Study On C-kit, The Candidate Gene Of Coat Color In Goat

According to the reported cattle C-kit DNA sequence (NW₀01495195) and goat C-kit mRNA sequence (D45168) from GenBank, partial C-kit gene fragments were amplified, which was 46647bp long, and had been submitted to GenBank, the accession number was HM130675. The amplified sequence of this experiment composed of two parts, the first part was from exon 2 to exon 5, in which ,exon 2 and exon 5 were incomplete and intron 2 missed about 715bp; the second part was from exon 8 to exon 21.According to the determined sequences, 20 polymorphic loci were found in goat C-kit gene, of which 1 was in exon, and 29 were in introns. According to HM130675, the mutation in exon was g.40545G>A resulting in Gly→Glu. The 19 mutations in introns were g.3800T>G, g.3939T>G, g.3948T>A, g.4125T>G, g.4233C>T, g.8048delA, g.32640delT, g.33781C>A, g.34431delT, g.35818insTCTC, g.36376A>C, g.37708A>T, g.38616A>T, g.38779A>T, g.39702T>C, g.39716insA, g.40259G>A, g.40923insT, and g.41218T>C.There was a missense mutation G→A at site 40545 in exon16. The gene frequency of allele A(65.98%) was significantly higher than allele G(34.52%) in these 341 individuals of 9 goat breeds or strains (Tangshan dairy goat, Liaoning cashmere goat, Jining gray goat, Chengdu ma goat, Reproduction strain of Nanjiang brown goat, Growth strain of Nanjiang brown goat, Black strain of Nanjing brown goat, Leizhou black goat, Chengde polled goat). Based on the gene frequencies of allele A, these populations were divided to three groups, the first group included Tangshan dairy goat, Liaoning cashmere goat and Jining gray goat, in which the frequencies were higher than 89.5%; the second group included Leizhou black goat and Chengde polled goat, in which the frequencies were around 64%; the third group included Chengdu ma goat and three strains of Nanjiang brown goat, in which the frequencies were lower than 50%. In the first group, Tangshan dairy goat and Liaoning cashmere goat are white coated, while the coat of Jining gray goat is composed of white and black fibers. The two breeds from the second group are both black. In the third group, except for the Nanjiang Brown goat black strain, which is black, the others all have brown coat color. The consistent clustering of coat color pattern and allele A frequency indicated some relationship between site g.40545G>A and coat color.As for the site g.35818insTCTC, the wild-type was designated as allele C, and the mutant-type was designated as allele T. Allele C has been shown to be superior in these analyzed populations (80.79%). Based on allele C frequencies, the involved populations were divided to two groups. The first group included Leizhou black goat, Chengde polled goat, Chengdu ma goat and three strains of Nanjiang brown goat, in which allele C frequencies were close to 1, while the other group included Tangshan dairy goat, Liaoning cashmere goat and Jining gray goat, with allele C frequencies of about 0.5. All the individuals from the first group are colored, while for the second group, except for Jining gray goat, whose coat is composed of black and white fibers, all the other populations are colorless (white). Population genetic analysis showed that the expected heterozygosity for the 9 involved populations are 0.31, indicating relatively rich genetic diversity.Population analysis via POPGENE showed that for the two mutations mentioned above, the homologies between different populations are from 0.5752 to 0.9990, the genetic distances are from 0.0010 to 0.5530, indicating rich genetic diversity. The UPGMA phylogenetic tree of the 9 goat populations was constructed according to Nei's genetic distance, in which, these populations were divided into 3 groups: Liaoning cashmere goat and Jining grey goat were clustered together, and then Tangshan Dairy Goat was clustered in; Reproduction strain and Growth strain of Nanjiang brown goat were clustered together, immediately followed by Black strain of Nanjing brown goat, then by Chengdu ma Goat; Leizhou black goat and Chengde polled goat were clustered together. Finally, the latter two groups were clustered, followed by the first group.The partial CDS of goat C-kit gene was obtained in this study, and 29 corresponding sequences from 7 species were downloaded from GenBank. These 30 sequences (2265bp) were aligned by BioEdit software and then analyzed by DnaSP software. 824 polymorphic loci were detected along the 2265bp long sequence, with mutation rate of 36.11%. Phylogenetic tree of the involved 9 goat populations was constructed according to nucleotide diversities. From the cluster analysis, we could see that goat and cattle clustered together firstly, then followed by pig, horse, dog, human, and finally by mouse. The cluster result is also consistent with the biological classification.