您好，欢迎访问安徽省农业科学院 机构知识库！

Genome-wide detection of genetic structure and runs of homozygosity analysis in Anhui indigenous and Western commercial pig breeds using PorcineSNP80k data

文献类型： 外文期刊

作者： Jiang, Yao 1 ; Li, Xiaojin 1 ; Liu, Jiali 2 ; Zhang, Wei 1 ; Zhou, Mei 1 ; Wang, Jieru 1 ; Liu, Linqing 1 ; Su, Shiguang 1 ; Zhao, Fuping 2 ; Chen, Hongquan 3 ; Wang, Chonglong 1 ;

作者机构： 1.Anhui Acad Agr Sci, Anhui Prov Key Lab Livestock & Poultry Prod Safet, Key Lab Pig Mol Quantitat Genet, Anhui Acad Agr Sci, Hefei 230031, Peoples R China

2.Chinese Acad Agr Sci, Minist Agr, Inst Anim Sci, Key Lab Anim Genet Breeding & Reprod Poultry, Beijing 100193, Peoples R China

3.Anhui Agr Univ, Coll Anim Sci & Technol, Hefei 230036, Peoples R China

关键词： Anhui indigenous pig breeds; genetic structure; runs of homozygosity; Inbreeding coefficient; ROH island

期刊名称：BMC GENOMICS （ 影响因子：4.547； 五年影响因子：4.931 ）

ISSN： 1471-2164

年卷期： 2022 年 23 卷 1 期

页码：

收录情况： SCI

摘要： Background Runs of homozygosity (ROH) are continuous homozygous regions typically located in the DNA sequence of diploid organisms. Identifications of ROH that lead to reduced performance can provide valuable insight into the genetic architecture of complex traits. Here, we systematically investigated the population genetic structure of five Anhui indigenous pig breeds (AHIPs), and compared them to those of five Western commercial pig breeds (WECPs). Furthermore, we examined the occurrence and distribution of ROHs in the five AHIPs and estimated the inbreeding coefficients based on the ROHs (F-ROH) and homozygosity (F-HOM). Finally, we identified genomic regions with high frequencies of ROHs and annotated candidate genes contained therein. Results The WECPs and AHIPs were clearly differentiated into two separate clades consistent with their geographical origins, as revealed by the population structure and principal component analysis. We identified 13,530 ROHs across all individuals, of which 4,555 and 8,975 ROHs were unique to AHIPs and WECPs, respectively. Most ROHs identified in our study were short (< 10 Mb) or medium (10-20 Mb) in length. WECPs had significantly higher numbers of short ROHs, and AHIPs generally had longer ROHs. F-ROH values were significantly lower in AHIPs than in WECPs, indicating that breed improvement and conservation programmes were successful in AHIPs. On average, F-ROH and F-HOM values were highly correlated (0.952-0.991) in AHIPs and WECPs. A total of 27 regions had a high frequency of ROHs and contained 17 key candidate genes associated with economically important traits in pigs. Among these, nine candidate genes (CCNT2, EGR2, MYL3, CDH13, PROX1, FLVCR1, SETD2, FGF18, and FGF20) found in WECPs were related to muscular and skeletal development, whereas eight candidate genes (CSN1S1, SULT1E1, TJP1, ZNF366, LIPC, MCEE, STAP1, and DUSP) found in AHIPs were associated with health, reproduction, and fatness traits. Conclusion Our findings provide a useful reference for the selection and assortative mating of pig breeds, laying the groundwork for future research on the population genetic structures of AHIPs, ultimately helping protect these local varieties.

  • 相关文献

[1]Genome-wide detection of genetic structure and runs of homozygosity analysis in Anhui indigenous and Western commercial pig breeds using PorcineSNP80k data. Jiang, Yao,Li, Xiaojin,Zhang, Wei,Zhou, Mei,Wang, Jieru,Liu, Linqing,Su, Shiguang,Wang, Chonglong,Liu, Jiali,Zhao, Fuping,Chen, Hongquan. 2022

作者其他论文 更多>>
置顶
购物车
反馈

© 京ICP备09089781号-29 主办单位：安徽省农业科学院

学术资源： 中国农业科学院 农业专业知识服务系统 农科联盟资源共建共享平台 中国农业科技文献与信息服务平台 中国农业期刊集成服务平台