Research On Origin And Domestication Of Chinese Domestic Rabbits Based On Genome Resequencing Data

Raising rabbits has a long history in China and it is one of the earliest recorded countries for rabbit husbandry.Domestic rabbits evolved from wild burrowing rabbits through long-term human domestication and selection.However,due to a lack of archaeological evidence for the domestication of burrowing rabbits in China and less research on the origin and domestication of rabbits,the origin and domestication process of domestic rabbits in China are not clear.Through long-term domestication,domestic rabbits have undergone significant changes in morphology,behavior,and physiological functions.Studying the genomic selection signals of domestic rabbits can help understand the genetic basis of their environmental adaptability and phenotype characteristics.To study the origin,domestication process,selectively important genomic regions,and genes of the Chinese domestic rabbit,we performed whole-genome resequencing on five Chinese domestic rabbit breeds from different regions,three introduced breeds,and one cultivated breed.In total,we obtained 2.8 terabytes of sequencing data from 142 rabbits,with an average sequencing depth of 15.31 X,and detected 18.85 million SNPs.The sequencing data was based on the rabbit reference genome(Ory Cun2.0)with a size of 2.74 GB.Through population genetics analysis,we found significant population differentiation between wild and domestic rabbits,with closer geographic breeds having closer genetic distances.Among the Chinese domestic rabbits,the Jiuyishan rabbit and the Laiwu black rabbit had the highest genetic diversity,while the Fujian white rabbit had the lowest.The genetic diversity level of local rabbits was similar to that of introduced breeds.We reconstructed the population history of rabbits and found that compared to other livestock,the domestication of rabbits was relatively late.The effective population size of each breed of rabbits and wild rabbits has a similar trend of change before 10,000 years ago,suggesting a common ancestor for Chinese and introduced rabbit breeds.By analyzing the evolutionary tree and population genetic structure,we found that some wild rabbits had a close genetic distance to domestic rabbits,indicating rich genetic heritage in domestic rabbits.Some of the domestic rabbit’s heritage came from the nominate subspecies of wild rabbits from northern Spain,while the Mediterranean subspecies of wild rabbits was not the main ancestor of modern domestic rabbits.Through the mitochondrial haplotype network analysis,we found that the ancestors of these two wild rabbit subspecies did not pass down mitochondrial information to the Chinese domestic rabbit population,suggesting that Chinese domestic rabbits may have had multiple ancestor populations in the early stages of domestication or that maternal replacement occurred during domestication.Furthermore,Chinese domestic rabbits may have different maternal ancestors from European rabbits,supporting the theory of multiple origins for Chinese domestic rabbits.Through gene flow studies,we found complex gene flow events between Chinese domestic rabbit breeds.The Sichuan white rabbit,Fujian white rabbit,and Minnan black rabbit populations had significant gene flow to Jiuyishan rabbit and Laiwu black rabbit.Chinese domestic rabbits also experienced lineage invasion from foreign breeds.To study the impact of domestication on the rabbit genome and genes related to rabbit phenotypes,we compared the genomes of wild and domestic rabbit populations and found that genes related to sensory,nervous system,fur color,and behavior were selected during domestication.Additionally,we used FST and ROD selection signal detection methods to identify genes such as TYR,GMR5,LUM,MYO3 B,GRIN3A,and GRIK2 that were subjected to high-intensity selection.This study analyzed the origin and domestication process of Chinese domestic rabbits and revealed genomic regions and genes related to rabbit breed characteristics,providing a foundation for the scientific utilization and protection of rabbit genetic resources and breed selection.