Genomic analysis of ionome-related QTLs in Arabidopsis thaliana

Abstract Ionome contributes to maintain cell integrity and acts as cofactors for catalyzing regulatory pathways. Identifying ionome contributing genomic regions provides a practical framework to dissect the genetic architecture of ionomic traits for use in biofortification. Meta-QTL (MQTL) analysis...

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Autores principales:	Nikwan Shariatipour, Bahram Heidari, Samathmika Ravi, Piergiorgio Stevanato
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/d909ff653f444f0bb5d694ae8193b4f9
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spelling	oai:doaj.org-article:d909ff653f444f0bb5d694ae8193b4f92021-12-02T17:37:23ZGenomic analysis of ionome-related QTLs in Arabidopsis thaliana10.1038/s41598-021-98592-72045-2322https://doaj.org/article/d909ff653f444f0bb5d694ae8193b4f92021-09-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-98592-7https://doaj.org/toc/2045-2322Abstract Ionome contributes to maintain cell integrity and acts as cofactors for catalyzing regulatory pathways. Identifying ionome contributing genomic regions provides a practical framework to dissect the genetic architecture of ionomic traits for use in biofortification. Meta-QTL (MQTL) analysis is a robust method to discover stable genomic regions for traits regardless of the genetic background. This study used information of 483 QTLs for ionomic traits identified from 12 populations for MQTL analysis in Arabidopsis thaliana. The selected QTLs were projected onto the newly constructed genetic consensus map and 33 MQTLs distributed on A. thaliana chromosomes were identified. The average confidence interval (CI) of the drafted MQTLs was 1.30 cM, reduced eight folds from a mean CI of 10.88 cM for the original QTLs. Four MQTLs were considered as stable MQTLs over different genetic backgrounds and environments. In parallel to the gene density over the A. thaliana genome, the genomic distribution of MQTLs over the genetic and physical maps indicated the highest density at non- and sub-telomeric chromosomal regions, respectively. Several candidate genes identified in the MQTLs intervals were associated with ion transportation, tolerance, and homeostasis. The genomic context of the identified MQTLs suggested nine chromosomal regions for Zn, Mn, and Fe control. The QTLs for potassium (K) and phosphorus (P) were the most frequently co-located with Zn (78.3%), Mn (76.2%), and Fe (88.2% and 70.6%) QTLs. The current MQTL analysis demonstrates that meta-QTL analysis is cheaper than, and as informative as genome-wide association study (GWAS) in refining the known QTLs.Nikwan ShariatipourBahram HeidariSamathmika RaviPiergiorgio StevanatoNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-14 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Nikwan Shariatipour Bahram Heidari Samathmika Ravi Piergiorgio Stevanato Genomic analysis of ionome-related QTLs in Arabidopsis thaliana
description	Abstract Ionome contributes to maintain cell integrity and acts as cofactors for catalyzing regulatory pathways. Identifying ionome contributing genomic regions provides a practical framework to dissect the genetic architecture of ionomic traits for use in biofortification. Meta-QTL (MQTL) analysis is a robust method to discover stable genomic regions for traits regardless of the genetic background. This study used information of 483 QTLs for ionomic traits identified from 12 populations for MQTL analysis in Arabidopsis thaliana. The selected QTLs were projected onto the newly constructed genetic consensus map and 33 MQTLs distributed on A. thaliana chromosomes were identified. The average confidence interval (CI) of the drafted MQTLs was 1.30 cM, reduced eight folds from a mean CI of 10.88 cM for the original QTLs. Four MQTLs were considered as stable MQTLs over different genetic backgrounds and environments. In parallel to the gene density over the A. thaliana genome, the genomic distribution of MQTLs over the genetic and physical maps indicated the highest density at non- and sub-telomeric chromosomal regions, respectively. Several candidate genes identified in the MQTLs intervals were associated with ion transportation, tolerance, and homeostasis. The genomic context of the identified MQTLs suggested nine chromosomal regions for Zn, Mn, and Fe control. The QTLs for potassium (K) and phosphorus (P) were the most frequently co-located with Zn (78.3%), Mn (76.2%), and Fe (88.2% and 70.6%) QTLs. The current MQTL analysis demonstrates that meta-QTL analysis is cheaper than, and as informative as genome-wide association study (GWAS) in refining the known QTLs.
format	article
author	Nikwan Shariatipour Bahram Heidari Samathmika Ravi Piergiorgio Stevanato
author_facet	Nikwan Shariatipour Bahram Heidari Samathmika Ravi Piergiorgio Stevanato
author_sort	Nikwan Shariatipour
title	Genomic analysis of ionome-related QTLs in Arabidopsis thaliana
title_short	Genomic analysis of ionome-related QTLs in Arabidopsis thaliana
title_full	Genomic analysis of ionome-related QTLs in Arabidopsis thaliana
title_fullStr	Genomic analysis of ionome-related QTLs in Arabidopsis thaliana
title_full_unstemmed	Genomic analysis of ionome-related QTLs in Arabidopsis thaliana
title_sort	genomic analysis of ionome-related qtls in arabidopsis thaliana
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/d909ff653f444f0bb5d694ae8193b4f9
work_keys_str_mv	AT nikwanshariatipour genomicanalysisofionomerelatedqtlsinarabidopsisthaliana AT bahramheidari genomicanalysisofionomerelatedqtlsinarabidopsisthaliana AT samathmikaravi genomicanalysisofionomerelatedqtlsinarabidopsisthaliana AT piergiorgiostevanato genomicanalysisofionomerelatedqtlsinarabidopsisthaliana
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Genomic analysis of ionome-related QTLs in Arabidopsis thaliana

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