Genetics and genomics studies of rice disease resistance and development of alternative disease management methods for bacterial panicle blight and sheath blight

Abstract

Bacterial panicle blight (BPB) and sheath blight (SB), caused by the bacteria Burkholderia glumae and B. gladioli, and the fungus Rhizoctonia solani, respectively, are two major rice diseases in southern rice growing regions of US. No completely resistant rice cultivars have been identified for these diseases. However, a medium-grain cultivar, Jupiter, showed partial resistance to BPB. In order to understand the mechanisms of rice resistance against BPB and SB, rice genetics and genomics studies have been conducted. Alternative methods to suppress BPB and SB were also studied. Broad-sense heritability and correlations were calculated for the traits, BPB and SB disease ratings, days to heading, and plant height, with recombinant inbred lines generated from a cross between Trenasse and Jupiter in replicated trials for two years. Days to heading and plant height had high heritability, and were negatively correlated with BPB and SB disease ratings. The traits with high heritability will not have environmental influence, and can be used as indirect selection tools. Study on genomic characteristics of five rice genotypes grown in Louisiana using their whole genome sequence data provides genome-wide DNA polymorphisms among them. These information will enable us to understand genetic elements for phenotypic variations among these genotypes, which will help to enhance the genetic studies of US rice cultivars. The sequence data were also used to develop microsatellites and single nucleotide polymorphism markers, which can be used for genetic mapping studies. Previous microarray studies showed that the gene encoding a NAC4-like transcription factor, named bacterial panicle blight response gene 1 (BPR1), was highly up-regulated in Jupiter upon B. glumae inoculation. Expression of BPR1 in response to B. glumae was not detected in both Jupiter and Trenasse at seedling and tillering stages. However, rapid induction of BPR1 expression was observed in Jupiter, but not in Trenasse, when it was treated with B. glumae or chemicals, such as ascorbic acid and jasmonic acid, at its heading stage, suggesting that BPR1 expression is tissue-specific, and might be involved in rice defense response against B. gluame. Several rice-associated bacteria (RAB) isolated from healthy rice leaves were tested for their ability to suppress BPB and SB in rice. Those RAB were able to suppress bacterial cell growth and sclerotia germination in vitro, and were able to reduce the BPB and SB symptoms in rice in the field. Based on the 16S rDNA sequencing analysis, those RABs were identified as Bacillus and Lysinibacillus