Evaluation of novel SNPs and haplotypes within the &amp;lt;i&amp;gt;ATBF1&amp;lt;/i&amp;gt; gene and their effects on economically important production traits in cattle

Han Xu,Xianyong Lan,Ruihua Dang,Chuzhao Lei,Sihuan Zhang,Xiaoyan Zhang,Hong Chen

doi:10.5194/aab-60-285-2017

Evaluation of novel SNPs and haplotypes within the &lt;i&gt;ATBF1&lt;/i&gt; gene and their effects on economically important production traits in cattle

Han Xu, Xianyong Lan + Show 5 more

Open Access

https://doi.org/10.5194/aab-60-285-2017

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Abstract

Abstract. AT motif binding factor 1 (ATBF1) gene can promote the expression level of the growth hormone 1 (GH1) gene by binding to the enhancers of the POU1F1 and PROP1 genes; thus, it affects the growth and development of livestock. Considering that the ATBF1 gene also has a close relationship with the Janus kinase–signal transductor and activator of transcription (JAK–STAT) pathway, the objective of this work was to identify novel single-nucleotide polymorphism (SNP) variations and their association with growth traits in native Chinese cattle breeds. Five novel SNPs within the ATBF1 gene were found in 644 Qinchuan and Jinnan cattle for first time using 25 pairs of screening and genotyping primers. The five novel SNPs were named as AC_000175:g.140344C>G (SNP1), g.146573T>C (SNP2), g.205468C>T (SNP3), g.205575A>G (SNP4) and g.297690C<T (SNP5). Among them, SNP1 and SNP2 were synonymous coding SNPs, while SNP5 was a missense coding SNP, and the other SNPs were intronic. Haplotype analysis found 18 haplotypes in the two breeds, and three and five closely linked loci were revealed in Qinchuan and Jinnan breeds, respectively. Association analysis revealed that SNP1 was significantly associated with the height across the hip in Qinchuan cattle. SNP2 was found to be significantly related to chest circumference and body side length traits in Jinnan cattle. SNP3 was found to have significant associations with four growth traits in Qinchuan cattle. Moreover, the different combined genotypes, SNP1–SNP3, SNP1–SNP4 and SNP2–SNP5 were significantly associated with the growth traits in cattle. These findings indicated that the bovine ATBF1 gene had marked effects on growth traits, and the growth-trait-related loci can be used as DNA markers for maker-assisted selection (MAS) breeding programs in cattle.

Highlights

With the fast improvement in living standards in developing countries, especially China, the demand for beef consumption has increased quickly
SNP3 and SNP4 were located at intron 3, and SNP4 was close to the exon 4 splicing site
The genotyping results can be seen from the agarose gel electrophoresis photos, which shows that singlenucleotide polymorphisms (SNPs) were named as AC_000175:g.140344C>G (SNP1)–SNP5 were successfully genotyped by their own methods (Fig. 2)

Summary

Introduction

With the fast improvement in living standards in developing countries, especially China, the demand for beef consumption has increased quickly. Cattle breed resources are very abundant in China, poor quality and low growth rate of many breeds are still barriers to an increase in cattle production. As the most practical and economic method, the MAS strategy relies on the numerous singlenucleotide polymorphisms (SNPs) associated with production traits. More functional SNPs, which could be applied in MAS breeding of domestic livestock, should be discovered. An example is the single A-to-G substitution near the ovine CLPG gene, which has been used for doublemuscle livestock breeding (Cockett et al, 1994)

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