GWAS And Selection Signal Analysis Of Litter-size And Body Size Traits Of Shanbei White Cashmere Goats

Northern Shaanxi white cashmere goat is an excellent local breed in Yulin City,Shaanxi Province,China and its surrounding areas.At the beginning of its breeding,it was mainly used for cashmere,and less attention was paid to its reproductive performance.According to statistics,the lambing rate of white cashmere goats in northern Shaanxi is only 104.8%,which has seriously hindered the development of its industry.In some studies,it was found that the reproductive performance of animals is often potentially related to the size of the body,so the breeding of northern Shaanxi white cashmere goats from two aspects of reproduction and body size may be an effective way to improve their reproductive performance.Genome-wide association analysis technology can directly correlate molecular markers and phenotypes in the whole genome,and then narrow the scope and screen candidate molecular markers related to phenotype.It is currently one of the main methods for studying functional genes of livestock;Genomic analysis of signals under selection can be used to detect candidate loci for differential traits between populations.Combining these two methods can help us screen more accurate and reliable molecular markers,and provide prior guidance for molecular marker-assisted breeding of northern Shaanxi white cashmere goats.In this study,whole genome resequencing was performed on 160 Shanbei white cashmere goats,and the corresponding phenotypic data such as litter size and body size were recorded at the same time.Combined with the resequencing data of 28 Jining green goats published on NCBI,inter-population analysis was carried out.The selection signal analysis was used to screen the molecular markers that affect the litter size and body size traits of northern Shaanxi white cashmere goats.The results are as follows:1 Genome-wide association analysis of northern Shaanxi white cashmere goatAccording to statistics on the phenotypes of 160 Shanbei cashmere goats collected,the average number of litter-size is 1.73,with a standard deviation of 0.71;the average body height is 59.33 cm,with a standard deviation of 4.74;the average body length is 64.99 cm,the standard deviation is 5.45.After Illumina library construction and sequencing,as well as subsequent variation detection and filtering,a variation set containing 2,368,352 SNPs was finally obtained for subsequent genome-wide association analysis.The correlation results detected five candidate genes significantly correlated with litter size,which were LOC102184340 and TUSC1 genes located on chromosome 8,LOC108637540 genes on chromosome 14,TRNAS-GGA and LOC108633784 genes on chromosome 24;Four gene significantly correlated with body height,namely CPS1 and KANSL1 L genes located on chromosome 2 and WBP11 and LOC108636046 genes located on chromosome 5;Nine candidate genes were significantly correlated with body length traits,including GNAT3 located on chromosome 4;LOC106502376 gene on chromosome 7;PDE2A,TRNAG-CCC and INPPL gene on chromosome 15;CSNK2A2,CCDC113 gene on chromosome 18,and LOC108638395,LOC102187988 gene on chromosome 20.These results can well provide a theoretical basis for molecular marker-assisted breeding.2 Analysis of group selection signalsFour selected signal detection methods of Fst,π ratio,XP-CLR,and XP-EHH were used for Shanbei white cashmere goats and Jining gray goats,and the top 1% of the results obtained by each method were used as basic candidate regions,the intersection between different methods is obtained as the final result.A total of 33 genes were screened out in this study.KEGG enrichment analysis of these genes showed that most of them were involved in Human T-cell leukemia virus 1 infection,Bladder cancer,Notch signaling pathway and other biological pathways were enriched,and GO enrichment analysis showed that these genes were involved in the Regulation of sodium ion transmembrane transport,DNA template transcription,Sarcolemma and Dystrophin-associated glycoprotein complex.Among them,C6H4orf22,ACTL10,ADAMTSL1,and CBFA2T2 are related to reproductive performance,and KAT2 B,DAG1,and KLHDC4 are related to the regulation of body size traits.LOC102184340 gene was screened in GWAS,Fst,XP-EHH and iHS selected signal analysis.The ruminant genome database showed that this gene was mainly expressed in the epidermis and adipoid system,with a small amount of expression in the reproductive and embryonic system.In summary,based on the resequencing data of 160 cashmere goats and 28 Jining green goats,this study screened out a series of candidate genes that potentially affect the reproductive and body size traits of northern Shaanxi white cashmere goats,which will be the basis for the follow-up study of northern Shaanxi white cashmere goats.The cultivation of large and high multiplication populations provides a theoretical basis.