A genome-wide association study suggests new candidate genes for milk production traits in Chinese Holstein cattle
- 30 August 2017
- journal article
- Published by Wiley in Animal Genetics
- Vol. 48 (6), 677-681
- https://doi.org/10.1111/age.12593
Abstract
A genome-wide association study (GWAS) was conducted on 15 milk production traits in Chinese Holstein. The experimental population consisted of 445 cattle, each genotyped by the GGP (GeneSeek genomic profiling)-BovineLD V3 SNP chip, which had 26 151 public SNPs in its manifest file. After data cleaning, 20 326 SNPs were retained for the GWAS. The phenotypes were estimated breeding values of traits, provided by a public dairy herd improvement program center that had been collected once a month for 3 years. Two statistical models, a fixed-effect linear regression model and a mixed-effect linear model, were used to estimate the association effects of SNPs on each of the phenotypes. Genome-wide significant and suggestive thresholds were set at 2.46E-06 and 4.95E-05 respectively. The two statistical models concurrently identified two genome-wide significant (P < 0.05) SNPs on milk production traits in this Chinese Holstein population. The positional candidate genes, which were the ones closest to these two identified SNPs, were EEF2K (eukaryotic elongation factor 2 kinase) and KLHL1 (kelch like family member 1). These two genes could serve as new candidate genes for milk yield and lactation persistence, yet their roles need to be verified in further function studies.Keywords
Funding Information
- National Natural Science Foundation of China (31402054)
- Key Project of Agricultural Fine Breeding of Shandong Province (2016LZGC030)
- Natural Science Foundation of Shandong Province (ZR2013CM013)
- Funds of Shandong “Double Tops” Program (SYL2017YSTD08)
- Modern Agricultural Industry Technology System (CARS-37)
- Tai Mountain Scholar Talent Team for Agricultural Breeding (2014LZ07-04)
This publication has 17 references indexed in Scilit:
- MEN1/Menin regulates milk protein synthesis through mTOR signaling in mammary epithelial cellsScientific Reports, 2017
- A Multiple-SNP Approach for Genome-Wide Association Study of Milk Production Traits in Chinese Holstein CattlePLOS ONE, 2014
- Genome‐wide association analysis identifies quantitative trait loci for growth in a Landrace purebred populationAnimal Genetics, 2014
- Association of polymorphisms in solute carrier family 27, isoform A6 (SLC27A6) and fatty acid-binding protein-3 and fatty acid-binding protein-4 (FABP3 and FABP4) with fatty acid composition of bovine milkJournal of Dairy Science, 2013
- Genome-wide association analysis of thirty one production, health, reproduction and body conformation traits in contemporary U.S. Holstein cowsBMC Genomics, 2011
- Association Between Polymorphisms in theSLC27A1Gene and Milk Production Traits in Chinese Holstein CattleAnimal Biotechnology, 2011
- A principal component regression based genome wide analysis approach reveals the presence of a novel QTL on BTA7 for MAP resistance in holstein cattleGenomics, 2010
- Nutrient availability and lactogenic hormones regulate mammary protein synthesis through the mammalian target of rapamycin signaling pathwayJournal of Dairy Science, 2010
- Initiation and elongation steps of mRNA translation are involved in the increase in milk protein yield caused by growth hormone administration during lactationJournal of Dairy Science, 2009
- PLINK: A Tool Set for Whole-Genome Association and Population-Based Linkage AnalysesAmerican Journal of Human Genetics, 2007