Effect of two non-synonymous ecto-5′-nucleotidase variants on the genetic architecture of inosine 5′-monophosphate (IMP) and its degradation products in Japanese Black beef
| Autor: | Masayuki Takeda, Tsuyoshi Ohtake, Tsuyoshi Abe, Hironori Sakuma, Nanae Sasago, Takatoshi Kojima, Yoshinobu Uemoto, Shinji Sasaki |
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| Jazyk: | angličtina |
| Rok vydání: | 2017 |
| Předmět: |
0301 basic medicine
Linkage disequilibrium lcsh:QH426-470 Protein Conformation lcsh:Biotechnology Genome-wide association study Single-nucleotide polymorphism NT5E Umami Biology Polymorphism Single Nucleotide Japanese Black cattle 03 medical and health sciences chemistry.chemical_compound Inosine Monophosphate lcsh:TP248.13-248.65 Genetic variation Genetics medicine Animals Humans GWAS Amino Acid Sequence Meat quality Inosine 5'-Nucleotidase Allele frequency Hypoxanthine Research IMP biochemical phenomena metabolism and nutrition Molecular Docking Simulation lcsh:Genetics 030104 developmental biology chemistry Cattle Genome-Wide Association Study Biotechnology medicine.drug |
| Zdroj: | BMC Genomics, Vol 18, Iss 1, Pp 1-15 (2017) BMC Genomics |
| ISSN: | 1471-2164 |
| DOI: | 10.1186/s12864-017-4275-4 |
| Popis: | Background 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. Results 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. Conclusion 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. Electronic supplementary material The online version of this article (doi: 10.1186/s12864-017-4275-4) contains supplementary material, which is available to authorized users. |
| Databáze: | OpenAIRE |
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