Using Genome-wide SNP Dataset To Reveal And Conserve Molecular Breed Characterization In Pigs

Livestock genetic resources is both the primary material for genetic improvement and the important safeguards for sustainable development of breeding project.Hence,it is greatly significant to explore and protect the excellent breed characterization to the maximum extent.The aim of this study is to dissect molecular breed feature of Taihu pigs,a Chinese excellent indigenous breed,based on whole-genome resequencing and to verify the mechanism involved in "prolificacy" using functional assays.Then,silico simulation experiment was established to evaluate the conservation effect on pig conserved stock based on whole-genome SNP marker.The thesis was studied in detail as below:?.Whole-genome resequencing reveals the breed characterization of prolificacy in Taihu pigWhole-genome resequencing was performed in four pools from six pig breeds,including Chinese high-fertility group(Taihu pig),Chinese low-fertility group(Tibetan pig and Diannan small ear pig),foreign high-fertility group(Landrace)and foreign low-fertility group(Duroc).After filtering the sweeps with the steps which consist of strong positive selection and highly differentiation of Taihu pig to the other control groups,39 putative selective sweeps involved in Taihu breed characterization were obtained.132,078 Taihu-specific SNPs were further obtained by analyzing the allele frequency difference.Genomic location enrichment analysis showed that Taihu-specific SNPs were mainly located in conserved noncoding regions.The top 1,000 genes having the most Taihu-specific SNPs were subjected to the GO overrepresentation analysis.GO terms associated with embryogenesis and morphogenesis were significantly enriched.Subsequent comparison between 39 putative selective sweeps and reproductive traits QTL indicated that one sweep(chr8:134.05-134.14Mb)was an important candidate genome region for pig fertility,which harboured the bone morphogenetic protein receptor type-1B gene(BMPR1B).The results from comparative genomics analysis showed a mammalian conserved estrogen receptor response element was located within the first BMPR1B intron.The evidence from luciferase assay showed that the binding activity with estrogen receptor I is stronger in Taihu-specific haplotype than Duroc's.Higher BMPR1B level was observed in endometrium from pregnant Meishan pig relative to Duroc.Meishan pig exhibited more abundant endometrial glands than Duroc using histological sections assay.Collectively,Taihu-specific haplotype could promote ESR1 binding activity,cis-regulate BMPR1B expression and further enhance the endometrial glands development.?.Investigation on changes of pig genetic diversity by genome-wide SNP dataWe established a simulation experiment according to the architecture of genome-wide SNPs in pigs to monitor dynamic changes of genetic diversity in pig conserved stock during 50 generations with current swine conservation program.The genetic diversity based on true identity-by-descent(IBD)probabilities has been first calculated with double-labelled SNPs.Meanwhile,He,Ho,Ae,Ao,Pp,GD_IBS and F were also applied to evaluate the genetic diversity of conserved stock.The results from all indicators showed that the genetic diversity of conserved population decreased-5%at the 10th generation under current conservation program;The correlation and sensitivity of He,Ho,Pp and GD_IBS were better than that of Ae,Ao and F.Particularly He exhibited the best.Furthermore,the results of parental genomic components analysis showed that-7.5%male families and-30%female families would be lost per 5 generations.To achieve the long-term conservation goal,it is necessary to introduce?10%genetic resources(either semen or embryos)of same breed from gene pool into conserved stock per 5 generations.In summary,we totally identified 3 9 sweeps involved in Taihu breed characterization based on whole genome resequencing.It is suggested BMPR1B gene played a key role in the prolificacy of Taihu pig based on comparative genomics analysis and functional experiments.Furthermore,we used genome-wide SNPs to simulate the pig conserved stock and monitored the dynamic changes of genetic diversity.This study provided a new insight for developing and conserving the breed characterization.