Rice
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...
Repetitive sequences, primarily transposable elements form an indispensable part of eukaryotic genomes. However, little is known about how these sequences originate, evolve and function in context of a genome. In an attempt to address this question, we performed a comparative analysis of repetitive DNA sequences in the genus Oryza, representing ~15 million years of evolution. Both Class I and Class...
Wild species of rice (genus Oryza) contain many useful genes but a vast majority of these genes remain untapped to date because it is often difficult to transfer these genes into cultivated rice (Oryza sativa L.). Chromosome segment substitution lines (CSSLs) and backcross inbred lines (BILs) are powerful tools for identifying these naturally occurring, favorable alleles in unadapted germplasm. In...
Long Terminal Repeat retrotransposons (LTR-RTs) are a major component of several plant genomes. Important insights into the evolutionary dynamics of these elements in a genome are provided by the comparative study of their insertion times. These can be inferred by the comparison of pairs of LTRs flanking intact LTR-RTs in combination with an estimated substitution rate. Over the past several years,...
We present an overview of a research platform that provides essential germplasm, genotypic and phenotypic data and analytical tools for dissecting phenotype–genotype associations in rice. These resources include a diversity panel of 400 Oryza sativa and 100 Oryza rufipogon accessions that have been purified by single seed descent, a custom-designed Affymetrix array consisting of 44,100 SNPs, an Illumina...
Australian Oryza are an understudied and underexploited genetic resource for rice improvement. Four species are indigenous: Oryza rufipogon, Oryza meridionalis, Oryza australiensis are widespread across northern Australia, whereas Oryza officinalis is known from two localities only. Molecular analysis of these wild populations is required to better define the distinctness of the taxa and the extent...
While cultivated rice, Oryza sativa, is arguably the world’s most important cereal crop, there is little comparative morphological information available for the grain of rice wild relatives. In this study, the endosperm of 16 rice wild relatives were compared to O. sativa subspecies indica and O. sativa subspecies japonica using scanning electron microscopy. Although the aleurone, starch granules,...
Zinc (Zn) is an essential micronutrient with numerous cellular functions in plants, and its deficiency represents one of the most serious problems in human nutrition worldwide. Zn deficiency causes a decrease in plant growth and yield. On the other hand, Zn could be toxic if excess amounts are accumulated. Therefore, the uptake and transport of Zn must be strictly regulated. In this review, the dominant...