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Variants in the 3' UTR of General Transcription Factor IIF, polypeptide 2 affect female calving efficiency in Japanese Black cattle

BACKGROUND: Calving 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 calve...

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Autores principales: Sasaki, Shinji, Ibi, Takayuki, Watanabe, Toshio, Matsuhashi, Tamako, Ikeda, Shogo, Sugimoto, Yoshikazu
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2013
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3656791/
https://www.ncbi.nlm.nih.gov/pubmed/23663537
http://dx.doi.org/10.1186/1471-2156-14-41
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author Sasaki, Shinji
Ibi, Takayuki
Watanabe, Toshio
Matsuhashi, Tamako
Ikeda, Shogo
Sugimoto, Yoshikazu
author_facet Sasaki, Shinji
Ibi, Takayuki
Watanabe, Toshio
Matsuhashi, Tamako
Ikeda, Shogo
Sugimoto, Yoshikazu
author_sort Sasaki, Shinji
collection PubMed
description BACKGROUND: Calving 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 (NCP(4)) 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 NCP(4) values selected from 15,225 animals. RESULTS: We identified genetic variants on bovine chromosome 12 (BTA12) that were associated with NCP(4). 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 NCP(4) 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. CONCLUSIONS: This GWAS has identified variants in the 3’ UTR of GTF2F2 that were associated with the NCP(4) 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.
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spelling pubmed-36567912013-05-18 Variants in the 3' UTR of General Transcription Factor IIF, polypeptide 2 affect female calving efficiency in Japanese Black cattle Sasaki, Shinji Ibi, Takayuki Watanabe, Toshio Matsuhashi, Tamako Ikeda, Shogo Sugimoto, Yoshikazu BMC Genet Research Article BACKGROUND: Calving 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 (NCP(4)) 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 NCP(4) values selected from 15,225 animals. RESULTS: We identified genetic variants on bovine chromosome 12 (BTA12) that were associated with NCP(4). 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 NCP(4) 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. CONCLUSIONS: This GWAS has identified variants in the 3’ UTR of GTF2F2 that were associated with the NCP(4) 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. BioMed Central 2013-05-10 /pmc/articles/PMC3656791/ /pubmed/23663537 http://dx.doi.org/10.1186/1471-2156-14-41 Text en Copyright © 2013 Sasaki et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Sasaki, Shinji
Ibi, Takayuki
Watanabe, Toshio
Matsuhashi, Tamako
Ikeda, Shogo
Sugimoto, Yoshikazu
Variants in the 3' UTR of General Transcription Factor IIF, polypeptide 2 affect female calving efficiency in Japanese Black cattle
title Variants in the 3' UTR of General Transcription Factor IIF, polypeptide 2 affect female calving efficiency in Japanese Black cattle
title_full Variants in the 3' UTR of General Transcription Factor IIF, polypeptide 2 affect female calving efficiency in Japanese Black cattle
title_fullStr Variants in the 3' UTR of General Transcription Factor IIF, polypeptide 2 affect female calving efficiency in Japanese Black cattle
title_full_unstemmed Variants in the 3' UTR of General Transcription Factor IIF, polypeptide 2 affect female calving efficiency in Japanese Black cattle
title_short Variants in the 3' UTR of General Transcription Factor IIF, polypeptide 2 affect female calving efficiency in Japanese Black cattle
title_sort variants in the 3' utr of general transcription factor iif, polypeptide 2 affect female calving efficiency in japanese black cattle
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3656791/
https://www.ncbi.nlm.nih.gov/pubmed/23663537
http://dx.doi.org/10.1186/1471-2156-14-41
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