Evaluation of novel SNPs and haplotypes within the <i>ATBF1</i> gene and their effects on economically important production traits in cattle

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 kinasesignal 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.

Detection of insertion/deletions (indels) of the &lt;i&gt;ATBF1&lt;/i&gt; gene and their effects on growth-related traits in three indigenous goat breeds

“…Sequencing maps showed the homozygotic insertion type (II) and the homozygotic deletion type (DD) of the P11-6-bp indel. width (HW) and circumference of the cannon bone (CCB) Yan et al, 2018).…”

“…It plays an important roles in regulating myogenesis and adipose tissue development (Klein et al, 1996;Berry et al, 2001;Huang et al, 2015) and has a close relationship with the lactation-related hypothalamic-pituitary-adrenal (HPA) axis pathway (PITX2/PITX1-HESX1-LHX3/LHX4-PROP1-POU1F1) (Goldberg et al, 2011;Ma et al, 2017) and JAK-STAT pathways in livestock science (Nagpal et al, 2002;Ruiz-Vela et al, 2009;Ma et al, 2017). ATBF1 not only activates the expression of the Pit1 (the pituitaryspecific transcription factor 1, also known as POU1F1) gene though interacting with a Pit1 enhancer (Qi et al, 2008;Araujo et al, 2013;Yan et al, 2018), but also potentially synergizes with PROP1 that can bind to the enhancer of the Pit1 gene and regulate the expression levels of the growth hormone (Li et al, 2013) prolactin and of TSH-β. STAT3, Pit1 and PROP1 genes play an important role in early embryo development and cell differentiation (Hirano et al, 2000;Ying et al, 2003;Laouar et al, 2003), so the ATBF1 gene was hypothesized to produce important effects on early develop-ment and cell differentiation; thus, it would affect the grow traits in animals.…”

“…In our team, Zhang et al (2015) first explored the single nucleotide polymorphisms (SNPs) and haplotype structure of the goat ATBF1 gene and analyzed its associa- tions with growth-related traits in two Chinese goat breeds. Xu et al (2017) identified crucial SNP variations within the ATBF1 gene in native Chinese cattle breeds. These functional experiments suggested that the ATBF1 gene would affect the growth traits of livestock.…”

“…The AT motif-binding factor (ATBF1), also known as zinc finger homeobox 3 (ZFHX3), is a crucial cancer suppressor gene. It is worth mentioning that ATBF1 could promote the expression levels of the growth hormone prolactin and TSH-β by binding to the enhancers of POU1F1 (also known as Pit1) and PROP1 (Darling et al, 1998;Qi et al, 2008;Araujo et al, 2013;Yan et al, 2018). These studies showed that the ATBF1 gene was hypothesized to produce important effects on cell differentiation and early development, suggesting that the ATBF1 gene would affect the growth traits in animals.…”