Screening of candidate genes related to differences in growth and development between Chinese indigenous and Western pig breeds.

Neijiang (NJ) and Yacha (YC) are two indigenous pig breeds in the Sichuan basin of China, displaying higher resistance to diseases, lower lean ratio, and slower growth rate than the commercial Western pig breed Yorkshire (YS). The molecular mechanisms underlying the differences in growth and development between these pig breeds are still unknown. In the present study, five pigs from NJ, YC, and YS breeds were subjected to the whole genome resequencing, and then the differential single-nucleotide polymorphisms (SNPs) were screened using a 10-kb window sliding in 1-kb step using the Fst method. Finally, 48,924, 48,543, and 46,228 nonsynonymous single-nucleotide polymorphism loci (nsSNPs) were identified between NJ and YS, NJ and YC, and YC and YS, which highly or moderately affected 2,490, 800, and 444 genes, respectively. Moreover, three nsSNPs were detected in the genes of acetyl-CoA acetyltransferase 1 (ACAT1) insulin-like growth factor 2 receptor (IGF2R), insulin-like growth factor 2 and mRNA-binding protein 3 (IGF2BP3), which potentially affected the transformation of acetyl-CoA to acetoacetyl-CoA and the normal functions of the insulin signaling pathways. Moreover, serous determinations revealed significantly lower acetyl-CoA content in YC than in YS, supporting that ACAT1 might be a reason explaining the differences in growth and development between YC and YS breeds. Contents of phosphatidylcholine (PC) and phosphatidic acid (PA) significantly differed between the pig breeds, suggesting that glycerophospholipid metabolism might be another reason for the differences between Chinese and Western pig breeds. Overall, these results might contribute basic information to understand the genetic differences determining the phenotypical traits in pigs.

The phylogeny analysis of MyoG gene in different pig breeds.

Ten different pig breeds with different genetic origin (they are eight Chinese Domestic breeds, one recently Developed breed and one Introduced breed respectively) were utilized in this study to analyze the phylogeny of MyoG gene. 63 individuals were sequenced to get their complete nucleotide sequences of MyoG gene. Different methods and software were used and 6 phylogenetic trees were got based on the complete nucleotide sequence. To test the validation of these phylogenetic trees, the topologic structure differences between different trees were compared. The results indicate that the Neighbour Joining tree of the MyoG gene (Figure 2, NJ tree) has the best topological structure. In this NJ tree, 6 Chinese Domestic breeds cluster in one branch, Dahe and Wuzhishan pig constructed a new branch, Dahewu pig, Duroc and Standard MyoG gene sequence (Genbank accession number X89007) are clustered in one branch, the results are concord with the breeding history of these breeds and can reflect their true genetic background. Same topologic structure and parameters were found between different phylogenetic trees got by different methods. The same parameters of these trees confirmed the fact that the MyoG gene is very conservative and there are very few mutation sites between different breeds.

[Developmental expression changes of insulin-like growth factors (IGFs) system genes in longissimus dorsi muscle of two pig breeds].

Real-time fluorescence quantitative PCR was applied to investigate the developmental expression patterns of insulin like growth factor-1 and -2 (IGF-1 and -2), insulin like growth factor receptor -1 and -2 (IGF-1R and -2R), insulin like growth factor binding protein-3 and -5 (IGFBP-3 and -5) genes at the age of birth (0), 1, 2, 3, 4, and 5 months in longissimus dorsi muscle of Landrace and Meishan pigs. The expression level of IGF-1 exhibited up-regulation, in contrast, the expression level of IGF-2 showed down-regulation after birth in the two pig breeds. These findings are consistent with the previous knowledge that IGF-2 is mainly expressed during the embryonic phase, IGF-1 is mainly expressed during the postnatal period, which could promote cell proliferation and ontogenesis. The expression patterns of IGFRs and IGFs were dissimilar from 0 to 5 months in the two pig breeds, which suggest that the expression changes of IGFRs may not be subjected to the regulation by local secretion of IGFs. Strikingly, at the age of 2 months, the expression levels of IGF-1R, IGF-2R, and IGFBP-3 reached their maximum peak values in Landrace pigs, which suggest that the 2 months after birth may be the most important growth stage for genes of insulin-like growth factors (IGFs) system to exert their biological functions from birth to 5 months. These results indicate that the mRNAs of IGFs system genes exhibit specific developmental expression changes between Landrace and Meishan pigs, and provides some data for further study on the mutual regulation mechanism of genes in IGFs system.