IDENTIFICATION OF IRON TOLERANT CANDIDATE LOCI IN RICE DETERMINED THROUGH GENOME-WIDE ASSOCIATION STUDY

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dc.contributor3Balai Besar Penelitian Tanah, KP. Taman Bogo, East Lampung, Lampung. 4Indonesian Centre for Rice Research, Jl. Raya 9, Sukamandi, Subang, West Java.en-US
dc.creatorUtami, M.Si., Dwinita Wikan; Indonesian Center for Agricultural Biotechnology and Genetic Resources Research and Development
dc.creatorRosdianti, Ida; Indonesian Center for Agricultural Biotechnology and Genetic Resources Research and Development
dc.creatorChrisnawati, Lili; Department of Biology, IPB University
dc.creatorSubardi, Subardi; Indonesian Soil Research Institute, Taman Bogo Experimental Station
dc.creatorNurani, Siti; Indonesian Center for Agricultural Biotechnology and Genetic Resources Research and Development
dc.creatorSuwarno, Suwarno; Indonesian Center for Rice Research
dc.date2020-06-30
dc.date.accessioned2020-11-06T02:30:39Z
dc.date.available2020-11-06T02:30:39Z
dc.descriptionIron (Fe) toxicity is a significant abiotic stress in swamp land. The study aimed to identify the candidate loci related to Fe toxicity tolerance through Genome-Wide Association Study (GWAS) approach.  The study used 288 rice accessions consisting of 192 breeding lines and 50 local landraces, and custom-designed 384 rice SNPs-chips. A field evaluation was conducted in inland swamp for two season periods (2014 and 2015). Phenotypic data and association mapping were analyzed using XLSTAT and TASSEL 3.0. The candidate loci were analyzed by functional gene detection of the significant SNPs aligned to the Rice Annotation Project and the Institute for Genomic Research databases. Three linkage disequilibrium (LD) blocks were detected in the Fe tolerant population around the significant SNPs. The first LD block was mapped in chromosome 1 (the AtIRT gene and qFETOX1; qFETOX1-3 QTLs loci) resembled partitioning of Fe-toxicity tolerant mechanism. The second LD blocks located in chromosome 2 (qFE-TOX-2-1 and qFETOX-2 QTLs loci) and chromosome 3 (qFETOX-3 QTL, OsNAS1 and OsNAS2 loci), probably contributed to Fe exclusion mechanism. The third LD blocks located in chromosome 4 (OsFRO2 and qFETOX-4 QTL loci) and chromosome 7 (OsIRT2 and NAS3 loci). The third LD block found on tolerant genotypes both on vegetative and generative stages. This condition indicated that these loci were presumed playing a role for Fe toxicity tolerance in rice. Result of the study are beneficial for determining the strategy on developing Fe-toxicity tolerant rice for specific swamp land type through breeding programs.en-US
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dc.identifierhttp://ejurnal.litbang.pertanian.go.id/index.php/ijas/article/view/10260
dc.identifier10.21082/ijas.v21n1.2020.p17-29
dc.identifier.urihttps://repository.pertanian.go.id/handle/123456789/10505
dc.languageeng
dc.publisherIndonesian Agency for Agricultural Research and Developmenten-US
dc.relationhttp://ejurnal.litbang.pertanian.go.id/index.php/ijas/article/view/10260/9198
dc.relationhttp://ejurnal.litbang.pertanian.go.id/index.php/ijas/article/downloadSuppFile/10260/898
dc.rightsCopyright (c) 2020 Indonesian Journal of Agricultural Scienceen-US
dc.rightshttp://creativecommons.org/licenses/by-sa/4.0en-US
dc.sourceIndonesian Journal of Agricultural Science; Vol 21, No 1 (2020): June 2020; 17-29en-US
dc.source2354-8509
dc.source1411-982X
dc.subjectGWAS; SNP markers; iron toxicity tolerance; rice landraceen-US
dc.titleIDENTIFICATION OF IRON TOLERANT CANDIDATE LOCI IN RICE DETERMINED THROUGH GENOME-WIDE ASSOCIATION STUDYen-US
dc.typeinfo:eu-repo/semantics/article
dc.typeinfo:eu-repo/semantics/publishedVersion
dc.typeen-US
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