Identification And Validation Of Candidate Genes Affecting Growth Traits In Rabbit Based On Whole Genome Resequencing

ABSTRCT In rabbit production,growth traits are important economic traits,and the growth rate directly affects the gross economic product of rabbit industry to a large extent.Growth traits are quantitative traits controlled by minor polygenes.Growth traits are quantitative traits controlled by micro-effect polygene.It is difficult to identify the key genes and variations that potentially affect the growth traits of rabbits by conventional genetic methods.Genome-wide resequencing technology provides an effective technical means to solve this problem.As one of the most recently domesticated species,the genetic diversity and genetic structure of rabbit remains to be further studied.Based on the above reasons,this study preliminarily clarified the genetic diversity and genetic structure of the four rabbit populations by genome-wide resequencing,and screened and verified the candidate genes and variations affecting the growth traits of rabbits.The main research contents and results are as follows:(1)Detection of rabbit genome genetic variation based on whole genome resequencingIn this study,the genome-wide resequencing technology was used to perform genome-wide resequencing on six Hyplus meat rabbits.Combined with the genomewide resequencing data of 31 rabbit individuals published in NCBI database,a total of 1556.12 Gb clean data was obtained,and the comparison rate of clean data to the reference genome was more than 98%.The average coating depth of each individual was more than 13.79×,and the genome coverage was more than 93%.By detecting the genetic variation information of SNPs,Indels and SVs in rabbit population,27,567,157 SNPs,9,061,538 Indels and 151,709 SVs variation sites were obtained.(2)Population genetic structure analysis and candidate gene identification of growth traits in rabbitsIn this study,phylogenetic tree analysis,population structure analysis and principal component analysis were used to classify the population of rabbits.The results showed that 37 rabbits could be divided into three groups.New Zealand white rabbits and Hyplus meat rabbits were used as a subgroup,while Watanabe heritable hyperlipidemic rabbits and Japanese white rabbits were used as a subgroup.The results of linkage disequilibrium decay analysis showed that,compared with the other three kinds of rabbits,the decay rate of the Hyplus meat rabbit was the slowest,indicating that the Hyplus meat rabbit may be subjected to more intense artificial selection.A total of 100 and 80 candidate genes that could potentially affect the phenotypes of the two strains of rabbits were screened by specific variation of Hyplus D strain and Hyplus E strain rabbits combined with RNA-seq data in previous studies in the laboratory and selective sweep analysis.Through functional enrichment analysis and literature review,it was found that UCP2,FRZB,SOCS2,CSRP3,MYL3,SMAD3,TIAM2,SRA1,AUTS2 and ROR2 might be candidate genes affecting rabbit growth traits.(3)Association analysis of CSRP3 and SMAD3 gene with rabbit growth traitsAccording to the above resequencing analysis,UCP2,CSRP3 and SMAD3 genes may be candidate genes affecting the growth traits of Hyplus meat rabbits.On this basis,5 candidate SNPs in UCP2 gene,7 candidate SNPs in CSRP3 gene and 17 candidate SNPs in SMAD3 gene were verified by PCR and first-generation sequencing.Among them,5 SNPs in UCP2 gene were specific in Hyplus D strain and Hyplus E strain rabbits.Linkage disequilibrium analysis showed that 7 SNPs of CSRP3 gene and 17 SNPs of SMAD3 gene were completely linked disequilibrium(r2 and D’ were both equal to 1)in Hyplus D strain rabbit population.Association analysis showed that the g.5372008 C>T locus of SMAD3 gene was significantly associated with 35-day-old body weight,49-day-old body weight and chest circumference of Hyplus D strain rabbits(P<0.05).However,the g.158134254 G>A locus of CSRP3 gene was not correlated with the growth traits of Hyplus D strain rabbits(P>0.05).In conclusion,this study used genome-wide resequencing technology to detect the genetic variation information at genome-wide level in rabbit population.The candidate genes and variations affecting the growth traits of rabbits were screened by specific variation combined with RNA-seq data in previous studies in the laboratory and selective sweep analysis,and the association analysis between the candidate gene variations and the growth traits of rabbits was carried out to verify the results of resequencing analysis.