Genome-wide Association Study And Genomic Mating Strategy For Growth Traits In Yunong-black Pigs

Growth traits,which can directly reflect the growth and development of pigs,are important reference indexes for breeding new breed selection.Traditional methods for genetic improvement of important traits in pigs has achieved remarkable results in the past,but traditional breeding methods have problems such as long cycles and high costs.Therefore,the implementation of new breeding theories and methods will be of great significance to accelerate the genetic improvement of pigs.In this paper,genome-wide association study and genome mating strategy were introduced into the research of pig breeding,in order to provide technical support for genetic improvement in pigs.Genome matching strategy is to use the genomic information of candidate animals to optimize the matching at the individual level,emphasizing the complementarity between parents,and achieving long-term sustainable genetic progress.However,the genome selection strategy is still in the stage of simulation research and has not been verified by actual breeding.Therefore,it is necessary to further explore the genome mating strategy.The main results obtained in this paper are as follows:(1)Statistical analysis of the phenotypic data in Yunong-black pigs shows that the mean values of the phenotypic data are:body length 119.71 ±7.52 cm,body height 70.01±4.16 cm,chest circumference 111.66±8.38 cm,cannon bone circumference 17.77±1.45 cm,legs buttocks circumference 86.23±9.22 cm,backfat thickness 1.86±0.47 cm,loin muscle depth 3.72±0.75 cm.the coefficient of variation are:6.28%,5.94%,7.50%,8.17%,9.43%,8.02%,9.93%.(2)Genome-wide association studies was performed on the growth traits of Yunong-black pig by FarmCPU model,as a result,a total of 27 genome-wide significant SNPs and 23 chromosome-wide significant SNPs were identified.Among them,there are 5 chromosome-wide significant SNPs for body length;7 genome-wide significant SNPs and 8 chromosome-wide significant SNPs for body height;4 chromosome-wide significant SNPs for chest circumference;2 chromosome-wide significant SNPs for cannon bone circumference;1 chromosome-wide significant SNPs for legs buttocks circumference;11 genome-wide significant SNPs and 3 chromosome-wide significant SNPs for backfat thickness;9 s genome-wide significant SNPs for loin muscle depth.(3)The Ensemble genome browser was used to search for candidate genes in the I Mb region of significant SNPs upstream and downstream,and a total of 38 candidate genes were identified in combination with literature reports.Among them,there are 4 genes for body length,KIAA1549L,KCNJ15,GALNT10 and TNFAIP6 genes;11 genes for body height,CCDC68,ADAMTSL1,NR5A1,C2orf42,PPP1R8,B4GALT6,GRM4,CPNE5,DICER1,ENOX1 and FMR1 genes;3 genes for chest circumference,SLITRK6,PHF12,and SLITRK6 genes;2 genes for cannon bone circumference,LRP11 and FBXO11 genes;1 candidate gene for legs buttocks circumference,DPP 10 gene;11 genes for backfat thickness,ZNF782,GOLGA3,VPS41,GPHN,MBIP MAGED1,CCSER1,CCDC198,PALM2AKAP2,TMEM272 and GUCY2D genes;and 6 genes for loin muscle depths,SF3B4,PARM1,HSF5,ITGA8,COL18A1 and SCML2 genes.(4)The genetic genetic parameters of the growth traits in Yunong-black pig were evaluated by using BLUP and GBLUP models.Traits that belong to low heritability(h2 ≤0.3)are:body length,body height,legs buttocks circumference,and traits that belong to medium heritability(0.3<h2≤ 0.5)are:chest circumference,cannon bone circumference,backfat thickness,loin muscle depths.Compared with the GBLUP method,the GBLUP-AD method that includes dominant genetic effect can improve the prediction accuracy by 4.17%to 30%.(5)In this experiment,the total genetic value and breeding value of the offspring produced between different combinations of all male and female pigs were calculated for each trait.Using the mating strategy that maximizes the genetic value of the offspring can increase genetic superiority by 0.9%to 16.7%.This study obtained SNPs significantly associated with growth traits and important candidate genes that affect growth traits.At the same time,it was found that the implementation of genome mating strategies that maximizes the total genetic value of the offspring can improve the growth performance of the offspring without adding the extra cost of breeding.The research results provide new molecular markers and breeding implementation methods for the genetic improvement of growth traits in Yunong-black pigs,and also enrich the genetic research content of growth traits.