title: Identifying novel QTLs for submergence tolerance in rice cultivars IR72 and Madabaru.
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 F(2:3) 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.
authors.affiliation: International Rice Research Institute, Metro Manila, Philippines. e.septiningsih@cgiar.org
authors.forename: Endang M
authors.initials: EM
authors.lastname: Septiningsih
authors.forename: Darlene L
authors.initials: DL
authors.lastname: Sanchez
authors.forename: Namrata
authors.initials: N
authors.lastname: Singh
authors.forename: Pamella M D
authors.initials: PM
authors.lastname: Sendon
authors.forename: Alvaro M
authors.initials: AM
authors.lastname: Pamplona
authors.forename: Sigrid
authors.initials: S
authors.lastname: Heuer
authors.forename: David J
authors.initials: DJ
authors.lastname: Mackill
mesh_terms: D000220:Adaptation, Biological / Q000235:genetics*; D001483:Base Sequence; D001947:Breeding / Q000379:methods*; D002874:Chromosome Mapping; D016000:Cluster Analysis; D019295:Computational Biology; D003433:Crosses, Genetic; D017931:DNA Primers / Q000235:genetics; D055868:Floods; D008126:Lod Score; D008969:Molecular Sequence Data; D012275:Oryza / Q000235:genetics* / Q000254:growth & development*; D010641:Phenotype; D040641:Quantitative Trait Loci / Q000235:genetics*; D012641:Selection, Genetic; D017422:Sequence Analysis, DNA; D013045:Species Specificity
chemical_list: D017931:DNA Primers
references.citation: Theor Appl Genet. 2005 May;110(7):1268-74
references.pmid: 15806347
references.citation: Bioinformatics. 2007 Jun 15;23(12):1527-36
references.pmid: 17459962
references.citation: Mol Gen Genet. 1997 Jun;255(1):1-8
references.pmid: 9230893
references.citation: Proc Natl Acad Sci U S A. 2008 Oct 28;105(43):16814-9
references.pmid: 18936491
references.citation: Mamm Genome. 2001 Dec;12(12):930-2
references.pmid: 11707780
references.citation: Nat Genet. 2006 May;38(5):594-7
references.pmid: 16642024
references.citation: Nature. 2006 Aug 10;442(7103):705-8
references.pmid: 16900200
references.citation: Ann Bot. 2009 Jan;103(2):151-60
references.pmid: 18974101
references.citation: Theor Appl Genet. 2007 Oct;115(6):767-76
references.pmid: 17657470
references.citation: Theor Appl Genet. 2003 Nov;107(8):1419-32
references.pmid: 14513215
references.citation: Bioinformatics. 2008 Mar 1;24(5):721-3
references.pmid: 18202029
references.citation: Theor Appl Genet. 2010 Nov;121(8):1441-53
references.pmid: 20652530
references.citation: Mol Gen Genet. 2000 May;263(4):681-9
references.pmid: 10852491
references.citation: Theor Appl Genet. 2003 Aug;107(3):479-93
references.pmid: 12736777
references.citation: Ann Bot. 2003 Jan;91 Spec No:243-53
references.pmid: 12509344