Study On The Genetic Polymorphisms Of CNV And The Relationship With Reproductive Traits Of Three Native Pig Breeds In Guizhou Province

In this study, a total of 120 Xiang pig population with large and small litter size and Kele pig were used to identify CNVs patterns based on Porcine SNP60 Genotyping data by CNVRuler and Penn CNV softwares. A total of 213 CNV regions(CNVRs) were deduced. Six candidate CNVs were chosen for subsequent polymorphism study in Xiang pig population with large and small litter size. We determined plenty of copy number variations at six CNV sites from two Xiang pig population with large and small litter size using quantitative real time PCR(q PCR) method, taking three pig breeds as control, which included Kele, Yorkshire and Nuogu pig breeds. The main results included:1. CNV36 presented polymorphism in the genome of Xiang pig. The gain event was dominant in Xiang pig population with large litter size, while the loss one was leading in the population with small litter size. Based on the chi-square test, the differences in the copy numbers of CNV36 was significant between the two Xiang pig populations(P<0.01). The major status of CNV36 were increase in Kele, Yorkshire and Nuogu pig breeds.Correlation analysis revealed that copy number of CNV36 was weak negative related to the bust of Xiang pig and body width and chest of Nuogu pig.2. For CNV74, the gain event was dominant in Xiang pig population with large litter size, while the loss event was leading in the population with small litter size. The differences in the copy numbers of CNV74 was significant between the two Xiang pig populations(P<0.01). Copy of CNV74 was decreased in Kele, Yorkshire and Nuogu pig breeds.And the CNV74 copy number was correlated with the nipple number, the first, second and third litter sizes in Xiang pig populations.3. The dominant type of CNV86 was gain events in Xiang pig population with large and small little size, while it was decrease in Kele, Yorkshire and Nuogu pig breeds. Thecopy number of CNV86 was weak positive related to the bust of Nuogu pig, negative related to the body height and pipe circumference of Kele, medium related to the body length, body width, body weight and bust of Kele pig.4. The loss events of CNV101 was higher in the Xiang pig population with a large and small little size, Kele, Nuogu and Yorkshire pig breeds. Correlation analysis revealed that the copy number of CNV101 was weak related to the body length of Xiang pig, the body height, body length, body width, body weight, bust and pipe circumference of Kele. It was slightly negative related to the body width and body weight of Nuogu pig.5. The gain events of CNV139 wasdominant in the Xiang pig population with large and small little size. However, it was decrease in Kele, Yorkshire and Nuogu pig breeds. The copy number of CNV139 was just weak negative related to the boby width and bust of Nuogu pig.6. Of CNV154 site, the gain event was dominant in the Xiang pig population with large litter size, while the loss one was leading in the population with small litter size. And the differences between two Xiang pig groups was significant(P<0.01). CNV154 were decreased in Kele, Yorkshire and Nuogu pig breeds. The correlationship was found out between the copy number of CNV154 and the nipple number, the first, second and third litter sizes of Xiang pig populations. It was weak negative correlated with the body width of Kele pig, the body width and bust in Nuogu pig.7. We futher detected the copy number variation of MTHFSD and PHB m RNA levelsusing real-time PCR method, which located in CNV74 and CNV154 regions, respectively. The results showed that copy number changes at m RNA leveland genome were consistent with each other.We detected six CNV variation from Xiang pig and other pig breeds. Two CNVs, CNV74 and CNV154, were found out to be correlated with the litter size of Xiang pig and was further confirmed based on the consistent copy changes of MTHFSD and PHB genes at both of m RNA and genomic levels. Thus it was speculated that the gene copy number variation in the CNV regions, in a certain extent, might affect on the pig growth and development. This results would provide a foundation for the mechanism of fecundity and growth and the breeding of native pig.