Genetic Diversity Of Six Native Goat Breeds In Yunnan

Domestic goats(Capra hircus)not only provide a variety of animal products to human society,but also play an important role in human history and culture.The genetic diversity of domestic goats has been the focus of genetic breeders,because the genetic diversity of species or populations is a result of long-term evolution and a prerequisite for their survival adaptation and evolution.There are many goat breeds with large quantities in Yunnan Province,but there are few molecular DNA-based studies for them.In this study,we obtained 481 bp fragment of mitochondrial DNA(mtDNA)D-loop region from 688 individuals of six local goat breeds(Maguan poll goat,Yunling goat,Shizong black goat,Luoping yellow goat,Zhaotong goat and Weixin white goat)and one introduced goat breed(Nubian goat)to investigate the genetic diversity and phylogeographic structure of Yunnan domestic goats.The results showed that Yunnan goat breeds presented higher level of genetic diversity.The haplotype diversity of each Yunnan goat breed ranged from 0.789±0.034(Weixin white goat)to 0.967±0.006(Nubian goat)and the nucleotide diversity ranged from 0.0275 ±0.00264(Weixin white goat)to 0.0382±0.00073(Shizong black goat).The phylogenetic analyses allowed us to classify Yunnan goats into two mtDNA lineages(A and B):both lineage A and B were widely distributed in Yunnan province;lineage A was predominant,accounted for 69.1%of all samples.Phylogenetic analysis combined with wild goat species sequences indicated that wild goat(Capra aegagrus)was probably the most important wild ancestor of six Yunnan goat populations.A combined analysis of previously reported sequences of Southeast Asian and our sequences belonging to lineage B suggested that the B2 subclade of lineage B might originated from southwestern China.There was no significant geographical structuring among Yunnan goat populations,indicating that there existed strong gene flow existed among goat populations,caused by the extensive transportation and frequent flow of goat populations.By comparing Yunling goats with Nubian goats,it was found that there are significant differences in disease resistance and production capability between these two breeds.Both of them are widely distributed and have a large number in Yunnan Province.Additionally,we also used the restriction-site-associated DNA sequencing(RAD-seq)to perform genome sequencing and population genetic difference analysis for Yunling goats(60 individuals)and Nubian goats(60 individuals).Our results showed that a total of 686.56 Gb data was obtained,with an average of 5.72 Gb per individual.The Q30 scores were more than 92.33%for all samples.A total of 11,668,890 SNPs was obtained by bioinformatics analysis,and the filtered 151,071 SNPs were used for subsequent population genetic analyses.Further analysis of the selection signature revealed that there were certain differentiations in the chromosomes of 8,9 and 13,16 between two goat populations.Eight selected regions and 91 selected candidate genes were identified by Fst analysis and Pi test,respectively.Functional analysis of these candidate genes found that some genes are associated with disease(DOK2,TIMM17A and LMODl),immunity(MAYS and DOCKS),and certain economic traits(MIR103,SPEF1 and CDC25B).For example,LMOD1 is associated with intestinal hypotonic syndrome,DOCK8 is associated with humoral immunity,SPEF1 and CDC25B are both reproductively related,and MIR103 controls milk fat accumulation in the mammary gland of goat during lactation.In summary,this study explored the mitochondrial genetic diversity and phylogeographic structure of six Yunnan goat populations,and found that Yunnan domestic goats showed high genetic diversity and no significant geographical structuring.And we also used RAD-seq technology to carry out population genetic analysis among Yunling goat and Nubian goat breeds,gene flow and differential genomic regions and related genes between them were found,which would provide an objective basis for trace the genetic differences among difference goat breeds.At the same time,this study will help to further understand the germplasm characteristics of indigenous goat breeds and better protect and develop goat breed resources.