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Domesticating Vigna stipulacea: Chromosome-Level genome assembly reveals VsPSAT1 as a candidate gene decreasing hard-seededness

To increase food production under the challenges presented by global climate change, the concept of de novo domestication—utilizing stress-tolerant wild species as new crops—has recently gained considerable attention. We had previously identified mutants with desired domestication traits in a mutage...

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Autores principales: Takahashi, Yu, Sakai, Hiroaki, Ariga, Hirotaka, Teramoto, Shota, Shimada, Takashi L., Eun, Heesoo, Muto, Chiaki, Naito, Ken, Tomooka, Norihiko
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10149957/
https://www.ncbi.nlm.nih.gov/pubmed/37139108
http://dx.doi.org/10.3389/fpls.2023.1119625
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author Takahashi, Yu
Sakai, Hiroaki
Ariga, Hirotaka
Teramoto, Shota
Shimada, Takashi L.
Eun, Heesoo
Muto, Chiaki
Naito, Ken
Tomooka, Norihiko
author_facet Takahashi, Yu
Sakai, Hiroaki
Ariga, Hirotaka
Teramoto, Shota
Shimada, Takashi L.
Eun, Heesoo
Muto, Chiaki
Naito, Ken
Tomooka, Norihiko
author_sort Takahashi, Yu
collection PubMed
description To increase food production under the challenges presented by global climate change, the concept of de novo domestication—utilizing stress-tolerant wild species as new crops—has recently gained considerable attention. We had previously identified mutants with desired domestication traits in a mutagenized population of the legume Vigna stipulacea Kuntze (minni payaru) as a pilot for de novo domestication. Given that there are multiple stress-tolerant wild legume species, it is important to establish efficient domestication processes using reverse genetics and identify the genes responsible for domestication traits. In this study, we identified VsPSAT1 as the candidate gene responsible for decreased hard-seededness, using a Vigna stipulacea isi2 mutant that takes up water from the lens groove. Scanning electron microscopy and computed tomography revealed that the isi2 mutant has lesser honeycomb-like wax sealing the lens groove than the wild-type, and takes up water from the lens groove. We also identified the pleiotropic effects of the isi2 mutant: accelerating leaf senescence, increasing seed size, and decreasing numbers of seeds per pod. While doing so, we produced a V. stipulacea whole-genome assembly of 441 Mbp in 11 chromosomes and 30,963 annotated protein-coding sequences. This study highlights the importance of wild legumes, especially those of the genus Vigna with pre-existing tolerance to biotic and abiotic stresses, for global food security during climate change.
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spelling pubmed-101499572023-05-02 Domesticating Vigna stipulacea: Chromosome-Level genome assembly reveals VsPSAT1 as a candidate gene decreasing hard-seededness Takahashi, Yu Sakai, Hiroaki Ariga, Hirotaka Teramoto, Shota Shimada, Takashi L. Eun, Heesoo Muto, Chiaki Naito, Ken Tomooka, Norihiko Front Plant Sci Plant Science To increase food production under the challenges presented by global climate change, the concept of de novo domestication—utilizing stress-tolerant wild species as new crops—has recently gained considerable attention. We had previously identified mutants with desired domestication traits in a mutagenized population of the legume Vigna stipulacea Kuntze (minni payaru) as a pilot for de novo domestication. Given that there are multiple stress-tolerant wild legume species, it is important to establish efficient domestication processes using reverse genetics and identify the genes responsible for domestication traits. In this study, we identified VsPSAT1 as the candidate gene responsible for decreased hard-seededness, using a Vigna stipulacea isi2 mutant that takes up water from the lens groove. Scanning electron microscopy and computed tomography revealed that the isi2 mutant has lesser honeycomb-like wax sealing the lens groove than the wild-type, and takes up water from the lens groove. We also identified the pleiotropic effects of the isi2 mutant: accelerating leaf senescence, increasing seed size, and decreasing numbers of seeds per pod. While doing so, we produced a V. stipulacea whole-genome assembly of 441 Mbp in 11 chromosomes and 30,963 annotated protein-coding sequences. This study highlights the importance of wild legumes, especially those of the genus Vigna with pre-existing tolerance to biotic and abiotic stresses, for global food security during climate change. Frontiers Media S.A. 2023-04-17 /pmc/articles/PMC10149957/ /pubmed/37139108 http://dx.doi.org/10.3389/fpls.2023.1119625 Text en Copyright © 2023 Takahashi, Sakai, Ariga, Teramoto, Shimada, Eun, Muto, Naito and Tomooka https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Plant Science
Takahashi, Yu
Sakai, Hiroaki
Ariga, Hirotaka
Teramoto, Shota
Shimada, Takashi L.
Eun, Heesoo
Muto, Chiaki
Naito, Ken
Tomooka, Norihiko
Domesticating Vigna stipulacea: Chromosome-Level genome assembly reveals VsPSAT1 as a candidate gene decreasing hard-seededness
title Domesticating Vigna stipulacea: Chromosome-Level genome assembly reveals VsPSAT1 as a candidate gene decreasing hard-seededness
title_full Domesticating Vigna stipulacea: Chromosome-Level genome assembly reveals VsPSAT1 as a candidate gene decreasing hard-seededness
title_fullStr Domesticating Vigna stipulacea: Chromosome-Level genome assembly reveals VsPSAT1 as a candidate gene decreasing hard-seededness
title_full_unstemmed Domesticating Vigna stipulacea: Chromosome-Level genome assembly reveals VsPSAT1 as a candidate gene decreasing hard-seededness
title_short Domesticating Vigna stipulacea: Chromosome-Level genome assembly reveals VsPSAT1 as a candidate gene decreasing hard-seededness
title_sort domesticating vigna stipulacea: chromosome-level genome assembly reveals vspsat1 as a candidate gene decreasing hard-seededness
topic Plant Science
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10149957/
https://www.ncbi.nlm.nih.gov/pubmed/37139108
http://dx.doi.org/10.3389/fpls.2023.1119625
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