| Taihu pig breeds have many outstanding economic traits,such as high prolificacy,high disease resistance,high resistance to crude feed,docile temperament and heterosis,especially they are the most prolific breeds of swine in the world.Revealing the molecular genetic mechanism of these complex trarits is an important issue for the genetic study.With the development of genetic study and biotechnologies as well as upgarating of study methods,the requirement to reveal the genetic mechanism of these complex traits in the genome level rathter than in the single or several genes level is becoming more intense.However,up to date,only few studies performed genetic variation analysis for Taihu pig breeds on the genome-wide.Moreover,these studies only contained few samples of one or several Taihu pig breeds.To our knowledge,the original survey of a genome-wide of genetic makers for all the six Taihu pig breeds has not yet been reported.What’s more,the genetic mechanism for their outstanding traits is still unclear.Additionally,the current classification of these breeds are mainly based on their characteristics of phenotype(such as body or ear size)or performance(reproductive or meat quality traits)(Resource 2011)as well as their locations.However,it has not been convinced from the terms of genetic characteristics.Therefore,this study will do the researches as follows:(1)Surveying the genome-wide of genetic variations for all the six Chinese Taihu pig breeds.(2)Applying the detected genetic markers for production practices such as breed conservation,etc,namely conducting the genetic diversity and population structure analysis to provide suggestions for breeds classification and future conservation.(3)Predicting their preliminary functions.(4)Applying the detected genetic markers for studies in revealing the genetic mechanism,namely performing the selection signature analysis to uncover the genetic mechansim of outstanding traits such as high prolificacy,high disease resistance for Taihu pig breeds.The results are as follows:(1)Genome variants detection.We detected genetic variants of 252 pigs related to the six breeds(Meishan,Erhualian,Mi,Fengjing,Shawutou and Jiaxing Black)in the Taihu Lake region using GGRS.In total,105,550 SNP,122,632 Indels,31,444 Insertions,44,056 Deletions and 455 CNVs(copy number variants)were identified in the genomes of the pigs.Among those SNPs,29,575(28%)were novel based on compariations with a database of known SNPs,it implied the specific of genetic variants in the Taihhu pig breeds.Further analyses indicated that SNPs were distributed in a relatively uniform fashion in the same chromosome,but its density for each chromosome were distributed in a non-uniform fashion(p < 0.001),and the distribution of the observed SNPs is skewed toward an intermediate frequency.These results are helpful to know the genome information of the Taihu pig breeds and to enrich the databse of genetic markers in the Chinese domestic pig breeds.(2)Genetic diversity and population structure analysis.The breed or sub-type classification of a population can bring a large effect for its protection and conservation.The requirement for effectively protecting and utilizing the genetic resource is to rationally classify them into the correct breed.The current classification of these breeds is mainly based on their characteristics of phenotype or performances as well as their locations.However,it has not been convinced from the terms of genetic characteristics.Therefore,we investigated the genetic diversity and population structure of the six Taihu pig breeds using whole-genome SNP data.Firstly,the allelic richness(AR),proportion of polymorphic markers(PN)and expected heterozygosity(HE)were used to investigate the genome-wide genetic variability within these six breeds.As a result,Mi and Duroc displayed the highest and least AR value compared with the other populations,PN value ranged from 0.946(Landrace)to 0.999(Erhualian),and HE value ranged from 0.343(Mi)to 0.375(Landrace).Secondly,the genetic differentiation shown by the fixation index(FST),principal component analysis(PCA),neighborjoining tree(NJ-tree)and STRUCTURE analysis were performed to investigate interpopulation genetic variability in the six Taihu pig breeds.The result of FST value indicated that the Middle Meishan and Small Meishan breeds exhibited a moderate level of genetic differentiation(FST = 0.099)that was greater than that of the Erhualian and Mi breeds(FST =0.055),which are now regarded as two breeds.What’s more,NJ-tree,PCA and STRUCTURE analysis showed that all the population could be well distinguished from each other(including the Middle Meishan and Small Meishan breeds).In conclusion,we confirmed the rationality of the current breed classification of the Chinese Taihu pig breeds,and we suggested that the Middle Meishan and Small Meishan breeds were separated into two breeds for conservation.(3)Genetic variants functional predicting analysis.We performed functional annotation analysis for these detected genetic variants based on the gene annotation databases(such as NCBI,QTL,KEGG,GO,etc).The results showed that the proportion of these variants in genetic regions ranged from 27.5% to 39.5%,and around 25% of them were in QTLs.The enrichment analysis for genes containing large-effect mutations for each type of variant suggested that they are enriched in different GOs and pathways,which indicated that the different types of variants may have different functions in the genome.SNPs were mainly related to adipose tissue.Indels were more related to disease.Both insertions and deletions were related to endocytosis,and CNVs were more related to nerve function.Moreover,we found the majority of QTLs with high density of variants were related to meat and carcass quality and health traits.Those findings can contribute to reveal Taihu pig breeds’ genetic variants distribution characteristics and functions and also provide valuable references for further studying their functions.(4)Selection signature analysis.Taihu pig breeds have experienced natural and artificial selection over a very long time and those factors might contribute to their current outstanding traits such as high prolificacy,high disease resistance.Therefore, in this study we used both Intra-population(REHH)and Inter-population(XPEHH)methods to detect genomic regions which might be under the process of selection for Taihu pig breeds.As a result,we found 282(REHH)and 112(XPEHH)selection signature candidate regions,corresponding to 159.78 Mb(6.15%)and 62.29 Mb(2.40%)of genomic regions.We found many genes or QTLs under the selection candidate regions were related to reproductive traits(such as TLR9 gene),coat color(such as KIT gene)and fat metabolism(such as CPT1 A gene and MAML3 gene).We further performed gene enrichments analysis for genes under selection candidate regions and found that most of the significant pathways were related to diseases such as autoimmune thyroid and asthma disease.Those findings were consistent with Taihu pig breeds’ traits characteristics of high prolificacy and high disease resistance.Therefore,the genes under selection candidate regions could be took as candidate genes set related to reproductive or disease resistance traits for future convincing. |
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