The Planteome project (http://www.planteome.org) provides a suite of reference and species-specific ontologies for plants and annotations to genes and phenotypes. Ontologies serve as common standards for semantic integration of a large and growing corpus of plant genomics, phenomics and genetics data. The reference ontologies include the Plant Ontology, Plant Trait Ontology and the Plant Experimental Conditions Ontology developed by the Planteome project, along with the Gene Ontology, Chemical Entities of Biological Interest, Phenotype and Attribute Ontology, and others. The project also provides access to species-specific Crop Ontologies developed by various plant breeding and research communities from around the world. We provide integrated data on plant traits, phenotypes, and gene function and expression from 95 plant taxa, annotated with reference ontology terms. The Planteome project is developing a plant gene annotation platform; Planteome Noctua, to facilitate community engagement. All the Planteome ontologies are publicly available and are maintained at the Planteome GitHub site (https://github.com/Planteome) for sharing, tracking revisions and new requests. The annotated data are freely accessible from the ontology browser (http://browser.planteome.org/amigo) and our data repository.

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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Plant breeders rely on molecular markers to guide the selection of traits that are difficult to phenotype or that show wide variation in field trials as they seek to uncover the intricate relationship between an organism's genotype and resulting phenotype. Specificity of molecular markers in wild potato (Solanum spp.) and other less‐adapted germplasm is complicated by the existence of homologous gene clusters. This study examines the consistency and effectiveness of two previously published cleaved amplified polymorphic sequence (CAPS) markers that have been shown to predict Verticillium wilt (VW) resistance. The genome of resistant diploid potato clone C287 was resequenced, and examination of the Ve locus indicated only two homologous regions when compared with the three found in the reference potato genome DM1‐3. The prevalence of each homologous region was examined within a panel of 83 diverse wild potato species. Both structural and genetic sequence variation is predicted to complicate the use of molecular markers developed within specific genetic backgrounds. This study demonstrates that primers designed in the noncoding flanking regions of gene homologs increases specificity and avoids off‐target binding. It is suggested that markers be developed by using more specific primers in these regions coupled with conserved primers within the gene's coding sequence.

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