Study On TYRP1 Gene Sequence And SNPs Of Goat

In this study, 55 TYRP1 complete coding sequences were obtained from NCBI, whose variations within and among species were discussed with the help of DnaSP, BioEdit, et al.. Results showed that humans, dogs, and especially cats had more genetic diversity than other species, and could be used to carry out correlation analysis between TYRP1 and coat color. Multi-species sequence comparisons via zPicture software identified two evolutionally conserved regions (from -1306 to -733 and from -642 to -515, based on AL138753) upstream of the transcriptional initiation site, as candidate regulatory units. With the help of ProtParam, SOPMA, SMART, MyHits, et al., the mouse TYRP1 protein was analyzed, which showed that it was 537 amino acids long, and was an unstable and hydrophilic, so it was inferred here that TYRP1 should be decorated and/or should work in the way of multi-enzyme complex. The molecular weight of mouse TYRP1 protein is 60.6 kDa. Minus the N-terminal signal sequence of about 20 amino acids, the remaining 58 kDa peptide plus 17 kDa modifying components (glycosyl- groups and Cu components) formed mature TYRP1 protein, the 75 kDa type-1 transmembrane glycoprotein. Alpha helix and random coil are the main secondary structures in TYRP1 protein, spreading within the entire protein sequence. Hydrophobicity profile and SMART analysis showed that there were three functional segments (1–24: signal peptide, 121–471: Pfam.Tyrosinase, 479–501: transmembrane domain) in TYRP1 protein. In addition, highly conserved amino acids and motifs among species were listed in our paper.According to the reported cattle and sheep TYRP1 gene sequences, along with the goat TYRP1 mRNA sequence in GenBank, pairs of primers were designed to have amplified almost complete goat TYRP1 gene, which was 17554bp long and had been submitted to GenBank (Accession no. HM070243). The connected coding region was 1614bp. Except for the intron 5, which has GC-AG as its splice sites, all the other introns are in accord with the canonical GT–AG rule. The transcriptional initiation site was identified to be at site 984; TATA box was determined to be from 944 to 950; M box was determined to be from 768 to 778, and the bicoid/Otx consensus elements were determined to be at 822-827 and 880-885.A total of 80 SNPs were screened, of which 12 were in exons, and 68 were in introns. Those SNPs in exons were g.1428C>T, g.1537G>T, g.3465C>G, g.3526G>A, g.10047G>A, g.13267A>G, g.17307A>G, g.17408T>G, g.17436A>G, g.17468C>G, g.17472T>A and g.17488C>A, among which, g.1428C>T existed in the 5'untranslated region, g.17468C>G, g.17472T>A and g.17488C>A existed in the 3'untranslated region, there were 7 missense mutations, g.1537G>T (p.Gly10Val), g.3465C>G (p.Asn186Lys), g.3526G>A (p.Gly207Ser), g.10047G>A (p.Ala334Thr), g.17307A>G (p.Ile493Val), g.17408T>G (p.Asn526Lys) and g.17436A>G (p.Met536Val). The 68 mutations in introns were g.1263A>C,g.1949T>C,g.1983G>T, g.1992T>C, g.1997C>A,g.2011G>C, g.2228A>T, g.2447G>A, g.2619T>G, g.2661G>A, g.2725A>G, g.2848T>C, g.3039C>T, g.3060G>A,g.3078G>C, g.3106A>G, g.3279T>C,g.4432A>G,g.4536T>C , g.4630A>G , g.4664C>T , g.4699C>T , g.5168A>G , g.5300A>G ,g.5425A>C, g.5434A>C, g.5955C>T, g.2957A>T, g.6191C>A, g.6216A>C, g.6217T>G, g.6210delA, g.6280A>G,g.6976G>A, g.7017C>T, g.7280T>C, g.7440T>C, g.8787C>T, g.8793G>A, g.8807G>A, g.8885T>C, g.9449C>T, g.9527T>C,g.10812A>G, g.10895A>T, g.11604T>A, g.11729T>A, g.12356T>G, g.12414C>G, g.12776G>A, g.12969G>A,g.13635G>A, g.13947C>T, g.14038T>A, g.14055A>G , g.14215T>C , g.14263C>T , g.14532T>C , g.14600C>T , g.14751G>C,g.16758C>T, g.16869A>G, g.16979A>G, and g.17130T>A. In addition, based on the SSR Tool, five and two SSR motifs were detected in intron 5 and intron 6 of goat TYRP1 gene, respectively, and it is noteworthy that 4 of the 5 SSR motifs in intron 5 are connected in tandem.Genetic diversity and coat color association analysis of two SNPs (g.1263A>C and g.1428C>T) upstream of the TYRP1 gene translational initiation site showed that both of the two sites had no high heterozygosity, while site g.1263A>C had ralatively higher heterozygosity than site g.1428C>T. Nanjiang Yellow Goat Black strain, Nanjiang Yellow Goat Fast Grow strain and Jining Gray Goat are deficient in heterozygotes for both g.1263A>C and g.1428C>T. Genotype and haplotype distribution among populations showed allele A at g.1263A>C and haplotype AC might be in favor of eumelanin biosynthesis and dark coat color, while mutation g.1428C>T occurred more recently in evolution and might have little effect on coat color. The population differentiation of g.1263A>C and g.1428C>T were 0.1119 and 0.0740, respectively, indicating relatively lower genetic diversity from interpopulation and relatively higher genetic diversity from intrapopulation.