| Pudong White pig(PW),the unique Chinese indigenous pig breed covered with whole white coat color and involved in < National List of Livestock or Poultry Genetic Resource Protection>,has many desirable economic traits like other Chinese indigenous pig breeds.Protecting this genetic resource is important for the sustainable development of livestock.However,as research continues,it couldn't meet the needs by exploring the breed characters only based on traditional methods such as performance measurement.It is becoming more and more important to Study its characters on genome-wide level.To our knowledge,researches about the characteristics of PW based on genome-wide markers have not yet been reported.Moreover,the declining size of PW,due to the impact of importation of exotic commercial pig breeds with good performance on economic traits such as growth rate and lean meat percentage,remind us that it is crucial to conserve and utilize this genetic resource.Therefore this study will focus on the following contents:(1)using GGRS technique to detect the genetic markers(SNP)of PW and control breeds(other indigenous pig breeds distributed in Jiangsu,Shanghai and Zhejiang province and main exotic commercial pig breeds in China)and to reveal the population structure of these populations.(2)preliminarily predicting functions of the SNPs to reveal the functional characteristics of PW.(3)performing the selection signature detection to reveal the molecular genetic mechanism of the characteristics of PW.(4)testing the effect of breeds conservation.(5)applying the prediction methods of heterosis and combining ability test to propose the rational scheme of hybridize breeding for the utilization of PW.(1)Studies of the characteristics of PW genome architecture.We used the GGRS to identify the SNPs of 47 PW,129 pigs from Jiangsu Province and 36 exotic pigs.Finally,a total of 183,872 SNPs were identified.Among these SNPs,about 68,104 SNPs may be monomorphic in PW.The SNPs were distributed in each chromosome with a relatively uniform fashion except for the isolated regions of some chromosomes.With the comparision of SNPs in the pig dbSNP,a total of 35,521 SNPs(26,084 SNPs were polymorphic in PW)were unreported ones,indicating the uniqueness of PW.It is important to reveal the origins and evolution of one population by exploring the genetic structure based on the genome-wide markers.In this study,the genetic structure and relationship between PW and other pig breeds has been investigated.The results showed the PW is a distinctive genetic resource and contains a unique genetic structure.The genetic distance between PW and Chinese indigenous pig breeds was shorter than that between PW and western breeds.(2)Studies of the functional characteristics of PW genome.It is important to reveal the gene expression regulation mechanism and genetic mechanism of biological traits by researching gene function.In order to further identify the characteristics of PW,we performed functional annotation analysis for the SNPs based on gene annotation databases.There are 1,389 loci that were monomorphic in PW but polymorphic in other populations located in exon region and they are associated with nervus and reproduction.Meanwhile,2,685 loci located in exon region were polymorphic in PW and they were significantly involved in the biological process of development,lipid synthesis and metabolism and immunity,etc.The result of QTL mapping analysis showed that the polymorphic loci in PW related with exterior,carcass and meat quality,reproduction were more than the monomorphic loci in PW but polymorphic in other populations.The results of IPA showed the polymorphic loci in PW related with disease,the development of the nervous system and embryo,while monomorphic loci in PW but polymorphic in other populations related with cell morphology and function,amino acid metabolism,reproductive system diseases,etc.(3)Studies on selection signature.PW have experienced natural and artificial selection through a long period domestication,which might contributed to its current characteristics.We used both intra-population and inter-population methods to detect the selection regions.The results showed that the genes under the candidate regions were mainly related with immunity,reproduction,growth,nervuss,digestive and fat etc.Those findings will improve our understanding of the characteristics of PW,and also be valuable for the future researching on the genetic mechanism of economic trarits of PW.(4)Studies on the conservation of PW.We analyzed the effect of PW conservation based on the pedigree and SNPs.The results showed PW displayed a lower level of the genetic diversity than other indigenous pig breeds,small effective population size and the obvious inbreeding,indicating this genetic resource needed protection urgently.In addition,we researched the effect of conservation for the reproductive traits and revealed the reason for the degradation of the reproductive performance by using the genome-wide SNPs.The result showed that the reason might be more reproductive-related loci were homozygous in PW compared with others.Nevertheless,a certain number of favorable alleles are still harbored in PW,which may result high heterosis in the offspring.Moreover,the result of PCA showed that PW displayed its uniqueness in the reproductive-related SNPs.In conclusion,our results may provide some valuable information for the breeding,conservation and utilization of this breed.(5)Studies on the utilization of PW.According to the theory of quantitative genetics,heterosis is proportional to the genetic distance between the two hybrid parents.In this study,we constructed heterosis prediction method based on the trait specific loci and combined with the result of PW hybridization experiment to determine the optimal model for hybrid utilization of PW.The candidate hybrid way as follows: two-way hybrid system(D×P,L×P,Y×P)and three-way hybrid system(D×LP,D×YP,Y×LP,L×YP,P×LY).With the consideration of the results of combining ability test(contained reproduction,growth,slaughter performance),the best cross pattern was P×LY. |
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