Please use this identifier to cite or link to this item: http://hdl.handle.net/2440/87442
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Type: Journal article
Title: Identifying novel QTLs for submergence tolerance in rice cultivars IR72 and Madabaru
Author: Septiningsih, E.
Sanchez, D.
Singh, N.
Sendon, P.
Pamplona, A.
Heuer, S.
Mackill, D.
Citation: Theoretical and Applied Genetics, 2012; 124(5):867-874
Publisher: Springer-Verlag
Issue Date: 2012
ISSN: 0040-5752
1432-2242
Statement of
Responsibility: 
Endang M. Septiningsih, Darlene L. Sanchez, Namrata Singh, Pamella M. D. Sendon, Alvaro M. Pamplona, Sigrid Heuer, David J. Mackill
Abstract: Short-term submergence is a recurring problem in many rice production areas. The SUB1 gene, derived from the tolerant variety FR13A, has been transferred to a number of widely grown varieties, allowing them to withstand complete submergence for up to 2 weeks. However, in areas where longer-term submergence occurs, improved varieties having higher tolerance levels are needed. To search for novel quantitative trait loci (QTLs) from other donors, an F2:3 population between IR72 and Madabaru, both moderately tolerant varieties, was investigated. After a repeated phenotyping of 466 families under submergence stress, a subset of 80 families selected from the two extreme phenotypic tails was used for the QTL analysis. Phenotypic data showed transgressive segregation, with several families having an even higher survival rate than the FR13A-derived tolerant check (IR40931). Four QTLs were identified on chromosomes 1, 2, 9, and 12; the largest QTL on chromosome 1 had a LOD score of 11.2 and R 2 of 52.3%. A QTL mapping to the SUB1 region on chromosome 9, with a LOD score of 3.6 and R 2 of 18.6%, had the tolerant allele from Madabaru, while the other three QTLs had tolerant alleles from IR72. The identification of three non-SUB1 QTLs from IR72 suggests that an alternative pathway may be present in this variety that is independent of the ethylene-dependent pathway mediated by the SUB1A gene. These novel QTLs can be combined with SUB1 using marker assisted backcrossing in an effort to enhance the level of submergence tolerance for flood-prone areas.
Keywords: DNA Primers; Cluster Analysis; Chromosome Mapping; Crosses, Genetic; Sequence Analysis, DNA; Breeding; Computational Biology; Adaptation, Biological; Species Specificity; Base Sequence; Lod Score; Phenotype; Quantitative Trait Loci; Molecular Sequence Data; Floods; Selection, Genetic; Oryza
Rights: © Springer-Verlag 2011
RMID: 0020134086
DOI: 10.1007/s00122-011-1751-0
Appears in Collections:Agriculture, Food and Wine publications

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