Association analysis of bovine Foxa2 gene single sequence variant and haplotype combinations with growth traits in Chinese cattle

Abstract

Forkhead box A2 (Foxa2) has been recognized as one of the most potent transcriptional activators that is implicated in the control of feeding behavior and energy homeostasis. However, similar researches about the effects of genetic variations of Foxa2 gene on growth traits are lacking. Therefore, this study detected Foxa2 gene polymorphisms by DNA pool sequencing, PCR-RFLP and PCR-ACRS methods in 822 individuals from three Chinese cattle breeds. The results showed that four sequence variants (SVs) were screened, including two mutations (SV1, g. 7005 C>T and SV2, g. 7044 C>G) in intron 4, one mutation (SV3, g. 8449 A>G) in exon 5 and one mutation (SV4, g. 8537 T>C) in the 3'UTR. Notably, association analysis of the single mutations with growth traits in total individuals (at 24months) revealed that significant statistical difference was found in four SVs, and SV4 locus was highly significantly associated with growth traits throughout all three breeds (P<0.05 or P<0.01). Meanwhile, haplotype combination CCCCAGTC also indicated remarkably associated to better chest girth and body weight in Jiaxian Red cattle (P<0.05). We herein described a comprehensive study on the variability of bovine Foxa2 gene that was predictive of molecular markers in cattle breeding for the first time.

Keywords: ANOVA; Analysis of variance; Association; Cattle; DLK1; Delta-like 1; EM; Expectation maximization; FTO; Fat mass and obesity associated; Forkhead box A2; Foxa2; Foxa2 gene; G6PC2; Growth traits; HNF-3; HWE; Haplotype combination; Hardy–Weinberg equilibrium; Hepatocyte nuclear factor 3; JX; Jiaxian Red; LD; Linkage disequilibrium; NY; Nanyang; PCR-ACRS; PCR-based amplification-created restriction site; PCR–RFLP; PIC; Polymerase chain reaction–restriction fragment length polymorphism; Polymorphism information content; QC; Qinchuan; SNPs; SVs; Sequence variant; Sequence variants; Single nucleotide polymorphisms; UTR; Unstranslated region(s); glucose-6-phosphatase catalytic subunit 2.