The effect of haplotype variation in the bovine PAX6 gene.
The transcription factor paired box 6 gene (PAX6) plays a key role during the early development of various organs. In this study, three single nucleotide polymorphisms (SNPs) have been identified in the introns 2, 8 and 11 of the bovine PAX6 gene. 8 haplotypes and 13 diplotypes were revealed and the linkage disequilibrium (LD) was assessed in 817 cows representing four main cattle breeds from China (Nanyang, NY; Qinchuan, QC; Jiaxian, JX; Chinese Holstein, CH). The LD analysis revealed that the additional three SNPs were not in strong LD, the wild haplotype (Hap 1: CTT) and mutant haplotype (Hap 8: TCC) have a frequency of 9.36, 35.61, 18.32, 57.15 % and 15.60, 14.19, 0.83, 0 % in the four cattle populations. The statistical analyses indicated that the SNP2 and 3 are associated with the body weight at birth, 6 and 12 months in NY and JX cattle population (P < 0.01 or P < 0.05); and significant association was detected between 19 (NY) or 13 (JX) diplotype (combined genotypes) and body weight at different ages (birth, 6 and 12 months). Our results provide evidence that some polymorphisms in PAX6 are associated with growth traits at some ages, and may be used as candidates for marker-assisted selection in beef cattle breeding program.
College of Animal Science and Technology, Northwest A&F University, No. 22 Xinong Road, Yangling, 712100, Shaanxi, China, hyzsci@126.com.
Yong-Zhen
YZ
Huang
Yong-Jie
YJ
Jing
Tian-Bao
TB
Wei
Xian-Yong
XY
Lan
Chu-Zhao
CZ
Lei
Chun-Lei
CL
Zhang
Hong
H
Chen
D000818:Animals; D001835:Body Weight / Q000235:genetics; D002417:Cattle / Q000235:genetics*; D002681:China; D005136:Eye Proteins / Q000235:genetics*; D005787:Gene Frequency / Q000235:genetics; D056726:Genetic Association Studies; D014644:Genetic Variation; D006239:Haplotypes / Q000235:genetics*; D018398:Homeodomain Proteins / Q000235:genetics*; D015810:Linkage Disequilibrium / Q000235:genetics; D000071841:PAX6 Transcription Factor; D051761:Paired Box Transcription Factors / Q000235:genetics*; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D019655:Quantitative Trait, Heritable; D012097:Repressor Proteins / Q000235:genetics*; D017422:Sequence Analysis, DNA
D005136:Eye Proteins; D018398:Homeodomain Proteins; D000071841:PAX6 Transcription Factor; D051761:Paired Box Transcription Factors; D012097:Repressor Proteins