title: QTL Mapping in Three Rice Populations Uncovers Major Genomic Regions Associated with African Rice Gall Midge Resistance.
abstract: African rice gall midge (AfRGM) is one of the most destructive pests of irrigated and lowland African ecologies. This study aimed to identify the quantitative trait loci (QTL) associated with AfRGM pest incidence and resistance in three independent bi-parental rice populations (ITA306xBW348-1, ITA306xTOG7106 and ITA306xTOS14519), and to conduct meta QTL (mQTL) analysis to explore whether any genomic regions are conserved across different genetic backgrounds. Composite interval mapping (CIM) conducted on the three populations independently uncovered a total of 28 QTLs associated with pest incidence (12) and pest severity (16). The number of QTLs per population associated with AfRGM resistance varied from three in the ITA306xBW348-1 population to eight in the ITA306xTOG7106 population. Each QTL individually explained 1.3 to 34.1% of the phenotypic variance. The major genomic region for AfRGM resistance had a LOD score and R2 of 60.0 and 34.1% respectively, and mapped at 111 cM on chromosome 4 (qAfrGM4) in the ITA306xTOS14519 population. The meta-analysis reduced the number of QTLs from 28 to 17 mQTLs, each explaining 1.3 to 24.5% of phenotypic variance, and narrowed the confidence intervals by 2.2 cM. There was only one minor effect mQTL on chromosome 1 that was common in the TOS14519 and TOG7106 genetic backgrounds; all other mQTLs were background specific. We are currently fine-mapping and validating the major effect genomic region on chromosome 4 (qAfRGM4). This is the first report in mapping the genomic regions associated with the AfRGM resistance, and will be highly useful for rice breeders.
authors: Biosciences eastern and central Africa (BecA), Nairobi, Kenya.
authors: Nasser
authors: N
authors: Yao
authors: Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei, Taiwan, ROC.|Institute of Plant Biology, National Taiwan University, Taipei, Taiwan, ROC.
authors: Cheng-Ruei
authors: CR
authors: Lee
authors: Department of Agriculture, Forestry and Nutrition Science, University of Alberta, 4-10 Agriculture/Forestry Centre, Edmonton, Canada.
authors: Kassa
authors: K
authors: Semagn
authors: AfricaRice, 01 BP 2031, Cotonou, Benin.
authors: Mounirou
authors: M
authors: Sow
authors: AfricaRice, PMB 5320, Ibadan, Oyo State, Nigeria.
authors: Francis
authors: F
authors: Nwilene
authors: AfricaRice, 01 BP 2031, Cotonou, Benin.
authors: Olufisayo
authors: O
authors: Kolade
authors: AfricaRice, 01 BP 2031, Cotonou, Benin.
authors: Roland
authors: R
authors: Bocco
authors: AfricaRice, PMB 5320, Ibadan, Oyo State, Nigeria.
authors: Olumoye
authors: O
authors: Oyetunji
authors: Institute for Genome Sciences and Policy, Department of Biology, Duke University, Durham, North Carolina, United States of America.
authors: Thomas
authors: T
authors: Mitchell-Olds
authors: AfricaRice, 01 BP 2031, Cotonou, Benin.
authors: Marie-Noëlle
authors: MN
authors: Ndjiondjop
mesh_terms: D000349:Africa; D000818:Animals; D032461:Chromosomes, Plant; D004175:Diptera; D005828:Genetics, Population; D012275:Oryza / Q000235:genetics* / Q000502:physiology; D010641:Phenotype; D016133:Polymerase Chain Reaction / Q000379:methods; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci