Genome-wide Association Study Of Body Conformation And Reproductive Traits By Whole Genome Resequencing In Dazu Black Goat(Capra Hircus)

As one of the oldest domesticated livestock,goats provide abundant meat,milk,and fiber.Most of the world’s goat population is found in South-East Asia and Africa,where goats are the major source of meat production.Owing to the rapid growth of the world’s population and increased demand for diversified meat,the goat industry has become increasingly important.Body conformation traits of goats directly reflect the body size,structure,and development,which are closely related to physiological function and production performance.Body height(BH),body length(BL),chest measurement(CM),chest width(CW),chest depth(CD),and cannon circumference(CC)are the most frequently used body conformation traits.The main function of the mammary gland is to provide nutrition and energy to the pups.The teat is an appendage of the mammary gland,and it is generally believed that the number of teats determines the lactation capacity and affects the health and growth performance of the lamb.In addition,the number of litter size produced by goats also has a significant impact on the development of the breeding stock and the goat breeding industry.Today,there are nearly 120,000 Dazu black goats(DBGs),which are raised in Dazu County of Chongqing(267～934 meters above sea level,Southwest China)and are mostly used for meat production.Screening single nucleotide polymorphic loci for optimal breeding and analyzing their associated genes and pathways using second-generation high-throughput sequencing and GWAS are of great importance to the goat industry.The main findings are as follows:Whole genome resequencing of Dazu black goat.In this study,DBGs(n=150)reared in Tengda breeding conservatory in Dazu district were used as the study subjects,and DNA was extracted from their jugular vein whole blood samples.Whole genome sequencing was performed based on the DNBSEQ-T7 platform after passing the test,and each individual generated 17.83 GB of raw data with an average depth of 6× and an average mapping rate of 99.06%.The raw data were filtered and compared to the goat genome(ARS1)by BWA software,and then the BAM files were sequenced using Picard and Samtools,followed by detection of genomic Single Nucletide Polymorphism(SNP)using GATK and annotation with ANNOVAR software.A total of 25,269,456 SNPs and 2,940,245 small indels were detected in the entire population,with 17,286,575 transitions and8,127,462 inversions,and a Ti/Tv ratio of 2.13.The population structure of goats was assessed by applying Principal Components Analysis(Principal Components Analysis,PCA)through the Facto Mine R package in R language software.The results indicated that there may be some degree of genetic drift between DBGs and other goat breeds.GWAS analysis of body conformation traits in Dazu black goats.In this study,GWAS analysis was performed on six body conformation traits(body height,body length,cannon circumference,chest depth,chest width,and chest circumference)in 150 DBGs.A total of 53 SNPs significant at genome-wide level were screened,and 45 candidate genes were annotated.Among them,28 candidate genes significantly associated with cannon circumference were mainly located on chromosome 8(UBAP1,CNTFR,RPP25 L,CCL19,CCL21,TLR4,BRINP1 and CDK5RAP2).Gene function queries and GO enrichment and KEGG pathway analysis revealed that these genes may be candidate genes in regulating muscle and bone development in goats.Therefore,PSTPIP2,C7orf57,CDKAL1,CCL19,FGF9,SGCG,SIPA1L1 and FIGN were considered as candidate genes affecting body conformation traits in goats.GWAS analysis of reproduction-related traits in Dazu black goats.In this study,10 different significantly SNPs associated with udder morphometry(udder length,teat diameter,teat length,supernumerary teats)were detected in total on chromosomes 3,15,18,23,24,26 and 29.A total of 18 potential SNPs associated with litter size(average number of litter size,average number of litter size in the first six litters)were localized on chromosomes 6,11,13,17,19,27 and 28,of which nine SNPs were located on chromosome 17.After gene annotation of the associated SNPs and combined with relevant references,the candidate genes associated with udder morphometry in DBGs were ATP1,LRRC4 C,SPCS2,XRRA1,CELF4,NTM,TMEM45 B,ATE1,FGFR2,etc.;the candidate genes associated with litter size in DBGs were ENSCHIG00000017110,SLC9A8,GLRB,GRIA2,GASK1 B,ENSCHIG00000026285,etc.The results revealed the genetic mechanisms of litter size and udder morphometry,which provide a reference for further improving the reproductive performance of goats.In conclusion,in this study,six body conformation traits and seven reproductive traits of 150 DBGs were studied,and the first genome resequencing of a large population of this native breed was carried out,and SNPs and candidate genes associated with the traits were identified through GWAS.This study will help to further investigate molecular genetic markers for morphological and litter size in goats,and these results have practical applications for genomic selection in goats.