Rice (Oryza sativa) is a staple food for more than half the world and a model for studies of monocotyledonous species, which include cereal crops and candidate bioenergy grasses. A major limitation of crop production is imposed by a suite of abiotic and biotic stresses resulting in 30%–60% yield losses globally each year. To elucidate stress response signaling networks, we constructed an interactome of 100 proteins by yeast two-hybrid (Y2H) assays around key regulators of the rice biotic and abiotic stress responses. We validated the interactome using protein–protein interaction (PPI) assays, co-expression of transcripts, and phenotypic analyses. Using this interactome-guided prediction and phenotype validation, we identified ten novel regulators of stress tolerance, including two from protein classes not previously known to function in stress responses. Several lines of evidence support cross-talk between biotic and abiotic stress responses. The combination of focused interactome and systems analyses described here represents significant progress toward elucidating the molecular basis of traits of agronomic importance.

The rice (Oryza sativa) genome contains 1,429 protein kinases, the vast majority of which have unknown functions. We created a phylogenomic database (http://rkd.ucdavis.edu) to facilitate functional analysis of this large gene family. Sequence and genomic data, including gene expression data and protein-protein interaction maps, can be displayed for each selected kinase in the context of a phylogenetic tree allowing for comparative analysis both within and between large kinase subfamilies. Interaction maps are easily accessed through links and displayed using Cytoscape, an open source software platform. Chromosomal distribution of all rice kinases can also be explored via an interactive interface.

Cloned DNA fragments from 14 characterized maize genes and 91 random fragments used for genetic mapping in maize were tested for their ability to hybridize and detect restriction fragment length polymorphisms in sorghum and other related crop species. Most DNA fragments tested hybridized strongly to DNA from sorghum, foxtail millet, Johnsongrass, and sugarcane. Hybridization to pearl millet DNA was generally weaker, and only a few probes hybridized to barley DNA under the conditions used. Patterns of hybridization of low-copy sequences to maize and sorghum DNA indicated that the two genomes are very similar. Most probes detected two loci in maize; these usually detected two loci in sorghum. Probes that detected one locus in maize generally detected a single locus in sorghum. However, maize repetitive DNA sequences present on some of the genomic clones did not hybridize to sorghum DNA. Most of the probes tested detected polymorphisms among a group of seven diverse sorghum lines tested; over one-third of the probes detected polymorphism in a single F2 population from two of these lines. Cosegregation analysis of 55 F2 individuals enabled several linkage groups to be constructed and compared with the linkage relationships of the same loci in maize. The linkage relationships of the polymorphic loci in the two species were usually conserved, but several rearrangements were detected.The tribe Andropogonae of the Gramineae contains several important crop species of which maize (Zea mays) is the best characterized genetically. Cloned maize DNA fragments that detect polymorphism and have been genetically mapped are available to the public (1-3). These probes have been used to generate a genetic map (1), to estimate evolutionary relationships between related species (4) If most maize restriction fragment length polymorphism (RFLP) probes hybridize sufficiently well to sorghum DNA, then it is possible to construct a genetic map of sorghum that can be directly compared to that of maize. Cloned DNA fragments that hybridize to single sites in the genomes ofboth species can be assumed to have arisen from a single sequence in a common ancestor. The genomic position of such orthologous (6) loci in each of the two species can be compared to outline the chromosomal rearrangements that have occurred during species divergence. Sorghum and maize have the same chromosome number (n = 10), but the nuclear DNA content of maize is over 3 times that of sorghum (7).The utility of genetic mapping in related species with common RFLP probes has been demonstrated in some of the solanaceous crops (6, 8). Tomato (Lycopersicon esculentum), garden pepper (Capsicum annuum), and potato (Solanum tuberosum) all have the same basic chromosome number (n = 12) and the nucleotide sequences of most genes are conserved well enough to permit heterologous hybridization. While few differences were found between the tomato and potato genomes, numerous rearrangements characterized the linkage map of pepper.The present study was undertaken to determine the...