ARS | Publication request: Identification of Candidate Genes in Rice for Resistance to Sheath Blight Disease by Whole Genome Sequencing

Submitted to: Journal of Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: August 17, 2011
Publication Date: January 12, 2012
Citation: Silva, J., Scheffler, B.E., Sanabria, Y., De Guzman, C., Galam, D., Farmer, A., Woodward, J., May, G., Oard, J. 2012. Identification of Candidate Genes in Rice for Resistance to Sheath Blight Disease by Whole Genome Sequencing. Journal of Theoretical and Applied Genetics. 124(1),pp. 63-74.

Interpretive Summary: The rice genome was sequenced many years ago and technology now allows for relatively cost effective resequencing of important rice cultivars. Using the high quality rice reference genome it is then possible to sequence other varieties using short DNA fragments and compare them to the reference genome. This is very similar to assembling a puzzle by looking at the finished picture on the box cover with the short DNA fragments representing the puzzle pieces. In this study, 13 important rice cultivars were resequenced to a genome equivalent of around 5X genome coverage. The sequences were then compared to the reference genome and differences at the single base pair level were noted. These differences are known as Single Nucleotide Polymorphisms (SNP). SNPs in the area of Sheath Blight resistance (a very important disease in rice production) were noted. This opens the possibility to uncover better DNA markers for breeding purpose, in relation to sheath blight resistance, and may point to the key genes associated with resistance.

Technical Abstract: Recent advances in whole genome sequencing have allowed identification of genes for disease susceptibility in humans. The objective of our research was to exploit whole genome sequences of 13 rice (Oryza sativa L.) inbred lines to identify non-synonymous SNPs (nsSNPs) and candidate genes for resistance to sheath blight, a disease of worldwide significance. Whole genome sequencing by the Illumina GA IIx platform across all lines produced an average 5X coverage with ~ 700 K variants detected per line when compared to the Nipponbare reference genome. Variants were found in 11 of 12 chromosomes. A “common variant” and a “principal component-biplot” filtering strategy were developed to identify nsSNPs between two groups of known resistant and susceptible lines. A total of 333 nsSNPs detected in the resistant lines were absent in the susceptible group. More than 200 genes containing the selected nsSNPs were assigned to 42 categories based on gene family / gene ontology. Several candidate resistance genes belonged to families reported in previous studies, and three new QTL regions with novel candidates were also identified. A subset of 24 nsSNPs detected in 23 genes was selected for further study. All nsSNPs in this subset were found in dbSNP. Individual alleles of the 24 nsSNPs were evaluated by PCR whose presence or absence corresponded to known resistant or susceptible phenotypes of nine additional lines. Sanger sequencing confirmed presence of 12 selected nsSNPs in two lines. “Resistant” nsSNP alleles were detected in an accession of O. nivara that suggests sources for SB resistance may occur in additional Oryza sp. Results from this study provide a foundation for future basic research and marker-assisted breeding of rice lines for sheath blight resistance.