A novel gene, Pi40(t), linked to the DNA markers derived from NBS-LRR motifs confers broad spectrum of blast resistance in rice

Rice blast disease caused by Magnaporthe grisea is a continuous threat to stable rice production worldwide. In a modernized agricultural system, the development of varieties with broad-spectrum and durable resistance to blast disease is essential for increased rice production and sustainability. In this study, a new gene is identified in the introgression line IR65482-4-136-2-2 that has inherited the resistance gene from an EE genome wild Oryza species, O. australiensis (Acc. 100882). Genetic and molecular analysis localized a major resistance gene, Pi40(t), on the short arm of chromosome 6, where four blast resistance genes (Piz, Piz-5, Piz-t, and Pi9) were also identified, flanked by the markers S2539 and RM3330. Through e-Landing, 14 BAC/PAC clones within the 1.81-Mb equivalent virtual contig were identified on Rice Pseudomolecule3. Highly stringent primer sets designed for 6 NBS-LRR motifs located within PAC clone P0649C11 facilitated high-resolution mapping of the new resistance gene, Pi40(t). Following association analysis and detailed haplotyping approaches, a DNA marker, 9871.T7E2b, was identified to be linked to the Pi40(t) gene at the 70 Kb chromosomal region, and differentiated the Pi40(t) gene from the LTH monogenic differential lines possessing genes Piz, Piz-5, Piz-t, and Pi-9. Pi40(t) was validated using the most virulent isolates of Korea as well as the Philippines, suggesting a broad spectrum for the resistance gene. Marker-assisted selection (MAS) and pathotyping of BC progenies having two japonica cultivar genetic backgrounds further supported the potential of the resistance gene in rice breeding. Our study based on new gene identification strategies provides insight into novel genetic resources for blast resistance as well as future studies on cloning and functional analysis of a blast resistance gene useful for rice improvement.

Comparative analysis of 5,211 leaf ESTs of wild rice (Oryza minuta)

The expressed sequence tags (ESTs) presented in this report are the first transcriptomes of wild rice. A cDNA library was constructed from 4-week-old leaf samples of greenhouse-grown Oryza minuta. The 5,211 cDNA clones of O. minuta represent 3,401 unique sequences, consisting of 2,787 singletons and 614 assembled sequences. Database comparisons of the cDNAs in GenBank's non-redundant databases using BLAST revealed that 4,957 of the 5,211 cDNAs (95.1%) showed a high degree of sequence homology to genes from other organisms. Most of the transcripts identified were genes related to metabolism, energy, protein biosynthesis and subcellular localization. The metabolism and energy categories of the O. minuta ESTs showed a considerably higher gene expression level than those of O. sativa ESTs. These data and genes can be utilized in rice breeding.

Identification of fungal ( Magnaporthe grisea) stress-induced genes in wild rice ( Oryza minuta)

To identify fungal stress-related genes in wild rice, Oryza minuta, we constructed a subtracted library using suppression subtractive hybridization in combination with mirror orientation selection. DNA chips containing 960 randomly selected cDNA clones were applied by reverse Northern analysis to eliminate false positive clones from the library and to prescreen differentially expressed genes. In total, 377 cDNA clones were selected on the basis of their signal intensities and expression ratios. Sequence analyses of these 377 cDNA fragments revealed that 180 of them (47.7%) represented unique genes. Of these 180 cDNAs, 89 clones (49.6%) showed significant homologies to previously known genes, while the remaining 91 did not match any known sequences. The putative functions of the 180 unique ESTs were categorized by aligning them with MIPS data. They were classified into seven different groups using microarray data-derived expression patterns and verified by Northern blotting.

Isolation and determination of anthocyanins in seed coats of black soybean (Glycine max (L.) Merr.)

Anthocyanin pigments in seed coats of black soybean (Glycine max (L.) Merr.) were extracted with 1% HCl-CH(3)OH, and the crude anthocyanin extract was purified by Shepadex LH-20 and Lichroprep RP-18 open-column chromatography. Three major anthocyanins were isolated, and their chemical structures were identified by spectroscopic methods (UV-visible, FABMS, (1)H and (13)C NMR, and by TLC). The complete structures of these anthocyanins were elucidated as delphinidin-3-glucoside, cyanidin-3-glucoside, and petunidin-3-glucoside. Among them, petunidin-3-glucoside was identified as a new anthocyanin in black soybeans. On the basis of RP-HPLC with a UV-vis detector, the contents of delphinidin-3-glucoside, cyanidin-3-glucoside, petunidin-3-glucoside, and total anthocyanins in seed coats of 10 black soybeans were found in the ranges of 0-3.71, 0.94-15.98, 0-1.41, and 1.58-20.18 mg/g, respectively. The results obtained in this study imply that the seed coats of black soybean can be used as a good source for cyanidin-3-glucoside and delphinidin-3-glucoside.