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Title of Journal: Theor Appl Genet

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Abbravation: Theoretical and Applied Genetics

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Springer-Verlag

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DOI

10.1007/978-3-662-43871-8_110

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1432-2242

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Identification of candidate genes in rice for resi

Authors: James Silva Brian Scheffler Yamid Sanabria Christian De Guzman Dominique Galam Andrew Farmer Jimmy Woodward Gregory May James Oard
Publish Date: 2011/09/07
Volume: 124, Issue: 1, Pages: 63-74
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Abstract

Recent advances in whole genome sequencing WGS 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 nonsynonymous SNPs nsSNPs and candidate genes for resistance to sheath blight a disease of worldwide significance WGS by the Illumina GA IIx platform produced an average 5× coverage with ~700 K variants detected per line when compared to the Nipponbare reference genome Two filtering strategies 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 Selected variants associated with resistance were found in 11 of 12 chromosomes More than 200 genes with selected nsSNPs were assigned to 42 categories based on gene family/gene ontology Several candidate genes belonged to families reported in previous studies and three new regions with novel candidates were also identified A subset of 24 nsSNPs detected in 23 genes was selected for further study 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 two accessions of O nivara that suggests sources for resistance occur in additional Oryza sp Results from this study provide a foundation for future basic research and markerassisted breeding of rice for sheath blight resistanceWe thank the RiceCAP project USDA/CSREES Grant 20043531714867 for generation of sequence data generation of the SB5 mapping population and associated QTL data We recognize the Louisiana Rice Research Board for partial funding of this research The Mississippi Rice Promotion Board funded the sequencing of the variety Bowman We acknowledge Dr Georgia Eizenga USDAARS Dale Bumpers National Rice Research Center for her generous gift of DNA isolated from two O nivara accessions

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