Relationship of polymorphisms within ZBED6 gene and growth traits in beef cattle

Abstract

ZBED6 is a novel transcription factor that was identified and shown to act as a repressor of IGF2 transcription in skeletal muscle. The aim of this study was to examine the association of the ZBED6 polymorphism with growth traits in beef cattle breed. Three single nucleotide polymorphisms (SNPs) were identified in the bovine ZBED6 by sequencing pooled DNA samples (Pool-Seq) and forced polymerase chain reaction-restriction fragment length polymorphism (Forced PCR-RFLP) methods. Overall, we reported one mutation (SNP1) in the promoter region and two missense mutations (SNP2 and 3) in the coding region (single exon) within the bovine ZBED6 gene, and the haplotype variability and extent of linkage disequilibrium (LD) in 1522 individuals representing four main cattle breeds from China (Nanyang, NY; Qinchuan, QC; Jiaxian, JX; and Chinese Holstein, CH). We also investigated haplotype frequencies and linkage disequilibrium coefficients for three SNPs in all study populations. LD and haplotype structure of ZBED6 were different between breeds. The result of haplotype analysis of three SNPs showed that eight different haplotypes were identified in all breeds. The wild-type haplotype (Hap 1: GCA) and mutant-type haplotype (Hap 8: AGG) shared by all four populations accounted for 15.1, 29.8, 21.7, 57.5% and 9.5, 8.6, 16.7, 0% of all haplotypes were observed in NY, QC, JX and CH, respectively. The statistical analyses indicated that three SNPs were significantly associated with growth traits in NY cattle population (P<0.05 or P<0.01) at five different ages. The results of this study suggest that the ZBED6 gene possibly is a strong candidate gene that affects growth traits in beef cattle breeding program.

Keywords: Association analysis; BW; CH; Cattle; Chinese Holstein; EMSA; GLM; Growth traits; HWE; Hardy–Weinberg equilibrium; He; IGF2; Insulin-like growth factor 2; JX; Jiaxian cattle; LD; LSM; NY; Nanyang; Ne; PIC; Polymorphism information content; QC; QTN; Qinchuan; SNPs; SPSS; ZBED6; Zinc finger, BED-type containing 6; base pair(s); body weight; bp; effective allele numbers; electrophoretic mobility shift assay; general linear models; heterozygosity; least square means estimates; linkage disequilibrium; quantitative trait nucleotide; single nucleotide polymorphisms; statistical product and service solutions.