Analysis of Structural Variants Reveal Novel Selective Regions in the Genome of Meishan Pigs by Whole Genome Sequencing

Structural variants (SVs) represent essential forms of genetic variation, and they are associated with various phenotypic traits in a wide range of important livestock species. However, the distribution of SVs in the pig genome has not been fully characterized, and the function of SVs in the economic traits of pig has rarely been studied, especially for most domestic pig breeds. Meishan pig is one of the most famous Chinese domestic pig breeds, with excellent reproductive performance. Here, to explore the genome characters of Meishan pig, we construct an SV map of porcine using whole-genome sequencing data and report 33,698 SVs in 305 individuals of 55 globally distributed pig breeds. We perform selective signature analysis using these SVs, and a number of candidate variants are successfully identified. Especially for the Meishan pig, 64 novel significant selection regions are detected in its genome. A 140-bp deletion in the Indoleamine 2,3-Dioxygenase 2 (IDO2) gene, is shown to be associated with reproduction traits in Meishan pig. In addition, we detect two duplications only existing in Meishan pig. Moreover, the two duplications are separately located in cytochrome P450 family 2 subfamily J member 2 (CYP2J2) gene and phospholipase A2 group IVA (PLA2G4A) gene, which are related to the reproduction trait. Our study provides new insights into the role of selection in SVs' evolution and how SVs contribute to phenotypic variation in pigs.

Molecular cloning, sequence characteristics, and tissue expression analysis of the SLC35D3 gene in lean, obese and mini-type pigs

Nowadays, with the development of people's life, obesity become one of the largest health problems today. Solute carrier family 35, member D3 (SLC35D3) protein has been reported to be involved in adipose deposition and metabolic control in mice. Because organ size in pig is comparable to that of the human, the pig is an ideal model that has been used to study diabetes mellitus, atherosclerosis, obesity, and other diseases. To better understand the structure and function of the SLC35D3 gene, the Meishan pig SLC35D3 gene was cloned and characterized, and its expression in different tissues was determined. The SLC35D3 cDNA consisted of a 1272 bp coding sequence that encoded a protein of 243 amino acids with a molecular mass of 44653.9 Da, and 966 bp 3′ untranslated regions. It is a pity that we have not got 5′ untranslated regions. Phylogenetic tree analysis revealed that porcine SLC35D3 had a closer genetic relationship and a shorter evolutionary distance with Vicugna; however, its evolutionary distance with that of the gorilla was longer than that of Vicugna. In addition, we quantified the SLC35D3 mRNA level by real-time polymerase chain reaction and detected expression in the liver, kidney, lung, heart, brain, LM, and spleen, as well as in the leaf lard, SAT, and PAT. In addition, we also tested the expression level of Meishan, Bama and Yorkshire in adipose tissue. The SLC35D3 mRNA level was highest in the leaf lard. These results serve as a foundation for further study on the porcine SLC35D3 gene.

Molecular cloning, sequence characteristics, and tissue expression analysis of the SLC35D3 gene in lean, obese and mini-type pigs

Nowadays, with the development of people's life, obesity become one of the largest health problems today. Solute carrier family 35, member D3 (SLC35D3) protein has been reported to be involved in adipose deposition and metabolic control in mice. Because organ size in pig is comparable to that of the human, the pig is an ideal model that has been used to study diabetes mellitus, atherosclerosis, obesity, and other diseases. To better understand the structure and function of the SLC35D3 gene, the Meishan pig SLC35D3 gene was cloned and characterized, and its expression in different tissues was determined. The SLC35D3 cDNA consisted of a 1272 bp coding sequence that encoded a protein of 243 amino acids with a molecular mass of 44653.9 Da, and 966 bp 3′ untranslated regions. It is a pity that we have not got 5′ untranslated regions. Phylogenetic tree analysis revealed that porcine SLC35D3 had a closer genetic relationship and a shorter evolutionary distance with Vicugna; however, its evolutionary distance with that of the gorilla was longer than that of Vicugna. In addition, we quantified the SLC35D3 mRNA level by real-time polymerase chain reaction and detected expression in the liver, kidney, lung, heart, brain, LM, and spleen, as well as in the leaf lard, SAT, and PAT. In addition, we also tested the expression level of Meishan, Bama and Yorkshire in adipose tissue. The SLC35D3 mRNA level was highest in the leaf lard. These results serve as a foundation for further study on the porcine SLC35D3 gene.

Impact of different sources of donor cells upon the nuclear transfer efficiency in Chinese indigenous Meishan pig

Somatic cell nuclear transfer (SCNT) is currently the most efficient and precise method to generate genetically tailored pig models for both agricultural and biomedical research. However, its efficiency is crucially dependent on the source of nuclear donor cells. In this study, we compared the cloning efficiency by using three lines of donor cells that are derived from fetal, newborn and adult fibroblasts of Chinese indigenous Meishan pig. We showed that cleavage rate and blastocyst formation rate of the reconstructed embryos were not significantly different between the fetal (80.7% and 15.6%) and newborn ear skin (77.5% and 12.3%) fibroblast groups (p>0.05), but in both groups these indices were significantly higher than that found in the adult ear skin (70.5% and 8.8%; p<0.05). Reconstructed embryos derived from fetal, newborn, and adult ear skin fibroblasts were transferred to four surrogates, respectively. For the fetal, newborn, and adult ear skin fibroblasts, the number of pregnancies were two (50.0%), two (50.0%), and one (25.0%), respectively, and the number of deliveries were two (50.0%), one (25.0%), and zero (0.0%), respectively. Seven and two cloned piglets were obtained from the fetal and newborn ear skin fibroblasts respectively, while no piglets were obtained from the adult ear skin fibroblasts. Two cloned piglets from the newborn ear skin fibroblasts died shortly after birth because of neonatal asphyxia caused by dystocia. The birth weights of the piglets derived from the fetal and newborn ear skin fibroblasts were 1230.5 and 1310.0g, respectively, which were statistically insignificant (p>0.05), but both were significantly higher than that of the control groups (p<0.05). Microsatellite analyses demonstrated that the genotypes of all cloned piglets were identical to their donor cells. Therefore, cloned pigs were successfully produced using two sources of donor cells isolated from the fetal and newborn ear skin fibroblasts of Meishan piglet, and indicating a better cloning efficiency than that obtained from adult fibroblasts. We concluded that the nuclear donor cell lines have significant impact on the developmental competence of cloned embryos as well as on the cloning efficiency of Meishan pig.