缺铁水稻根转录本微点阵分析

水稻不仅是非常重要的粮食作物 ,也是用于研究的模式植物之一 .由于水稻基因组测序的完成 ,用功能基因组学的现代方法来研究缺铁相关基因的表达调控是最高效的方法之一。在前期工作的基础上 ,精心设计了缺铁和EDTA鳌合二价铁诱导5天的水稻根实验 ,并进行了转录水平的微点阵 (microarray)分析。但只获得了第 5天的结果。在 10 5 31个水稻cDNA芯片图谱中 ,缺铁和加铁比较发现了 4 5 1个差异点。对缺铁诱导的 4 5 1个差异cDNA逐一地进行NCBI (美国国家生物技术信息中心 )的BLAST(局部定位排列搜索工具 )数据库检索、分析和归类。发现其中缺铁与加铁 ( -Fe/Fe -EDTAratio)之间的相对表达水平(REL)在 2 - 9.175之间的缺铁诱导上调基因为 2 0 3个 ,缺铁诱导的下调基因为 2 4 8个。对每一类上调基因都逐一地进行了NCBI-PubMed的文献检索。利用国际网络数据库进行了功能鉴定。     

Feedback inhibition of photosynthesis in rice measured by O2 dependent transients

The kinetic properties of photosynthesis (both transient and steady-state) were monitored using three non-invasive techniques to evaluate limitations on triose-phosphate (triose-P) conversion to carbohydrate in rice. These included analyzing the O₂ sensitivity of CO₂ fixation and the assimilatory charge (AC) using gas exchange (estimate of the ribulose 1,5- bisphosphate pool) and measuring Photosystem II activity by chlorophyll fluorescence analysis under varying light, temperature and CO₂ partial pressures. Photosynthesis was inhibited transiently upon switching from 20 to 2 kPa O₂ (reversed O₂ sensitivity), the degree of which was correlated with a terminal, steady-state suppression of low O₂ enhancement of photosynthesis. Under current ambient levels of CO₂ and moderate to high light, the transient pattern was more obvious at 18 °C than at 26 °C while at 34 °C no tra nsient response was observed. The transient inhibition at 18 °C ranged from 15% to 31% depending on the pre-measurement temperature. This pattern, symptomatic of feedback, was observed with increasing light and CO₂ partial pressures with the degree of feedback decreasing from moderate (18 °C) up to high temperature (34 °C). Under feedback conditions, the rate of assimilation is shifted from being photorespiration limited to being triose-P utilization limited. Transitory changes in CO₂ assimilation rates (A) under low O₂ indicative of feedback coincided with a transitory drop in assimilatory charge (AC) and inhibition of electron transport. In contrast to previous studies with many C₃ species, our studies indicate that rice shows susceptibility to feedback inhibition under moderate temperatures and current atmospheric levels of CO₂.     

Evolutionary trajectory of phytoalexin biosynthetic gene clusters in rice

Plants frequently possess operon‐like gene clusters for specialized metabolism. Cultivated rice, Oryza sativa, produces antimicrobial diterpene phytoalexins represented by phytocassanes and momilactones, and the majority of their biosynthetic genes are clustered on chromosomes 2 and 4, respectively. These labdane‐related diterpene phytoalexins are biosynthesized from geranylgeranyl diphosphate via ent‐copalyl diphosphate or syn‐copalyl diphosphate. The two gene clusters consist of genes encoding diterpene synthases and chemical‐modification enzymes including P450s. In contrast, genes for the biosynthesis of gibberellins, which are labdane‐related phytohormones, are scattered throughout the rice genome similar to other plant genomes. The mechanism of operon‐like gene cluster formation remains undefined despite previous studies in other plant species. Here we show an evolutionary insight into the rice gene clusters by a comparison with wild Oryza species. Comparative genomics and biochemical studies using wild rice species from the AA genome lineage, including Oryza barthii, Oryza glumaepatula, Oryza meridionalis and the progenitor of Asian cultivated rice Oryza rufipogon indicate that gene clustering for biosynthesis of momilactones and phytocassanes had already been accomplished before the domestication of rice. Similar studies using the species Oryza punctata from the BB genome lineage, the distant FF genome lineage species Oryza brachyantha and an outgroup species Leersia perrieri suggest that the phytocassane biosynthetic gene cluster was present in the common ancestor of the Oryza species despite the different locations, directions and numbers of their member genes. However, the momilactone biosynthetic gene cluster evolved within Oryza before the divergence of the BB genome via assembly of ancestral genes.     

Genome-wide DNA polymorphism and transcriptome analysis of an early-maturing rice mutant

In order to develop a rice population with improved important traits such as flowering time, we developed 2,911 M₂ targeting-induced local lesions in genomes (TILLING) lines by irradiating rice seeds with γ-rays. In all, 15 M₃ lines were obtained from 3 different M₂ lines that exhibited an early-maturing phenotype: these plants matured approximately 25 days faster than wild-type (WT) plants. To identify genome-wide DNA polymorphisms, we performed whole-genome resequencing of both the plant types, i.e., WT and early-maturing TILLING 1 (EMT1), and obtained mapped reads of 118,488,245 bp (99.53 %) and 128,489,860 bp (99.72 %), respectively; Nipponbare was used as the reference genome. We obtained 63,648 and 147,728 single nucleotide polymorphisms (SNPs) and 33,474 and 31,082 insertions and deletions (InDels) for the WT and EMT1, respectively. Interestingly, there was a higher number of SNPs (2.6-fold) and slightly lower number of InDels (0.9-fold) in EMT1 than in WT. The expression of at least 202 structurally altered genes was changed in EMT1, and functional enrichment analysis of these genes revealed that their molecular functions were related to flower development. These results might provide a critical insight into the regulatory pathways of rice flowering.     

Evolutionary history and positional shift of a rice centromere

Rice centromere 8 was previously proposed to be an "immature" centromere that recently arose from a genic region. Our comparative genomics analysis indicates that Cen8 was formed at its current location at least 7-9 million years ago and was physically shifted by a more recent inversion of a segment spanning centromeric and pericentromeric regions.