Search Results (3)

In direct seeding, hypoxia is a major stress faced by rice plants. Therefore, dissecting the response mechanism of rice to hypoxia stress and the molecular regulatory network is critical to the development of hypoxia-tolerant rice varieties and direct seeding of rice. This review summarizes the morphological, physiological, and ecological changes in rice under hypoxia stress, the discovery of hypoxia-tolerant and germination-related genes/QTLs, and the latest research on candidate genes, and explores the linkage of hypoxia tolerance genes and their distribution in indica and japonica rice through population variance analysis and haplotype network analysis. Among the candidate genes, OsMAP1 is a typical gene located on the MAPK cascade reaction for indica–japonica divergence; MHZ6 is involved in both the MAPK signaling and phytohormone transduction pathway. MHZ6 has three major haplotypes and one rare haplotype, with Hap3 being dominated by indica rice varieties, and promotes internode elongation in deep-water rice by activating the SD1 gene. OsAmy3D and Adh1 have similar indica–japonica varietal differentiation, and are mainly present in indica varieties. There are three high-frequency haplotypes of OsTPP7, namely Hap1 (n = 1109), Hap2 (n = 1349), and Hap3 (n = 217); Hap2 is more frequent in japonica, and the genetic background of OsTPP7 was derived from the japonica rice subpopulation. Further artificial selection, natural domestication, and other means to identify more resistance mechanisms of this gene may facilitate future research to breed superior rice cultivars. Finally, this study discusses the application of rice hypoxia-tolerant germplasm in future breeding research. Full article

SNORKEL1 (SK1) and SNORKEL2 (SK2) are ethylene responsive factors that regulate the internode elongation of deepwater rice in response to submergence. We previously reported that normal cultivated rice lacks SK genes because the Chromosome 12 region containing SK genes was deleted from its genome. However, no study has analyzed how the genome defect occurred in that region by comparing normal cultivated rice and deepwater rice. In this study, comparison of the sequence of the end of Chromosome 12, which contains SK genes, between normal and deepwater rice showed that complicated genome changes such as insertions, deletions, inversions, substitutions, and translocation occurred frequently in this region. In addition to SK1 and SK2 of deepwater rice, gene prediction analysis identified four genes containing AP2/ERF domains in normal cultivated rice and six in deepwater rice; we called these genes SK-LIKE (SKL) genes. SKs and SKLs were present in close proximity to each other, and the SKLs in normal cultivated rice were in tandem. These predicted genes belong to the same AP2/ERF subfamily and were separated into four types: SK1, SK2, SKL3, and SKL4. Sequence comparison indicated that normal cultivated rice possesses a gene with high homology to SK2, which we named SKL1. However, none of the predicted SKLs except for SKL3s were expressed during submergence. Although SKL3s were expressed in both normal and deepwater rice, normal rice does not undergo internode elongation, suggesting that its expression does not contribute to internode elongation. Plants overexpressing SKL1, which showed the most homology to SK2, underwent internode elongation similar to plants overexpressing SK1 and SK2 under normal growth conditions. A yeast one-hybrid assay showed that the C-end of SKL1 has transcription activity, as do the C-ends of SK1 and SK2. Our results suggested that SKLs were derived via gene duplication, but were not expressed and pseudogenized in normal cultivated rice during sequence evolution. Full article

Rice varieties that can survive under submergence conditions respond to flooding either by enhancing internode elongation or by quiescence of shoot elongation. Despite extensive efforts to identify key metabolites triggered by complete submergence of rice possessing SUBMERGENCE 1 (SUB1) locus, metabolic responses of internode elongation of deepwater rice governed by the SNORKEL 1 and 2 genes remain elusive. This study investigated specific metabolomic responses under partial submergence (PS) to deepwater- (C9285) and non-deepwater rice cultivars (Taichung 65 (T65)). In addition, we examined the response in a near-isogenic line (NIL-12) that has a C9285 genomic fragment on chromosome 12 introgressed into the genetic background of T65. Under short-term submergence (0–24 h), metabolite profiles of C9285, NIL-12, and T65 were compared to extract significantly changed metabolites in deepwater rice under PS conditions. Comprehensive metabolite and phytohormone profiling revealed increases in metabolite levels in the glycolysis pathway in NIL-12 plants. Under long-term submergence (0–288 h), we found decreased amino acid levels. These metabolomic changes were opposite when compared to those in flood-tolerant rice with SUB1 locus. Auxin conjugate levels related to stress response decreased in NIL-12 lines relative to T65. Our analysis helped clarify the complex metabolic reprogramming in deepwater rice as an escape strategy. Full article