Microarray analysis of broad-spectrum resistance derived from an indica cultivar Rathu Heenati

Rathu Heenati (RHT) is a Sri Lankan rice cultivar that carries a brown planthopper (BPH) resistance gene, Bph3, and shows broad-spectrum resistance to all four biotypes of BPH. The BPH-resistance loci in RHT has been studied extensively and assigned to four different rice chromosomes (3, 4, 6, and 10) by different research groups, but the gene has not been cloned previously. An Affymetrix rice genome array containing 48,564 japonica and 1,260 indica sequences was used to analyze the potential resistance-related genes on the four chromosomes by comparative analysis of the differentially expressed genes between resistant and susceptible rice cultivars exposed to BPH attack. The microarray results showed that at least 17 genes related to induced resistance and at least 193 genes related to constitutive resistance in RHT. On chromosome 3, the AOC4 was hypothesized to be the most important candidate gene. On chromosome 6, no valuable candidate resistance gene was identified in the Bph3 localization region. In the three Quantitative trait locus regions of chromosomes 3, 4, and 10, the numbers of constitutive and induced resistance-related genes found were 17, 26, and 12, respectively. The major probe on chromosome 10 represents a constitutive expression gene with a very high absolute fold-change of 2,588.82. The microarray analysis indicated that BPH resistance in RHT is probably controlled by a series of resistance-related genes. This study provides valuable information for cloning, functional analysis and marker-assisted breeding of these BPH resistance genes.