Evaluating haplotype associations for brown planthopper resistance in rice using the HAPLOANNOTATOR bioinformatics tool

Abstract

Abstract Arthropod pests are a major contributor to rice production losses at a global scale and are predicted to increase in severity due to anthropogenic activity. It is generally recognised that an urgent requirement is to understand the genomic basis of crop-insect resistance to develop successful selective crop breeding programs capable of sustainably supporting future generations of human civilization. We evaluated phenotypic assay of rice resistance against its predominant arthropod pest, Nilaparvata lugens (brown planthopper; BPH) in Thailand. Using four geographically distinct BPH populations against a 227 strong rice accession panel, we identified eight key functional gene haplotypes (FGHs) in rice that statistically associate with high BPH resistance. Three of these were shown to associate with high resistance against all populations of examined BPH which likely represents two BPH biotypes. Finally, correlation analyses failed to detect strong signals of FGH pyramiding indicating that identified FGHs may be capable of conferring resistance independently. Our work relies on a newly developed bioinformatics tool, haploAnnotator, that provides graphical and statistical annotation of FGHs and should prove valuable to breeding research among all crops (not only rice) that possess a published genome.