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Title: Identification of a putative pyridoxamine 5'-phosphate oxidase gene linked with 4-pyridoxate accumulation in seeds of Brachypodium distachyon through metabolite quantitative trait locus mapping

Author
item ONDO, YOSHIHIKO - Riken Institute
item SAWADA, YUJI - Riken Institute
item SHIMIZU, MINAMI - Riken Institute
item TAKAHAGI, KOTARO - Riken Institute
item UEHARA-YAMAGUCHI, YUKIKO - Riken Institute
item HIRAI, MASAMI - Riken Institute
item Garvin, David
item MOCHIDA, KEIICHI - Riken Institute

Submitted to: International Journal of Molecular Sciences
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/27/2019
Publication Date: 5/11/2019
Citation: Ondo, Y., Sawada, Y., Shimizu, M., Takahagi, K., Uehara-Yamaguchi, Y., Hirai, M., Garvin, D.F., Mochida, K. 2019. Identification of a putative pyridoxamine 5'-phosphate oxidase gene linked with 4-pyridoxate accumulation in seeds of Brachypodium distachyon through metabolite quantitative trait locus mapping. International Journal of Molecular Sciences. 20(9):2348. https://doi.org/10.3390/ijms20092348.
DOI: https://doi.org/10.3390/ijms20092348

Interpretive Summary: Cereal grains such as wheat and rice are a major food source for billions of humans. They contain protein, carbohydrates, vitamins and minerals that are essential dietary components. Through breeding, it may be possible to improve the nutritional value of these crops. However, this requires that genetic variation exists that can be exploited by breeders. In this study, the model grass Brachypodium was used to demonstrate that genetic variation for levels of a number of chemical compounds including a form of vitamin B6 exists between different genotypes. Subsequently, through molecular mapping, the chromosome locations of genes that underly variation for vitamin B6 levels were identified. The gene having the strongest effect is located on chromosome 3. Additional molecular mapping focused specifically on this region of chromosome 3 identified a gene involved in the synthesis of vitamin B6, and found that DNA sequence variation in this gene is likely to be the cause of a portion of the vitamin B6 level variability. This research demonstrates that it is possible to genetically dissect variation in grain seed chemical content including vitamins, and to identify the genes that cause this variation. The information obtained here can be translated to wheat, for development of nutritionally enhanced wheat grain that will improve the health status of segments of humans who rely upon wheat as a staple food crop.

Technical Abstract: Metabolite accumulation influences crop traits such as grain quality. To explore the diversity of seed metabolites in a temperate model grass, we comparatively quantified 183 compounds in mature seeds of 58 natural accessions of Brachypodium distachyon by a widely targeted metabolome analysis. Specifically, we found 32 metabolites that exhibited significant differential accumulation between the accessions, Bd21 and Bd3-1. Using a recombinant inbred line (RIL) population developed from a cross between these two accessions, we identified quantitative trait loci (QTLs) linked with variation in levels of 4-pyridoxate, a compound associated with vitamin B6 metabolism. For the most significant QTL detected on chromosome 3, we narrowed down candidate genes to Bradi3g23340, which encodes a putative pyridoxine/pyridoxamine 5'-phosphate oxidase that catalyses the synthesis of pyridoxal-5'-phosphate in vitamin B6 metabolism. Further, we found that contrasting SNP haplotypes in the coding region of Bradi3g23340 were consistently associated with 4-pyridoxate accumulation patterns in some of the RILs; thus, we hypothesized that non-synonymous substitutions in Bradi3g23340 may affect 4-pyridoxate accumulation in seeds of Bd21 and Bd3-1. Taken together, our findings revealed a likely gene related to metabolic phenotypes in B. distachyon.