QTL Mapping in Three Rice Populations Uncovers Major Genomic Regions Associated with African Rice Gall Midge Resistance.
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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.
Published Version (Please cite this version)10.1371/journal.pone.0160749
Publication InfoYao, N; Lee, C-R; Semagn, K; Sow, M; Nwilene, F; Kolade, O; ... Ndjiondjop, M-N (2016). QTL Mapping in Three Rice Populations Uncovers Major Genomic Regions Associated with African Rice Gall Midge Resistance. PLoS One, 11(8). pp. e0160749. 10.1371/journal.pone.0160749. Retrieved from http://hdl.handle.net/10161/14984.
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Newman Ivey White Professor of Biology in Trinity College of Arts and Sciences
We study genetic variation in plant populations, focusing on genes that influence traits controlling plant performance in an environmental context – a central theme throughout our research in natural and agricultural populations. Much of our work is focused on the genes that affect ecological success and evolutionary fitness in natural environments. Similarly, the interaction of crop plants with their biotic and abiotic environments is controlled by complex trait variation which can be elu