National Livestock Breeding Center, Nishigo, Fukushima, 961-8511, Japan.
Present address: Graduate School of Agricultural Science, Tohoku University, Sendai, Miyagi, 980-0845, Japan.
BMC Genomics. 2017 Nov 13;18(1):874. doi: 10.1186/s12864-017-4275-4.
Umami is a Japanese term for the fifth basic taste and is an important sensory property of beef palatability. Inosine 5'-monophosphate (IMP) contributes to umami taste in beef. Thus, the overall change in concentration of IMP and its degradation products can potentially affect the beef palatability. In this study, we investigated the genetic architecture of IMP and its degradation products in Japanese Black beef. First, we performed genome-wide association study (GWAS), candidate gene analysis, and functional analysis to detect the causal variants that affect IMP, inosine, and hypoxanthine. Second, we evaluated the allele frequencies in the different breeds, the contribution of genetic variance, and the effect on other economical traits using the detected variants.
A total of 574 Japanese Black cattle were genotyped using the Illumina BovineSNP50 BeadChip and were then used for GWAS. The results of GWAS showed that the genome-wide significant single nucleotide polymorphisms (SNPs) on BTA9 were detected for IMP, inosine, and hypoxanthine. The ecto-5'-nucleotidase (NT5E) gene, which encodes the enzyme NT5E for the extracellular degradation of IMP to inosine, was located near the significant region on BTA9. The results of candidate gene analysis and functional analysis showed that two non-synonymous SNPs (c.1318C > T and c.1475 T > A) in NT5E affected the amount of IMP and its degradation products in beef by regulating the enzymatic activity of NT5E. The Q haplotype showed a positive effect on IMP and a negative effect on the enzymatic activity of NT5E in IMP degradation. The two SNPs were under perfect linkage disequilibrium in five different breeds, and different haplotype frequencies were seen among breeds. The two SNPs contribute to about half of the total genetic variance in IMP, and the results of genetic relationship between IMP and its degradation products showed that NT5E affected the overall concentration balance of IMP and its degradation products. In addition, the SNPs in NT5E did not have an unfavorable effect on the other economical traits.
Based on all the above findings taken together, two non-synonymous SNPs in NT5E would be useful for improving IMP and its degradation products by marker-assisted selection in Japanese Black cattle.
鲜味是日本的一个术语，代表第五种基本味道，也是牛肉可口性的一个重要感官特性。肌苷 5'-单磷酸（IMP）有助于牛肉产生鲜味。因此，IMP 及其降解产物的总体浓度变化可能会影响牛肉的可口性。在这项研究中，我们研究了日本黑牛肉中 IMP 及其降解产物的遗传结构。首先，我们进行了全基因组关联研究（GWAS）、候选基因分析和功能分析，以检测影响 IMP、肌苷和次黄嘌呤的因果变异。其次，我们使用检测到的变异评估了不同品种的等位基因频率、遗传方差的贡献以及对其他经济性状的影响。
共对 574 头日本黑牛进行了 Illumina BovineSNP50 BeadChip 基因分型，然后用于 GWAS。GWAS 的结果表明，IMP、肌苷和次黄嘌呤的 BTA9 上存在全基因组显著的单核苷酸多态性（SNP）。编码用于 IMP 胞外降解为肌苷的酶 NT5E 的外核苷酸酶（NT5E）基因位于 BTA9 上的显著区域附近。候选基因分析和功能分析的结果表明，NT5E 中的两个非同义 SNP（c.1318C>T 和 c.1475T>A）通过调节 NT5E 的酶活性，影响牛肉中 IMP 和其降解产物的含量。Q 单倍型对 IMP 有正效应，对 IMP 降解中 NT5E 的酶活性有负效应。在五个不同品种中，这两个 SNP 处于完全连锁不平衡状态，不同品种的单倍型频率不同。这两个 SNP 对 IMP 的总遗传方差贡献约为一半，IMP 及其降解产物的遗传关系结果表明，NT5E 影响 IMP 及其降解产物的总体浓度平衡。此外，NT5E 中的 SNP 对其他经济性状没有不利影响。
基于所有上述发现，NT5E 中的两个非同义 SNP 可用于通过日本黑牛的标记辅助选择来改善 IMP 和其降解产物。
