The Study Of Taihu Pigs' Molecular Germplasm Characteristics Based On Whole Genome Sequencing

Taihu pigs is one of the most famous local pig breeds in C hina,and it has the unique germplasm characteristics,such as high fecundity traits,good meat quality,and crude feed tolerance.What's more its high reproductive performance is famous all over the world.So Taihu pigs is known as C hina's national treasure,and it has been highly concerned by the C hinese and international pig producers and pig breeding researchers.However,the genetic mechanism of Taihu pigs characteristics is not clear,which also includes phenotypic characteristics and high germplasm propagation production performance of functional genes or genomic regions and other aspects need to be further analysis and verification.In this study,the reserch objects were divided into four groups: 12 Taihu pigs(6 Er Hualian pigs and 6 FengJing pigs),12 Duroc pigs,12 C hinese native pigs(6 Diannan small ear pigs and 6 Tibetan pigs),and 12 Landrace pigs,which are not relationship between each other.And then the four groups were researched with mixed pool whole genome re-sequencing,and the sequencing dep th was 10-fold coverage for each group and total clean data was 119 Gb.Comparing with the reference genome(Sus scrofa 10.2.75),we got more than 21 million SNPs,and 2.6 mill ion InDels,and There are 2511464 SNP mutation informations and 362974 InDel variation informations are unique to Taihu pigs.There are two selective sweep methods,which are Zhp test based on heterozygosity and Fst test based on difference of population.Then the selective sweep was analyzed to the Taihu group and other three groups,with 100 kb size windows and 50 kb sliding step,and calculated hp values,Zhp values and Fst values of each window based on the degree of selection.In these selected areas which are under the threshold of Zhp <-4,or the minimum Fst>0.35,we got a total of 360 candidate genes in Taihu pigs.By GO enrichment analysis and KEGG pathway analysis,we found these genes mainly related to reproduction,tooth development,fat metabolism,collagen metabolism and neural development negatively regulate biological processes and ovarian steroidogenic pathway.It is follow with interest that we found the high reproductive related important functional genes in Taihu pigs,such as BMPR1 B and BMP15,which provides a new way for further analysis and improvement of the molec ular mechanism of the high reproductive germplasm characteristics in Taihu pigs.Based on mapping analysis,the location of 43 candidate regions were associated with the characteristics of Taihu pig germplasm.This study found the selected region and functional genes in Taihu pigs from whole genome sequence,and revealed the 43 specific areas are molecular mechanism of Taihu pigs' germplasm gharacteristics,and 360 functional genes are the molecular mechanism of germplasm characteristics of Taihu pigs.