Cattle Genetics and Breeding Group, Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China.
Animal Science and Technology College, Beijing University of Agriculture (BUA), Beijing 102206, China.
Sci Rep. 2016 Nov 28;6:38073. doi: 10.1038/srep38073.
Average daily gain (ADG) is the most economically important trait in beef cattle industry. Using genome-wide association study (GWAS) approaches, previous studies have identified several causal variants within the PLAG1, NCAPG and LCORL genes for ADG in cattle. Multi-strategy GWASs were implemented in this study to improve detection and to explore the causal genes and regions. In this study, we conducted GWASs based on the genotypes of 1,173 Simmental cattle. In the SNP-based GWAS, the most significant SNPs (rs109303784 and rs110058857, P = 1.78 × 10) were identified in the NCAPG intron on BTA6 and explained 4.01% of the phenotypic variance, and the independent and significant SNP (rs110406669, P = 5.18 × 10) explained 3.32% of the phenotypic variance. Similarly, in the haplotype-based GWAS, the most significant haplotype block, Hap-6-N1416 (P = 2.56 × 10), spanned 12.7 kb on BTA6 and explained 4.85% of the phenotypic variance. Also, in the gene-based GWAS, seven significant genes were obtained which included DCAF16 and NCAPG. Moreover, analysis of the transcript levels confirmed that transcripts abundance of NCAPG (P = 0.046) and DCAF16 (P = 0.046) were significantly correlated with the ADG trait. Overall, our results from the multi-strategy GWASs revealed the DCAF16-NCAPG region to be a susceptibility locus for ADG in cattle.
平均日增重（ADG）是肉牛业中最重要的经济性状。利用全基因组关联研究（GWAS）方法，先前的研究已经在牛的 PLAG1、NCAPG 和 LCORL 基因中发现了几个与 ADG 相关的因果变异。本研究采用多策略 GWAS 方法提高检测能力，探索因果基因和区域。本研究基于 1173 头西门塔尔牛的基因型进行了 GWAS。在基于 SNP 的 GWAS 中，在 BTA6 上的 NCAPG 内含子中鉴定到了最显著的 SNP（rs109303784 和 rs110058857，P=1.78×10），解释了表型方差的 4.01%，独立且显著的 SNP（rs110406669，P=5.18×10）解释了表型方差的 3.32%。同样，在基于单倍型的 GWAS 中，最显著的单倍型块 Hap-6-N1416（P=2.56×10）跨越 BTA6 的 12.7kb，解释了表型方差的 4.85%。此外，在基于基因的 GWAS 中，获得了七个显著的基因，包括 DCAF16 和 NCAPG。此外，转录水平的分析证实 NCAPG（P=0.046）和 DCAF16（P=0.046）的转录水平与 ADG 性状显著相关。总体而言，我们的多策略 GWAS 结果表明 DCAF16-NCAPG 区域是牛 ADG 的易感位点。
