Correlation Analysis of ALX4 Gene Polymorphism and Cashmere Traits in Cashmere Goats (Capra hircus)
ZHANG Zhi-Long1,2, WU Tie-Cheng2, LI Yu-Rong2, MA Yue-Jun2, ZHAO Xia2, ZHAO Sheng-Guo1, LIU Bin2,*, CAI Yuan1,*
1 College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China;
2 Animal Husbandry Institute of Inner Mongolia Autonomous Region Academy of Agricultural and Husbandry Sciences, Hohhot 010031, China
Abstract：During the development of cashmere goat (Capra hircus), different gene expression regulation plays an important role in hair follicle metabolism. In this study, ALX4 (aristaless-like homeobox 4) was selected as the candidate gene to verify the correlation between ALX4 gene and cashmere goat traits, and to provide a basis for molecular marker-assisted selection of cashmere goats. The blood DNA of 20 cashmere goats with maximum and minimum was first extracted, and the 3'-UTR, 5'-UTR, exon, and promoter sequences of the ALX4 gene were amplified and sequenced by PCR amplification technology. According to the results of Blast comparison, SNP loci with mutations in ALX4 gene were counted, and 315 cashmere goat individuals were detected using KASP (kompetitive allele-specific PCR)genotyping technology. The correlation analysis between SNPs loci and villi traits was performed using a general linear model. The results showed that SNP1 (T-1700C) exists in the promoter region of ALX4 gene, SNP2 (T-14621C), SNP3 (T-15433C), SNP4 (G-16377C), SNP5 (A-17780G) and SNP6 (A-18044G) in the 3'-UTR. Among them, the frequency of CG genotype of SNP4 locus of ALX4 gene is the highest (0.4459), which is the dominant genotype, and the G allele is the dominant allele; the frequency of GG genotype of SNP6 locus is the highest (0.5641), which is the dominant genotype, and the G allele is the dominant allele. All SNP loci were in Hardy-Weinberg equilibrium in cashmere goat population (P>0.05), and the homozygosity was higher and the heterozygosity was lower in the population. The effective allele of SNP4 (1.8947) was the highest among all SNPs, and that of SNP1 was the highest. The number of effective alleles (1.2534) was the lowest than other SNPs; except for SNP1 in low polymorphism (PIC<0.25), all other SNPs loci were in moderately high (0.5>PIC>0.25). Correlation analysis showed that the SNP4 locus of ALX4 gene was significantly associated with wool length traits (P<0.05), the wool length of individuals with GG genotype was significantly higher than those of CC and CG individuals (P<0.05); the SNP6 was significantly associated with cashmere fineness traits (P<0.05) the cashmere fineness of AA individuals was significantly higher than that of GG and AG individuals (P<0.05); A total of 12 haplotypes were constructed using PHASE software, with 4 haplotypes having a frequency>5%, which were: H1 (TCCAA, 20.384%), H4 (TCCGG, 15.029%), H7 (TCGGG, 38.498%), and H12 (CTGGG, 22.248%). In the haplotype combination of 5 SNPs of the ALX4 gene, there were 9 haplotype combinations with a frequency>5%. Correlation analysis of these 9 haplotype combinations with cashmere production traits indicated that different haplotype combinations of 5 SNPs in the 3'-UTR region of ALX4 gene were significantly associated with wool length correlation (P<0.05), the wool length of H1H1 individuals was significantly higher than that of HIH7, H1H12, H4H7 and H7H7 (P<0.05). The above results indicate that the ALX4 gene can be used as a key gene for molecular marker-assisted breeding in cashmere goats. In the breeding work of cashmere goats, individuals with AG genotypes at the SNP6 locus can be selected for ultrafine cashmere goat breeding.
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