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.

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Grain quality plays a crucial economic role for producers, millers, and exporters of rice (Oryza sativa L.). The objective of this research was to develop a japonica‐based rice recombinant inbred line (RIL) mapping population to assist in the identification of genomic regions associated with whole‐grain milling (head rice), five additional seed‐related characters, and two agronomic traits. The ‘Cypress’/‘LaGrue’ mapping population (Reg. No. MP‐4, NSL 466304) was developed under the Rice Coordinated Agricultural Project (RiceCAP) and released by the Louisiana State University Agricultural Center, Baton Rouge, LA in 2009. The mapping population consisted of 298 F2:6 RILs from which a linkage map was constructed using simple sequence repeat (SSR) markers to identify the quantitative trait loci underlying the above mentioned traits. To complement the SSR marker information, the DNA sequence of the two parental nuclear genomes at fivefold coverage has been determined. A database consisting of single nucleotide polymorphisms between the two parents has been posted at a public website. This mapping population and related datasets represent a valuable resource for basic rice genomic and applied marker‐assisted breeding efforts in grain quality and associated traits.

Development of cultivars resistant to sheath blight (SB) disease caused by Rhizoctonia sotaníKuhn is an important breeding objective for the southern U.S. rice (Oryza sativa L.) industry. The aim of this research was to explore performance, genotype (G) and genotype x environment (GE) interactions, and stability for SB resistance of 322 doubled-haploid (DH) lines of the SB2 mapping population produced by the RiceCAP project. Analysis was performed by heritability-adjusted genotype plus genotype x environment interaction (HA-GGE) biplot analysis, Hühn's nonparametric stability statistics, median polish, and additive main effects and multiplicative interaction (AMMI). Genetic material was evaluated in replicated plots for 2 yr (2006 and 2007) in Louisiana and Arkansas. A single mega-environment was identified consisting of the four year-location combinations. Heritability-adjusted genotype plus genotype x environment interaction biplot analyses identified 11 DH lines with high and stable levels of resistance at both locations. Five susceptible DH lines were also identified with greater stability than the susceptible parent used to develop the SB2 population. Results from Hühn's nonparametric approach and median polish complemented those of HA-GGE biplot analysis. Material identified in this study represents a potential source of high and stable SB resistance for eultivar development that warrants additional field-plot evaluation.

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