A simple extraction method was developed for obtaining the white tip nematode, Aphelenchoides besseyi Christie, from single seeds of rice, Oryza sativa. The method was as follows: Individual rice seeds were split longitudinally and then transferred into single pipet tips. Tips containing a split seed were then singly placed upright in glass vials with water to extract the nematodes. This method...

Miniature inverted-repeat transposable elements (MITEs) are predicted to play important roles on genome evolution. We developed a BLASTN-based approach for de novo identification of MITEs and systematically analyzed MITEs in rice genome. The genome of rice cultivar Nipponbare (Oryza sativa ssp. japonica) harbors 178,533 MITE-related sequences classified into 338 families. Pairwise nucleotide di...

Asian rice, Oryza sativa is a cultivated, inbreeding species that feeds over half of the world's population. Understanding the genetic basis of diverse physiological, developmental, and morphological traits provides the basis for improving yield, quality and sustainability of rice. Here we show the results of a genome-wide association study based on genotyping 44,100 SNP variants across 413 div...

The brassinosteroid-SIGNALING KINASE (BSK) belongs to the receptor-like cytoplasmic kinase XII subgroup. BSK1 regulates development and immunity in Arabidopsis. However, the function of rice (Oryza sativa) BSK1 is largely unknown. Here, we report that the expression level of OsBSK1-2 is induced after a chitin or fagellin22 (flg22) treatment. Silencing OsBSK1-2 in rice results in compromised res...

Rice blast is caused by the fungus Magnaporthe grisea, which elaborates specialized infection cells called appressoria to penetrate the tough outer cuticle of the rice plant Oryza sativa. We found that the formation of an appressorium required, sequentially, the completion of mitosis, nuclear migration, and death of the conidium (fungal spore) from which the infection originated. Genetic interv...

Rice (Oryza sativa), a major staple food, is usually milled to remove the oil-rich aleurone layer that turns rancid upon storage, especially in tropical areas. The remaining edible part of rice grains, the endosperm, lacks several essential nutrients, such as provitamin A. Thus, predominant rice consumption promotes vitamin A deficiency, a serious public health problem in at least 26 countries,...

Rice (Oryza sativa L.) produces diterpene phytoalexins, such as momilactones, oryzalexins, and phytocassanes. Using rice genome information and in vitro assay with recombinant enzymes, we identified genes (OsKS4 and OsKS10) encoding the type-A diterpene cyclases 9beta-pimara-7,15-diene synthase and ent-sandaracopimaradiene synthase which are involved in the biosynthesis of momilactones A, B and...

Genealogical patterns in different genomic regions may be different due to the joint influence of gene flow and selection. The existence of two subspecies of cultivated rice provides a unique opportunity for analyzing these effects during domestication. We chose 66 accessions from the three rice taxa (about 22 each from Oryza sativa indica, O. sativa japonica, and O. rufipogon) for whole-genome...

Rice is an important crop throughout the world and is the staple food for about half the world's population. For better breeding and improved production, we need to know the function of rice molecules which facilitate their function through interactions with each other. The database of interacting proteins in Oryza sativa (DIPOS) provides comprehensive information of interacting proteins in ric...

Sewage sludge at the rate of 0, 40, 80, 120 and 240 t/ha showed that the number of filled grains per panicle, dry weight of grains and weight of 1000 grains of rice (Oryza sativa L.) were the significantly highest where 240 tons of sewage sludge per hectare was added. The contents of N, P, K, Ca, Mg, Fe, Cu, Zn and Pb in rice grains increased significantly with increasing rate of sewage sludge ...