Wu Yang, Fan Huizhong, Wang Yanhui, Zhang Lupei, Gao Xue, Chen Yan, Li Junya, Ren HongYan, Gao Huijiang
Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, China.
Department of life sciences, National Natural Science Foundation of China, Beijing, China.
PLoS One. 2014 Oct 20;9(10):e109330. doi: 10.1371/journal.pone.0109330. eCollection 2014.
Recent advances in high-throughput genotyping technologies have provided the opportunity to map genes using associations between complex traits and markers. Genome-wide association studies (GWAS) based on either a single marker or haplotype have identified genetic variants and underlying genetic mechanisms of quantitative traits. Prompted by the achievements of studies examining economic traits in cattle and to verify the consistency of these two methods using real data, the current study was conducted to construct the haplotype structure in the bovine genome and to detect relevant genes genuinely affecting a carcass trait and a meat quality trait. Using the Illumina BovineHD BeadChip, 942 young bulls with genotyping data were introduced as a reference population to identify the genes in the beef cattle genome significantly associated with foreshank weight and triglyceride levels. In total, 92,553 haplotype blocks were detected in the genome. The regions of high linkage disequilibrium extended up to approximately 200 kb, and the size of haplotype blocks ranged from 22 bp to 199,266 bp. Additionally, the individual SNP analysis and the haplotype-based analysis detected similar regions and common SNPs for these two representative traits. A total of 12 and 7 SNPs in the bovine genome were significantly associated with foreshank weight and triglyceride levels, respectively. By comparison, 4 and 5 haplotype blocks containing the majority of significant SNPs were strongly associated with foreshank weight and triglyceride levels, respectively. In addition, 36 SNPs with high linkage disequilibrium were detected in the GNAQ gene, a potential hotspot that may play a crucial role for regulating carcass trait components.
高通量基因分型技术的最新进展为利用复杂性状与标记之间的关联来绘制基因图谱提供了机会。基于单个标记或单倍型的全基因组关联研究（GWAS）已经确定了数量性状的遗传变异和潜在遗传机制。受牛经济性状研究成果的启发，并为了使用真实数据验证这两种方法的一致性，本研究旨在构建牛基因组的单倍型结构，并检测真正影响胴体性状和肉质性状的相关基因。利用Illumina BovineHD BeadChip，引入942头具有基因分型数据的年轻公牛作为参考群体，以鉴定肉牛基因组中与前腿重量和甘油三酯水平显著相关的基因。基因组中总共检测到92,553个单倍型块。高连锁不平衡区域延伸至约200 kb，单倍型块大小从22 bp到199,266 bp不等。此外，个体单核苷酸多态性（SNP）分析和基于单倍型的分析检测到这两个代表性性状的相似区域和常见SNP。牛基因组中分别有12个和7个SNP与前腿重量和甘油三酯水平显著相关。相比之下，分别有4个和5个包含大多数显著SNP的单倍型块与前腿重量和甘油三酯水平强烈相关。此外，在GNAQ基因中检测到36个具有高连锁不平衡的SNP，该基因可能是调节胴体性状组成部分的关键热点。
