Whole-genome sequencing reveals patterns of runs of homozygosity underlying genetic diversity and selection in domestic rabbits

作者：Xinxin Ping, Yuan Chen, Hui Wang, Zhuoya Jin, Qianting Duan, Ren Zhanjun, Xianggui Dong · 发表于：BMC Genomics · 年份：2025 · DOI：10.1186/s12864-025-11616-8 · 被引用次数：5 · 研究领域：Rabbits: Nutrition, Reproduction, Health、Genetic Mapping and Diversity in Plants and Animals、Genetic diversity and population structure

Runs of homozygosity (ROH) are continuous segments of homozygous genotypes inherited from both parental lineages. These segments arise due to the transmission of identical haplotypes. The genome-wide patterns and hotspot regions of ROH provide valuable insights into genetic diversity, demographic history, and selection trends. In this study, we analyzed whole-genome resequencing data from 117 rabbits to identify ROH patterns and inbreeding level across eleven rabbit breeds, including seven Chinese indigenous breeds and four exotic breeds, and to uncover selective signatures based on ROH islands. We detected a total of 31,429 ROHs across the autosomes of all breeds, with the number of ROHs (N ROH ) per breed ranging from 1316 to 7476. The mean sum of ROHs length (S ROH ) per individual was 493.84 Mb, covering approximately 22.79% of the rabbit autosomal genome. The majority of the detected ROHs ranged from 1 to 2 Mb in length, with an average ROH length (L ROH ) of 1.84 Mb. ROHs longer than 6 Mb constituted only 0.83% of the detected ROHs. The average inbreeding coefficient derived from ROHs (F ROH ) was 0.23, with F ROH values ranging from 0.14 to 0.38 across breeds. Among Chinese indigenous breeds, the Jiuyishan rabbit exhibited the highest values of N ROH , S ROH , L ROH , and F ROH , whereas the Fujian Yellow rabbit had the lowest F ROH values. In exotic rabbit breeds, the Japanese White rabbit displayed the highest values for N ROH , S ROH , L ROH , and F ROH , while the ...