Variants in the 3 UTR of General Transcription Factor IIF, polypeptide 2 affect female calving efficiency in Japanese Black cattleReport as inadecuate




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BMC Genetics

, 14:41

Complex traits and quantitative genetics

Abstract

BackgroundCalving efficiency can be described as the measure of a cow’s ability to produce viable offspring within a specific period of time. This trait is crucial in beef cattle because calves are necessary both for the production of beef and for heifer replacements. Recently, the number of calves produced at 4 years of age NCP4 has been used to evaluate the calving efficiency of Japanese Black cattle. To identify variants associated with calving efficiency in Japanese Black cattle, we conducted a genome-wide association study GWAS using 688 animals with extreme NCP4 values selected from 15,225 animals.

ResultsWe identified genetic variants on bovine chromosome 12 BTA12 that were associated with NCP4. The General Transcription Factor IIF, polypeptide 2 GTF2F2, located in the 132 kbp-associated region, proved to be in strong linkage disequilibrium. We found 15 associated variants in the promoter and the 3- UTR regions. Consistent with this finding, transcripts of GTF2F2 derived from the haplotype Q with the increased number of calves were 1.33-fold more abundant than q-derived transcripts. Furthermore, luciferase assays revealed that the activity of the 3- UTR, a region that includes nine SNPs, was higher in constructs with the Q haplotype than in those with the q haplotype by approximately 1.35-fold. In contrast, the activity of the promoter region did not differ between haplotypes. The association was replicated in an independent sample of 827 animals that were randomly selected from the remainder of the cohort from the same farms used in the GWAS. In the replicated population, the frequency of the Q haplotype is 0.313, and this haplotype accounts for 2.69% of the total phenotypic variance. The effect of the Q to q haplotype substitution on NCP4 was 0.054 calves. These findings suggest that variants in the 3- UTR of GTF2F2 affect the level of GTF2F2 mRNA, which is associated with calving efficiency.

ConclusionsThis GWAS has identified variants in the 3’ UTR of GTF2F2 that were associated with the NCP4 of Japanese Black cattle, and this association was validated in an independent sample. The Q haplotype will be immediately useful in improving the calving efficiency of Japanese Black cattle.

KeywordsCalving efficiency Number of calves produced at 4 years of age NCP4 Genome-wide association study General Transcription Factor IIF, polypeptide 2 GTF2F2 Beef cattle AbbreviationsGWASGenome-wide association study

NCP4Number of calves produced at 4 years of age

QTLQuantitative trait locus or loci

BTABovine Bos taurus chromosome

SNPSingle nucleotide polymorphism

LDLinkage disequilibrium

PCRPolymerase chain reaction.

Electronic supplementary materialThe online version of this article doi:10.1186-1471-2156-14-41 contains supplementary material, which is available to authorized users.

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Author: Shinji Sasaki - Takayuki Ibi - Toshio Watanabe - Tamako Matsuhashi - Shogo Ikeda - Yoshikazu Sugimoto

Source: https://link.springer.com/



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