Wild Rice Oryza Rufipogon Griff Research Articles

Differences Between the Strength of Preference-Performance Coupling in Two Rice Stemborers (Lepidoptera: Pyralidae, Crambidae) Promotes Coexistence at Field-Plot Scales.

Two stem-boring moths, the yellow stemborer (YSB) Scirpophaga incertulas (Walker), and the striped stemborer (SSB), Chilo suppressalis (Walker), damage rice in Asia. YSB is the dominant species in much of tropical Asia. Both species are oligophagous on domesticated and wild rice. We investigated the roles of host plant preferences and larval performance in determining the larval densities of both species in rice plots. In screenhouse experiments, YSB showed significant preference–performance coupling. Adults preferred high-tillering rice varieties during early vegetative growth. In contrast, SSB did not demonstrate oviposition preferences under the same screenhouse conditions, but did oviposit less on the wild rice Oryza rufipogon Griff. than on domesticated rice varieties during a choice experiment. Despite differences in preference–performance coupling, larval survival and biomass across 10 varieties were correlated between the two species. YSB and SSB larvae occurred in relatively high numbers on rice varieties with large tillers (IR70, IR68, and T16) in wet and dry season field experiments. However, whereas YSB was the dominant species on IR68 and IR70, it was relatively less abundant on T16, where SSB dominated. Results suggest that YSB preferentially attacked fast-growing rice varieties with high tiller numbers early in the crop cycle. Meanwhile SSB, which has weak preference–performance coupling, occurred in rice plants with large tillers that were relatively free of YSB later in the crop cycle. These factors may allow the species to coexist. We discuss the implications of proximate and ultimate factors influencing stemborer co-occurrence for the sustainable production of rice in tropical Asia.

Morphological and Molecular Data Reveal Three Distinct Populations of Indian Wild Rice Oryza rufipogon Griff. Species Complex.

Wild relatives of crops possess adaptive mutations for agronomically important traits, which could play significant role in crop improvement for sustainable agriculture. However, global climate change and human activities pose serious threats to the natural habitats leading to erosion of genetic diversity of wild rice populations. The purpose of this study was to explore and characterize India’s huge untapped wild rice diversity in Oryza rufipogon Griff. species complex from a wide range of ecological niches. We made strategic expeditions around diversity hot spots in 64 districts of nine different agro-climatic zones of the country and collected 418 wild rice accessions. Significant variation was observed among the accessions for 46 morphological descriptors, allowing classification into O. nivara, O. rufipogon, and O. sativa f. spontanea morpho-taxonomic groups. Genome-specific pSINE1 markers confirmed all the accessions having AA genome, which were further classified using ecotype-specific pSINE1 markers into annual, perennial, intermediate, and an unknown type. Principal component analysis revealed continuous variation for the morphological traits in each ecotype group. Genetic diversity analysis based on multi-allelic SSR markers clustered these accessions into three major groups and analysis of molecular variance for nine agro-climatic zones showed that 68% of the genetic variation was inherent amongst individuals while only 11% of the variation separated the zones, though there was significant correlation between genetic and spatial distances of the accessions. Model based population structure analysis using genome wide bi-allelic SNP markers revealed three sub-populations designated ‘Pro-Indica,’ ‘Pro-Aus,’ and ‘Mid-Gangetic,’ which showed poor correspondence with the morpho-taxonomic classification or pSINE1 ecotypes. There was Pan-India distribution of the ‘Pro-Indica’ and ‘Pro-Aus’ sub-populations across agro-climatic zones, indicating a more fundamental grouping based on the ancestry closely related to ‘Indica’ and ‘Aus’ groups of rice cultivars. The Pro-Indica population has substantial presence in the Eastern Himalayan Region and Lower Gangetic Plains, whereas ‘Pro-Aus’ sub-population was predominant in the Upper Gangetic Plains, Western Himalayan Region, Gujarat Plains and Hills, and Western Coastal Plains. In contrast ‘Mid-Gangetic’ population was largely concentrated in the Mid Gangetic Plains. The information presented here will be useful in the utilization of wild rice resources for varietal improvement.

Lowered Diversity and Increased Inbreeding Depression within Peripheral Populations of Wild Rice Oryza rufipogon.

BackgroundThe distribution of genetic variability from the interior towards the periphery of a species’ range is of great interest to evolutionary biologists. Although it has been long presumed that population genetic variation should decrease as a species’ range is approached, results of empirical investigations still remain ambiguous. Knowledge regarding patterns of genetic variability as well as affected factors is particularly not conclusive in plants.Methodology/Principal FindingsTo determine genetic divergence in peripheral populations of the wild rice Oryza rufipogon Griff. from China, genetic diversity and population structure were studied in five northern & northeastern peripheral and 16 central populations using six microsatellite loci. We found that populations resided at peripheries of the species possessed markedly decreased microsatellite diversity than those located in its center. Population size was observed to be positively correlated with microsatellite diversity. Moreover, there are significantly positive correlations between levels of microsatellite diversity and distances from the northern and northeastern periphery of this species. To investigate genetic structure and heterozygosity variation between generations of O. rufipogon, a total of 2382 progeny seeds from 186 maternal families were further assayed from three peripheral and central populations, respectively. Peripheral populations exhibited significantly lower levels of heterozygosities than central populations for both seed and maternal generations. In comparisons with maternal samples, significantly low observed heterozygosity (HO) and high heterozygote deficit within populations (FIS) values were detected in seed samples from both peripheral and central populations. Significantly lower observed heterozygosity (HO) and higher FIS values were further observed in peripheral populations than those in central populations for seed samples. The results indicate an excess of homozygotes and thus high inbreeding depression in peripheral populations.Conclusions/SignificanceOur results together suggest that historical contraction of geographical range, demographic changes, and environmental conditions near the northern and northeastern margins of O. rufipogon favor inbreeding and possibly selfing, leading to the rapidly decreased effective population size. Genetic drift, reduced gene flow, and possible local selection, consequently lead to lowered gene diversity, accelerated genetic divergence and increased inbreeding depression found in peripheral populations of O. rufipogon. Given these characteristics observed, northern and northeastern peripheral populations deserve relatively different conservation strategies for either germplasm sampling of ex situ conservation or setting in situ reserves for the adaptation to possible environmental changes and the future germplasm utilization of wild rice.

Morphological characterization of wild rice (Oryza rufipogon Griff.) of NBU campus (West Bengal) for in situ conservation and germplasm enhancement

Asian wild rice Oryza rufipogon Griff. (Poaceae) is considered as a progenitor of the cultivated rice (Oryza sativa L). lt is a source of many biotic and abiotic stress tolerance genes and these are utilized for genetic improvement of cultivated rice. Thus it needs immediate attention with high priority so that we could not loss this agriculturally important Oryza gene pool. Natural population of Oryza rufipogon in the North Bengal University campus is characterized based on phylogeographic and morphological parameters for conservation purposes. Twenty-five plants were considered randomly to measures twenty-six different types of morphological passport data for genetic relatedness analysis within the population. Diagnostic characters are provided to delineate the species morphologically. Plant is annual ecotype having short to intermediate culms height (64 cm-145 cm), and 0.5- 1.6 cm in thickness. Profuse fibrous roots of 2 mm thick and 3-9 cm long creamy-white in colour grows from the floating nodes, node region is solid and pinkish in colour (5-7 mm long). Flag leaf length ranges from 13 cm-40 cm with 0.3 cm 1.8 cm width. Flag leaf blade attitude is varying from deflexed to horizontal to semierect. Auricle was hard, curved, glabrous and 13-15.5 mm in size. Two-cleft ligule length ranges 17 mm to 35 mm. Panicle length varies from 15.4 cm 30 cm with l cm-8 cm wide with 5-13 primary branches. Attitude ofprimary branches is spreading, well exserted (100%), alternately arranged on the wavy axis. Length of the lemma varies 6-11 mm and 1.4-2.3 mm wide, lemma-awn junction marked by a pinkish pubescent constriction with 23-80 mm long red awn. Yellow colour anthers vary in length 4-8 mm long. Stigma was bifurcated (>2 mm) and purple in colour comes out from the spike lets. Seeds (blackish) are harvested during November-December and vary in length (7.5 mm - 10 mm). Density of fertile spikelets ranges from 15 to 82. Grain length/breadth ratio was 3.73 (average) and average kernel length/breadth ratio was 3.99. The results suggest that the population of NBU campus are genetically diversified, heterogeneous and should be conserved in situ to protect this precious genetic resource as separate ecological race (ecotype or intergrade) for germplasm enhancement.

Identification of a Resistance Gene bls1 to Bacterial Leaf Streak in Wild Rice Oryza rufipogon Griff.

Bacterial leaf streak (BLS) of rice, caused by Xanthomonas oryzae pv. oryzicola (Xoc) is a worldwide destructive disease. Development of resistant varieties is considered to be one of the most effective and eco-friendly ways to control the disease. However, only a few genes/QTLs having resistance to BLS have been identified in rice until now. In the present study, we have identified and primarily mapped a BLS-resistance gene, bls1, from a rice line DP3, derived from the wild rice species Oryza rufipogon Griff. A BC2F2 (9311/DP3//9311) population was constructed to map BLS-resistance gene in the rice line DP3. The segregation of the resistant and susceptible plants in BC2F2 in 1:3 ratio (χ2=0.009, χ20.05, 1=3.84, P>0.05), suggested that a recessive gene confers BLS resistance in DP3. In bulked segregant analysis (BSA), two SSR markers RM8116 and RM584 were identified to be polymorphic in resistant and susceptible DNA bulks. For further mapping the resistance gene, six polymorphic markers around the target region were applied to analyze the genotypes of the BC2F2 individuals. As a result, the BLS-resistant gene, designated as bls1, was mapped in a 4.0-cM region flanked by RM587 and RM510 on chromosome 6.

Identification of SUB1A alleles from wild rice Oryza rufipogon Griff.

Submergence stress is a major constraint to rice production in South and Southeast Asia. Most rice (Oryza sativa L.) cultivars die within a week of complete submergence, while a small number of accessions are submergence-tolerant for up to 2 weeks or more. These cultivars have the tolerant allele of the SUB1A gene, one of three ERF genes at this locus on rice chromosome 9. In all O. sativa varieties studied, the SUB1A gene is limited to a subset of indica accessions of O. sativa. Thus far, there has been no published report of the SUB1A gene in wild rice species. Here we report evidence of the SUB1A gene found in wild species of O. rufipogon Griff. accessions by the use of degenerate primers corresponding to the most highly conserved regions of the SUB1 locus. The results indicated that two SUB1A-like alleles, e.g. OrSub1A-1 and OrSub1A-2, were identified from two O. rufipogon accessions. Submergence treatment shows that both of the accessions with SUB1A-like genes were submergence-intolerant. This preliminary study provides insight into the origin and allelic variation of SUB1A, an agronomically important gene that is rapidly being introduced into widely-grown rice cultivars.

Diversity and high nitrogenase activity of endophytic diazotrophs isolated from Oryza rufipogon Griff.

Diversity and nitrogenase activity of endophytic diazotrophs colonized in the wild rice Oryza rufipogon Griff grown in Boluo, Huilai County in Guangdong Province and Lingshui County in Hainan Province were studied. Thirty-seven isolates obtained from Oryza rufipogon were identified as putative endophytic nitrogen-fixing bacteria by ARA (acetylene reduction assay) test and further confirmed by PCR amplification of nifH gene fragments. All obtained strains have ARA activity and the same sized nifH gene fragments. Above the similarity level of 80%, the obtained isolates were assigned as Group I to VIII by the clustering of IS-PCR fingerprints. The SDS-PAGE whole-cell protein patterns were similar to those of IS-PCR fingerprints. Components and contents of fatty acid methyl esters (FAMEs) were used to differentiate the representative strains (Ls13, Ls8, BL1, BL12, HL6, Ls4) from Group I to Group VI. The six representative strains showed significant difference in contents and components of cellular fatty acid methyl ester. 16S rDNA sequencing analysis showed that strains of Group I to VII were located in Enterobacteraceae (γ-proteobacteria). Strains of Group I and Group II were closely related to Klebsiella sp.; Strain Ls8 of Group II was a little far away from the genus of Pantoea (homology level 96% with Pantoea agglomerans), which may represent a new species or genus in Enterobacteraceae; Strains of Groups IV and V belonged to different Enterobacter sp.; Strain Ls4 and Ls 9 representing Group VI were close to Citrobacter amalonaticus with 98% sequence similarity; Strain Ls15 of Group VII showed 98% sequence identity with Pantoea sp.; Strains of Group VIII were assigned to the genus Ideonella (β-proteobacteria). Based on the above results, endophytic diazotrophs isolated from O. rufipogon showed great diversity and some diazotrophs showed high nitrogenase activity with 42.52 μmol/mL·h C2H4. Inoculation to rice tests indicated that the isolated endophytic diazotrophs significantly promoted the rice growth.

Assessment of population genetic structure in common wild rice Oryza rufipogon Griff. using microsatellite and allozyme markers

The genetic structure of five natural populations of common wild rice Oryza rufipogon Griff. from China, was investigated with 21 microsatellite loci and compared to estimates of genetic diversity and genetic differentiation detected by 22 allozyme loci. Microsatellite loci, as expected, have much higher levels of genetic diversity (mean values of A = 3.1, P = 73.3%, Ho = 0.358 and He = 0.345) than allozyme loci (mean values of A = 1.2, P = 12.7%, Ho = 0.020 and He = 0.030). Genetic differentiation detected by microsatellite loci ( FST = 0.468, mean I = 0.472) was higher than that for allozyme loci ( FST =0.388, mean I = 0.976). However, microsatellite markers showed less deviation from Hardy-Weinberg expectation (Wright's inbreeding coefficient FIS = -0.069) than do allozymes ( FIS = 0.337). These results suggest that microsatellite markers are powerful high-resolution tools for the accurate assessment of important parameters in population biology and conservation genetics of O. rufipogon, and offer advantages over allozyme markers.

Genetic erosion in northern marginal population of the common wild rice Oryza rufipogon Griff. and its conservation, revealed by the change of population genetic structure.

In order to monitor genetic erosion within the northern marginal population of common wild rice Oryza rufipogon Griff. from Dongxiang, Jiangxi Province, China, allozyme diversity encoded by 22 loci was analyzed electrophoretically from all the existing subpopulations in 1980, 1985 and 1994. The sample collected from the nine large subpopulations in 1980 showed the highest levels of genetic diversity (A = 1.27, P = 18.20%, Ho = 0.042 and He = 0.049) and a slight deviation from Hardy-Weinberg expectation (F = 0.143), the sample from five moderate ones in 1985 displayed medium levels of genetic diversity (A = 1.14, P = 13.60%, Ho = 0.008 and He = 0.049) and a great deviation from Hardy-Weinberg expectation (F = 0.837), and the sample from two small ones in 1994 demonstrated the lowest levels of genetic diversity (A = 1.09, P = 9.10%, Ho = 0.000 and He = 0.043) and the largest deviation from Hardy-Weinberg expectation (F = 1.000). The results not only documented the genetic erosion stemmed from the extinction of the subpopulations, but also revealed the drastic change of the population genetic structure due to the reduction of the population. Finally, some conservation strategies for the population are proposed.

Allozyme variation and population genetic structure of common wild rice Oryza rufipogon Griff. in China

In order to determine the genetic diversity and genetic structure of populations in common wild rice Oryza rufipogon, an endangered species, allozyme diversity was analyzed using 22 loci in 607 individuals of 21 natural populations from the Guangxi, Guangdong, Hainan, Yunnan, Hunan, Jiangxi and Fujian provinces in China. The populations studied showed a moderate allozyme variability (A=1.33, P=22.7%, Ho=0.033 and He=0.068), which was relatively high for the genus Oryza. The levels of genetic diversity for Guangxi and Guangdong were significantly higher than those for the other regions, and thus South China appeared to be the center of genetic diversity of O. rufipogon in China. A moderate genetic differentiation (FST=0.310, I=0.964) was found among the populations studied. Interestingly, the pattern of population differentiation does not correspond to geographic distance. An estimate of the outcrossing rate (t=0.324) suggests that the species has a typical mixed-mating system. The deficit of heterozygotes (F=0.511) indicates that some inbreeding may have taken place in outcrossing asexual populations because of intra-clone outcrossing events and ”isolation by distance” as a result of human disturbance. In order to predict the long-term genetic survival of fragmented populations, further studies on gene flow among the remaining populations and the genetic effects of fragmentation are proposed. Finally, some implications for the conservation of endangered species are suggested.