Genome-Wide Scan for Runs of Homozygosity Identifies Candidate Genes Related to Economically Important Traits in Chinese Merino
Genome-Wide Scan for Runs of Homozygosity Identifies Candidate Genes Related to Economically Important Traits in Chinese Merino
复制标题
DOI：
10.3390/ani10030524
复制
发表时间：
2020-03-01
期刊：
影响因子：
3
通讯作者：
Li, Wenrong
中科院分区：
文献类型：
--
作者：
He, Sangang;Di, Jiang;Li, Wenrong
纯合子简单摘要序列（Simple Summary Runs of homozygosity， ROH）通常用于估计近交系数和识别牲畜种群的选择特征。本研究确定了中国美利奴的ROH模式，估计了近交水平，并确定了ROH高频率的基因组区域（ROH热点）。结果表明，中国美利奴羊基因组的ROH丰度较低。近交水平相对较低。共鉴定出13个卢武铉热点，共190个基因。选择特征重叠的ROH热点可能与体型、角性状、免疫性状和环境适应性有关。研究结果可为确定中国美利奴经济性状的候选基因提供参考。摘要本研究利用OvineSNP50全基因组基因分型阵列，对635只中国美利奴羊的纯合性（ROH）运行数、长度和频率进行了估算，并鉴定出ROH频率较高的基因组区域。634只动物共检出6039个超过1mb的ROH。平均每只动物的ROH数量为9.23个，平均长度为5.87 Mb，其中大部分ROH小于10 Mb，占检测到的总数的88.77%。另外，oar21染色体和OAR3染色体的卢武铉覆盖率分别最高和最低。OAR1显示的ROH数量最多，OAR24显示的ROH数量最少。结果表明，在1 Mb以上的ROH中，近交系数为0.023。在1、2、3、5、6、10、11和16号染色体上有13个区域含有ROH热点。在OAR6和OAR11的基因组区域中，NCAPG/LCORL、FGF11和TP53被鉴定为与体型相关的候选基因，而OAR10的基因组区域中含有负责角性状的RXFP2基因。这些结果表明中国美利奴对定向性状选择具有适应性。
Simple Summary Runs of homozygosity (ROH) are commonly used to estimate inbreeding coefficients and identify selection signatures in livestock population. The present study determined ROH patterns, estimated the inbreeding levels, and identified the genome regions with high ROH frequency (ROH hotspots) in Chinese Merino. Our results showed that the genome of Chinese Merino harbored lower ROH abundance. Moreover, the inbreeding levels were relatively low. Thirteen ROH hotspots consisting of 190 genes were identified. The ROH hotspots overlapped the selective signatures might be associated with body size, horn traits, immune traits and environment adaption. These findings could contribute to an optimum breeding program by identifying the candidate genes related to economically traits in Chinese Merino.Abstract In this study, we estimated the number, length, and frequency of runs of homozygosity (ROH) in 635 Chinese Merino and identified genomic regions with high ROH frequency using the OvineSNP50 whole-genome genotyping array. A total of 6039 ROH exceeding 1 Mb were detected in 634 animals. The average number of ROH in each animal was 9.23 and the average length was 5.87 Mb. Most of the ROH were less than 10 Mb, accounting for 88.77% of the total number of detected ROH. In addition, Ovies aries chromosome (OAR) 21 and OAR3 exhibited the highest and lowest coverage of chromosomes by ROH, respectively. OAR1 displayed the highest number of ROH, while the lowest number of ROH was found on OAR24. An inbreeding coefficient of 0.023 was calculated from ROH greater than 1 Mb. Thirteen regions on chromosomes 1, 2, 3, 5, 6, 10, 11, and 16 were found to contain ROH hotspots. Within the genome regions of OAR6 and OAR11, NCAPG/LCORL, FGF11 and TP53 were identified as the candidate genes related to body size, while the genome region of OAR10 harbored RXFP2 gene responsible for the horn trait. These findings indicate the adaptive to directional trait selection in Chinese Merino.