Genome-wide Scan In Seven Indigenous Pakistani Goat Breeds And Candidate Gene Analysis Of High Altitude Adaptation In The Tibetan Goats

Goat breeds have been selected for meat,milk,prolificacy,pashmina（cashmere）and skins in countries with climatic conditions that range from tropical and subtropical to high mountains in dry,humid,and cold environments.The wide diversity of these breeds in morphological characteristics and production performance should have immense merits for selection and genetic improvement.Bari（BAR）,Bugi Toori（BUT）,Kamori（KMR）,Pateri（PTR）,Tapri（TPR）,White Tapri（WTP）and Black Tapri（BTR）are among the main breeds in the Sindh province of Pakistan.The phenotypic diversity of these Pakistani goat breeds mainly reflects in coat color,milk production,ear length and body size,milk production and reproductive traits.Firstly,we investigated the genetic diversity,evolutionary relationship,population structure,and differentiation within and between seven indigenous Pakistani goat populations by 50K SNP arrays.Analysis of the genotyping data showed different levels of genetic polymorphism.In the present study,Proportion of polymorphic SNPs(P_N),Observed heterozygous（H_O）and Expected heterozygous（H_E）were used to estimate genetic diversity between individuals.The P_N was comparable among the breeds and ranged from 0.565 to 0.971 with the highest value in PTR and the lowest value in BUT.The H_O and H_E were quite similar across seven Pakistan goat breeds.Further,principal component analysis（PCA）was performed among all individuals.The first（PC1）explained18.95%,the second（PC2）8.25%and the third（PC3）6.15%of the observed variation.Contrasting PCI vs.PC2 and PC1vs.PC3 resulted in clear segregations of BAR and BTR from other breeds.In order to better understand the genetic characterization of Pakistani local goat breeds,an NJ tree was constructed,indicating a clear separation between most breeds.The KMR and PTR branched close to each other and BUT and BAR showed longer branch.The pairwise FST value ranged from 0.0354 to 0.3028 among seven goat breeds.BUT and BAR showed the highest level of differentiation（0.3028）.Secondly,a total of 2,508 putative selection signals were reported in the genome of Pakistani goats.The 26 most significant windows in at least four breeds contained known candidate genes,such as coat color variation（KIT）,reproduction（BMPR1B,GNRHR,INSL6,JAK2,EGR4）,body size（SOCS2）,ear size（MSBR）and milk composition（ABCG2,SPP1,CSN1S2,CSN2,CSN3,PROLACTIN）.This study provides valuable insights into the genetic diversity of Pakistani goats and contributes toward a better understanding of the genetic architecture of coat color,milk composition,and reproduction traits of Pakistani goats.However,the successive collection of more data and subsequent validation of the results of future studies is necessary.Among the most severe environmental challenges to confront animal is the low oxygen availability of high-altitude regions such as the Tibetan Plateau.Tibetan goats are the main livestock for people living in Qinghai–Tibetan plateau at China.These goats exhibit the distinct physiological and phenotypic characteristic with respect to lowland goat populations.These traits allow them to adapt hypoxia conditions of the Tibetan plateau during the long-term selection.Therefore,it provides an outstanding model for understanding the genetic mechanism of hypoxia adaptations and the hypoxia-related disease development.Our previous exome sequencing of five Chinese cashmere breeds revealed a candidate gene,DSG2,and DSG3 responsible for the high-altitude adaptation in Tibetan goat.DSG2 and DSG3 genes are desmoglein proteins coding gene.These are located in a cluster on goat chromosome 24,consisting of 16 exons and spanning more than 30 kb.DSG2 is widely expressed in all desmosomes containing tissue,including myocardial and stratifying epithelial.While DSG3 is expressed in stratifying epithelial tissues and its role in the cardiovascular system remains unknown.In this study,the entire region of DSG2 and DSG3（³0 kb）were re-sequenced in ten Chinese native goat populations.In DSG2 gene,thirteen significant SNPs loci were found between the lowland and highland goat populations.There were three intronic SNPs and ten exonic with five synonymous mutations and five non-synonymous substitutions.One intronic SNP3 and three exonic SNP1,SNP8,SNP9 were highly significant and reflect a remarkable difference between high and low altitude goat breeds.The mutant allele frequency was rare in four,low in three,equitably average in two lowland goat populations,but higher in one highland goat population.The pair-wise genetic distance（FST）between lowland and highland goat breeds ranged from 0.00 to 0.55.The significant thirteen loci were ranged from 0.42 to0.55.Similarly,in DSG3,twenty-seven SNPs variants were found between the lowland andhighland goat populations.The genetic distance（FST）of these SNPs between lowland and highland populations ranged from 0.00 to 0.58.We further conducted statistical analysis including correlation coefficient analysis,linkage disequilibrium,and haplotype network construction in DSG3.We found three non-synonymous candidate SNPs（R392Q,T394I,G417S）and two synonymous SNPs in DSG3 that were significantly segregated between high-and low-altitude goats,indicating the contribution of DSG2/DSG3 to the high altitude adaptation of Tibetan goat.