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

Abstract

Background: 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.

Results: 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 Flemish Giant rabbit had the lowest values for these metrics. Additionally, we identified 17 ROH islands in Chinese indigenous breeds and 22 ROH islands in exotic rabbit breeds, encompassing 124 and 186 genes, respectively. In Chinese indigenous breeds, we identified prominent genes associated with reproduction, including CFAP206, RNF133, CPNE4, ASTE1, and ATP2C1, as well as genes related to adaptation, namely CADPS2, FEZF1, and EPHA7. In contrast, the exotic breeds exhibited a prevalence of genes associated with fat deposition, such as ELOVL3 and NPM3, as well as growth and body weight related genes, including FAM184B, NSMCE2, and TWNK.

Conclusions: This study enhances our understanding of genetic diversity and selection pressures in domestic rabbits, offering valuable implications for breeding management and conservation strategies.

Keywords: Genome resequencing; Inbreeding; ROH island; Rabbit; Runs of homozygosity.

Fig. 1

Distribution patterns of genomic ROHs across different rabbit breeds. (a) Total number of ROHs and ROH categories by length in various rabbit breeds. (b) Distribution of ROH length categories across rabbit autosomes. (c) Correlation analysis between N_ROH and S_ROH in the rabbit population. (d-f) ROH-related metrics in various rabbit breeds: N_ROH represents the total number of ROHs. S_ROH represents the mean sum length of ROH, and L_ROH represents the average length of ROH

Fig. 2

Inbreeding coefficient and effective population size. (a) Inbreeding coefficient based on ROHs (F_ROH). (b) Comparison of inbreeding coefficient based on different metrics across various rabbit breeds. (c) Inbreeding Coefficient based on SNP heterozygosity (F_HOM). (d) Correlation between different inbreeding coefficients. (e) Correlation of F_ROH and F_HOM in each breed. (f-g) Effective population size over generations

Fig. 3

Distribution of ROH islands in different rabbit populations. (a-b) Manhattan plots illustrating the percentage occurrence of each SNP within ROH regions for Chinese indigenous rabbits (a) and exotic rabbits (b)

Fig. 4

Gene enrichment analysis within ROH islands in Chinese indigenous and exotic rabbits. (a-b) Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of genes derived from ROH islands for Chinese indigenous rabbits (a) and exotic rabbits (b)