Genome wide association study identifies 20 novel promising genes associated with milk fatty acid traits in Chinese Holstein

Cong Li; Dongxiao Sun; Shengli Zhang; Sheng Wang; Xiaoping Wu; Qin Zhang; Lin Liu; Yanhua Li; Lv Qiao

doi:10.1371/journal.pone.0096186

Genome wide association study identifies 20 novel promising genes associated with milk fatty acid traits in Chinese Holstein

PLoS One. 2014 May 23;9(5):e96186. doi: 10.1371/journal.pone.0096186. eCollection 2014.

Authors

Cong Li¹, Dongxiao Sun¹, Shengli Zhang¹, Sheng Wang¹, Xiaoping Wu¹, Qin Zhang¹, Lin Liu², Yanhua Li², Lv Qiao²

Affiliations

¹ Key Laboratory of Animal Genetics and Breeding of Ministry of Agriculture, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China.
² Beijing Dairy Cattle Center, Beijing, China.

Abstract

Detecting genes associated with milk fat composition could provide valuable insights into the complex genetic networks of genes underling variation in fatty acids synthesis and point towards opportunities for changing milk fat composition via selective breeding. In this study, we conducted a genome-wide association study (GWAS) for 22 milk fatty acids in 784 Chinese Holstein cows with the PLINK software. Genotypes were obtained with the Illumina BovineSNP50 Bead chip and a total of 40,604 informative, high-quality single nucleotide polymorphisms (SNPs) were used. Totally, 83 genome-wide significant SNPs and 314 suggestive significant SNPs associated with 18 milk fatty acid traits were detected. Chromosome regions that affect milk fatty acid traits were mainly observed on BTA1, 2, 5, 6, 7, 9, 13, 14, 18, 19, 20, 21, 23, 26 and 27. Of these, 146 SNPs were associated with more than one milk fatty acid trait; most of studied fatty acid traits were significant associated with multiple SNPs, especially C18:0 (105 SNPs), C18 index (93 SNPs), and C14 index (84 SNPs); Several SNPs are close to or within the DGAT1, SCD1 and FASN genes which are well-known to affect milk composition traits of dairy cattle. Combined with the previously reported QTL regions and the biological functions of the genes, 20 novel promising candidates for C10:0, C12:0, C14:0, C14:1, C14 index, C18:0, C18:1n9c, C18 index, SFA, UFA and SFA/UFA were found, which composed of HTR1B, CPM, PRKG1, MINPP1, LIPJ, LIPK, EHHADH, MOGAT1, ECHS1, STAT1, SORBS1, NFKB2, AGPAT3, CHUK, OSBPL8, PRLR, IGF1R, ACSL3, GHR and OXCT1. Our findings provide a groundwork for unraveling the key genes and causal mutations affecting milk fatty acid traits in dairy cattle.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
Cattle / genetics*
Chromosomes, Mammalian / genetics
Fatty Acids / chemistry
Fatty Acids / metabolism*
Genome-Wide Association Study*
Milk / metabolism*
Phenotype
Polymorphism, Single Nucleotide

Substances

Fatty Acids

Grants and funding

This work was supported by the High Technology Research and Development Program of China (2013AA102504), National Key Technologies R & D Program (2011BAD28B02, 2012BAD12B01), Beijing Dairy Industry Innovation Team, 948 Program (2011-G2A), Beijing Research and Technology program (D121100003312001), and Program for Changjiang Scholar and Innovation Research Team in University (IRT1191). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.