| Laiwu pigs are local pig breeds in Laiwu District,Jinan City,Shandong Province,China.They have the highest intramuscular fat(IMF)content in the world.And other excellent characteristics,so it has become a high-quality resource for genetic improvement,and has been highly valued by the government,academia,industry and other circles.The purpose of this study is to analyze the genetic variation of Laiwu pigs at the current and historical levels,the association between historical selection imprints and their germplasm characteristics,and to analyze their genetic mechanisms.In addition,Laiwu pigs,as China’s precious genetic resources,need to be protected and used urgently.On the one hand,because the status,genetic structure,pedigree and pedigree of the existing Laiwu pig population are still unclear,it is difficult to carry out its protection work.The differences in germplasm characteristics of breed pigs in the genomic structure need to be analyzed.Therefore,based on the simplified genome sequencing of Laiwu pigs and five imported breeds of pigs,Laiwu pig chip data and Laiwu pig pedigree data,the following work was carried out:1.Based on the GGRS simplified genome sequencing platform,this study examined 259988 SNPs in the Laiwu pig population and five imported breed pig populations.The average sequencing depth of each individual was 8X,and the average sequencing coverage was 2.3% of the genome.Among them,there are 220366 SNPs in Laiwu pigs.SNPs are evenly distributed on each chromosome in the genome.The overall average value of MAF is 0.247,indicating that the population has excellent genetic diversity.Comparing the SNP database,31334 SNPs were newly discovered in Laiwu pigs.Among the SNPs detected on the Y chromosome,the newly discovered SNPs accounted for 82.93%.Using the GO and KEGG databases to map the four types of SNP datasets respectively,the results showed that 3.88%-4.21% of the SNPs fell into the exon region.The functional annotation analysis of these SNPs revealed that Laiwu pig SNPs were fat,reproduction and immune There are polymorphisms in other aspects and unique polymorphisms in meat quality traits;SNPs between Laiwu pigs and imported breeds are mostly related to growth and development,immunity,and fat metabolism.QTL mapping analysis showed that most of the traits mapped to SNP in Laiwu pigs were meat quality,ketone body traits and reproductive traits.These studies revealed rich genetic variation information on the Laiwu pig genome,and the newly discovered SNPs reflected the uniqueness of the Laiwu pig population.This study also provided a molecular theoretical basis for revealing the function of genetic variation in Laiwu pigs and differences in germplasm characteristics caused by differences in the genome structure between Laiwu pigs and imported breeds.2.In order to study the changes experienced by Laiwu pigs at the genomic level in the historical process,and to reveal the evolutionary characteristics of Laiwu pigs and their relationship with germplasm characteristics,this study uses the REHH and ROH methods to detect selection signals in Laiwu pig population,Get 31 extremely significant signals(P <0.001)and 21 significant signals(top1%),respectively.These signals are mainly related to meat quality-related fat metabolism,deposition and testicular development,sperm formation,litter and other reproductive characteristics.In order to explore the differences in the selection signals left on the genome between the Laiwu pigs and the introduced breeds,this study uses the PLS method to divide them into two categories for detection.The SNP locus with top3% PLS value was selected to map 1502 genes.Through enrichment analysis,it was found that significant signals were mainly related to obesity and growth and development,immunity,reproduction and muscle development.The results of this chapter provide a theoretical basis for the analysis of the genetic mechanism of high intramuscular fat content in the Laiwu pig population,as well as the genetic mechanism of Laiwu pigs and imported breeds in body size,meat quality,reproduction,growth,and immunity.At the same time,it showed that Laiwu pigs and imported breeds had unique advantages in their respective germplasm characteristics,provided theoretical guidance for their subsequent cross-breeding use and reasonable selection,and gave full play to the advantages of Laiwu pigs.3.By investigating Laiwu pig farms,the problems in the management and application of genealogical information records of local pig breeding farms are discussed.By using the guidelines of the local pig breed registration platform to recode the individual ear names of Laiwu pigs,the pedigree of individuals in the herd was combed.On the basis of combing,the pedigree structure analysis was performed using R language package and MEGA drawing evolutionary tree software.The problems of discontinuous,complete and inaccurate genealogy were systematically corrected through the establishment of electronic archives and platform registration.A molecular pedigree of 163 Laiwu pigs was constructed by combining 38452 SNPs and file genealogy of 107 Laiwu pigs obtained from the data of pig 50 K chip.The analysis of pedigree structure showed that the average inbreeding coefficient of the individuals in the group was 0.0215,but the actual average inbreeding coefficient was 0.035,and the effective content of the group reached 92,indicating that some individuals in the group did not use the same breeding method.The population was divided into 13 families,but the number of individuals in each family was uneven.The genetic correlation between the molecular genealogy and the archive genealogy is 0.636.Both are divided into 13 families,and the genetic relationship between individuals in the population is more accurate.This survey shows that the pedigrees of local pig breeding farms still have problems such as the completeness and accuracy of breeding effectiveness evaluation and breeding utilization.The pedigree information should be accurately recorded and breeding software should be used in the future.In addition,the construction of molecular pedigrees To some extent,the errors in traditional genealogy have been corrected.4.This chapter studies the comprehensive evaluation of breeding individuals in Laiwu pigs and the selection of breeding and screening issues.Using the phenotypic data of the ancestors of Laiwu pigs in the herds and the molecular pedigree of the herds in the herds,one step estimation(SSBLUP)method is used to estimate 5 Breeding values for meat quality traits.A breeding population of Laiwu pigs was established by combining the breeding values of intramuscular fat content traits and genotype data of genes affecting intramuscular fat content.Using PLINK software,we genotyped each individual that affected the fat content gene in Laiwu pigs.The results showed that there were 32 individuals with dominant genotype(TT type)and 21 individuals with disadvantaged genotype(CC type).The effect value of TT genotype was 0.0329 higher than that of CC genotype.Based on the effects of breeding values and genotypes,all individuals were comprehensively evaluated,and 38 populations with high estimated breeding values for the genome were selected to carry out subsequent select ion and selection of Laiwu pigs. |
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