Update of Genome-Filtered Markers for Complex Rice Disease Resistance in Doubled-Haploid and Backcross Populations

Various strategies such as QTL mapping, genomic selection and genotype by sequencing have been proposed to identify molecular markers and superior individuals for plant improvement. An alternative strategy has recently exploited filtering of genomic data to identify variants associated with Mendelian disorders in humans. Based on success in recent human studies, the objective of our research is to identify nsSNPs and other variants associated with sheath blight (SB) resistance in rice using a modified genomic filtering approach for 13 elite rice lines. Genomic filtering was used to identify variants between contrasting phenotypes for SB resistance with subsequent evaluation in the SB2 doubled haploid segregating population and > 30 inbred lines. Crosses between SB resistant and susceptible varieties were carried out to generate 1866 BC₁F₁ plants that were advanced to create 768 BC₂F₁ populations based on selected markers and whole plant phenotypes. A total of 58 selected lines containing different combinations of putative resistant SB alleles were used to develop > 400 doubled-haploid lines. Future research will focus on evaluation of our doubled-haploids and various inbred lines under different field and greenhouse environments.