基于SNP芯片数据分析不同奶牛场基因组近交系数及筛选功能性基因

doi:10.11843/j.issn.0366-6964.2023.07.017

摘要/Abstract

摘要： 旨在利用基因组长纯合片段（runs of homozygosity，ROH）信息评估河南省不同中国荷斯坦牛群体的全基因组近交水平，并通过ROH检测鉴定基因组ROH富集区域，筛选与奶牛经济性状相关的候选基因。本研究基于GGP Bovine 150K芯片对来自河南省7个牧场900头荷斯坦牛进行全基因组ROH检测，统计ROH在荷斯坦群体中的数目、长度及频率，根据ROH计算基因组近交系数（F_ROH），并对高频ROH区域进行基因注释。结果表明，在全部900个体中共检测出55 908个ROH片段，平均长度4.23 Mb。7个牧场平均近交系数（F_ROH）的变化范围从0.082（H7）到0.123（H2），平均F_ROH为0.106。在ROH的高频区域内共鉴定到79个与奶牛经济性状相关的基因，如与牛体型、体高有关的基因AKAP3、C5H12orf4、FGF6，与胴体及繁殖性状相关的基因CAPN3，与妊娠维持和胎儿生长直接相关的基因CHST14，影响牛奶蛋白质组成的基因IL5RA，参与调节胎儿卵泡生成的基因FGF10。其中，在14号染色体上检测到一个高频率的ROH区域（22.78~23.38 Mb），超过80%的个体都在该区域内发生ROH片段，并在此区域鉴定到与生长和饲料转化率相关的基因TGS1、LYN、CHCHD7。基于ROH信息的奶牛近交评估可为奶牛场的选种选配提供指导，在高频ROH区域鉴定到的候选基因可作为奶牛分子育种中进行标记辅助选择的基因。

关键词: 长纯合片段(ROH), 基因组近交系数, 候选基因, 中国荷斯坦牛

Abstract: This study aimed to estimate whole-genome inbreeding levels of Chinese Holstein cattle from different herds in Henan province by using the runs of homozygosity (ROH), and identify ROH enriched regions and screen candidate genes associated with the traits of economic interest. A total of 900 Chinese Holstein cattle form 7 dairy herds in Henan province were used to detect genome-wide ROH by the GGP Bovine 150K Beadchip. The number, length and frequency of ROH in Holstein population was counted. The genome inbreeding coefficient(F_ROH) was calculated according to ROH, and the high frequency ROH regions were annotated. ROH was identified in all animals, 55 908 ROH were identified, with a mean length of 4.23 Mb. The estimated inbreeding coefficients of ROH in 7 herds ranged from 0.082 (H7) to 0.123 (H2), with an average F_ROH of 0.106 in all animals.Moreover, 79 genes related to the economic traits of dairy cows in the genomic region with high frequency ROH were identified. Among these genes, AKAP3, C5H12orf4, and FGF6 were related to the body size and height of cattle, CAPN3 was associated with carcass and reproductive traits, CHST14 was directly related to pregnancy maintenance and fetal growth, the traits of milk protein composition were affected by IL5RA, and FGF10 was involved in regulating fetal folliculogenesis. Notably, a high-frequency ROH region was detected on chromosome 14(22.78-23.38 Mb), where more than 80% of individuals carried ROH fragments. The genes TGS1, LYN and CHCHD7 related to growth and feed conversion were identified in this region. Evaluation of dairy cattle inbreeding based on ROH information could be a useful tool for selection and mating strategies. The candidate genes identified could be used for marker-assisted selection in dairy cattle breeding.

Key words: runs of homozygosity (ROH), genomic inbreeding coefficient, candidate gene, Chinese Holstein cattle

中图分类号:

S823.91

王振宇, 张赛博, 刘文慧, 梁栋, 任小丽, 闫磊, 闫跃飞, 高腾云, 张震, 黄河天. 基于SNP芯片数据分析不同奶牛场基因组近交系数及筛选功能性基因[J]. 畜牧兽医学报, 2023, 54(7): 2848-2857.

WANG Zhenyu, ZHANG Saibo, LIU Wenhui, LIANG Dong, REN Xiaoli, YAN Lei, YAN Yuefei, GAO Tengyun, ZHANG Zhen, HUANG Hetian. Genomic Inbreeding Coefficient Analysis and Functional Gene Screening in Different Dairy Farms Based on SNP Chip Data[J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(7): 2848-2857.

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