of 8 Holstein bulls with extremely high and low EBVs for milk PP and FP, we identified a total of 14,821 CNVs, 487 differential CNVRs between groups, and 10 genes, which were suggested as promising candidate genes for milk protein and fat traits.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-017-3636-3) contains supplementary material, which is available to authorized users.

High-density genotyping reveals signatures of selection related to acclimation and economically important traits in 15 local sheep breeds from Russia

“…SPP1 is associated with milk protein percentage, milk yield, milk protein yield, and lactation regulation in dairy cattle [57]. Signatures of selection near the SNCA, potentially related to milk protein and fat traits in dairy cattle [58] were reported by DSMC for the Kulundin, Volgograd, Krasnoyarsk, and Baikal breeds. Two family members, the ACSS1 and ACSS2 previously associated with the mammary gland function and milk fatty acid composition in sheep [59,60], cattle [61], and yaks [62] were the top-ranked genes in positively selected regions reported by DCMS.…”

Detection of CNV in the SH3RF2 gene and its effects on growth and carcass traits in chickens

“…CNV is an important source of genetic variation complementary to SNP. CNV is associated with not only disease and abnormal development in livestock and poultry but also physical appearance and many economic traits [10][11][12][13]. For example, Wright [14] found that the first intron CNV of the SOX5 gene is related to crown type.…”

A global analysis of CNVs in Chinese indigenous fine-wool sheep populations using whole-genome resequencing

“…A total of 7228 CNVRs were obtained after merging overlapping CNVs, which greatly exceeded the numbers previously reported for sheep based on SNP50 chip and SNP600 chip studies [11,13,15,16]. This difference was not surprising, as the genomic coverage of SNP chips is poor, which results in the detection of longer CNVRs [17,18]. The CNVRs detected in this study accounted for 2.17% of the sheep reference genome, which falls within the range (0.8%-5.12%) reported for horses, pigs, cattle and chickens [19][20][21][22].…”