To identify senescence-associated genes (SAGs) in rice leaves, senescence was induced by transferring rice seedlings into darkness. Senescence up-regulated cDNAs were obtained by PCR-based subtractive hybridization. Among 14 SAG clones characterized, 11 were found to be associated with both dark-induced and natural leaf senescence. Three clones were associated only with dark-induced leaf senescence. The possible physiological roles of these SAGs during rice leaf senescence are discussed.

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SUMMARYRice (Oryza sativa) is one of the world's most important crops. Rice researchers make extensive use of insertional mutants for the study of gene function. Approximately half a million flanking sequence tags from rice insertional mutant libraries are publicly available. However, the relationship between genotype and phenotype is very weak. Transgenic plant assays have been used frequently for complementation, overexpression or antisense analysis, but sequence changes caused by callus growth, Agrobacterium incubation medium, virulence genes, transformation and selection conditions are unknown. We used high-throughput sequencing of DNA from rice lines derived from Tainung 67 to analyze non-transformed and transgenic rice plants for mutations caused by these parameters. For comparison, we also analyzed sequence changes for two additional rice varieties and four T-DNA tagged transformants from the Taiwan Rice Insertional Mutant resource. We identified single-nucleotide polymorphisms, small indels, large deletions, chromosome doubling and chromosome translocations in these lines. Using standard rice regeneration/transformation procedures, the mutation rates of regenerants and transformants were relatively low, with no significant differences among eight tested treatments in the Tainung 67 background and in the cultivars Taikeng 9 and IR64. Thus, we could not conclusively detect sequence changes resulting from Agrobacterium-mediated transformation in addition to those caused by tissue culture-induced somaclonal variation. However, the mutation frequencies within the two publically available tagged mutant populations, including TRIM transformants or Tos17 lines, were about 10-fold higher than the frequency of standard transformants, probably because mass production of embryogenic calli and longer callus growth periods were required to generate these large libraries.

Proteins abundant in seeds during the late stages of development, late embryogenesis abundant (LEA) proteins, are associated with desiccation tolerance. More than 100 of the group I LEA genes, also termed Em genes, have been identified from plants, bacteria and animals. The wide distribution indicates the functional importance of these genes. In the present study, we characterized a novel Em-like gene, OsLEA1a of rice (Oryza sativa). The encoded OsLEA1a protein has an N-terminal sequence similar to that of other plant Em proteins but lacks a 20-mer motif that is the most significant feature of typical Em proteins. The location of the sole intron indicates that the second exon of OsLEA1a is the mutated product of a typical Em gene. Transcriptome analysis revealed OsLEA1a mainly expressed in embryos, with no or only a few transcripts in osmotic stress-treated vegetative tissues. Structural analysis revealed that the OsLEA1a protein adopts high amounts of disordered conformations in solution and undergoes desiccation-induced conformational changes. Macromolecular interaction studies revealed that OsLEA1a protein interacts with non-reducing sugars and phospholipids but not poly-l-lysine. Thus, although the OsLEA1a protein lost its 20-mer motif, it is still involved in the formation of bioglasses with non-reducing sugars or plasma membrane. However, the protein does not function as a chaperone as do other groups of hydrophilic LEA proteins. The orthologs of the OsLEA1a gene had been identified from various grasses but not in dicot plants. Genetic analysis indicated that rice OsLEA1a locates at a 193 kb segment in chromosome 1 and is conserved in several published cereal genomes. Thus, the ancestor of Em-like genes might have evolved after the divergence of monocot plants.

BackgroundGenetic data for traditional Taiwanese (Formosan) agriculture is essential for tracing the origins on the East Asian mainland of the Austronesian language family, whose homeland is generally placed in Taiwan. Three main models for the origins of the Taiwanese Neolithic have been proposed: origins in coastal north China (Shandong); in coastal central China (Yangtze Valley), and in coastal south China. A combination of linguistic and agricultural evidence helps resolve this controversial issue.ResultsWe report on botanically informed linguistic fieldwork of the agricultural vocabulary of Formosan aborigines, which converges with earlier findings in archaeology, genetics and historical linguistics to assign a lesser role for rice than was earlier thought, and a more important one for the millets. We next present the results of an investigation of domestication genes in a collection of traditional rice landraces maintained by the Formosan aborigines over a hundred years ago. The genes controlling awn length, shattering, caryopsis color, plant and panicle shapes contain the same mutated sequences as modern rice varieties everywhere else in the world, arguing against an independent domestication in south China or Taiwan. Early and traditional Formosan agriculture was based on foxtail millet, broomcorn millet and rice. We trace this suite of cereals to northeastern China in the period 6000–5000 BCE and argue, following earlier proposals, that the precursors of the Austronesians, expanded south along the coast from Shandong after c. 5000 BCE to reach northwest Taiwan in the second half of the 4th millennium BCE. This expansion introduced to Taiwan a mixed farming, fishing and intertidal foraging subsistence strategy; domesticated foxtail millet, broomcorn millet and japonica rice; a belief in the sacredness of foxtail millet; ritual ablation of the upper incisors in adolescents of both sexes; domesticated dogs; and a technological package including inter alia houses, nautical technology, and loom weaving.ConclusionWe suggest that the pre-Austronesians expanded south along the coast from that region after c. 5000 BCE to reach northwest Taiwan in the second half of the 4th millennium BCE.Electronic supplementary materialThe online version of this article (10.1186/s12284-018-0247-9) contains supplementary material, which is available to authorized users.