Sasaki Shinji, Ibi Takayuki, Matsuhashi Tamako, Takeda Kenji, Ikeda Shogo, Sugimoto Mayumi, Sugimoto Yoshikazu
National Livestock Breeding Center, Odakura, Nishigo, Fukushima, 961-8511, Japan.
Graduate School of Environmental and Life Science, Okayama University, Tsushima-naka, Okayama, 700-8530, Japan.
BMC Genet. 2015 Oct 20;16:123. doi: 10.1186/s12863-015-0282-0.
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.
雌性生育力是动物繁殖所需的一项基本特征，在过去20年里日本黑牛的雌性生育力逐渐下降。为了鉴定日本黑牛中与之相关的基因变异，我们将雌性生育力作为一种衡量指标来描述从第一胎到第四胎受孕所需人工授精次数的平均倒数（ANAI4），并使用来自10399头动物中具有极端ANAI4值的430头动物进行了全基因组关联研究（GWAS）。
我们发现，激活素受体IIA基因（ACVR2A）上游区域的2个变异，即一个单核苷酸多态性（SNP；g.48476925C>T）和一个3bp插入缺失（g.48476943_48476946insGGC）与ANAI4相关。由该SNP和3bp插入缺失所定义的Q单倍型的日本黑牛中，ANAI4增加，其ACVR2A转录本比q衍生的转录本丰富1.29 - 1.32倍。与此一致，报告基因检测结果显示，具有Q单倍型的报告基因构建体中ACVR2A启动子的活性比具有q单倍型的构建体高约1.2倍。在垂体促性腺细胞系中，外源性ACVR2A的表达诱导了促卵泡激素β多肽（FSHB）启动子的报告基因活性随激活素A呈剂量依赖性增加。这些发现表明，具有Q单倍型的ACVR2A上游区域的序列变异增加了ACVR2A转录，进而诱导了FSHB表达。使用1433头动物的样本群体重复了这一关联；Q单倍型的频率为0.39，从Q到q单倍型的替换导致ANAI4增加了0.02。
这项GWAS鉴定出了ACVR2A上游区域的变异与日本黑牛的雌性生育力相关。这些变异影响了ACVR2A mRNA表达水平，这可能导致等位基因失衡。使用1433头动物的样本群体重复了这一关联。因此，结果表明Q单倍型可作为选择具有优良雌性生育力的日本黑牛的有用标记。
