Deciphering the Genetic Basis of Allelopathy in japonica Rice Cultivated in Temperate Regions Using a Genome-Wide Association Study

[EN] Allelopathy has been considered as a natural method of weed control. Despite the nature of allelochemical compounds has been studied, little is known about the genetic basis underlying allelopathy. However, it is known that rice exhibits diverse allelopathic potentials across varieties, and bre...

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Authors: Garcia-Romeral, Julia, Castanera, Raúl, Casacuberta, Josep, Domingo, Concha
Format: article
Publication Date:2024
Country:España
Institution:Universitat Politècnica de València (UPV)
Repository:RiuNet. Repositorio Institucional de la Universitat Politécnica de Valéncia
Language:English
OAI Identifier:oai:riunet.upv.es:10251/221785
Online Access:https://riunet.upv.es/handle/10251/221785
Access Level:Open access
Keyword:Allelopathy
QTL
Genome Wide Association Study (GWAS)
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dc.title.none.fl_str_mv Deciphering the Genetic Basis of Allelopathy in japonica Rice Cultivated in Temperate Regions Using a Genome-Wide Association Study
title Deciphering the Genetic Basis of Allelopathy in japonica Rice Cultivated in Temperate Regions Using a Genome-Wide Association Study
spellingShingle Deciphering the Genetic Basis of Allelopathy in japonica Rice Cultivated in Temperate Regions Using a Genome-Wide Association Study
Garcia-Romeral, Julia
Allelopathy
QTL
Genome Wide Association Study (GWAS)
title_short Deciphering the Genetic Basis of Allelopathy in japonica Rice Cultivated in Temperate Regions Using a Genome-Wide Association Study
title_full Deciphering the Genetic Basis of Allelopathy in japonica Rice Cultivated in Temperate Regions Using a Genome-Wide Association Study
title_fullStr Deciphering the Genetic Basis of Allelopathy in japonica Rice Cultivated in Temperate Regions Using a Genome-Wide Association Study
title_full_unstemmed Deciphering the Genetic Basis of Allelopathy in japonica Rice Cultivated in Temperate Regions Using a Genome-Wide Association Study
title_sort Deciphering the Genetic Basis of Allelopathy in japonica Rice Cultivated in Temperate Regions Using a Genome-Wide Association Study
dc.creator.none.fl_str_mv Garcia-Romeral, Julia
Castanera, Raúl
Casacuberta, Josep
Domingo, Concha
author Garcia-Romeral, Julia
author_facet Garcia-Romeral, Julia
Castanera, Raúl
Casacuberta, Josep
Domingo, Concha
author_role author
author2 Castanera, Raúl
Casacuberta, Josep
Domingo, Concha
author2_role author
author
author
dc.contributor.none.fl_str_mv Agencia Estatal de Investigación
European Regional Development Fund
Ministerio de Ciencia, Innovación y Universidades
Repositorio Institucional de la Universitat Politècnica de València Riunet
dc.subject.none.fl_str_mv Allelopathy
QTL
Genome Wide Association Study (GWAS)
topic Allelopathy
QTL
Genome Wide Association Study (GWAS)
description [EN] Allelopathy has been considered as a natural method of weed control. Despite the nature of allelochemical compounds has been studied, little is known about the genetic basis underlying allelopathy. However, it is known that rice exhibits diverse allelopathic potentials across varieties, and breeding for rice plants exhibiting allelopathic potential conferring an advantage against weeds in paddy fields would be highly desirable. Knowledge of the gene factors and the identification of the genomic regions responsible for allelopathy would facilitate breeding programs. Taking advantage of the existing genetic diversity in rice, particularly in temperate japonica rice, we conducted a comprehensive investigation into the genetic determinants that contribute to rice allelopathy. Employing Genome-Wide Association Study, we identified four Quantitative Trait Loci, with the most promising loci situated on chromosome 2 and 5. Subsequent inspection of the genes located within these QTLs revealed genes associated with the biosynthesis of secondary metabolites such as Phenylalanine Ammonia Lyase (PAL), a key enzyme in the synthesis of phenolic compounds, and two genes coding for R2R3-type MYB transcription factors. The identification of these two QTLs associated to allelopathy in rice provides a useful tool for further exploration and targeted breeding strategies.
publishDate 2024
dc.date.none.fl_str_mv 2024
2024-12-01
dc.type.none.fl_str_mv journal article
http://purl.org/coar/resource_type/c_6501
VoR
http://purl.org/coar/version/c_970fb48d4fbd8a85
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format article
dc.identifier.none.fl_str_mv https://riunet.upv.es/handle/10251/221785
url https://riunet.upv.es/handle/10251/221785
dc.language.none.fl_str_mv Inglés
eng
language_invalid_str_mv Inglés
language eng
dc.relation.none.fl_str_mv Agencia Estatal de Investigación http://dx.doi.org/10.13039/501100011033 Plan Estatal de Investigación Científica y Técnica y de Innovación 2017-2020 PID2019-104099RR-I00 MEJORA DE LA RESISTENCIA A ESTRES ABIOTICO Y BIOTICO DE VARIEADES DE ARROZ PARA HACER FRENTE AL CAMBIO CLIMATICO
Agencia Estatal de Investigación http://dx.doi.org/10.13039/501100011033 Plan Estatal de Investigación Científica y Técnica y de Innovación 2017-2020 PID2019-106374RB-I00 TRANSPOSONES, UNA FUENTE IMPORTANTE DE VARIABILIDAD GENETICA EN PLANTAS CULTIVADAS
Agencia Estatal de Investigación http://dx.doi.org/10.13039/501100011033 Plan Estatal de Investigación Científica y Técnica y de Innovación 2017-2020 PID2019-108829RB-I00 LA BELLEZA DE LO PROFUNDO: APLICACIONES DEL DEEP LEARNING A LA PREDICCION GENOMICA
Agencia Estatal de Investigación http://dx.doi.org/10.13039/501100011033 Plan Estatal de Investigación Científica y Técnica y de Innovación 2017-2020 PLEC2021-007786 Estrategias integradas para el desarrollo de un sistema de producción sostenible de arroz: desarrollo de nuevas herramientas para promover la transición agro-ecológica (BestRice)
Agencia Estatal de Investigación http://dx.doi.org/10.13039/501100011033 Plan Estatal de Investigación Científica y Técnica y de Innovación 2021-2023 PID2022-143167NB-I00 LOS TRANSPOSONES, UN MOTOR DE LA EVOLUCION DE LOS GENOMAS DE PLANTAS
Agencia Estatal de Investigación http://dx.doi.org/10.13039/501100011033 PRE2019-089034
Agencia Estatal de Investigación http://dx.doi.org/10.13039/501100011033 IJC2020-045949-I
dc.rights.none.fl_str_mv open access
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dc.publisher.none.fl_str_mv Springer (Biomed Central Ltd.)
publisher.none.fl_str_mv Springer (Biomed Central Ltd.)
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spelling Deciphering the Genetic Basis of Allelopathy in japonica Rice Cultivated in Temperate Regions Using a Genome-Wide Association StudyGarcia-Romeral, JuliaCastanera, RaúlCasacuberta, JosepDomingo, ConchaAllelopathyQTLGenome Wide Association Study (GWAS)[EN] Allelopathy has been considered as a natural method of weed control. Despite the nature of allelochemical compounds has been studied, little is known about the genetic basis underlying allelopathy. However, it is known that rice exhibits diverse allelopathic potentials across varieties, and breeding for rice plants exhibiting allelopathic potential conferring an advantage against weeds in paddy fields would be highly desirable. Knowledge of the gene factors and the identification of the genomic regions responsible for allelopathy would facilitate breeding programs. Taking advantage of the existing genetic diversity in rice, particularly in temperate japonica rice, we conducted a comprehensive investigation into the genetic determinants that contribute to rice allelopathy. Employing Genome-Wide Association Study, we identified four Quantitative Trait Loci, with the most promising loci situated on chromosome 2 and 5. Subsequent inspection of the genes located within these QTLs revealed genes associated with the biosynthesis of secondary metabolites such as Phenylalanine Ammonia Lyase (PAL), a key enzyme in the synthesis of phenolic compounds, and two genes coding for R2R3-type MYB transcription factors. The identification of these two QTLs associated to allelopathy in rice provides a useful tool for further exploration and targeted breeding strategies.This work was supported by MICIU/AEI/10.13039/501100011033, FEDER UE and Next GenerationEU/PRTR (Grant PLEC2021-007786 and PID2019-104099RR-I00 to CD, Grants PID2019-106374RB-I00 and PID2022-143167NB-I00 to JC and Grant PID2019-108829RB-I00 to RC), as well as JGR fellowship PRE2019-089034 and RC fellowship IJC2020-045949-I).Springer (Biomed Central Ltd.)Agencia Estatal de InvestigaciónEuropean Regional Development FundMinisterio de Ciencia, Innovación y UniversidadesRepositorio Institucional de la Universitat Politècnica de València Riunet20242024-12-01journal articlehttp://purl.org/coar/resource_type/c_6501VoRhttp://purl.org/coar/version/c_970fb48d4fbd8a85info:eu-repo/semantics/articleapplication/pdfhttps://riunet.upv.es/handle/10251/221785reponame:RiuNet. Repositorio Institucional de la Universitat Politécnica de Valénciainstname:Universitat Politècnica de València (UPV)InglésengAgencia Estatal de Investigación http://dx.doi.org/10.13039/501100011033 Plan Estatal de Investigación Científica y Técnica y de Innovación 2017-2020 PID2019-104099RR-I00 MEJORA DE LA RESISTENCIA A ESTRES ABIOTICO Y BIOTICO DE VARIEADES DE ARROZ PARA HACER FRENTE AL CAMBIO CLIMATICOAgencia Estatal de Investigación http://dx.doi.org/10.13039/501100011033 Plan Estatal de Investigación Científica y Técnica y de Innovación 2017-2020 PID2019-106374RB-I00 TRANSPOSONES, UNA FUENTE IMPORTANTE DE VARIABILIDAD GENETICA EN PLANTAS CULTIVADASAgencia Estatal de Investigación http://dx.doi.org/10.13039/501100011033 Plan Estatal de Investigación Científica y Técnica y de Innovación 2017-2020 PID2019-108829RB-I00 LA BELLEZA DE LO PROFUNDO: APLICACIONES DEL DEEP LEARNING A LA PREDICCION GENOMICAAgencia Estatal de Investigación http://dx.doi.org/10.13039/501100011033 Plan Estatal de Investigación Científica y Técnica y de Innovación 2017-2020 PLEC2021-007786 Estrategias integradas para el desarrollo de un sistema de producción sostenible de arroz: desarrollo de nuevas herramientas para promover la transición agro-ecológica (BestRice)Agencia Estatal de Investigación http://dx.doi.org/10.13039/501100011033 Plan Estatal de Investigación Científica y Técnica y de Innovación 2021-2023 PID2022-143167NB-I00 LOS TRANSPOSONES, UN MOTOR DE LA EVOLUCION DE LOS GENOMAS DE PLANTASAgencia Estatal de Investigación http://dx.doi.org/10.13039/501100011033 PRE2019-089034Agencia Estatal de Investigación http://dx.doi.org/10.13039/501100011033 IJC2020-045949-Iopen accesshttp://purl.org/coar/access_right/c_abf2Reconocimiento (by)http://creativecommons.org/licenses/by/4.0/info:eu-repo/semantics/openAccessoai:riunet.upv.es:10251/2217852026-06-13T07:49:27Z
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