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The herbicide glyphosate became widely used in the United States and other parts of the world after the commercialization of glyphosate-resistant crops. These crops have constitutive overexpression of a glyphosate-insensitive form of the herbicide target site gene, 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS). Increased use of glyphosate over multiple years imposes selective genetic pressure on weed populations. We investigated recently discovered glyphosate-resistant Amaranthus palmeri populations from Georgia, in comparison with normally sensitive populations. EPSPS enzyme activity from resistant and susceptible plants was equally inhibited by glyphosate, which led us to use quantitative PCR to measure relative copy numbers of the EPSPS gene. Genomes of resistant plants contained from 5-fold to more than 160-fold more copies of the EPSPS gene than did genomes of susceptible plants. Quantitative RT-PCR on cDNA revealed that EPSPS expression was positively correlated with genomic EPSPS relative copy number. Immunoblot analyses showed that increased EPSPS protein level also correlated with EPSPS genomic copy number. EPSPS gene amplification was heritable, correlated with resistance in pseudo-F 2 populations, and is proposed to be the molecular basis of glyphosate resistance. FISH revealed that EPSPS genes were present on every chromosome and, therefore, gene amplification was likely not caused by unequal chromosome crossing over. This occurrence of gene amplification as an herbicide resistance mechanism in a naturally occurring weed population is particularly significant because it could threaten the sustainable use of glyphosate-resistant crop technology.5-enolpyruvylshikimate-3-phosphate synthase | herbicide resistance | mobile genetic element | evolution | Palmer amaranth

Rice, the primary source of dietary calories for half of humanity, is the first crop plant for which a high-quality reference genome sequence from a single variety was produced. We used resequencing microarrays to interrogate 100 Mb of the unique fraction of the reference genome for 20 diverse varieties and landraces that capture the impressive genotypic and phenotypic diversity of domesticated rice. Here, we report the distribution of 160,000 nonredundant SNPs. Introgression patterns of shared SNPs revealed the breeding history and relationships among the 20 varieties; some introgressed regions are associated with agronomic traits that mark major milestones in rice improvement. These comprehensive SNP data provide a foundation for deep exploration of rice diversity and gene-trait relationships and their use for future rice improvement.introgression ͉ Oryza sativa ͉ resequencing ͉ SNP discovery T he genomes of domesticated rice, Oryza sativa, contain a wealth of information that can explain the large morphological, physiological, and ecological variation observed in the many varieties cultivated for food. To meet population demands by 2025, rice production must increase by 24% (1). The innovative use of genetic diversity will play a key role in reaching this ambitious goal.The availability of complete genome sequences provides a starting point to understanding the tremendous diversity of the rice gene pool at a fine scale. Among the organisms with a high-quality genome sequence from at least one individual or strain, such as human, mouse, and Arabidopsis, genomewide surveys of SNP variation in small or moderately sized samples have captured significant portions of within-species variation. In human and mouse, for example, a sampling of 71 and 15 individuals captured 80% and 43% of the genotypic variation, respectively (2, 3). In the model plant, Arabidopsis, 20 diverse varieties captured Ͼ90% of the common genotypic variation in the species (4).We initiated the OryzaSNP project (www.OryzaSNP.org) to discover genetic variation within 20 rice varieties and landraces. These varieties, the OryzaSNPset collection (Table S1), are genetically diverse and actively used in international breeding programs because of their wide range of agronomic attributes (5). Most varieties belong to the 2 main groups, indica and japonica, including tropical and temperate japonica, whereas others represent the aus, deep water, and aromatic rice groups. Adapting a hybridization approach previously used for human, mouse, and Arabidopsis (3, 6, 7), we determined SNP variation in 100 Mb of the rice genome, representing Ϸ80% of the nonrepetitive portion of the 390-Mb Nipponbare reference genome (8). Here, we describe the discovery of 159,478 high-quality, nonredundant SNPs distributed across the entire genomes of the OryzaSNPset. Relative to the model dicotyledenous plant Arabidopsis (4), typical haplotype blocks in indica rice varieties are longer (Ϸ200 kb). Observed patterns of shared SNPs among groups indicate introgression caused by rece...

Feeding a growing world population amidst climate change requires optimizing the reliability, resource use, and environmental impacts of food production. One way to assist in achieving these goals is to integrate beneficial plant microbiomes—i.e., those enhancing plant growth, nutrient use efficiency, abiotic stress tolerance, and disease resistance—into agricultural production. This integration will require a large-scale effort among academic researchers, industry researchers, and farmers to understand and manage plant-microbiome interactions in the context of modern agricultural systems. Here, we identify priorities for research in this area: (1) develop model host–microbiome systems for crop plants and non-crop plants with associated microbial culture collections and reference genomes, (2) define core microbiomes and metagenomes in these model systems, (3) elucidate the rules of synthetic, functionally programmable microbiome assembly, (4) determine functional mechanisms of plant-microbiome interactions, and (5) characterize and refine plant genotype-by-environment-by-microbiome-by-management interactions. Meeting these goals should accelerate our ability to design and implement effective agricultural microbiome manipulations and management strategies, which, in turn, will pay dividends for both the consumers and producers of the world food supply.

Rice feeds more than half of the world's population. Rice blast, caused by the fungal pathogen Magnaporthe oryzae, and bacterial blight, caused by the bacterial pathogen Xanthomonas oryzae pv. oryzae, are major constraints to rice production worldwide. Genome sequencing and extensive molecular analysis has led to the identification of many new pathogen-associated molecular patterns (PAMPs) and avirulence and virulence effectors in both pathogens, as well as effector targets and receptors in the rice host. Characterization of these effectors, host targets, and resistance genes has provided new insight into innate immunity in plants. Some of the new findings, such as the binding activity of X. oryzae transcriptional activator-like (TAL) effectors to specific rice genomic sequences, are being used for the development of effective disease control methods and genome modification tools. This review summarizes the recent progress toward understanding the recognition and signaling events that govern rice innate immunity.