| Seed industry is the strategic and basic core industry of the country.Pig breeding is the premise of high-quality development of pig industry.Guanzhong black pig is a variety bred by Lu Xingzhong ’s older experts in the 1980 s,which has the advantages of strong resistance and good meat quality.At the same time,there are also shortcomings such as slow growth rate and low litter size.In order to comprehensively utilize the excellent performance of pig breeds at home and abroad,the research group began in 2017 to carry out the cultivation of new varieties of Qinchuan black pig with Guanzhong black pig as female parent and large white pig as male parent.On the other hand,the rapid development of high-throughput sequencing technology in recent years has made genome-wide association analysis and genome selection breeding widely used.Using bioinformatics methods for genetic diversity,genetic relationship and dominant gene screening can accelerate the process of generation selection.In this study,G1 generation Qinchuan black pigs were used as the research object.Based on 542 growth traits and 99 whole genome resequencing data,genetic parameter estimation,signal selection and genome-wide association analysis were used to mine key genes regulating growth traits.The main results are as follows :1.The construction of molecular pedigree divided Qinchuan black pigs into 4families,which was consistent with the results of principal component analysis.The blood composition of families 1 and 3 was similar,and the linkage disequilibrium of families 2 and 4 was low.The results of runs of homozygosity(ROH)showed that the inbreeding coefficient ranged from 0.07 to 0.10,with an average of 0.08.2.The significance test results of fixed effects showed that the birth season effect had a very significant effect on the early growth traits of Qinchuan black pigs(P <0.01).The results of genetic parameter estimation showed that the heritability of each growth trait in the two stages ranged from 0.31 to 0.51,which belonged to the medium heritability level,except that the heritability of circumference at 2 months old was 0.02.The genetic correlation of 2 months was 0.07-0.98,and the phenotypic correlation was0.62-0.89.The genetic correlation was 0.53-0.99 and the phenotypic correlation was0.65-0.83 at 4 months of age.3.A total of 43 candidate genes related to growth and reproduction,such as MPP7,CHD9,TMEM170 B and CSN1S2,were screened by the selection signal detection between Qinchuan black pig and large white pig populations.These genes are enriched in pathways related to bone growth and development,embryonic development and organ growth,reproductive hormone synthesis and secretion;qTL mapping showed that 43 genes were mapped to growth,reproduction,meat quality and immune traits.Haplotype analysis showed that the haplotypes of MPP7,UCK2 and FARP1 genes in some individuals were the same as those in Large White pigs.4.The genome-wide association study(GWAS)of growth traits in Qinchuan black pigs identified 13 significant SNPs associated with body length traits at 2 months of age.A total of 30 candidate genes,such as ABHD5,MAP3K1 and FAM180 A,were identified to be associated with 2-month-old body length traits.Functional annotation revealed that these genes were associated with bone development,average birth weight and disease resistance.In summary,the molecular pedigree constructed in this study,the results of estimated genetic parameters and the key genes of growth traits screened not only provide data support for subsequent selection and mating,but also lay a theoretical foundation for accelerating the cultivation of new varieties of Qinchuan black pig by genome selection technology. |
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