| Shanghai White Pig(Shang line)is a kind of local meat-fat dual-purpose breed cultivated through more than ten years of breeding.It has good characteristics such as good meat quality,more litter size,higher carcass lean meat percentage and resistance to roughage.As early as 1986,it was included in the "Chinese Pig Breeds",and in 2012 it was included in the "List of Shanghai Livestock and Poultry Genetic Resources Protection." Shanghai White Pigs(Shang line)used to be the dam line of the swine hybrids sold to Hong Kong for a long time,but with the introduction of west pig breeds seriously impacting the domestic pig market,the size of Shanghai White Pig(Shang line)has been greatly affected.The production index has experienced a certain degree of decline.In response to this problem,the genetic variation and genetic diversity of the Shanghai White pig(Shang line)genome were tested using the independently developed Genotyping by Genome Reducing and Sequencing(GGRS)platform.The traits such as reproduction,carcass meat quality were also systematically measured in Shanghai White Pig(Shang line)current core population.Based on genetic variation information and production performance,the Shanghai white pig(Shang line)hybridization utilization model was further proposed.The research aims were to fully analyze the germplasm characteristics of Shanghai White Pig(Shang line)and provided a theoretical basis for the protection,breeding,development and utilization of Shanghai White Pig(upper line).The main findings are as follows:1.Genome genetic variation detection of Shanghai white pigs(Shang line)In this study,the GGRS was used to sequence the genome of 82 Shanghai White pig(Shang line)populations.After the quality control,a total of approximately 365 million high-quality reads were obtained in Shanghai White Pigs,of which,the minimum number of detected reads and the largest one were 0.84 and 19.41 million,respectively.The average number of reads per individual was 4.45 million,the average genome sequencing coverage was 2.93%and the average sequencing depth was 3.95.After SNP calling and filtering,a total of 328,586 SNPs and 693,220 InDels were detected in Shanghai White(Shang line).Further analysis showed that the distribution of SNPs and Indels on chromosomes was relatively uniform,but there were differences in the distribution of numbers and densities on different chromosomes.At the same time,based on the genomic variation information,the Shanghai White Pig(Shang line)digital preservation database was constructed and integrated into the Chinese local pig breeding registration platform(http://www.pigbreeds.org.cn).This work effectively enriched the genetic variation database of local pig breeds in China.2.Genome functional characteristics of Shanghai White pig(Shang line)In order to reveal the genetic mechanism of Shanghai white pig(Shang line)germplasm characteristics,the detected SNPs and InDel were annotated by the genes information,QTLs and pathway enrichment.The structure annotations showed that the number of SNP and InDel corresponding genes were 11,496 and 13,216,respectively.According to the structural regions of the genes,the distribution characteristics of SNPs and InDel in all functional gene intervals were consistent,with the majority of SNPs and InDel mutations were distributed in the intergenic regions,which were 74.61%and 83.38%,respectively.The introns were followed by 22.76%and 14.98%,respectively.The results of gene enrichment analysis of large effect mutations showed that there are differences in pathways for different types of enrichment.Most of the SNP enrichment pathwayst are related to the synthesis and regulation of protein macromolecules.For example,protein metabolism(GO:0019538),macromolecular metabolism(GO:0043170),etc.InDel,on the other hand,has been enriched in tissues,organs,and disease-related pathways such as single-multicellular organism(GO:0044707)and Arrhythmogenic right ventricular cardiomyopathy(ssc05412).In addition,we also found that genes containing SNP and InDel were mainly concentrated in the QTL range of meat and carcass traits and health traits.These results are conducive to the understanding of the genome functional characteristics of Shanghai white pig(Shang line),and provide reference for further revealing the genetic mechanism of its germplasm characteristics.3.Analysis of genetic diversity and population structure of Shanghai white pig(Shang line)and other pig breedsTo reveal the genetic diversity and population structure of the Shanghai white pig(Shang line)population,genetic variation detected by the same GGRS method in six local breeds from the Taihu(Meishan pig,Erhualian,Fengjing pigs,Mi pigs,Shawutou,Jiaxing black pigs)and five western-introduced breeds(Duroc,Landrace,Yorkshire,Pietrain,and Berkshire pigs)were integrated to perform analysis.The statistical results of genetic diversity parameters showed that the proportion of polymorphic markers(PN)in Shanghai White pig(Shang line)was 0.731,the allelic richness(AR)was 1.709,and the expected heterozygosity(HE)was 0.221,which was higher than Taihu pig breeds and Western pig breeds.Genetic distance analysis between populations showed that Shanghai White pigs(Shang line)were closer to Western pig breeds than Taihu pig breeds;principal component analysis,cluster analysis and population structure analysis showed that Shanghai White Pigs(Shang line)can form independent groups.The above results show that from the molecular level,Shanghai White Pig(Shang line)has a unique genetic structure,and its protection,development,and utilization should be further strengthened.4.Performance measurement and hybridization utilization model prediction of Shanghai White Pig(upper line)Shanghai White Pig(Shang line)was purified and rejuvenated,and was tested for production performance.The results showed that the number of first-born was 10.98,and the number of pluriparity reached 12.22 for Shanghai White Pig(Shang line),both of which were degraded to a certain degree,and the fattening performance and slaughter performance were maintained at a good level.The variation coefficients of average daily gain,thickness,water keeping,rate fat and intramuscular fat is relatively large,but still has a certain potential for breeding.According to the basic theory of quantitative genetics,heterosis is directly proportional to the genetic distance between the parents of the cross.This study focused on multiple indicators of reproduction,fattening,carcass and meat quality,and through the hybridization experiment of Landrace(L)and Shanghai white pig(SH),we verified the reliability of prediction of binary hybridization based on genome-wide genetic variation information.Meanwhile,comprehensively considering the management,cost,and current market demand for high-quality pork,and constructed a trait-specific heterosis prediction method to determine the most suitable combination that the Shanghai white pig(Shang line)was the terminal sire and the hybrid combination of the Landrace and Yorkshire sows was dam.The work lays the foundation for the efficient hybridization and utilization of the Shanghai white pig(Shang line).In summary,the Shanghai white pig(Shang line)has degraded in reproductive performance,but the fattening performance and slaughter performance maintain a relatively high level;the study established a digital conversation database for Shanghai White Pig(Shang line),effectively enriching genetic variation database of Chinese local pig breeds;Genetic diversity of Shanghai White pigs(Shang line)were higher than Taihu pigs and Western pig breeds;Population structure analysis showed that Shanghai White pigs(Shang line)could form independent groups with a unique genetic structure;Genes containing SNPs and InDel were mainly mapped on QTLs for meat quality,carcass traits,and health traits;Based on a trait-specific heterosis prediction method,the hybrid combination(S×LY)is the best combination of the mating lines. |
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