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Carbon isotope discrimination (∆13C) is considered as an index of leaf-level water use efficiency, an important objective for plant breeders seeking to conserve water resources. We report in rice a genetic analysis for ∆13C, leaf structural parameters, gas exchange, stomatal conductance, and leaf abscisic acid (ABA) concentrations. Doubled haploid and recombinant inbred populations, both derived from...
The beet armyworm (Spodoptera exigua) and the rice water weevil (Lissorhoptrus oryzophilus) are two important insect pests in rice production. To identify insect-responsive genes in rice, we performed a deep transcriptome analysis of Nipponbare rice leaves infested with both beet armyworm and water weevil using massively parallel signature sequencing (MPSS). Many antisense, alternative, and novel...
A secreted cellulase of Xanthomonas oryzae pv. oryzae induces innate immune responses in rice including a hypersensitive response (HR) like reaction. Microarray analysis was conducted using RNA isolated 12 h following ClsA treatment of leaves. BLAST searches were performed for the 267 (152 up- and 115 downregulated) differentially expressed (≥2-fold) genes. A number of defense and stress-response...
Diseases caused by fungal and bacterial pathogens like Magnaporthe oryzae and Xanthomonas oryzae pv. oryzae are responsible for considerable yield loss. Up to now, in rice, the modification of the expression of more than 60 genes from diverse origins has shown beneficial effects with respect to disease resistance. In this paper, we review this large set of data to identify the best genes and strategies...
Germin-like protein (GLP) markers were associated with quantitative trait loci (QTL) for resistance to the rice blast pathogen, Magnaporthe oryzae in multiple rice (Oryza sativa) mapping populations. Twelve paralogous OsGLP gene family members are located within the physical QTL region on chromosome 8, and gene silencing studies suggest that they contribute collectively to the resistance phenotype...
WRKY transcription factors regulate diverse plant processes including responses to biotic stresses. Our previous studies indicate that OsWRKY62, an OsWRKY IIa subfamily member, functions as a negative regulator of the rice defense against Xanthomonas oryzae pv. oryzae. Here, we report that a large inverted repeat construct designed to knock down the expression of the four OsWRKY IIa subfamily members...
One of the major challenges in genetics has been to identify the nucleotide polymorphisms responsible for phenotypic variation. Through intensive analysis, several major quantitative trait loci (QTLs) for agronomic traits in rice have been identified and the underlying candidate genes have been delimited. Advanced mapping populations, including chromosome segment substitution lines, have enhanced...
The main objectives of the “Oryza Map Alignment Project” (OMAP) are to characterize the rice genome from a comparative standpoint by establishing a genus-wide and genome-scale comparative framework from representative species. Here, we report our progress in the analyses of these datasets and emerging “comparative phylogenomics” insights into Oryza evolution at two different resolutions—chromosomal...
In plants, polyglutamylated folate forms account for a significant proportion of the total folate pool. Polyglutamylated folate forms are produced by the enzyme folylpolyglutamate synthetase (FPGS). The FPGS enzyme is encoded by two genes in rice, Os03g02030 and Os10g35940. Os03g02030 represents the major expressed form in developing seed. To determine the function of this FPGS gene in rice, a T-DNA...
Iron (Fe) is an important micronutrient for living organisms. Fe deficiency severely impairs plant growth and is a widespread human dietary problem, with particularly high numbers of affected children and females. Rice (Oryza sativa) is a source of energy for more than half of the world’s population. Thus, understanding the mechanisms of Fe uptake and translocation in rice is of utmost importance...
Leaf photosynthesis, an important determinant of yield potential in rice, can be estimated from measurements of chlorophyll content. We searched for quantitative trait loci (QTLs) for Soil and Plant Analyzer Development (SPAD) value, an index of leaf chlorophyll content, and assessed their association with leaf photosynthesis. QTL analysis derived from a cross between japonica cultivar Sasanishiki...
This study characterized Pokkali-derived quantitative trait loci (QTLs) for seedling stage salinity tolerance in preparation for use in marker-assisted breeding. An analysis of 100 SSR markers on 140 IR29/Pokkali recombinant inbred lines (RILs) confirmed the location of the Saltol QTL on chromosome 1 and identified additional QTLs associated with tolerance. Analysis of a series of backcross lines...
Histone modifications play pivotal roles in chromatin remodeling and gene regulation. Rice genome possesses multiple genes encoding different classes of histone modification enzymes. Specific histone modification patterns in rice are associated with either heterochromatic or euchromatic regions or related to gene expression. Functional studies of several rice genes encoding histone deacetylases and...
Over the past two decades, genetic dissection of complex phenotypes of economic and biological interest has revealed the chromosomal locations of many quantitative trait loci (QTLs) in rice and their contributions to phenotypic variation. Mapping resolution has varied considerably among QTL studies owing to differences in population size and number of DNA markers used. Additionally, the same QTLs...
Two types of innate immune receptors, pattern recognition receptors, and resistance proteins, play crucial roles in plant innate immunity; however, the molecules activated by the receptors and how immune responses are transmitted are not well understood. Evidence has been accumulating for a decade that Rac, a small guanosine triphosphatase (GTPase; also known as Rop) belonging to the Rho-type small...
Among the planthoppers of rice, the brown planthopper (BPH) is a major threat to rice production and causes significant yield loss annually. Host-plant resistance is an important strategy to reduce the damage caused by BPH and increase rice productivity. Twenty-one major genes for BPH resistance have been identified by using standard evaluation methods developed at the International Rice Research...
Rice landraces tolerant of up to 2 weeks of complete submergence were collected from farmers’ fields in the 1950s. Success in fine mapping of SUBMERGENCE 1 (SUB1), a robust quantitative trait locus from the submergence tolerant FR13A landrace, has enabled marker-assisted breeding of high-yielding rice capable of enduring transient complete submergence. At the molecular level, SUB1 is a variable polygenic...
The advent of next-generation sequencing technologies opens a new era for discovering genome diversity and genetic mapping. A sequencing-based method was recently developed to genotype recombinant populations with considerably improved resolution and reduced time and cost. To effectively implement this method, here we report the development of an analytic pipeline, sequencing enabled genotyping for...
In rice-consuming countries, specific varieties are recognized as premium, “gold standard” varieties, while others are recognized as being superior but second best, despite being identical using the current suite of tools to evaluate quality. The objectives of this study were to determine if there are distinguishable differences in sensory properties of premium and second best varieties and whether...
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