Genetic Variation And Expression Pattern Of NPC1 & NPC2 Genes In Four Chinese Cattle Breeds

Niemann-Picktype C(NPC) is autosomal recessive lipid accumulation disease, directly related to NPC1 gene and NPC2 gene. The functional defects of NPC1 and NPC2 genes can cause this disease. NPC1 gene and NPC2 gene play an important role in lipid metabolism and participate in in the cholesterol transportation process in SREBP pathway. At present, most studies are focused on human and mouse. The research of NPC1 and NPC2 gene on livestock is rare. Because of their important roles on fat metabolism and the potential research value on body size traits, bioinformatics analyses were conducted in this research. The genetic characteristics of bovine NPC1 and NPC2 gene were studied, and the association analyses were calculated. The expression pattern of bovine NPC1 and NPC2 gene in fetal cattle, calf and adult cattle were also studied in this research. The main results and conclusions are as follows:1. Genetic variations and their correlation with body size traitsBy DNA pooling sequence, 4 coding SNPs were found in Chinese bovine NPC1 gene: NPC1-SNP1, g.G10710A; NPC1-SNP2, g.C21992T; NPC1-SNP3, g.C22007T; NPC1-SNP4, g.T36976 C. 3 SNPs were found in Chinese bovine NPC2 gene: NPC2-SNP1, g.T2456C; NPC2-SNP2, g.T4762C; NPC2-SNP3, g. A8349 G.In the 2.0-year-old Qinchuan cattle population, the NPC1-SNP4 was associated with body weight(P < 0.05), in the 3.5-year-old Qinchuan population, NPC1-SNP1 was associated with heart girth, hip width, and body weight(P < 0.01 or P < 0.05), because of the strong linkage between NPC1-SNP2 and NPC1-SNP3, the two loci were significantly associated with hip width(P < 0.05). The NPC1 gene combined genotypes were associated with heart girth, hip width and body weight(P < 0.01).In the 2.0-year-old Jinnan cattle population, NPC2-SNP1 was associated with body height, height at hip cross, body length, heart girth and body weight(P < 0.05 or P < 0.01), NPC2-SNP2 was associated with height at hip cross, heart girth, and body weight(P < 0.05). NPC2-SNP3 was associated with height at hip cross(P < 0.05). The combined genotypes NPC2 gene was associated with height at hip cross(P < 0.05). The H05H05 individuals have much larger body size values.In the 2.0-year-old Qinchuan cattle population, the NPC2-SNP3 was significantly associated with heart girth, rump length and body weight(P < 0.05). In this population, the NPC2 gene combined genotypes were associated with body height(P < 0.05), the H02H07(CT-CT-GG) individuals have larger body height than the other individuals.So, NPC1 and NPC2 genes can be used as molecular markers in Chinese beef cattle breeding.2. Bioinformatics analysesThe bovine NPC1 gene is located in the 24 th chromosome. It contains 25 exons and encodes 1277 amino acid. There are 132 leucines, accounting for 10.3%, the highest proportion. While the proportion for serine is the second highest, accounting for 7.6%. Tryptophan accounts for the lowest proportion, only 1.4%. The molecular formula of NPC1 protein is C6450H9787N1623O1840S75 and the in vitro half-lives of it is 30 h. The instability index(II) of bovine NPC1 protein is computed to be 40.55. This classifies the protein as unstable. The bovine NPC2 gene is located in the 10 th chromosome. It contains 4 exons and encodes 149 amino acids. Among them, there are 18 valines, accounting for 12.1%, followed by 13 serines(8.7%). The proportion of histidine is the lowest, only 1.3%. The molecular formula of bovine NPC2 protein is C754H1175N193O215S8. The in vitro half-lives of it is 30 h. The instability index(II) of bovine NPC2 protein is computed to be 37.18. This classifies the protein as stable. So, NPC1 and NPC2 protein show different properties in the amino acid composition, physical and chemical properties.3. Expression pattern analysisNPC1 gene was slightly expressed in heart, muscle and highly expressed in spleen, lung and small intestine. During the period of the fetal cattle, the NPC1 gene was expressed at a low level in all issues. During the period of the calf, the NPC1 gene was highly expressed followed by the expression level in the adult cattle period. NPC2 gene was slightly expressed in heart and nearly not expressed in muscle. But NPC2 gene was highly expressed in spleen, kidney and stomach. Unlike NPC1, NPC2 gene was expressed at low level in adult cattle. To sum up, the bovine NPC1 and NPC2 gene expressed the highest in the calf, and mainly expressed in spleen, lung.