Physiological basis of salt stress tolerance in rice expressing the antiapoptotic gene SfIAP

Programmed cell death-associated genes, especially antiapoptosis-related genes have been reported to confer tolerance to a wide range of biotic and abiotic stresses in dicotyledonous plants such as tobacco (Nicotiana tabacum L.) and tomato (Solanum lycopersicum L.). This is the first time the antiapoptotic gene SfIAP was transformed into a monocotyledonous representative: rice (Oryza sativa L.). Transgenic rice strains expressing SfIAP were generated by the Agrobacterium-mediated transformation method and rice embryogenic calli, and assessed for their ability to confer tolerance to salt stress at both the seedling and reproductive stages using a combination of molecular, agronomical, physiological and biochemical techniques. The results show that plants expressing SfIAP have higher salt tolerance levels in comparison to the wild-type and vector controls. By preventing cell death at the onset of salt stress and maintaining the cell membrane’s integrity, SfIAP transgenic rice plants can retain plant water status, ion homeostasis, photosynthetic efficiency and growth to combat salinity successfully.

A 3-hour quantitative comparison of glucose-based versus rice-based oral rehydration solution intake by children with diarrhoea in Port Moresby General Hospital

Measurements were made of the intake of a WHO/UNICEF glucose-based and a rice cereal-based oral rehydration solution (ORS) by children with diarrhoea. Twenty children who presented to the Children's Outpatient Department at Port Moresby General Hospital with acute diarrhoea and mild dehydration were randomly assigned to an ORS and measurements were taken over the following 3 hours. For data analysis, the patients were paired by weight. Testing the means of the paired samples by t test showed that there was no significant difference between the amount of rice ORS and the amount of glucose ORS taken over 3 hours. The discovery of oral rehydration solution (ORS) for the treatment of diarrheal disease has been heralded as the most important medical discovery of the century. Cereal-based ORS is able to decrease stool output and the duration of diarrheal illness more than the standard glucose-based ORS, through the increased absorption provided by oligosaccharides without the imposition of a greater osmotic penalty. Moreover, the peptides in cereals enhance amino acid and water absorption, while providing nutritional benefits. UNICEF's glucose-based ORS is becoming more widely used in Papua New Guinea (PNG). 20 children aged 6-37 months (mean age, 15 months) who presented to the Children's Outpatient Department at Port Moresby General Hospital during September-October 1993 with acute diarrhea and mild dehydration were randomly assigned to receive either a rice-based ORS or standard glucose ORS, and measurements were taken over the following 3 hours. The patients were paired by weight for analysis. No statistically significant difference was found between the amount of rice ORS and the amount of glucose ORS taken over 3 hours.

Acceptability of a rice-based oral rehydration solution in Port Moresby General Hospital's Children's Outpatient Department

The guardians of children brought to the Port Moresby General Hospital's Children's Outpatient Department with a chief complaint of diarrhoeal disease were questioned regarding their preference of glucose-based vs rice-based oral rehydration solution (ORS) in order to determine the acceptability of a rice-based ORS. Of the 93 guardians interviewed, greater than 60% preferred the glucose-based solution in its mixability, appearance and taste, and 65% initially reported that their children preferred the taste of the glucose solution. However, after a 30-minute trial, only 58% of children still preferred the glucose solution. In a country where diarrhoeal disease is a leading cause of child death and guardians are the primary health care providers, the acceptability of an ORS is critical to the morbidity and mortality of Papua New Guinea's children. Killing an estimated 2.9 million children annually, diarrheal disease is the second leading cause of child mortality worldwide. Diarrheal disease is also the second leading cause of child mortality in Papua New Guinea (PNG), killing an average 193 inpatient children per year over the period 1984-90. However, despite the high level of diarrhea-related mortality and the proven efficacy of oral rehydration therapy (ORT) in managing diarrhea-related dehydration, standardized ORT has been underutilized in PNG. The current glucose-based oral rehydration solution (ORS) does not reduce the frequency or volume of a child's diarrhea, the most immediate concern of caregivers during episodes of illness. Cereal-based ORS, made from cereals which are commonly available as food staples in most countries, better address the short-term concerns of caregivers while offering a superior nutritional profile. A sample of guardians of children brought to the Port Moresby General Hospital's Children's Outpatient Department complaining of child diarrhea were asked about their preferences on glucose-based versus rice-based ORS in order to determine the acceptability of a rice-based ORS. More than 60% of the 93 guardians interviewed preferred the glucose-based solution for its mixability, appearance, and taste. 65% initially reported that their children preferred the taste of the glucose solution. However, after a 30-minute trial, only 58% of children still preferred the glucose solution.

Rice responses to soil management in a rice-based cropping system in the semi-arid tropics of southern Lombok, Eastern Indonesia

This paper is the first of a series that investigates whether new cropping systems with permanent raised beds (PRBs) or Flat land could be successfully used to increase farmers' incomes from rainfed crops in Lombok in Eastern Indonesia. This paper discusses the rice phase of the cropping system. Low grain yields of dry-seeded rice (Oryza sativa) grown on Flat land on Vertisols in the rainfed region of southern Lombok, Eastern Indonesia, are probably mainly due to (a) erratic rainfall (870-1220 mm/yr), with water often limiting at sensitive growth stages, (b) consistently high temperatures (average maximum - 31 C), and (c) low solar radiation. Farmers are therefore poor, and labour is hard and costly, as all operations are manual. Two replicated field experiments were run at Wakan (annual rainfall = 868 mm) and Kawo (1215 mm) for 3 years (2001/2002 to 2003/2004) on Vertisols in southern Lombok. Dry-seeded rice was grown in 4 treatments with or without manual tillage on (a) PRBs, 1.2 m wide, 200 mm high, separated by furrows 300 mm wide, 200 mill deep, with no rice sown in the well-graded furrows, and (b) well-graded Flat land. Excess surface water was harvested from each treatment and used for irrigation after the vegetative stage of the rice. All operations were manual. There were no differences between treatments in grain yield of rice (mean grain yield = 681 g/m(2)) which could be partly explained by total number of tillers/hill and mean panicle length, but not number of productive tillers/hill, plant height or weight of 1000 grains. When the data from both treatments on PRBs and from both treatments on Flat land, each year at each site were analysed, there were also no differences in grain yield of rice (g/m(2)). When rainfall in the wet season up to harvest was over 1000 mm (Year 2; Wakan, Kawo), or plants were water-stressed during crop establishment (Year 1; Wakan) or during grain-fill (Year 3: Kawo), there were significant differences in grain yield (g/1.5 m(2)) between treatments; generally the grain yield (g/1.5 m(2)) on PRBs with or without tillage was less than that on Flat land with or without tillage. However, when the data from both treatments on PRBs and from both treatments on Flat land, each year at each site, were analysed, the greater grain yield of dry-seeded rice on Flat land (mean yield 1 092 g/1.5 m(2)) than that on PRBs (mean 815 g/1.5 m(2)) was mainly because there were 25% more plants on Flat land. Overall when the data in the 2 outer rows and the 2 inner rows on PRBs were each combined, there was a higher number of productive tillers in the combined outer rows (mean 20.7 tillers/hill) compared with that in the combined inner rows on each PRB (mean 18.2 tillers/hill). However, there were no differences in grain yield between combined rows (mean 142 g/m row). Hence with a gap of 500 mm (the distance between the outer rows of plants on adjacent raised beds), plants did not compensate in grain yield for missing plants in furrows. This suggests that rice (a) also sown in furrows, or (b) sown in 7 rows with narrower row-spacing, or (c) sown in 6 rows with slightly wider row-spacing, and narrower gap between outer rows on adjacent beds, may further increase grain yield (g/1.5 m(2)) in this system of PRBs. The growth and the grain yield (y in g/m(2)) of rainfed rice (with rainfall on-site the only source of water for irrigation) depended mainly on the rainfall (x in mm) in the wet season up to harvest (due either to site or year) with y = 1. 1x -308; r(2) = 0.54; p < 0.005. However, 280 mm (i.e. 32%) of the rainfall was not directly used to produce grain (i.e. when y = 0 g/m(2)). Manual tillage did not affect growth and grain yield of rice (g/m(2); g/1.5 m(2)), either on PRB or on Flat land.

Curvularia tsudae comb. nov. et nom. nov., formerly Pseudocochliobolus australiensis, and a revised synonymy for Curvularia australiensis

Cultures originally identified as Drechslera australiensis, from seeds of Chloris gayana in Japan, were the basis for Tsuda and Ueyama's new combination, Bipolaris australiensis, and its associated sexual morph Pseudocochliobolus australiensis. By studying ex-type materials of both Drechslera australiensis, which was originally isolated from seeds of Oryza sativa in Australia, and Pseudocochliobolus australiensis, we show by morphological and molecular phylogenetic analysis that these two specimens represent different species. Taxonomic confusion is resolved by the transfer of Pseudocochliobolus australiensis to Curvularia tsudae comb. nov. et nom. nov., together with a revised synonymy for Curvularia australiensis. © 2014 The Mycological Society of Japan.

Curvularia tsudae comb. nov. et nom. nov., formerly Pseudocochliobolus australiensis, and a revised synonymy for Curvularia australiensis

Cultures originally identified as Drechslera australiensis, from seeds of Chloris gayana in Japan, were the basis for Tsuda and Ueyama's new combination, Bipolaris australiensis, and its associated sexual morph Pseudocochliobolus australiensis. By studying ex-type materials of both Drechslera australiensis, which was originally isolated from seeds of Oryza sativa in Australia, and Pseudocochliobolus australiensis, we show by morphological and molecular phylogenetic analysis that these two specimens represent different species. Taxonomic confusion is resolved by the transfer of Pseudocochliobolus australiensis to Curvularia tsudae comb. nov. et nom. nov., together with a revised synonymy for Curvularia australiensis.

DNA Free Energy-Based Promoter Prediction and Comparative Analysis of Arabidopsis and Rice Genomes

The cis-regulatory regions on DNA serve as binding sites for proteins such as transcription factors and RNA polymerase. The combinatorial interaction of these proteins plays a crucial role in transcription initiation, which is an important point of control in the regulation of gene expression. We present here an analysis of the performance of an in silico method for predicting cis-regulatory regions in the plant genomes of Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa) on the basis of free energy of DNA melting. For protein-coding genes, we achieve recall and precision of 96% and 42% for Arabidopsis and 97% and 31% for rice, respectively. For noncoding RNA genes, the program gives recall and precision of 94% and 75% for Arabidopsis and 95% and 90% for rice, respectively. Moreover, 96% of the false-positive predictions were located in noncoding regions of primary transcripts, out of which 20% were found in the first intron alone, indicating possible regulatory roles. The predictions for orthologous genes from the two genomes showed a good correlation with respect to prediction scores and promoter organization. Comparison of our results with an existing program for promoter prediction in plant genomes indicates that our method shows improved prediction capability.

Rice LHS1/OsMADS1 Controls Floret Meristem Specification by Coordinated Regulation of Transcription Factors and Hormone Signaling Pathways

SEPALLATA (SEP) MADS box transcription factors mediate floral development in association with other regulators. Mutants in five rice (Oryza sativa) SEP genes suggest both redundant and unique functions in panicle branching and floret development. LEAFY HULL STERILE1/OsMADS1, from a grass-specific subgroup of LOFSEP genes, is required for specifying a single floret on the spikelet meristem and for floret organ development, but its downstream mechanisms are unknown. Here, key pathways and directly modulated targets of OsMADS1 were deduced from expression analysis after its knockdown and induction in developing florets and by studying its chromatin occupancy at downstream genes. The negative regulation of OsMADS34, another LOFSEP gene, and activation of OsMADS55, a SHORT VEGETATIVE PHASE-like floret meristem identity gene, show its role in facilitating the spikelet-to-floret meristem transition. Direct regulation of other transcription factor genes like OsHB4 (a class III homeodomain Leu zipper member), OsBLH1 (a BEL1-like homeodomain member), OsKANADI2, OsKANADI4, and OsETTIN2 show its role in meristem maintenance, determinacy, and lateral organ development. We found that the OsMADS1 targets OsETTIN1 and OsETTIN2 redundantly ensure carpel differentiation. The multiple effects of OsMADS1 in promoting auxin transport, signaling, and auxin-dependent expression and its direct repression of three cytokinin A-type response regulators show its role in balancing meristem growth, lateral organ differentiation, and determinacy. Overall, we show that OsMADS1 integrates transcriptional and signaling pathways to promote rice floret specification and development.

Evaluación de cinco genotipos de arroz en el sistema clearfield, en época de riego en la finca Altamira, San Lorenzo, Boaco

El arroz (Oryza sativa L.) es uno de los cultivos más importantes del sector agropecuario nacional y uno de los principales alimentos en la dieta de los nicaragüenses, entre las limitantes en la producción está la infestación de los campos por malezas, el sistema de producción clearfield es una alternativa para garantizar una desinfección de arroz rojo que causa bajas en el rendimiento y calidad. El objetivo del estudio fue evaluar cinco genotipos de arroz en condiciones de manejo del sistema clearfield en época de riego en la finca Altamira, San Lorenzo, Boaco, Nicaragua. El ensayo se estableció en la Finca Arrocera "Altamira", a una altitud de 340 m.s.n.m, se utilizó un diseño de bloques completos al azar (BCA) con cinco tratamientos (Aitamira-120, CFX-18, IW-888, Puita Guanacaste, y IW-735) en cuatro repeticiones. Las variables evaluadas fueron comportamiento agronómico, presencia de enfermedades y productividad agrícola e industriaL Los resultados encontrados fueron los siguientes; los genotipos de mayor altura fueron IW-735 y Altamira-120; el genotipo Puíta presentó la escala mas alta de acame. No hubo diferencia entre genotipos para la variable macollamiento, el periodo de maduración más corto fue de el genotipo CFX-18 y el más largo Altamira 120. La incidencia de enfermedades Ryzoctonia y Pyricularia en los genotipos fue baja en el periodo del ensayo, el genotipo con mayor rendimiento agrícola e industrial fue IW-888 con 12 600.00 kg ha-1 en campo (Pr :S 0.05~ 0.0012)

Evaluation of Waterhyacinth and Paddy Straw Waste for Culture of Oyster Mushrooms

Waterhyacinth ( Eichhornia crassipes (Mart.) Solms.) was evaluated at ratios of 25, 50 and 75% with paddy straw ( Oryza sativa L.) for oyster mushroom ( Pleurotus sajor-caju) cultivation. There was an increase in yield with decreasing ratio waterhyacinth.

Evaluation of Water hyacinth and Paddy Straw Waste for Culture of Oyster Mushrooms

Waterhyacinth ( Eichhornia crassipes (Mart.) Solms.) was evaluated at ratios of 25, 50 and 75% with paddy straw ( Oryza sativa L.) for oyster mushroom ( Pleurotus sajor-caju) cultivation. There was an increase in yield with decreasing ratio waterhyacinth.

Viability of seeds in food products proposed for field trips in Galapagos

Seeds of 14 plant species extracted from food products proposed for field trips in Galapagos were tested for viability. Strawberry Fragaria ananasa and Blackberry Rubus glaucus jams (Snob and Gustadina brands) contained no viable seeds. Schullo brand granola contained inviable Sesame Sesamum indicum seed, but Sesame in granolas prepared in Galapagos was viable. Sesame seed in bread was viable but Flax Linum usitatissimum seed in bread was not. Brown Rice Oryza sativa and Sunflower seeds Helianthus annuus were both viable. Fresh Apple Malus domestica, Naranjilla Solanum quitoense, Cucumber Cucumis sativus, Pineapple Ananas comosus, Pear Pyrus communis, Bell Pepper Capsicum annuum, Tomato Solanum lycopersicum, Grape Vinis vinifera all contained viable seeds. We recommend prohibiting any product with viable seeds from field trips to uninhabited areas. CDF Contribution Number 1009.

稻属C染色体组物种的群体遗传学和物种形成研究

植物近缘物种系统发育和物种形成过程一直以来都是植物进化生物学研究中最基本的问题之一，是人们理解自然界物种多样性产生和变化的前提。近缘物种间通常形态相似，遗传和分子水平的分化很小且常受诸如渐渗杂交、谱系分选、种内重组等微观进化事件的影响，导致植物近缘物种间系统发育和物种形成过程研究极为困难。在过去十多年中，生物技术的革新和理论方法的发展极大地推动了进化生物学研究，促进了人们对一些重要模式生物与其近缘种间的系统发育关系和物种分化过程的认识，如人、果蝇、线虫、拟南芥和玉米等。然而，迄今在植物中，许多重要类群及其近缘种的系统发育和物种形成过程研究仍不多见，包括在具有特殊重要性的栽培作物中，如稻属（Oryza L.）。由于属内包含有重要粮食作物水稻，稻属向来都是禾本科内备受关注的一个类群。本研究中，我们通过多基因序列的方法，探讨了稻属C染色体组三个近缘二倍体物种的系统发育和物种形成过程，主要研究结果如下。 为选择适宜的实验策略和保证序列数据的真实性，我们利用不同聚合酶扩增自交的栽培稻Oryza sativa ssp. japonica和异交的O. longistaminata不同类型的基因片段，采用克隆测序的方法，评估聚合酶链式扩增反应（PCR）中产生的非真实变异的状况。我们使用exTaq、exTaq和Pfu混和酶和PfuUltraTM酶三种不同聚合酶扩增了Adh1、GPA1和Waxy三个基因片段。在检测到的非真实变异中，PCR 错误的类型主要为单碱基变异和不同等位基因间重组，其中以单碱基变异为主，且突变类型以转换占绝大多数。比较不同酶扩增错误的结果表明，高保真PfuUltraTM酶对PCR反应错误有显著的改善，在扩增产物的单克隆中几乎检测不到PCR噪音，错误率仅为0.0001%，而exTaq和混和酶的错误率分别为0.096%和0.073%。从不同物种比较结果来看，exTaq酶和Pfu酶混用时在自交的O. sativa ssp. japonica内对PCR错误也表现明显的改善，但在异交的O. longistaminata中改善效应不太明显。在三个不同基因位点上，PCR扩增错误出现频率随扩增区域增长而变大。在PfuUltraTM酶的扩增产物中发现重组最少，exTaq和混和酶重组较多，且混和酶对重组改善效果不明显。基于不同聚合酶扩增错误对比研究结果，我们认为，由于能保证序列变异的真实性且不遗漏等位基因，核基因的克隆测序较宜于分离杂合个体中不同的等位基因。 基于随机挑取4个叶绿体和10个核基因位点，利用12份Oryza officinalis、8份O. eichingeri和4份O. rhizomatis材料，对稻属C染色体组三个近缘二倍体物种的系统发育关系作了深入分析。利用不同的系统发育分析方法对单基因位点序列和合并序列数据作了分析，结果表明，稻属C染色体组三个近缘种间呈多歧分支。因此，三个二倍体C染色体组物种可能经快速辐射分化形成。在不同核基因和叶绿体基因的系统发育树中各分支枝长均很短，也表明C染色体组的三个物种可能在较短时期内分化出。不同基因间拓扑结构不一致主要受谱系随机分选的影响。此外，C染色体组不同物种间的种间渐渗和不同等位基因重组对系统发育树的冲突也有影响。值得注意的是，C染色体组三个物种的辐射分化不排除由于相邻两次物种形成事件间隔时间太近、目前数据量不够而无法分辨的可能。在本研究中，我们发现，对于系统发育重建困难的类群，利用等位基因构建物种谱系树有助于挖掘不同基因间结果不一致的因素。 基于10个随机选取的核基因序列数据，利用物种水平的取样方式和群体遗传学分析方法，我们研究了稻属C染色体组三个近缘物种O. officinalis、O. eichingeri和O. rhizomatis的核苷酸多态性，并根据多态性水平和式样，推测了三个近缘种分化的历史。结果表明，在C染色体组的三个近缘种中，仅分布于斯里兰卡的O. rhizomatis的核苷酸多态性水平相对最低（θsil = 0.0038），而间断分布于非洲和斯里兰卡的O. eichingeri最高（θsil = 0.0057）。与被子植物其他类群相比，稻属C染色体组三个物种的核苷酸多态性水平显得较低，O. eichingeri的核苷酸多态性仅约为玉米及其近缘野生种的23-46%和拟南芥的35%。C染色体组内三个野生种相对较低的核苷酸多态性水平可能起因于其较小的祖先有效群体。物种形成模型分析表明，O. officinalis和其近缘种从最近共同祖先分化开后可能经历了居群缩减的历史，且自最近共同祖先分开后，三个物种彼此间并无显著的基因交流。基于分子钟粗略估算了C染色体三个物种分化时间，结果表明，三个物种彼此在很短的时期内分开，约0.63-0.68 Myr。同时，O. eichingeri在非洲和斯里兰卡两个地理宗的分异时间约为0.37 Myr，且推测斯里兰卡的O. eichingeri主要由西非经长距离扩散传播到斯里兰卡。

水稻Phi类谷胱甘肽转移酶基因家族的功能分化研究

在植物中大多数功能基因是以基因家族的形式存在的，而基因重复则是基因家族的一种重要的进化方式。很多基因往往是由重复事件产生形成不同的拷贝，进而分化形成基因家族。谷胱甘肽转移酶（GSTs）是一类古老、庞大、行使解毒、抗逆、信号转导等多种功能的一个基因家族。本研究以栽培水稻（Oryza sativa ssp. japonica c.v. Nipponbare）为研究材料，以栽培水稻的Phi类GST的5个基因（OsGSTF3、OsGSTF6、OsGSTF14、OsGSTF15、OsGSTF16）为研究对象，分析了它们的系统发生和起源历史、不同组织的差异性表达、编码蛋白质的功能差异等问题，探讨了基因重复后5个基因的功能变化，主要结果如下： 1. OsGSTF3、OsGSTF14、OsGSTF15、OsGSTF16由串联重复产生，而OsGSTF6则由DNA转座产生;它们起源时间早在稻属（Oryza）分化之前。 2. 对水稻不同部位组织的RT-PCR结果表明这5个基因在水稻中的特异性表达组织部位有较大差异：OsGSTF3基因在叶、叶鞘、茎、根4个部位均有大量表达;OsGSTF6基因仅在叶中有表达;OsGSTF14基因在叶鞘、茎2个部位中有表达;OsGSTF15基因在茎、根2个部位中有表达;OsGSTF16则在叶、茎、根3个部位中有表达。 3. 将这5个基因连接原核表达载体PET30a并转化大肠杆菌BL21（DE3），获得了高表达菌株。将表达菌株进行大量表达，表达形式分析显示OsGSTF3蛋白是可溶性表达，而其余4个蛋白以包涵体的形式表达。通过亲和层析获得了纯化的OsGSTF3融合蛋白，OsGSTF3融合蛋白对底物CDNB和NBD-Cl具有高活性，酶动力学分析显示OsGSTF3融合蛋白对GSH与NBD-Cl有较高的亲和力，热力学分析显示该蛋白在40℃以下是热稳定的。通过对包涵体进行洗涤、亲和层析获得了纯化的OsGSTF6、OsGSTF14、OsGSTF15、OsGSTF16的融合蛋白，OsGSTF14融合蛋白对NBD-Cl有微弱活性，OsGSTF15融合蛋白对NBC有较高的活性，而没有检测到OsGSTF6与OsGSTF16融合蛋白的活性。