Current advances in sequencing technologies and bioinformatics revealed the genomic background of rice, a staple food for the poor people, and provided the basis to develop large genomic variation databases for thousands of cultivars. Proper analysis of this massive resource is expected to give novel insights into the structure, function, and evolution of the rice genome, and to aid the development of rice varieties through marker assisted selection or genomic selection. In this work we present sequencing and bioinformatics analyses of 104 rice varieties belonging to the major subspecies of Oryza sativa. We identified repetitive elements and recurrent copy number variation covering about 200 Mbp of the rice genome. Genotyping of over 18 million polymorphic locations within O. sativa allowed us to reconstruct the individual haplotype patterns shaping the genomic background of elite varieties used by farmers throughout the Americas. Based on a reconstruction of the alleles for the gene GBSSI, we could identify novel genetic markers for selection of varieties with high amylose content. We expect that both the analysis methods and the genomic information described here would be of great use for the rice research community and for other groups carrying on similar sequencing efforts in other crops.

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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23The genetic arms race between pathogen and host plant is a tug of war that has been ongoing for 24 millennia. The "battles" are those of disruption, restoration of signaling and information 25 transmission on a subcellular level. One such battle occurs between rice an important crop that 26 feeds 50% of the world population and the sheath blight disease (SB) caused by the fungus 27 Rhizoctonia solani. It results in 10 30% global yield loss annually and can reach 50% under 28 severe outbreak. Many Receptor like kinases (RLKs) are recruited as soldiers in these battles. 29 Wall Associated Receptor Kinases (WAKs) a subfamily of receptor-like kinases have been 30 shown to play a role in fungal defense. Here we show that rice gene OsWAK91, present in the 31 major SB resistance QTL region on Chromosome 9 is a key component in defense against rice 32 sheath blight. An SNP mutation C/T separates susceptible variety, Cocodrie (CCDR) from the 33 resistant line MCR010277 (MCR). The resistant allele C results in the stop codon loss that 34 results in 68 amino acids longer C terminus carrying longer protein kinase domain and 35 phosphorylation sites. Our genotype and phenotype analysis of the top 20 individuals of the 36 double haploid SB population shows a strong correlation with the SNP. The susceptible allele 37 appears as a recent introduction found in the japonica subspecies reference genome and a 38 majority of the tropical and temperate japonica lines sequenced by the 3000 rice genome project. 39 Multiple US commercial varieties with japonica background carry the susceptible allele and are 40 known for SB susceptibility. This discovery opens the possibility of introducing resistance 41 alleles into high yielding commercial varieties to reduce yield losses incurred by the disease.42 43 103 point. Expression of known genes from each line, at each time point, was compared in a pairwise 104 fashion against the untreated, Day-0 sample for differential gene expression analysis. For CCDR 105 there were 105, 367 and 377 transcripts from 79, 281 and 320 genes at the Day-0 to Day-1, Day-106 0 to Day-3, and Day-0 to Day-5 comparisons, respectively. Whereas, in the MCR line, there 107 were 148 and 597 transcripts from 119 and 443 genes in the Day-0 to Day-3, and Day-0 to Day-5 108 comparisons, while there were no statistically significant differences in expression observed at 109 Day 0 to 1 (Figure-1B). In the Day-0 to Day-3 comparison, 17 common genes were up-regulated 110 in both the CCDR and MCR lines, and one common gene was down-regulated. Similarly, in the 111 6Day 0 to 5 comparison, 63 common genes in the CCDR and MCR lines were up-regulated, while 112 8 genes were down-regulated ( Figure 1B). In the susceptible CCDR line, there was a larger 113 number of differentially-expressed genes at Day-1, and increasing numberson and Day-3, unlike 114

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