Screening Of Candidate Genes Related To Economic Traits Based On Whole Genome Resequencing In Goat(Capra Hircus)

Goats(Capra hircus) have been used for their milk,meat,hair and skins over much of the world.However,the studies for deciphering genetic mechanism of appearance,productive and reproductive traits on goats were performed by mainly means of validating physiological candidate genes that came from other previous researches,which largely neglected systematic biology and had low accuracy for causative genes.The everincreasing development of high throughput sequencing technology provides the possibility for genome-wide screening of candidate genes related to economic traits in this species.This study collected a total of 12 blood samples of unrelated individuals from Dazu black female goats(DBG,n=6)and Inner Mongolia cashmere female goats(IMCG,n=6).Genomic DNA was extracted using a Tiangen DNA isolation kit and used to construct 350 bp paired-end sequencing libraries.Each library was sequenced with Illumina HiSeq PE150 platform according to the manufacturer's instructions at Novogene(Tianjin,China).Raw data were processed to filter out the adaptors and low quality reads resulted in clean reads using BWA software.After alignment,variation calling was performed per individual using SAMtools package.All the called variations were annotated using the ANNOVAR package.We used the Cluster 3.0 software for performing PCA analysis with the population scale single nucletide polymorphisms(SNPs).Genetic structure was estimated using the program ADMIXTURE Version 1.22 and the neighbor-joining(NJ)tree was constructed using MEGA 5.2 procedure based on genome-wide SNPs.Comparative analysis of variations was performed via incorporating those same SNPs at each group and comparing those different SNPs between the two populations,exonic mutations of which were annotated to genes.Selective sweep analyses were performed by calculating heterozygosity(Hp)and population differentiation(Fst).In addition,those regions that have low ZHp value and high ZFst value were scanned as candidates.To know the biological function of genes within candidate regions,the analysis of Gene Ontology(GO)and Kyoto Encyclopedia of Genes and Genomes(KEGG)pathways were performed using Goseq(Bioconductor 2.12)and KOBAS(kobas2.0–20120208),respectively.The results generated 192.747 Gb raw data and identified more than 5.03 million SNPs.Population substructure(PCA,ADMIXTURE and NJ tree)demonstrated that the clear genetic divergence between DBG and IMCG,which showed that the individuals chosen could be used for further exploring their genomic features.The results analyzed by comparative genomics showed that there are separately 1,873 and 1,706 unique SNPs in the set of DBG and IMCG,exotic variations of which are 21 and 17,matching to 16 and 14 genes,respectively.In addition,we identified 155 and 294 candidate regions harboring 86 and 97 genes based on allele frequency differences(Hp)in DBG and IMCG,respectively.Populations differentiation reflected by Fst values detected 368 putative selective sweep regions including 164 genes.The top 1.0% regions of both low heterozygosity and high genetic differentiation contained 239(135 genes)and 176(106 genes)candidate regions in DBG and IMCG,respectively.These genes were related to physical,reproductive and productive traits through enrichment analyses of GO and KEGG,reference or literature reports and experimental verifications.Such as the missense mutation(rs647214940)at the caprine KIT locus determines dominant white coat color phenotype and FGF5 may be a crucial regulator of hair length but to be further verification.BIRC6 gene likely regulate seasonality of goats,olfaction and hypothalamic-pituitary-gonadal axis are important regular regions for “male effect” on goat.In addition,the rs659097694 site within EGLN1 gene may be causative for high-altitude adaptation of IMCG.The works performed here screened of a large set of candidate genes associated with economic traits by means of the procedures including whole genome resequencing,calling variations,population structure,comparative analysis of variations and selective signature,which laid the foundation for future studying genetic mechanism of economic traits in this species.