Markers-traits association for iron toxicity tolerance in selected Indonesian rice varieties

Nugraha Y, Utami DW, Rosdianti I, Ardie SW, Ghulammahdi M, Suwarno, Aswidinnoor H. 2016. Markers-traits association for iron toxicity tolerance in selected Indonesian rice varieties. Biodiversitas 17: 753-763. Ferrous iron toxicity is a mineral disorder frequently occurring under flooded soils condi...

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Autores principales:	YUDHISTIRA NUGRAHA, DWINITA W UTAMI, IDA ROSDIANTI, SINTHO WAHYUNING ARDIE, MUNIF GHULAMMAHDI, SUWARNO SUWARNO, HAJRIAL ASWIDINNOOR
Formato:	article
Lenguaje:	EN
Publicado:	MBI & UNS Solo 2016
Materias:	golden gate assay, grain yield, leaf bronzing scores, principle component analysis, single nucleotide polymorphism Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/c931c1e1658e4f53a7941b2c677e6852
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spelling	oai:doaj.org-article:c931c1e1658e4f53a7941b2c677e68522021-11-14T02:27:09ZMarkers-traits association for iron toxicity tolerance in selected Indonesian rice varieties1412-033X2085-472210.13057/biodiv/d170251https://doaj.org/article/c931c1e1658e4f53a7941b2c677e68522016-09-01T00:00:00Zhttps://smujo.id/biodiv/article/view/548https://doaj.org/toc/1412-033Xhttps://doaj.org/toc/2085-4722Nugraha Y, Utami DW, Rosdianti I, Ardie SW, Ghulammahdi M, Suwarno, Aswidinnoor H. 2016. Markers-traits association for iron toxicity tolerance in selected Indonesian rice varieties. Biodiversitas 17: 753-763. Ferrous iron toxicity is a mineral disorder frequently occurring under flooded soils condition where rice is cultivated. Here we study identification the Single Nucleotide Polymorphism (SNPs) markers associated with iron toxicity tolerance characters. The phenotypical data was collected from exploiting of twenty-four rice genotypes that were grown under Yoshida + 0.2% agar solution with treatment of 400 mg. L-1 Fe2+ and control conditions. The same genotypes were grown in iron toxicity acute and control sites at Taman Bogo, Lampung Province, Indonesia. The Principle Component Analysis (PCA) of the phenotypic data showed that 18 rice genotypes were selected representing grouping of related characters to iron toxicity condition. The genotyping of selected genotypes was carried out using multiplexes of 384 SNPs Golden Gate IlluminaÂ© assay. We identified, TBGI380435 which located on 14.45 Mbp of chromosome 9 was associated to leaf bronzing and relative shoot weight characters in the greenhouse experiment. The marker was associated with heavy metal transport detoxification (HTDT). The results are expected to assist in locating the potential candidate genes or Fe toxicity tolerance and to allow for precise marker-assisted selection. This research will serve for rice improvement through marker-assisted breeding and genomic selection in Indonesia. Keywords: Golden gate assay, grain yield, leaf bronzing scores, principle component analysis, single nucleotide polymorphism Abbreviations: SNPs = Single Nucleotide Polymorphisms, AM = Association Mapping, LD= Linkage Disequilibrium, GG= Golden Gate Assay, NGS= Next Generation sequencing ,QTL = Quantitative Trait Loci, LBS = Leaf Bronzing Score, PCA = Principle Component Analysis, SES = Standard Evaluation System For Rice, GLM = General Linear Model, PC = Principle Component, HTDT = Heavy Metal Transport DetoxificationYUDHISTIRA NUGRAHADWINITA W UTAMIIDA ROSDIANTISINTHO WAHYUNING ARDIEMUNIF GHULAMMAHDISUWARNO SUWARNOHAJRIAL ASWIDINNOORMBI & UNS Soloarticlegolden gate assay, grain yield, leaf bronzing scores, principle component analysis, single nucleotide polymorphismBiology (General)QH301-705.5ENBiodiversitas, Vol 17, Iss 2 (2016)
institution	DOAJ
collection	DOAJ
language	EN
topic	golden gate assay, grain yield, leaf bronzing scores, principle component analysis, single nucleotide polymorphism Biology (General) QH301-705.5
spellingShingle	golden gate assay, grain yield, leaf bronzing scores, principle component analysis, single nucleotide polymorphism Biology (General) QH301-705.5 YUDHISTIRA NUGRAHA DWINITA W UTAMI IDA ROSDIANTI SINTHO WAHYUNING ARDIE MUNIF GHULAMMAHDI SUWARNO SUWARNO HAJRIAL ASWIDINNOOR Markers-traits association for iron toxicity tolerance in selected Indonesian rice varieties
description	Nugraha Y, Utami DW, Rosdianti I, Ardie SW, Ghulammahdi M, Suwarno, Aswidinnoor H. 2016. Markers-traits association for iron toxicity tolerance in selected Indonesian rice varieties. Biodiversitas 17: 753-763. Ferrous iron toxicity is a mineral disorder frequently occurring under flooded soils condition where rice is cultivated. Here we study identification the Single Nucleotide Polymorphism (SNPs) markers associated with iron toxicity tolerance characters. The phenotypical data was collected from exploiting of twenty-four rice genotypes that were grown under Yoshida + 0.2% agar solution with treatment of 400 mg. L-1 Fe2+ and control conditions. The same genotypes were grown in iron toxicity acute and control sites at Taman Bogo, Lampung Province, Indonesia. The Principle Component Analysis (PCA) of the phenotypic data showed that 18 rice genotypes were selected representing grouping of related characters to iron toxicity condition. The genotyping of selected genotypes was carried out using multiplexes of 384 SNPs Golden Gate IlluminaÂ© assay. We identified, TBGI380435 which located on 14.45 Mbp of chromosome 9 was associated to leaf bronzing and relative shoot weight characters in the greenhouse experiment. The marker was associated with heavy metal transport detoxification (HTDT). The results are expected to assist in locating the potential candidate genes or Fe toxicity tolerance and to allow for precise marker-assisted selection. This research will serve for rice improvement through marker-assisted breeding and genomic selection in Indonesia. Keywords: Golden gate assay, grain yield, leaf bronzing scores, principle component analysis, single nucleotide polymorphism Abbreviations: SNPs = Single Nucleotide Polymorphisms, AM = Association Mapping, LD= Linkage Disequilibrium, GG= Golden Gate Assay, NGS= Next Generation sequencing ,QTL = Quantitative Trait Loci, LBS = Leaf Bronzing Score, PCA = Principle Component Analysis, SES = Standard Evaluation System For Rice, GLM = General Linear Model, PC = Principle Component, HTDT = Heavy Metal Transport Detoxification
format	article
author	YUDHISTIRA NUGRAHA DWINITA W UTAMI IDA ROSDIANTI SINTHO WAHYUNING ARDIE MUNIF GHULAMMAHDI SUWARNO SUWARNO HAJRIAL ASWIDINNOOR
author_facet	YUDHISTIRA NUGRAHA DWINITA W UTAMI IDA ROSDIANTI SINTHO WAHYUNING ARDIE MUNIF GHULAMMAHDI SUWARNO SUWARNO HAJRIAL ASWIDINNOOR
author_sort	YUDHISTIRA NUGRAHA
title	Markers-traits association for iron toxicity tolerance in selected Indonesian rice varieties
title_short	Markers-traits association for iron toxicity tolerance in selected Indonesian rice varieties
title_full	Markers-traits association for iron toxicity tolerance in selected Indonesian rice varieties
title_fullStr	Markers-traits association for iron toxicity tolerance in selected Indonesian rice varieties
title_full_unstemmed	Markers-traits association for iron toxicity tolerance in selected Indonesian rice varieties
title_sort	markers-traits association for iron toxicity tolerance in selected indonesian rice varieties
publisher	MBI & UNS Solo
publishDate	2016
url	https://doaj.org/article/c931c1e1658e4f53a7941b2c677e6852
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_version_	1718430042045808640

Markers-traits association for iron toxicity tolerance in selected Indonesian rice varieties

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