Genetic Diversity And Genome-Wide Association Analysis Of Reproductive Traits In Zaozhuang Heigai Pigs

Zaozhuang Heigai pig is an ancient pig breed in Zaozhuang city,Shandong Province,which has the characteristics of rough feeding tolerance and strong stress resistance.Due to the continuous introduction of foreign pig breeds in the last century,the protection of Zaozhuang Heigai pig was greatly impacted.In order to protect this genetic resource,shandong province carried out protective breeding work,after more than ten years of closed-breeding,the scale of core population has been expanded to a certain extent.In order to explore the genetic diversity of Zaozhuang Heigai pig and dig into its excellent genetic resources,the research results can be better applied to practice,so that the genetic resources of the newly approved excellent national and local livestock and poultry breeds can be better fully protected and innovatively utilized.In this study,90 Zaozhuang Heigai pigs were selected as the research objects.Ear tissue was collected and DNA was extracted.Using a50K Single nucleotide polymorphism（SNP）chip to conduct genotyping and after quality control of genotype data,the following studies were carried out.The genetic diversity,relationship,inbreeding number and population structure of 90Zaozhuang Heigai pigs（all sows）were analyzed.The results showed that:A total of 51315SNP loci were detected in 90 Zaozhuang Heigai pigs,and the number of SNPS through quality control was 39,076.The average detection rate of SNP chip genotyping was 98.86%,indicating that the CHIP is suitable for analyzing Zaozhuang Heigai pig.The number of effective alleles was 1.4223,the average polymorphic information content was 0.249,and the proportion of polymorphic markers was 0.830,indicating that the genetic diversity of Zaozhuang Heigai pig was rich.The average observed heterozygosity was 0.3497 and the average expected heterozygosity was 0.3441.The effective population content was 4.44.The average 1-ibs（Identical by state）genetic distance was 0.271,and the results of genetic distance and G matrix showed that there was a large genetic relationship between individuals.The results of NJ evolutionary tree showed that 90 populations of Zaozhuang Heigai pigs were divided into 8 lineages.ROH（Runs of homozygosity fragments）had 2366 fragments,of which 66.77%were between 1 and 10Mb,and the number of inbred lines was 0.104.This indicates that the inbreeding degree of this population is low.From the attenuation degree of LD（Linkage disequilibrium）,it can be seen that SSC4,SSC11,SSC12,SSC16 and SSC17had high r~2phenomenon with too large spacing.It is estimated that the effective population size was about 135 in 50 generations 20 years ago.These results showed that Zaozhuang Heigai pig.had a relatively pure pedigree and rich genetic diversity,and there was no population separation in this population.Genome-wide association analysis（GWAS）was used to explore four reproductive traits of Zaozhuang Heigai pigs:Candidate genes related to Number born alive（TNB）,Total Number born alive（NBA）,Birth weight（BW）and Birth litter weight（BLW）.PLINK v1.09software was used to match phenotypic data with genotype data for quality control and then used for subsequent GWAS analysis.Locate significant loci of the traits and SNP to be measured.Related genes were analyzed by GO and KEGG enrichment analysis to identify candidate genes for reproductive traits.In this study,we added permanent environmental effects that were different from traditional GWAS using the repeatability model of GMAT genome relationship matrix module and single trait analysis module.After Bonferroni correction,the threshold of genomic significance was 0.05/39018=1.28E-06,the threshold of genomic significance was 0.01/39018=2.56E-07,and the threshold of chromosomal significance was 1/39018=2.56E-05.A total of 9 SNPS were detected that were significantly associated with target traits,including 5 SNPS that were significantly associated with BLW,2SNPS that were significantly associated with BW,and 1 SNP that was significantly associated with NBA.No SNP was detected in TNB.Finally,five candidate genes were found,including MED8,WAC and IFNK for BLW,DCP2 and OPRM1 for BW.In conclusion,this study provides a reference for better protection and utilization of Germplasm resources of Zaozhuang Heigai pig.lays a foundation for further exploration of genetic variation of reproductive traits,and also provides more possibilities for molecular breeding of Zaozhuang Heigai pig in the future.