绵羊全基因组ROH检测及候选基因鉴定

doi:10.11843/j.issn.0366-6964.2019.08.004

摘要/Abstract

摘要： 旨在利用长纯合片段（runs of homozygosity，ROH）信息评估不同绵羊群体的近交情况，并鉴定与绵羊经济性状相关的基因。本研究基于Illumina Ovine SNP50芯片对来自10个绵羊群体共440个个体进行全基因组ROH检测，统计ROH在不同绵羊群体中的数目、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，在10个绵羊群体中共检测到25 920个ROH片段，不同绵羊群体ROH的数目、长度、频率及分布存在明显差异。ROH平均数目的变化范围从10.17个（苏尼特羊）到95.99个（杜泊羊），平均长度的变化范围从2.04 Mb（四川藏羊）到4.71 Mb（罗布羊），平均F_ROH的变化范围从0.010（苏尼特羊）到0.172（杜泊羊）。引进品种的（杜泊羊和德美羊）平均F_ROH明显高于地方品种。在地方绵羊群体中，西藏藏羊（0.085）具有最高的平均F_ROH。在高频ROH区域鉴定到26个与绵羊经济性状相关的基因，如与生长发育相关的基因NCAPG、LCORL、PRKAA2、FAIM2和HYDIN，与脂肪代谢相关的基因LEPR、WNT10B和NCKAP5L，与肉质及胴体性状相关的基因CDIPT、CAPN3和FGF9。基于ROH评估的近交情况可为绵羊种群育种和保种提供参考依据，鉴定到的候选基因可以作为绵羊标记辅助选择重要的基因。

Abstract: The aim of this study was to evaluate inbreeding among different sheep populations and detect genes related to economic traits of sheep based on the information of runs of homozygosity (ROH). Based on Illumina Ovine SNP50 BeadChip, we performed genome-wide ROH scan for 440 individuals from 10 sheep populations. The number, length and frequency of ROH were counted in each population and the genomic inbreeding coefficient(F_ROH) was calculated based on ROH. The genomic regions with high frequency in ROH were annotated. A total of 25 920 ROH fragments were identified in the 10 sheep populations. The number, length, frequency and distribution of ROH varied among these sheep populations. The average number of ROH per population ranged from 10.17 (Sunite) to 95.99 (Dorper), the average length of ROH per population ranged from 2.04 Mb (Tibetan sheep from Sichuan) to 4.71 Mb (Lop), and the average genomic inbreeding coefficients (F_ROH) ranged from 0.010 (Sunite) to 0.172 (Dorper) in sheep populations. The average F_ROH in commercial sheep breeds from abroad (Dorper and German Mutton Merino sheep) were higher than that in the indigenous sheep populations in China. Among Chinese indigenous sheep populations, Tibetan sheep from Tibet (0.085) had the highest average genomic inbreeding coefficient. Moreover, twenty-six genes related to economic traits of sheep located in the genomic regions with high frequency in ROH were identified. Among these genes, NCAPG, LCORL, PRKAA2, FAIM2 and HYDIN were associated with growth and development traits, LEPR, WNT10B and NCKAP5L were related to fat metabolism, and CDIPT, CAPN3 and FGF9 involved in meat quality and carcass traits. The inbreeding coefficients calculated based on ROH would provide reference for breeding and preservation of the 10 sheep populations and the candidate genes identified could be used for marker-assisted selection in sheep breeding.

中图分类号:

S826.2

刘家鑫, 魏霞, 邓天宇, 谢锐, 韩建林, 杜立新, 赵福平, 王立贤. 绵羊全基因组ROH检测及候选基因鉴定[J]. 畜牧兽医学报, 2019, 50(8): 1554-1566.

LIU Jiaxin, WEI Xia, DENG Tianyu, XIE Rui, HAN Jianlin, DU Lixin, ZHAO Fuping, WANG Lixian. Genome-wide Scan for Run of Homozygosity and Identification of Corresponding Candidate Genes in Sheep Populations[J]. ACTA VETERINARIA ET ZOOTECHNICA SINICA, 2019, 50(8): 1554-1566.

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