Diversity Of Rice Varieties Research Articles

Genetic structure and diversity of indigenous rice (Oryza sativa) varieties in the Eastern Himalayan region of Northeast India

The Eastern Himalayan region of Northeast (NE) India is home to a large number of indigenous rice varieties, which may serve as a valuable genetic resource for future crop improvement to meet the ever-increasing demand for food production. However, these varieties are rapidly being lost due to changes in land-use and agricultural practices, which favor agronomically improved varieties. A detailed understanding of the genetic structure and diversity of indigenous rice varieties is crucial for efficient utilization of rice genetic resources and for developing suitable conservation strategies. To explore the genetic structure and diversity of rice varieties in NE India, we genotyped 300 individuals of 24 indigenous rice varieties representing sali, boro, jum and glutinous types, 5 agronomically improved varieties, and one wild rice species (O. rufipogon) using seven SSR markers. A total of 85 alleles and a very high level of gene diversity (0.776) were detected among the indigenous rice varieties of the region. Considerable level of genetic variation was found within indigenous varieties whereas improved varieties were monoporphic across all loci. The comparison of genetic diversity among different types of rice revealed that sali type possessed the highest gene diversity (0.747) followed by jum (0.627), glutinous (0.602) and boro (0.596) types of indigenous rice varieties, while the lowest diversity was detected in agronomically improved varieties (0.459). The AMOVA results showed that 66% of the variation was distributed among varieties indicating a very high level of genetic differentiation in rice varieties in the region. Two major genetically defined clusters corresponding to indica and japonica groups were detected in rice varieties of the region. Overall, traditionally cultivated indigenous rice varieties in NE India showed high levels of genetic diversity comparable to levels of genetic diversity reported from wild rice populations in various parts of the world. The efforts for conservation of rice germplasm in NE India should consider saving rice varieties representing different types with specific emphasis given to sali and jum types. The protection against the loss of vast genetic diversity found in indigenous rice varieties in NE India is crucial for maintaining future food security in the changing world.Electronic supplementary materialThe online version of this article (doi:10.1186/2193-1801-2-228) contains supplementary material, which is available to authorized users.

Starch of diverse Mexican rice cultivars: physicochemical, structural, and nutritional features

AbstractStructure‐function relationship of rice starch is scarce in the literature. Starch was isolated from diverse Mexican rice varieties and their swelling power (SP), soluble solids (ss), thermal and pasting properties, XRD pattern, in vitro starch digestibility, and AP chain‐length distribution were evaluated. Rice starches with low SP at 60°C had higher temperature and enthalpy of gelatinization. The peak viscosity of rice starches ranged between 2426 and 3519 cP, and the samples presented high values for setback due to the AM content. Rice starches presented the typical A‐type XRD pattern with crystallinity values between 32.7 and 36.3%. Rice starches presented high amounts of short chains (A and B1), and differences were found among the cultivars. AM content for rice starches ranged between 18.4 and 22.9%, and the main fraction recorded by HPSEC was the Fraction III (short chains) with values around 60%. The uncooked rice starch samples presented high values of slowly digestible starch (SDS) and rapidly digestible starch (RDS), and differences were found among the cultivars. In cooked samples decreased SDS and increased RDS and RS. Onset temperature and enthalpy of gelatinization were correlated with the percentage of A‐chains and an opposite pattern was found with the percentage of B1 chains. AP structural characteristics affect the functional, physicochemical, and digestibility properties of rice starches.

Identification of Rice Transcription Factors Associated with Drought Tolerance Using the Ecotilling Method

The drought tolerance (DT) of plants is a complex quantitative trait. Under natural and artificial selection, drought tolerance represents the crop survival ability and production capacity under drought conditions (Luo, 2010). To understand the regulation mechanism of varied drought tolerance among rice genotypes, 95 diverse rice landraces or varieties were evaluated within a field screen facility based on the ‘line–source soil moisture gradient’, and their resistance varied from extremely resistant to sensitive. The method of Ecotype Targeting Induced Local Lesions in Genomes (Ecotilling) was used to analyze the diversity in the promoters of 24 transcription factor families. The bands separated by electrophoresis using Ecotilling were converted into molecular markers. STRUCTURE analysis revealed a value of K = 2, namely, the population with two subgroups (i.e., indica and japonica), which coincided very well with the UPGMA clusters (NTSYS-pc software) using distance-based analysis and InDel markers. Then the association analysis between the promoter diversity of these transcription factors and the DT index/level of each variety was performed. The results showed that three genes were associated with the DT index and that five genes were associated with the DT level. The sequences of these associated genes are complex and variable, especially at approximately 1000 bp upstream of the transcription initiation sites. The study illuminated that association analysis aimed at Ecotilling diversity of natural groups could facilitate the isolation of rice genes related to complex quantitative traits.

Impacts of Seed Clubs in Ensuring Local Seed Systems in the Mekong Delta, Vietnam

The formal seed sector only meets a small proportion of farmers' rice seed requirements in the Mekong Delta, Vietnam. To cope with the growing demands, farmers have organized themselves in seed clubs to produce and supply the needed seeds themselves. This study assesses the status of rice seed production and proposes a model of how to ensure adequate seed supply in the Mekong Delta. Data of total seed production, distribution, prices, and used varieties of each crop season was collected from 19 seed stations and 309 seed clubs in all the 13 provinces of the Delta for the whole year of 2008. One hundred sixty none farmers were interviewed about seed demand and supply. Effective demand of seed in the Mekong Delta was about 0.55 million tons/year. The formal seed system met 3.5% and the informal seed system supplied more 16% of needed amounts. The informal system had significantly lower seed prices, but more diversity of rice varieties than the formal seed system. Both seed systems supplied seeds of rice varieties that had not yet been certified by the formal sector. Thus, new varieties were of high demand. Socialization of seed production was recommended to ensure the local seed supply systems for developing sustainable agriculture in the future. Results of this study indicate status of seed demands and supply to improve and link developing among seed systems in the Mekong Delta.

Genetic Variation in Biomass Traits among 20 Diverse Rice Varieties

Biofuels provide a promising route of producing energy while reducing reliance on petroleum. Developing sustainable liquid fuel production from cellulosic feedstock is a major challenge and will require significant breeding efforts to maximize plant biomass production. Our approach to elucidating genes and genetic pathways that can be targeted for improving biomass production is to exploit the combination of genomic tools and genetic diversity in rice (Oryza sativa). In this study, we analyzed a diverse set of 20 recently resequenced rice varieties for variation in biomass traits at several different developmental stages. The traits included plant size and architecture, aboveground biomass, and underlying physiological processes. We found significant genetic variation among the 20 lines in all morphological and physiological traits. Although heritability estimates were significant for all traits, heritabilities were higher in traits relating to plant size and architecture than for physiological traits. Trait variation was largely explained by variety and breeding history (advanced versus landrace) but not by varietal groupings (indica, japonica, and aus). In the context of cellulosic biofuels development, cell wall composition varied significantly among varieties. Surprisingly, photosynthetic rates among the varieties were inversely correlated with biomass accumulation. Examining these data in an evolutionary context reveals that rice varieties have achieved high biomass production via independent developmental and physiological pathways, suggesting that there are multiple targets for biomass improvement. Future efforts to identify loci and networks underlying this functional variation will facilitate the improvement of biomass traits in other grasses being developed as energy crops.

Capillary electrophoresis for analysis of microheterogeneous glutelin subunits in rice (Oryza sativa L.)

Glutelin, the major storage protein of rice seed, consists of microheterogenous subunits and partially exists in a macromolecular form that is polymerized by intersubunit disulfide bonds. In order to analyze the glutelin subunits using high-throughput CE, we first identified a sample preparation procedure suitable for CE. The polymerized glutelin treated with a reductant could not dissociate into its constituent monomer subunits when it was dissolved in an acidic solution. However, the glutelin dissociated into its subunits and component α and β polypeptides when it was denatured and reduced by an appropriate amount of urea and 2-mercaptoethanol at a specific incubation time and temperature. The molecular species of the completely dissociated α and β polypeptides were identified and quantitatively analyzed by CE using glutelin mutants. The CE analysis also demonstrated that the actual subunit variation in terms of the charge and/or size of the β polypeptides is much smaller than predicted when compared with that of α polypeptides, even under denaturing and reducing condition. Thus, the combined analytical system described here will be useful for basic and applied research, such as the kinetic characterization of higher-order structure and the quantitative evaluation of glutelin in a large number of diverse rice varieties.

SNP haplotypes of the BADH1 gene and their association with aroma in rice (Oryza sativa L.)

Betaine aldehyde dehydrogenase (BADH) is a key enzyme involved in the synthesis of glycinebetaine—a powerful osmoprotectant against salt and drought stress in a large number of species. Rice is not known to accumulate glycinebetaine but it has two functional genes coding for the BADH enzyme. A non-functional allele of the BADH2 gene located on chromosome 8 is a major factor associated with rice aroma. However, similar information is not available regarding the BADH1 gene located on chromosome 4 despite the similar biochemical function of the two genes. Here we report on the discovery and validation of SNPs in the BADH1 gene by re-sequencing of diverse rice varieties differing in aroma and salt tolerance. There were 17 SNPs in introns with an average density of one per 171 bp, but only three SNPs in exons at a density of one per 505 bp. Each of the three exonic SNPs led to changes in amino acids with functional significance. Multiplex SNP assays were used for genotyping of 127 diverse rice varieties and landraces. In total 15 SNP haplotypes were identified but only four of these, corresponding to two protein haplotypes, were common, representing more than 85% of the cultivars. Determination of population structure using 54 random SNPs classified the varieties into two groups broadly corresponding to indica and japonica cultivar groups, aromatic varieties clustering with the japonica group. There was no association between salt tolerance and the common BADH1 haplotypes, but aromatic varieties showed specific association with a BADH1 protein haplotype (PH2) having lysine144 to asparagine144 and lysine345 to glutamine345 substitutions. Protein modeling and ligand docking studies show that these two substitutions lead to reduction in the substrate binding capacity of the BADH1 enzyme towards gamma-aminobutyraldehyde (GABald), which is a precursor of the major aroma compound 2-acetyl-1-pyrroline (2-AP). This association requires further validation in segregating populations for potential utilization in the rice breeding programs.

Rice landrace diversity in Nepal. Socio-economic and ecological factors determining rice landrace diversity in three agro-ecozones of Nepal based on farm surveys

In Nepal, in traditional rice farming systems many diverse landraces are grown in all of the rice agro-ecosystems from low to high altitude. Three case study sites were selected to represent the major rice agro-ecozones: Bara (100–150 m) for the low-altitude terai (plain); Kaski (700–1,206 m) for the mid-hill zone; and Jumla (2,200–3,000 m) for the high-hill zone. The diversity in rice varieties was compared in these three sites and nine survey villages in a series of surveys conducted in 1998, 1999 and 2006. The level and distribution of diversity on farm varied with the physical and socio-economic settings of the farming communities. The mid-hill site (Kaski) had the highest rice landrace diversity. This was adapted to the diverse agro-ecosystems found there and there was equal diversity in Kule khet (irrigated lands by seasonal canals) and Sim khet (marshy wet land). The next most diverse system was Nicha khet (irrigated lowlands) in Bara, the low-altitude site. The high-hill site (Jumla) had the lowest rice diversity. Across all sites many of the landraces were rarely grown and then only in small areas, reflecting the specialized uses to which they were put. At all sites the most common single landrace occupied less than half of the rice area. Resource-rich farmers were the more important custodians of on-farm rice varietal diversity across the sites. There was more rice diversity in favourable environments than in less favourable ones. This was true whether diversity was measured across sites or across rice domains within sites.

Cultivation Practices and Knowledge of Local Rice Varieties among Benuaq Farmers in Muara Lawa District West Kutai, East Kalimantan-Indonesia

This research aim to study how Benuaq society around Muara Lawa District, manage agriculture system and internal knowledge about rice varieties. This research use ethnobotanical approach: collecting ethnobotanical data of rice varieties and traditional system of swidden cultivation. Data was obtained by using direct participatory technique by interviewing the people (key informants) about their practice and perception. The interviews were unstructured open-ended discussion onknowledge and farming activities including about diversity in rice varieties. Subsequently, quantitative data from questionnaires was combined with depth-interview data from key informants. The Benuaq indigenous systems, practices, and cultivation preferences held by the Benuaq are guarded toward maintaining their rice diversity. The Benuaq systems of upland rice cultivation, site selection for umaq establishment, plant species for fertility indicator, and cultivation of wide ranges of upland rice varieties indicate their sophisticate knowledge in agriculture. Unfortunately there has been degradation in the indigenous knowledge among the young Benuaqs.Key words: Benuaq, ethnobotanical, indigenous, upland rice.

Pre-sowing treatment for improving seed quality in West African rice varieties: i. seed germination and vigor

Ten diverse modem West AJrican rice varieties were exposed to six dry heat temperatures (400C, 450C, 500C, 550C, 600C and control (32 0 C) Jor 24 hours and the reaJte r seed germination, speed oj germination and seedling vigor were investigated. Dry heat temperatures significantly stimulated seed germination above the control. Temperatures oj 400C, 450C and 500C significantly promoted seed germination, seedling vigor and speed oj germination oj the rice varieties. Although heat intensities at 550C and 60 0 C had no adverse effects on both seed germination and speed oj germination, 600C heat treatment specifically Jailed to increase seedling vigor. Dry heat temperatures generally promoted seed germination oj TOx 4004 43-12-1 and WITA 12; speed oj germination oj ITA 230 and seedling vigor oj BW348-1, ITA230, SIPI1692033, TOx 4004-43-1-2-1 and WITA 12. There was enhanced seed germination oj WITA 12 at all the heat intensities except at 600C. High dry heat temperatures (500C, 55 0 C and 600C) Jor 24 hours was suffICient to break seed dormancy that promoted seed germinatation in BW 348-1, WITA 1, CISADANE and WAB 189-B-B-B-Hl. Seed dormancy in ITA 230, WITA 12 and TOx 4004-43-1-2-1 was almost completely broken under natural conditions. BenefiCial carry-over effects beyond seed germination and vigor stages uXJUld needJurther investigations.

Rhizosphere dynamics of inoculated cyanobacteria and their growth-promoting role in rice crop.

Nitrogen fixing cyanobacteria are the predominant flora in waterlogged paddy fields which contribute significantly towards nitrogen budgeting in these ecosystems. Their establishment and role in plant growth promotion and soil microbial activity is poorly known. Under greenhouse conditions, pots were inoculated with one of a set of twenty cyanobacterial strains isolated from the rhizosphere of diverse rice and wheat varieties. Several strains established in the soil and persisted up to the harvest stage in soil and roots, significantly enhancing soil microbial biomass carbon, available nitrogen, and related soil microbiological parameters, and increased grain yields and grain weight. This can help in selecting promising strains for developing carrier-based inoculants to promote the growth of crop and soil microflora, leading to enhanced soil fertility and crop yields.

Development of minisatellite markers in phytopathogenic fungus, Magnaporthe grisea

AbstractSixteen polymorphic minisatellite markers suitable for biodiversity and population genetic studies were developed for the phytopathogenic fungus, Magnaporthe grisea. Polymorphism was evaluated using 23 isolates collected from diverse geographical locations and rice varieties in Yunnan Province, China. Each locus had various alleles ranging from three to 16. This is the first description of minisatellite nucleotide sequence from the fungus.

Sequencing Multiple and Diverse Rice Varieties. Connecting Whole-Genome Variation with Phenotypes

The International Rice Functional Genomics Consortium (IRFGC) has initiated a project to provide the rice research community with access to extensive information on genetic variation present within and between diverse rice cultivars and landraces, as well as the genetic resources to exploit that

POTENTIAL FOR UTILISING WILD RICE SPECIES AS SOURCES OF RESISTANCE TO THE WHITEBACKED PLANTHOPPER, SOGATELLA FURCIFERA (HORVATH) (HOMOPTERA: DELPHACIDE)

Three species of wild rice and eight genetically diverse rice varieties were evaluated for resistance to Sogetella furcifera (Horvath) using seedbox screening test. The wild rice species. Oryza officinalis, O, latifolia and O.punctata and eight genetically diverse rice varieties viz., N 22 (Wbph1). ARC 10239 (Wbph2). Pth 33 (Wbph3). Podwi AS (wbph4), N'diang Marie (Whph5) IR 2035-117-3 (Wbph1+ Wbph2). Chaia Anaser (Wbphl+ Whph 3) and TN (no resistance gene) were included in the study. In the free choice screening test, wild rices maintained their extremely high level of resistance even after prolonged exposure to S. furcifera nymphs while plant damage ratings of cultivated rices increased progressively. The quantity of food ingested and assimilated by S. furcifera was significantly less on wild rices than on cultivated varieties. Compared to resistant varieties with diverse genes, S. furcifera caged on wild rices had slow nymphal development, reduced longevity and low fecundity. Egg hatchability was adversely affected on wild rices particularly on O. officinalis. Population growth was also less on wild rices. Steam distillate extracts of wild rices were more toxic to the first instar nymphs of S. furcifera than the extracts of resistant varieties with diverse genes.

Mode of Feeding and Growth of Nephotettix virescens (Homoptera: Cicadellidae) on Selected Resistant and Susceptible Rice Varieties

The feeding activity of a leafhopper, Nephotettix virescens (Distant), on nine genetically diverse rice varieties was monitored with an electronic recording device. The varieties tested were the leafhopper resistant ‘Pankhari 203’ ( Glh 1), ‘ASD7’ ( Glh 2), ‘IR8’ ( Glh 3), ‘Ptb 8’ ( Glh 4), ‘ASD8’ ( Glh 5), ‘IR36’ ( Glh 6), ‘Moddai Karuppan’ ( Glh 7), the highly resistant ‘IR29’ (resistance gene not identified), and the susceptible ‘Taichung Native 1’ (TN1) (no resistance gene). Distinct differences in waveforms for probing, salivation, phloem feeding, and xylem drinking were recorded on resistant and susceptible rice plants. The waveforms indicated that the insect fed primarily from the phloem of susceptible ‘TN1’ plants, but switched to the xylem on resistant varieties. N. virescens made a significantly higher number of brief and repeated probes on resistant varieties than on susceptible ‘TN1’ plants. However, differences in the mean duration of salivation on resistant and susceptible varieties were not associated with resistance. Bulk seedling screening of the test varieties and the insect‘s growth on them were used as criteria for evaluation of resistance to N. virescens for comparison with results of electronic recording.