Dataset Information

Variants in the 3' UTR of general Transcription factor IIF, polypeptide 2 affect female calving efficiency in Japanese Black cattle.

ABSTRACT:

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 (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.

Results

We 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.

Conclusions

This 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.

SUBMITTER: Sasaki S

PROVIDER: S-EPMC3656791 | biostudies-literature | 2013 May

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Variants in the 3' UTR of general Transcription factor IIF, polypeptide 2 affect female calving efficiency in Japanese Black cattle.

Sasaki Shinji S Ibi Takayuki T Watanabe Toshio T Matsuhashi Tamako T Ikeda Shogo S Sugimoto Yoshikazu Y

BMC genetics 20130510

<h4>Background</h4>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 (NCP4) has been used to evaluate the calving efficiency of Japanese Black cattle. To identify variants associated with calving efficiency in Japanese Black cattle, ...[more]

PMID: 23663537

Similar Datasets

Project description:We evaluated the genetic relationships (1) among feed efficiency traits with different fattening periods, (2) between feed efficiency traits and growth traits, and (3) between feed efficiency traits and carcass traits, to determine the influence of genetic factors on feed efficiency traits. In total, 4,578 Japanese Black cattle from a progeny testing program were used. Residual feed intake (RFI), residual BW gain (RG), and residual intake and BW gain (RIG) were defined as feed efficiency traits, and were measured for the first half (approximately 9 to 15 months of age), latter half (approximately 15 to 21 months of age), and total period of fattening (approximately 9 to 21 months of age). A single-trait animal model for estimating heritability and a two-trait animal model for estimating genetic and phenotypic correlations were used. The heritability estimates for RFI, RG, and RIG were different in each fattening period, ranging from 0.36 to 0.46, 0.19 to 0.28, and 0.28 to 0.34, respectively, and the heritability estimates for the total fattening period were greater than those for the first and latter halves separately. RIG showed the greatest preferred genetic correlation, with a greater feed conversion ratio than the other feed efficiency traits (ranging from -0.84 to -0.96). RG in the first and latter halves of the fattening period had different genetic correlations with the growth starting point (0.82 and -0.06, respectively) and maturity rate (0.49 and -0.51, respectively) of the Gompertz growth curve parameters, and is strongly dependent on the different fattening periods. Feed efficiency traits in different fattening periods had low genetic correlations with the carcass traits (from -0.05 to 0.19 for RFI; from 0.02 to 0.31 for RG; and from -0.11 to 0.20 for RIG). This study indicated the possibility for genetic improvement through the selection of high-RIG animals to decrease feed intake and increase BW gain without any unfavorable correlated responses affecting mature (asymptotic) weight and carcass grade.

Project description:Female fertility, a fundamental trait required for animal reproduction, has gradually declined in the last 2 decades in Japanese Black cattle. To identify associated genetic variants in Japanese Black cattle, we evaluated female fertility as a metric to describe the average inverse of the number of artificial inseminations required for conception from the first through the fourth parity (ANAI4) and conducted a genome-wide association study (GWAS) using 430 animals with extreme ANAI4 values from 10,399 animals.We found that 2 variants, namely a single-nucleotide polymorphisms (SNP; g.48476925C?>?T) and a 3-bp indel (g.48476943_48476946insGGC), in the upstream region of the activin receptor IIA gene (ACVR2A) were associated with ANAI4. ACVR2A transcripts from Japanese Black cattle of the Q haplotype, defined by the SNP and the 3-bp indel, with increased ANAI4 were 1.29-1.32-fold more abundant than q-derived transcripts. In agreement, reporter assay results revealed that the activity of the ACVR2A promoter was higher in reporter constructs with the Q haplotype than in those with the q haplotype by approximately 1.2 fold. Expression of exogenous ACVR2A induced dose-dependent increases of reporter activity from the follicle-stimulating hormone, beta polypeptide (FSHB) promoter in response to activin A in a pituitary gonadotrophic cell line. The findings suggested that sequence variations in the upstream region of ACVR2A with the Q haplotype increased ACVR2A transcription, which in turn induced FSHB expression. This association was replicated using a sample population size of 1,433 animals; the frequency of the Q haplotype was 0.39, and Q-to-q haplotype substitution resulted in an increase of 0.02 in terms of ANAI4.This GWAS identified variants in the upstream region of ACVR2A, which were associated with female fertility in Japanese Black cattle. The variants affected the level of ACVR2A mRNA expression, which could lead to an allelic imbalance. This association was replicated with a sample population of 1,433 animals. Thus, the results suggest that the Q haplotype could serve as a useful marker to select Japanese Black cattle with superior female fertility.

Dataset Information

Variants in the 3' UTR of general Transcription factor IIF, polypeptide 2 affect female calving efficiency in Japanese Black cattle.

Background

Results

Conclusions

Publications

Variants in the 3' UTR of general Transcription factor IIF, polypeptide 2 affect female calving efficiency in Japanese Black cattle.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure