The CNV map construction and ROH analysis of Pinan cattle.

IF 3.5 2区生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

BMC Genomics Pub Date : 2025-05-14 DOI:10.1186/s12864-025-11626-6

Xingya Song, Zijing Zhang, Shengyan Xing, Xian Liu, Yuqiao Zhang, Jiamei Wang, Shijie Lyu, Xiangnan Wang, Xingshan Qi, Weidong Ma, Chuzhao Lei, Eryao Wang, Yongzhen Huang

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Abstract

Pinan cattle, as the progeny of crossbreeding improvement between Nanyang cattle and Piedmontese, have attracted attention for their excellent growth performance. In this study, we constructed a copy number variation map by whole genome resequencing of 132 Pinan cattle. In the genome of Pinan cattle, deletion-type copy number variants occupied a higher proportion and only 3.31% of CNVRs overlapped with exonic regions. It showed that Pinan cattle was clearly distinguishable from other breeds and Pinan cattle was closer to Nanyang cattle by population genetic structure analysis based on CNVRs. The degree of inbreeding in the Pinan cattle population was explored by ROH analysis, which showed that the degree of inbreeding in Pinan cattle was lower than that in European beef cattle, suggesting that the risk of inbreeding was low. Candidate genes related to muscle development (CADM3, CNTFR, DOCK3), reproductive traits (SCAPER), embryonic development (RERE) and immune traits (CD84) were identified by V_ST selection analysis, ROH islands and iHS selection analysis, which provided a new scientific basis for the genetic basis of the excellent traits in Pinan cattle.

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品南牛CNV图谱构建及ROH分析。

品南牛作为南洋牛与皮埃蒙特牛杂交改良的后代，因其优良的生长性能而备受关注。通过对132头品南牛的全基因组重测序，构建了拷贝数变异图谱。在品南牛基因组中，缺失型拷贝数变异所占比例较高，仅有3.31%的CNVRs与外显子区域重叠。基于CNVRs的群体遗传结构分析表明，品南牛与其他品种有明显区别，品南牛与南阳牛更接近。通过ROH分析探讨了品南牛群体的近交程度，结果表明品南牛的近交程度低于欧洲肉牛，表明近交风险较低。通过VST选择分析、ROH孤岛分析和iHS选择分析，鉴定出与肌肉发育（CADM3、CNTFR、DOCK3）、生殖性状（SCAPER）、胚胎发育（RERE）和免疫性状（CD84）相关的候选基因，为品南牛优良性状的遗传基础提供了新的科学依据。

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来源期刊

BMC Genomics 生物-生物工程与应用微生物

CiteScore

7.40

自引率

4.50%

发文量

769

审稿时长

6.4 months

期刊介绍： BMC Genomics is an open access, peer-reviewed journal that considers articles on all aspects of genome-scale analysis, functional genomics, and proteomics. BMC Genomics is part of the BMC series which publishes subject-specific journals focused on the needs of individual research communities across all areas of biology and medicine. We offer an efficient, fair and friendly peer review service, and are committed to publishing all sound science, provided that there is some advance in knowledge presented by the work.