Liu Mei, Li Bo, Shi Tao, Huang Yongzhen, Liu George E, Lan Xianyong, Lei Chuzhao, Chen Hong
College of Animal Science and Technology, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Northwest A&F University, No. 22 Xinong Road, Yangling, 712100, Shaanxi, People's Republic of China.
Animal Genomics and Improvement Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD, 20705, USA.
J Appl Genet. 2019 May;60(2):199-207. doi: 10.1007/s13353-019-00496-w. Epub 2019 Apr 17.
Sonic Hedgehog (Shh) regulates many key developmental processes during vertebrate limb development, fat formation, and skeletal tissue regeneration. Current whole genome sequencing data have identified a copy number variation mapping to bovine Sonic Hedgehog gene (SHH-CNV). The object of this study was to characterize the SHH-CNV distributions in 648 individuals from 11 Chinese cattle populations and further to investigate the associations of the copy number changes with gene expression and cattle growth traits. The SHH-CNV showed a high variance within Chinese indigenous yellow cattle. Compared to yak and dairy cattle, the beef cattle like Luxi and Xianan breed had significantly higher median copy numbers, suggesting the diversity of SHH-CNV in beef cattle selections. The negative correlation of SHH-CNV with SHH transcriptional level in adult adipose tissue (P < 0.01) indicated the dosage effects of SHH-CNV related to bovine fat formation. Association analysis of SHH-CNV and body size traits was conducted in five breeds. The results revealed that the copy number gain type of SHH-CNV exhibited significantly better chest depth in 24 months old Qinchuan cattle, and better body weight, body length, and chest girth in 18 months old Nanyang cattle, whereas the normal copy number had superior chest girth and body weight in adult Jinnan cattle (P < 0.05 or P < 0.01). In summary, this research uncovered meaningful effects of SHH-CNV on gene expression and cattle phenotypic traits, indicating its potential applications for genetic improvement of beef cattle.
音猬因子（Shh）在脊椎动物肢体发育、脂肪形成和骨骼组织再生过程中调节许多关键的发育进程。当前的全基因组测序数据已鉴定出一个映射至牛音猬因子基因的拷贝数变异（SHH-CNV）。本研究的目的是表征11个中国牛种群648个个体中SHH-CNV的分布情况，并进一步研究拷贝数变化与基因表达及牛生长性状之间的关联。SHH-CNV在中国本土黄牛中表现出高度的变异性。与牦牛和奶牛相比，像鲁西和西南牛这样的肉牛品种具有显著更高的中位数拷贝数，这表明在肉牛选育中SHH-CNV具有多样性。SHH-CNV与成年脂肪组织中SHH转录水平呈负相关（P < 0.01），这表明SHH-CNV与牛脂肪形成相关的剂量效应。对五个品种进行了SHH-CNV与体尺性状的关联分析。结果显示，SHH-CNV的拷贝数增加型在24月龄的秦川牛中胸深显著更好，在18月龄的南阳牛中体重、体长和胸围更好，而正常拷贝数在成年晋南牛中胸围和体重更优（P < 0.05或P < 0.01）。总之，本研究揭示了SHH-CNV对基因表达和牛表型性状的重要影响，表明其在肉牛遗传改良中的潜在应用价值。
