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PMID: 21901547 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

Identification of candidate genes in rice for resistance to sheath blight disease by whole genome sequencing.

TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik ·Vol. 124 ·No. 1 ·2012-01-00 ·Pages 63-74

Silva J, Scheffler B, Sanabria Y, De Guzman C, Galam D, Farmer A, Woodward J, May G, Oard J

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 non-synonymous 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 marker-assisted breeding of rice for sheath blight resistance.

MeSH Terms
Chromosomes, Plant Disease Resistance/genetics Genes, Plant Genome, Plant Genotype Oryza/genetics,microbiology Plant Diseases/genetics,microbiology Polymorphism, Single Nucleotide Rhizoctonia/physiology
Authors & Affiliations
9 authors, click to expand affiliations / ORCID
Silva James
School of Plant, Environmental, and Soil Sciences, Louisiana State University Agricultural Center, 104 Sturgis Hall, Baton Rouge, LA, 70803, USA.
Scheffler Brian
Sanabria Yamid
De Guzman Christian
Galam Dominique
Farmer Andrew
Woodward Jimmy
May Gregory
Oard James
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Article Info
Journal
TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik
Abbr.
Theor Appl Genet
ISSN
1432-2242
DOI
10.1007/s00122-011-1687-4
Published
2012-01-00
Epub
2011-00-07
Pages
63-74
Language
English
Region
Germany
NLM ID
0145600
Subset
IM
External Links
PubMed source DOI: 10.1007/s00122-011-1687-4 View journal details
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