Microsatellite Markers Revealed the Genetic Diversity of an Old Japanese Rice Landrace ‘Echizen’

Landraces of rice (Oryza sativa L.) are valuable sources of genetic variation that have been lost in advanced cultivars. Seeds of a rice landrace stored for almost 100 years were found on Sado Island in Niigata prefecture, Japan. This report aims to present basic data on the genetic variation of this landrace, which was known as ‘Echizen’. Five samples of ‘Echizen’, consisting of two old samples, one sample maintained on farm, and two lines regenerated from old seeds were compared with other advanced cultivars and landraces using 19 microsatellite markers. Among the five samples of Echizen, the two stored samples showed greater diversity than the other samples. Cluster analysis based on the UPGMA method also showed that old Echizen was a diverse landrace that could cover the genetic diversity of most Japanese rice cultivars.     

Genetic Erosion from Modern Varieties into Traditional Upland Rice Cultivars (Oryza sativa L.) in Northern Thailand

The purpose of this study was to assess the extent of genetic erosion of traditional upland germplasm in northern Thailand as a result of gene-flow from distinct strains carrying different genotypes. Even modern variety specific markers have not been developed, there is a comparative population in Laos. Thus, both populations were compared with various characters to evaluate gene-flow from modern variety to landraces. Glutinous and glabrous strains are predominated in Laos. However, such strains were drastically decreased in north–east Thailand. Gene diversity is higher in Thailand, compared to Laos at seven isozyme loci. This was a result of the higher frequencies of Indica strains and heterozygotes in Thailand. Plastid type was also determined by using an INDEL marker. Nearly half of Indica strains carried the Japonica plastid. Heterozygotes also tended to carry Japonica cytoplasm. Such nuclear–cytoplasm substituted strains and heterozygotes were probably generated by natural hybridization. Japonica strains tended to be a maternal donor rather than Indica ones. Or Indica strains would easily release pollens, which grow outside of upland fields.     

粳稻资源热粳35遗传图谱构建与耐热QTL分析

为了揭示耐热粳稻资源热粳35的遗传特性,以热粳35/协B F2群体为研究材料,构建了包含140个SSR标记的分子图谱;借助构图分子数据分析标记基因型的分离情况,并进行耐热性QTL分析。结果表明,该图谱覆盖基因组全长2 157.7 c M,标记间平均图距15.4 c M,45个(28.5%)标记极显著偏向亲本或杂合子(P0.01)。在第1、第3、第4、第6、第7和第8号染色体上发现9个偏分离热点区域。其中,有4个偏分离热点区域可能与孢子体或配子体选择有关,在第4、第8和第12号染色体上共检测到3个耐热性QTL。本研究结果为耐热粳稻资源的遗传机理解析和新品种选育提供了参考信息。     

根区一次施氮提高水稻氮肥利用效率的效果和原理

我国水稻氮肥施用量大,农民习惯氮肥表面撒施,氮肥通过氨挥发以及径流等途径损失严重,造成经济损失和环境污染。农村劳动力缺乏,土地流转迅速,省时省力、节肥高效的施肥方式亟待探索和推广。大田条件下,在环太湖水稻高施氮区,比较常规氮肥用量下(225 kg/hm2)的农民习惯分次施用(40%︰30%︰30%分次施用)与根区一次施用(偏根系5 cm,土表下10 cm穴施)两种施肥方式对水稻产量及氮肥利用率的影响。结果表明不种植水稻的前提下,习惯施氮处理表层土壤NH_4~+-N最高,自表层向下逐渐降低,各层养分均随时间推移而下降。根区一次施氮可显著提高施肥点周围土壤中的NH_4~+-N含量及其贮存时间,施肥后30,60和90 d,根区施氮处理NH_4~+-N最高值分别达到542.6、412.1和39.8 mg/kg。且根区一次施氮处理施肥点周围土壤高NH_4~+-N含量至少可保持60 d。种植水稻后,相对习惯分次施氮而言,根区一次施氮显著提高水稻分蘖数、各器官的氮含量、氮积累量及氮肥利用效率。根区一次施氮处理水稻氮积累量高达196.7 kg/hm2,相对习惯施氮增加34.9%。氮肥表观利用率分别达到59.8%(差值法)和42.5%(15N标记法),相对习惯施肥分别增加22.6和30.6个百分点。肥料氮损失由分次施用的73.0%下降到29.7%。根区一次施氮显著增加肥料养分在土壤中的贮存时间,降低肥料养分损失的风险,提高水稻氮肥利用效率,是一种节肥高效的施肥方式,值得进一步研发施肥机械和推广应用。     

Physiological enhancement of early growth of rice seedlings (Oryza sativa L.) by production of phytohormone of N2-fixing methylotrophic isolates

Three plant-growth promoting, N₂-fixing methylotrophic strains isolated from rice cultivars (Oryza sativa L.), viz, Methylobacterium sp. CBMB20, Enterobacter sp. CBMB30, Burkholderia sp. CBMB40, were selected, and their activities in promoting the early growth of rice were studied. Seeds treated with the methylotrophic strains improved seed germination, seedling vigor index (SVI), and biomass of rice seedlings. The methylotrophic population in the treated seedlings increased in the vegetative stages when compared to seeding stages. Treated seedlings showed a higher accumulation of plant hormones viz trans-zeatin riboside, isopentenyladenosine, and indole-3-acetic acid than untreated seedlings. Plant hormones were detected immunologically using the phytodetek kit. Conformational evidence suggested that cytokinins were produced by the epiphytic bacteria colonizing the plants rather than by the plants themselves. In addition, the inoculated early stage rice seedlings also exhibited a wide range of acetylene reduction activity. The results suggest the potential use of these bacteria to stimulate germination, SVI, and biomass production, which is mediated by production of plant hormone accumulation and nitrogen fixation.     

Exploration, collection and characterisation of Basmati rice germplasm in India

Eighty-eight long, slender, scented Basmati rice germplasms were collected from North India during an exploration mission. Morpho-agronomic characterisation of the accessions revealed a significant variability in leaf length, culm length, culm number and panicle length.     

Selection of efficient vesicular-arbuscular mycorrhizal fungi for wetland rice (Oryza sativa L.)

Summary We tested the response of the wetland rice cultivar Prakash to inoculation with ten vescular-arbucular mycorrhizal (VAM) fungi (three selected from the first screening and seven isolated from local paddy fields) in a pot experiment under flooded conditions in order to select the most efficient mycorrhizal fungi to inoculate the rice nursery. A sandy clay loam soil was used as the substrate, fertilized with the recommended N and K levels (100 kg N ha^–1 as ammonium sulphate and 50 kg K ha^–1 as muriate of potash) and half the recommended level of P (25 kg ha^–1 as super phosphate). The inoculation was made into dry nursery beds and the beds were flooded when the seedlings were about 25 cm high, in 15 days. Twenty-eight-day old seedlings were transferred to pots filled with well puddled soil flooded with 5 cm of standing water. Based on the increase in grain yield and total biomass, Glomus intraradices and Acaulospora sp. were considered efficient and suitable for inoculation into rice nurseries.     

Nitrogen contribution to wetland rice by green manuring with Sesbania spp. in an alkaline soil

Summary Two annual species of Sesbania, S. aculeata and Sesbania sp. PL Se-17, were field evaluated as green manure for wetland rice in an alkaline soil. The two species were raised as a catch crop during summer in a wheat-rice rotation, and added as 24.7 and 20.8 t ha^–1 of green matter, 116 and 98 kg N ha^–1, respectively, after 45 days of growth. For the optimum green manuring effect on rice grain yield and N uptake, S. aculeata required 5 days of decomposition (after turning in and before rice transplantation), whereas no decomposition period was necessary for Sesbania sp. PL Se-17. The effect on grain yield and N uptake of rice was equivalent to an application of 122 and 78 kg ha^–1 of chemical N, for the two species, respectively. There was no residual effect of the green manuring on the soil N status after rice harvest.     

Genetic Relationships and Variation among Biotypes of Dallisgrass (Paspalum dilatatum Poir.) and Related Species Using Random Amplified Polymorphic DNA Markers

The genus Paspalum L. consists of more than 400 species. Around twenty-five informal groups of species are recognized in Paspalum and the Dilatata group is of special interest because its members are excellent potential forage grasses. Seventy-five germplasm accessions, representing 15 taxa, were analyzed using randomly amplified polymorphic DNA (RAPD). Polymorphisms were observed with twenty-two primers in the Dilatata group and 16 of those were analyzed. Four hundred and four different RAPD fragments were generated, resulting in an average of 25.2 bands per primer. Among the 404 markers analyzed, 48 (11.88%) were exclusive for the P. dilatatum Poir. biotypes, 31 (7.67%) were exclusive to taxa belonging to other groups included in this study, 28 markers (6.93%) were diagnosed for other species of the Dilatata group and 16 (3.96%), for natural hybrids. Extensive RAPD variation was found among the species studied. Inter- and intra-taxonomic polymorphisms were detected. A dendrogram based on the RAPD data shows some clusters corresponding to the same taxa. However, the biotypes of P. dilatatum do not form a cluster. The present work confirms that the RAPD technique can be used to determine genetic relationships between the taxa belonging to the Dilatata group.     

磷胁迫下蔗糖对水稻苗期根适应性和磷酸转运蛋白基因表达的影响

磷是植物生长和发育中最重要的必须元素之一。尽管土壤中磷资源很丰富,但大部分磷是以植物不能吸收利用的固定态和有机态存在,特别是以酸性土壤为主的南方稻田,水稻缺磷现象非常严重。理解和掌握水稻对低磷的适应机制有助于利用分子手段培育磷高效利用水稻品种。为阐明蔗糖提高水稻耐低磷的机制,本研究对水稻幼苗进行不同磷、糖处理,分析水稻幼苗在不同磷糖配比培养基中的根系结构、无机磷、酸性磷酸酶活性的变化,并利用定量RT-PCR技术分析水稻磷酸转运蛋白基因(OsPT)和酸性磷酸酶基因(OsSAP1)的表达。试验设2个磷浓度:无磷和85 mg·L?1KH2PO4,2个蔗糖浓度:无糖和3%蔗糖,正交设计。结果表明,在低磷胁迫时添加蔗糖,能使水稻幼苗的根总长度、总根数、根冠比显著增加,根分泌的酸性磷酸酶活性降低,但水稻体内的磷酸转运酶活性提高。11个与磷具有高度亲和力的磷酸转运酶的表达发生了改变,其中根优势表达的4个基因OsPT2、OsPT3、OsPT4、OsPT6对磷、糖的影响最为敏感,暗示了蔗糖是通过调节磷转运蛋白维持磷的吸收和平衡。增加根系的蔗糖分配能够提高水稻幼苗对磷胁迫的耐受性。     

Genetic Diversity in Accessions of Wild Rice Oryza granulata from South and Southeast Asia

Oryza granulata, an upland wild rice species, represents an unique germplasm for possessing abilities of tolerance to shade and drought, immune to bacterial blight and resistance to brown planthopper. Although low degree of genetic variability has been revealed within its populations, little genetic information at the species level is available in determining rational conservation strategies. Here we used dominant DNA marker random amplified polymorphism DNA (RAPD) to assess the genetic variability among 23 accessions of O. granulata that collected from main distribution areas worldwide. Twenty decamer primers generated a total of 243 bands, with 83.5% of them (203 bands) being polymorphic. Calculation of Shannon index of diversity revealed an average value of 0.42 ± 0.25, indicating that O. granulata maintains a relatively high degree of genetic diversity on the species level. Analysis of genetic dissimilarity (GD) showed that genetic differentiation occurred among studied accessions, which supports the feasibility of current ex situ conservation strategies. We also suggested that information based on population studies, which could be achieved by international co-operation, is needed to conserve this widespread germplasm more effectively.     

水稻多逆境响应基因OsMsr8的克隆与表达

非生物胁迫是引起全世界作物减产的主要因素, 利用分子生物学技术提高作物耐逆性已成为作物改良的新途径。本课题组采用Affymetrix水稻表达芯片分析了超级稻亲本“培矮64S”全基因组表达模式, 发现了众多逆境相关基因。OsMsr8基因受低温、干旱等多逆境因子诱导, 在孕穗期干旱胁迫下表达水平显著上调。qRT-PCR分析试验数据与芯片结果基本吻合。利用生物信息学方法对所获得序列进行开放阅读框、序列同源性分析, 预测了编码蛋白质产物的理化性质。该基因ORF全长为834 bp, 编码277个氨基酸残基, 不含内含子, 无典型的基因保守结构域。在不同物种中有高相似性的蛋白, 功能未知。对启动子区域进行分析, 发现含有多种与逆境诱导相关的调控元件, 推测该基因与植物耐逆性有一定关系。     

Genetic Effects on Grain Characteristics of <Emphasis Type="Italic">indica</Emphasis> Black Rice and their Useson Indirect Selections for some Mineral Element Contents in Grains

Complete diallel crosses with Oryza sativa L., six varieties of black rice and one variety of aromatic white rice were conducted to study the seed, maternal and cytoplasmic genetic effects on grain characteristics such as 100-grain weight, length, width and shape and their genetic correlations with Fe, Zn, Mn and P mineral contents in kernels by using the genetic model on quantitative traits of seed in parents and their F₁s and F₂s. The seed genetic effects were found more important than the maternal genetic effects for grain characteristics, and seed additive effects constituted a major part of their genetic effects. The heritabilities of seed effects were high for 100-grain weight, width and shape and moderate for grain length. Single seed selection based on the 100-grain weight, width and shape was advocated in early generations, whereas single plant and seed selection based on grain length were advocated in late generations. Significant genetic correlations including seed additive, dominance, cytoplasmic, maternal additive and dominance between 100-grain weight, length, width and shape and Fe, Zn, Mn and P mineral contents were observed. Indirect selection of grain characteristics may be one of the breeding methods to select for higher contents of Fe, Zn, Mn and P in black pericarp indica rice.     

Agro-morphological diversity scenario in upland rice germplasm of Jeypore tract

The Jeypore tract of Orissa is one of the secondary centers of origin of cultivated rice. Recent exploration to that tract has resulted in a collection of 120 accessions of upland rice germplasm. They have been conserved in both National active collection and base collection centres for further utilisation as and when it will be required. Also a historical perspective on the genetical diversity of rice germplasm of the region has been highlighted. The characterization data revealed enormous morphological as well as agronomical variability among the landraces.     

Diversity in Phenotypic Profiles in Landrace Populations of Vietnamese Rice: A Case Study of Agronomic Characters for Conserving Crop Genetic Diversity on Farm

Phenotypic variation of agronomic characters in aromatic rice (Oryza sativa L.) was analyzed in order to elucidate the genetic diversity of the populations of rice landraces. Thirteen populations in Namdinh province, in the Red River Delta of Vietnam, were studied in both of farmers fields and an experimental field. Only small differences were found in agronomic characters among the populations, including populations containing different varieties. Variations among the populations in the frequency distributions of several characters suggested different degrees of diversity among the populations even among populations with the same variety name. The phenotypic profiles of farmers fields were different from those in an experimental field suggesting the environmental differences between them. One variety cultivated in the Myloc district had different phenotypic characters from the other varieties in the Haihau district more clearly in the experimental field. Since the small phenotypic variation in each of farm might be due to the genetic drift and selection by the farmers, on farm conservation of the landraces of rice is considered to be under a force to decrease phenotypic diversity. The present study suggests that the targeting several farms with different phenotypic profiles contribute to the conservation of regional genetic diversity of the landraces of rice.     

RAPD and seed coat morphology variation in annual and perennial species of the genus Cicer L.

Molecular and morphological variation of six perennial and five annual species including domesticated chickpea, C. arietinum, were inferred on the basis of RAPD and S.E.M. seed coat features using three outgroup taxa (Lens ervoides, Lathyrus japonica and Pisum sativum). Of the 66 decamer arbitrary primers tested, eight primers revealed 87 informative fragments. Neighbor-joining cluster analysis using Jaccard's coefficient of similarity on the basis of polymorphic fragments indicated a narrow variation in C. arietinum and recognized two major clusters in the genus Cicer. The first one included four species of sect. Monocicer: C. echinospermum, C. arietinum, C. reticulatum and Iranian material of C. bijugum. The second cluster contained annual and perennial species belonging to sections Chamaecicer, Polycicer and Acanthocicer. The character state of morphological and ecological traits on the RAPD phenogram indicated no monophyletic incision. Our results suggested that the high genetic difference between annual and perennial species might be regarded as a rapid speciation of section Monocicer. Reconsideration of traditional classification of sections Polycicer and Acanthocicer is necessary. The Desi and Kabuli types of C. arietinum could not be separately grouped at the DNA level, and the low level of genetic variation of C. arietinum may result from a bottleneck during the domestication process.     

Origin of Weedy Rice Grown in Bhutan and the Force of Genetic Diversity

In Bhutan, weedy rice (Oryza sativa L.) was grown together with cultivated rice on terraced paddy fields lower than 2620 m above sea level. Seeds of cultivars and weedy strains were collected at 22 collection sites located from 1000 to 2620 m above sea level. Cultivars with round seeds were frequently found in fields higher than 2250 m, and those with slender seeds in fields lower than 1630 m. All cultivars and weedy strains were divided into indica or japonica types by isozyme (multi-locus) and morpho-physiological (multicharacter) analyses. Japonica cultivars predominated in highland; Indica cultivars predominated in lowland. Plastid type was confirmed by the length polymorphism for the ORF100 region. The japonica cultivars carried non-deletion type ORF100. The indica cultivars carried deletion type ORF100. In contrast, weedy strains showed discrepancy in the combination of the nuclear and cytoplasm types. An intermediate type was found in weedy strains for isozyme genotypes. A recombinant type, which has indica genotypes for isozyme analysis with japonica cytoplasm, and vice versa, was frequently found in weedy strains. These findings suggested that weedy strains would be generated by natural hybridization between indica and japonica. Further, they might fail to recombine their prior genotypes sets for isozyme and cytoplasm. Morphophysiological characters did not show such a tendency. Morpho-physiological analysis of highland plants, in particular, showed indica cultivars and weedy strains with japonica cytoplasm. Hypervariable nuclear microsatellite analysis was then used to compare cultivars and weedy strains. Identical alleles were shared between indica and japonica, and also between cultivars and weedy strains. This suggested that there was gene-flow resulting from natural hybridization.     

Denitrification losses from puddled rice soils in the tropics

Summary Although denitrification has long been considered a major loss mechanism for N fertilizer applied to lowland rice (Oryza sativa L.) soils, direct field measurements of denitrification losses from puddled rice soils in the tropics have only been made recently. This paper summarizes the results of direct measurement and indirect estimation of denitrification losses from puddled rice fields and reviews the status of research methodology for measurement of denitrification in rice fields. The direct recovery of (N₂+N₂O)-¹⁵N from ¹⁵N-enriched urea has recently been measured at sites in the Philippines, Thailand, and Indonesia. In all 12 studies, recoveries of (N₂+N₂O)-¹⁵N ranged from less than 0.1 to 2.2% of the applied N. Total gaseous N losses, estimated by the ¹⁵N-balance technique, were much greater, ranging from 10 to 56% of the applied urea-N. Denitrification was limited by the nitrate supply rather than by available C, as indicated by the values for water-soluble soil organic C, floodwater (nitrate+nitrite)-N, and evolved (N₂+N₂O)-¹⁵N from added nitrate. In the absence of runoff and leaching losses, the amount of (N₂+N₂O)-¹⁵N evolved from ¹⁵N-labeled nitrate was consistently less than the unrecovered ¹⁵N in ¹⁵N balances with labeled nitrate, which presumably represented total denitrification losses. This finding indicates that the measured recoveries of (N₂+N₂O)-¹⁵N had underestimated the denitrification losses from urea. Even with a probable two-or threefold underestimation, direct measurements of (N₂+N₂O)-¹⁵N failed to confirm the appreciable denitrification losses often estimated by the indirect difference method. This method, which determines denitrification losses by the difference between total ¹⁵N loss and determined ammonia loss, is prone to high variability. Measurements of nitrate disappearance and ¹⁵N-balance studies suggest that nitrification-denitrification occurs under alternate soil drying and wetting conditions both during the rice cropping period and between rice crops. Research is needed to determine the magnitude of denitrification losses when soils are flooded and puddled for production of rice.     

The Weedy Rice Complex in Costa Rica. I. Morphological Study of Relationships Between Commercial Rice Varieties,Wild <Emphasis Type="Italic">Oryza</Emphasis> Relatives and Weedy Types

Weedy rice is a complex of Oryza morphotypes widely distributed in commercial rice fields, which interfere with rice cultivation, seed production, industrial processing and commercialization of this crop in several countries. The objective of this study was to characterize the weedy rice complex of Costa Rica by comparing it with the cultivated and wild rice species found in the country. A collection of weedy rice accessions, representative of the morphotypes found in the country, was established and characterized. Their morphometric relationships were established by comparing 27 morphological traits with commercial rice cultivars, landraces and wild Oryza species and by performing a multivariate analysis. Twenty-one weedy rice morphotypes were identified among 735 weedy accessions by using a three-digit code based on seed characters. Three principal components (PCs) explained 66.25% of the variation observed. The first PC accounted for 36.21% of the variation and separated CCDD genome type Oryza latifolia and O. grandiglumis from AA genome species O. sativa, O. glumaepatula, O. rufipogon and O. glaberrima. The second (18.9%) and third (11.14%) PCs separated the weedy morphotype groups from the AA genome species O.sativa, O. glaberrima and O. rufipogon. The weedy morphotypes were scattered between the indica commercial rice varieties, the cluster landraces–glaberrima and O. rufipogon. Additionally, a group of morphotypes showed intermediate characteristics between O. sativa and O. rufipogon, suggesting that hybridization could have taken place in the past between these species. None of the morphotypes collected in Costa Rica clustered with the allotetraploids CCDD species or O. glumaepatula.     

Cassava Genetic Resources: Extinct Everywhere in Brazil

Wild cassava, Manihot spp. are sources of many useful characters. Their occurrence in natural habitats is diminishing day after day and a number of them almost have come to extinction. It is suggested that in situ conservation should be followed. It is appealed to concerned authorities to make an effort for their salvation.