生长抑制因子基因 ZBED6 在秦川牛肉牛中的表达、SNP 鉴定、连锁不平衡及单倍型关联分析。
Expression, SNP identification, linkage disequilibrium, and haplotype association analysis of the growth suppressor gene ZBED6 in Qinchuan beef cattle.
机构信息
a College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture , Yangling , Shaanxi , China.
出版信息
Anim Biotechnol. 2014;25(1):35-54. doi: 10.1080/10495398.2013.814572.
Zinc finger, BED-type containing 6 (ZBED6) is a novel transcription factor that was identified and shown to act as a repressor of IGF2 transcription in skeletal muscle myogenesis and development. The aims of this study were to determine ZBED6 expression level and examine the association of the ZBED6 polymorphism with growth traits in Qinchuan beef cattle. The bovine ZBED6 mRNA was detected in eight tissues by quantitative real-time PCR (qPCR), being highly expressed in skeletal muscle. Three single nucleotide polymorphisms (SNPs) were identified the bovine ZBED6 by sequencing pooled DNA samples (Pool-Seq) and forced polymerase chain reaction-restriction fragment length polymorphism (forced PCR-RFLP) methods. In this study, we reported one mutation in the promoter and two missense mutations in the coding regions within the bovine ZBED6 gene, and the haplotype variability and extent of linkage disequilibrium (LD) in 817 individuals from the Qinchuan (QC) and Chinese Holstein (CH). We also investigated haplotype structure and linkage disequilibrium coefficients for three SNPs of ZBED6 in the study populations. The result of haplotype analysis of three SNPs showed that eight different haplotypes were identified in two breeds. The wild-type haplotype (Hap 1: GCA) and mutant-type haplotype (Hap 8: AGG) shared by two populations accounted for 29.8%, 57.5%, and 8.6%, 0% of all haplotypes observed in QC and CH, respectively. The statistical analyses indicated that three SNPs, 23 combined genotypes, and 8 haplotypes were significantly associated with different growth traits in the QC cattle population (P < 0.05 or P < 0.01). The mutant-type variants and mutant haplotype were superior for growth traits; the heterozygote diplotype was associated with higher growth traits compared to the wild-type homozygote. The results of this study suggest that the ZBED6 gene possibly is a strong candidate gene that affects growth traits in QC beef cattle breeding program.
锌指，BED 型包含 6 个（ZBED6）是一种新的转录因子，在骨骼肌的发生和发育过程中被鉴定为 IGF2 转录的抑制剂。本研究的目的是确定 ZBED6 的表达水平，并研究 ZBED6 多态性与秦川牛肉牛生长性状的关系。通过定量实时 PCR（qPCR）检测了 8 种组织中的牛 ZBED6mRNA，发现其在骨骼肌中高度表达。通过测序混合 DNA 样本（Pool-Seq）和强制聚合酶链反应-限制性片段长度多态性（forced PCR-RFLP）方法，在牛 ZBED6 中鉴定了 3 个单核苷酸多态性（SNP）。本研究报道了牛 ZBED6 基因启动子中的一个突变和编码区中的两个错义突变，以及秦川牛（QC）和中国荷斯坦牛（CH）817 个体中的单倍型变异和连锁不平衡（LD）程度。还研究了 ZBED6 三个 SNP 的研究群体中的单倍型结构和连锁不平衡系数。三个 SNP 的单倍型分析结果表明，在两个品种中鉴定出了 8 种不同的单倍型。两个群体共有的野生型单倍型（Hap1：GCA）和突变型单倍型（Hap8：AGG）分别占 QC 和 CH 所有观察到的单倍型的 29.8%、57.5%和 8.6%、0%。统计分析表明，三个 SNP、23 个联合基因型和 8 个单倍型与 QC 牛群的不同生长性状显著相关（P < 0.05 或 P < 0.01）。突变型变体和突变单倍型在生长性状上具有优势；与野生型纯合子相比，杂合子二倍体与更高的生长性状相关。本研究结果表明，ZBED6 基因可能是影响秦川牛肉牛育种计划生长性状的一个强候选基因。
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