Marker traits association of agronomical traits correlated with stagnant flooding tolerance in rice

In deep-water areas, the water depth increases gradually throughout the year and maintains up to more than 50 cm of deep of water for long period. In these situations, elongation ability is necessary to allow the plants to keep up with rising floodwater. The elongation of internode during submergenc...

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Published inJournal of physics. Conference series Vol. 835; no. 1; pp. 12002 - 12009
Main Authors Sitaresmi, T, Utami, D W, Suwarno, W B, Ardie, S W, Susanto, U, Aswidinnoor, H
Format Journal Article
LanguageEnglish
Published Bristol IOP Publishing 17.05.2017
Subjects
Agricultural biotechnology
Agronomy
Ammonium bromides
Cetyltrimethylammonium bromide
Deoxyribonucleic acid
DNA
Elongation
Flooding
Floods
Floodwater
Kinases
Markers
Physics
Plant stress
R&D
Research & development
Software
Water depth
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Summary:In deep-water areas, the water depth increases gradually throughout the year and maintains up to more than 50 cm of deep of water for long period. In these situations, elongation ability is necessary to allow the plants to keep up with rising floodwater. The elongation of internode during submergence is regulated by environmental and hormonal factors. The objective of this study was aimed to identify the SNP markers on 384 SNPs linked with agronomical and morphological traits related to stagnant flooding tolerance. The research were conducted at Indonesian Center for Rice Research and Indonesian Centre for Agricultural Biotechnology and Genetic Resources Research and Development. The phenotypical data was collected from F2 from bi-parental crossing of IR 42 and IRRI 119. IR 42 was sensitive parent, and IRRI 119 was tolerant. DNA extraction for rice was using a modified version of Murray and Thompson method using cetyl tri-methyl-ammonium bromide (CTAB). The genotyping was carried out using 384 SNPs Golden Gate Illumina assay. Association analysis between SNP markers and phenotypical data was performed using General Linear Model in Tassel versus 5.0 software program. Based on GLM analysis, the significant marker for plant height with P value < 0.05 are TBGI275345, TBGI275367, and TBGI424383. The significant marker for number of tiller are TBGI000722, TBGI258600, TBGI270843, TBGI271066, TBGI271076, TBGI272122, TBGI272241, and TBGI327790. Two of them, TBGI424383 and TBGI271066 were expected associated with family of protein kinase which play role in plant stress signalling.
ISSN:1742-6588
1742-6596
DOI:10.1088/1742-6596/835/1/012002