Genome-wide Selection Signal Analysis Of Boer Goat

Boer goats were first domesticated in South Africa in the early 19th century.They have attracted attention worldwide due to their stable production performance,fast growth rate and increased meat production.Since the middle of the last century,Boer goats have been introduced by many countries around the world,such as Australia,the United States and Asian countries.In particular,Australia has continued to carry out strong artificial breeding on the growth performance of South African Boer goats,making the growth performance of Australian Boer goats renowned around the world and designating them as the‘meat production machine’.At present,China has abundant local goat genetic resources and has a large number of dominant genotypes in economic traits such as reproduction.However,the overall meat production performance of the goat population in China is poor,and the growth rate is slow,which is also one of the important reasons that restrict the development of the meat goat industry in our country.As early as 1995,China began to introduce Boer goats,and domestic studies on the adaptability,growth performance and hybrid improvement of Boer goats have been carried out.Boer goats have made significant contributions to the improvement of the growth rate of goats in our country.Thus,Boer goats have accumulated a large number of dominant genotypes in their populations with economic traits such as meat production performance and growth speed as they have undergone long-term artificial selection.Therefore,screening of candidate genomic regions and candidate genes related to the growth performance of Boer goats using genome-wide selection signal analysis is helpful to the development of genetic markers for economic traits such as goat growth and meat production.Combined with public data databases that have been published from Europe,Africa and Asia,this study used whole-genome high-throughput sequencing technology to carry out whole-genome resequencing of 46 Australian Boer goats（individual sequencing depth>10×,case group）.The whole-genome resequencing data（control group）of 81 local goats that have not clearly undergone strong manual selection were scanned for the whole-genome selection signal,and candidate genes were identified.The main results are as follows:（1）The results of the SNP data set showed that a total of 13,795,202 SNPs were detected in all individuals.Using F fixation index(F_ST)and population nucleotide polymorphism ratio(π_case/π_control),a 40 kb sliding window and a 20 kb step were used to perform selection signal analysis on a total of 128,929 windows in the whole genome.Through the intersection of the top 5% of the windows for each of the two parameters,1,741 high selection signal windows were screened,and 453 candidate genes were annotated in them.Through gene enrichment analysis,439 candidate genes were enriched into 2,739 GO terms and 247 known signalling pathways.Amongst them,we found 30 candidate genes related to muscle development（e.g.POPDC2,LBX1,LOMD3,TBX5）and a large number of candidate genes related to reproduction,immunity and metabolism（e.g.BRCA2,ITFG2,USE1）.（2）A total of 1,122,858 InDels were identified in the results of the indel data set.F_ST was used to calculate the signal analysis results of each indel site selection between populations,and a total of 11,229 InDels were selected based on the top 1% of the high signal value.In these Indels,2,573 candidate genes were annotated.The results of gene function enrichment showed that 1,200 candidate genes were enriched to 5,999 GO terms and 319 known signal pathways.Amongst them,we found 88 candidate genes related to muscle development and regulation（e.g.MEF2C,MYOZ2,TCF4）and a large number of candidate genes related to reproduction,immunity and metabolism（e.g.SRD5A1,FBXW11,INSR,STXBP3）.（3）In the results of copy number variation（CNV）,a total of 10,338 CNVs were identified.F_STand V_STwere used to calculate the selection signal of each CNV between populations.After taking the intersection of the first 1% high signal value CNV of each parameter,a total of 40 CNVs were screened,and 28 candidate genes were annotated,including EDNRA,CYBA,and MVD.Amongst them,20 candidate genes were extensively enriched into 238 GO terms and 33 known signal pathways related to growth,development and immunity.In conclusion,this study identified a large number of chromosomal regions and candidate genes for goat growth and development through the analysis of the selection signal of the entire genome of the Australian Boer goat.This study provides a basis for future research on economic traits such as goat growth and development.Whilst the mechanism provides the basis of genetic theory,it also contributes to the development of selective genetic markers for goat molecular breeding.