Yao Nasser, Lee Cheng-Ruei, Semagn Kassa, Sow Mounirou, Nwilene Francis, Kolade Olufisayo, Bocco Roland, Oyetunji Olumoye, Mitchell-Olds Thomas, Ndjiondjop Marie-Noëlle
Biosciences eastern and central Africa (BecA), Nairobi, Kenya.
Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei, Taiwan, ROC.
PLoS One. 2016 Aug 10;11(8):e0160749. doi: 10.1371/journal.pone.0160749. eCollection 2016.
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.
非洲稻瘿蚊（AfRGM）是灌溉和低地非洲生态环境中最具破坏性的害虫之一。本研究旨在鉴定三个独立的双亲亲本水稻群体（ITA306xBW348 - 1、ITA306xTOG7106和ITA306xTOS14519）中与非洲稻瘿蚊害虫发生率和抗性相关的数量性状位点（QTL），并进行元QTL（mQTL）分析，以探索是否有任何基因组区域在不同遗传背景下是保守的。对这三个群体独立进行的复合区间作图（CIM）共发现了28个与害虫发生率（12个）和害虫严重程度（16个）相关的QTL。每个群体中与非洲稻瘿蚊抗性相关的QTL数量从ITA306xBW348 - 1群体中的3个到ITA306xTOG7106群体中的8个不等。每个QTL单独解释了1.3%至34.1%的表型变异。非洲稻瘿蚊抗性的主要基因组区域的LOD值和R²分别为60.0和34.1%，位于ITA306xTOS14519群体中第4号染色体上111 cM处（qAfrGM4）。元分析将QTL数量从28个减少到17个mQTLs，每个mQTL解释1.3%至24.5%的表型变异，并将置信区间缩小了2.2 cM。在第1号染色体上只有一个微效mQTL在TOS14519和TOG7106遗传背景中是常见的；所有其他mQTLs都是背景特异性的。我们目前正在对第4号染色体上的主效基因组区域（qAfRGM4）进行精细定位和验证。这是关于绘制与非洲稻瘿蚊抗性相关的基因组区域的首次报道，对水稻育种者将非常有用。
