Development, genetic mapping of candidate gene-based markers and their significant association with the shoot fly resistance quantitative trait loci in sorghum [Sorghum bicolor (L.) Moench]

The associations of candidate genes with quantitative trait loci (QTL) for insect resistance provide primary insight into the molecular mechanisms of resistance. The objectives of the present study were to genetically map the candidate genes and identify their association with shoot fly resistance, and update the genetic map with new markers to locate additional QTL. In this study, 80 candidate gene (CG)-based markers were developed, targeting the seven most important shoot fly resistance genomic regions reported in our previous study. Of the 17 polymorphic CGs, the allelic polymorphisms of seven genes were significantly associated with 18 major QTL for component traits of resistance in multiple QTL mapping (MQM), and two genes in the single-marker analysis. MQM with an updated map revealed 20 new QTL with LOD and R ² (%) values ranging from 2.6 to 15.6 and 5.5 to 34.5?%, respectively. The susceptible parent 296B contributed resistance at 10 QTL. Interestingly, an orthologous insect resistance gene Cysteine protease-Mir1 (XnhsbmSFC34/SBI-10), previously presumed to be a CG based on synteny with maize, was significantly associated with major QTL for all traits (except seedling vigor) explaining 22.1?% of the phenotypic variation for deadhearts%, a direct measure of shoot fly resistance. Similarly, a NBS?CLRR gene (XnhsbmSFCILP2/SBI-10), involved in rice brown planthopper resistance, was associated with deadhearts% and number of eggs per plant. Beta-1,3-glucanase (XnhsbmSFC4/SBI-10), involved in aphid and brown planthopper resistance, was associated with deadhearts% and leaf glossiness. Comparative QTL analysis revealed the existence of common QTL for shoot fly and other important sorghum insect pests such as greenbug, head bug, and midge. Finally, the associated CGs should aid in elucidating the molecular basis of resistance, high-resolution mapping, and map-based cloning of major QTL, besides providing powerful gene tags for marker-assisted selection of shoot fly resistance.