scholarly journals DNA Sequencing and Bioinformatics Analysis of Clone pOr78 from the Species Specific Suppression Subtractive Hybridization Library Constructed from Endemic Wild Rice Species O. rhizomatis

2017 ◽  
Vol 5 (2) ◽  
pp. 133-140
Author(s):  
Gowri Rajkumar ◽  
Jagathpriya Weerasena ◽  
Kumudu Fernando
Keyword(s):  
Wild Rice ◽  
Lipid Transfer Protein ◽  
Subtractive Hybridization ◽  
Lipid Transfer ◽  
Biotic And Abiotic Stress ◽  
Cultivated Rice ◽  
Novel Genes ◽  
Wild Rice Species ◽  
Species Specific ◽  
Ssh Library

Oryza rhizomatis is an endemic wild rice species in Sri Lanka with some unique characteristics of biotic and abiotic stress resistance. Hence characterization of desirable novel genes found in Oryza rhizomatis will be useful for transferring traits to commercial varieties. Therefore, in this study, a species-specific cDNA library was constructed from the wild rice species O. rhizomatis to isolate and characterize novel genes which are specifically present in this species but absent in cultivated rice (Oryza sativa). Forty recombinant clones were randomly selected from the cDNA SSH library and the inserts were sequenced. Sequence analysis of all forty clones indicated that the suppression and hybridization procedures in the library construction were successful as most of the clones have significant alignment with other wild rice species than O. sativa used as a reference cDNA for construction of subtraction library in this study. Therefore the genes which were specifically expressed in the wild rice species O. rhizomatis enriched in the SSH library. From this study it was possible to characterize O. rhizomatis nsLTP1 proteins (non specific Lipid Transfer Protein 1) super family AAI_LTSS which are found to be involved in control of pathogen attack related responses in plants.Int. J. Appl. Sci. Biotechnol. Vol 5(2): 133-140

Origin and evolution of aus type fragrant rice (Oryza sativa L.) : A review

2020 ◽  
Vol 57 (3) ◽  
pp. 169-180
Author(s):  
S Das ◽  
CM Khanda
Keyword(s):  
Wild Rice ◽  
Oryza Sativa L ◽  
Abiotic Stress Tolerance ◽  
Japonica Rice ◽  
Biotic And Abiotic Stress ◽  
Cultivated Rice ◽  
Significant Group ◽  
Origin And Evolution ◽  
Fragrant Rice ◽  
Wild Rice Species

Diversity in wild forms and landraces of a crop in a region is an indicator and the core tenet of determining its centre of origin. Jeypore tract of Odisha with diverse rice forms is considered as the earliest, independent rice domestication region of aus ecotype. The aus group of Asian cultivated rice is a distinct population with unique alleles for biotic and abiotic stress tolerance and high genetic diversity even in its fragrant accessions, detected at the molecular level. Annual wild rice Oryza nivara is considered as the progenitor of aus rice. The aus type fragrant rice is the original crop of Indian sub-continent, domesticated in hill areas by primitive tribes, around 4500 years ago. The Chinese japonica rice which came to India later, inherited chloroplast and nuclear genome from wild aus rice and the resulting hybrids formed the aromatic group. Loss or gain of phenotypic characters is the common feature of evolution. The aus landraces possessing characters such as black hull, red pericarp, poor panicle features, low grain yield, associated with wild rice species have evolved into cultivated forms from the intermediate stages of domestication. Considering the archeological evidences, genetic inferences and correlations of different investigations relating to aus type fragrant rice, Jeypore tract is regarded as the place of origin and evolution of this small but significant group of fragrant rice.

Whole grain morphology of Australian rice species

2009 ◽  
Vol 8 (1) ◽  
pp. 74-81 ◽  
Author(s):  
S. Kasem ◽  
D. L. E. Waters ◽  
N. Rice ◽  
F. M. Shapter ◽  
R. J. Henry
Keyword(s):  
Wild Rice ◽  
Grain Morphology ◽  
Whole Grain ◽  
Cultivated Rice ◽  
Rice Varieties ◽  
Wild Rice Species ◽  
Breeding Programmes ◽  
Standard Classification ◽  
Novel Alleles ◽  
Grain Colour

The grain morphology of 17 wild rice relatives were studied by light and scanning electron microscopy and compared to two cultivated rice varieties (Oryza sativa cv. Nipponbare and O. sativa cv. Teqing). Observations were made of the grain colour, size and shape. Grains from wild rice species exhibited a variety of colours that have potential aesthetic and nutritional value. The grains of these species exhibited a wide array of sizes and shapes, but still fell within the standard classification scale that rice breeders use for routine breeding evaluation. These results highlight the potential of these species as whole grain foods or as sources of novel alleles in conventional rice breeding programmes.

scholarly journals Identification and Expression Analysis of the CsMYB Gene Family in Root Knot Nematode-Resistant and Susceptible Cucumbers

2020 ◽  
Vol 11 ◽  
Author(s):  
Chunyan Cheng ◽  
Qingrong Li ◽  
Xing Wang ◽  
Ying Li ◽  
Chuntao Qian ◽  
...  
Keyword(s):  
Gene Family ◽  
Expression Analysis ◽  
Lipid Transfer Protein ◽  
Major Gene ◽  
Regulation Mechanism ◽  
Lipid Transfer ◽  
Biotic And Abiotic Stress ◽  
Root Knot Nematode ◽  
Element Analysis ◽  
Resistance Response

MYB (myeloblastosis) transcription factors (TFs) play important roles in controlling various physiological processes in plants, such as responses to biotic and abiotic stress, metabolism, and defense. A previous study identified a gene, Csa6G410090, encoding a plant lipid transfer protein (LTP), as a possible regulator in cucumber (Cucumis sativus L.) of the resistance response to root-knot nematode (RKN) [Meloidogyne incognita Kofoid and White (Chitwood)]. Myb-type DNA-binding TFs were presumed to regulate downstream genes expression, including LTPs, however, the regulation mechanism remained unclear. To elucidate whether and which MYB TFs may be involved in regulation of the resistance response, this study identified 112 genes as candidate members of the CsMYB gene family by combining CDD and SMART databases, using the Hidden Markov Model (HMM) and manual calibration. Within this group, ten phylogenetic subgroups were resolved according to sequence-based classification, consistent with results from comprehensive investigation of gene structure, conserved motifs, chromosome locations, and cis-element analysis. Distribution and collinearity analysis indicated that amplification of the CsMYB gene family in cucumber has occurred mainly through tandem repeat events. Spatial gene expression analysis showed that 8 CsMYB genes were highly expressed at differing levels in ten different tissues or organs. The roots of RKN-resistant and susceptible cucumbers were inoculated with M. incognita, finding that CsMYB (Csa6G538700, Csa1G021940, and Csa5G641610) genes showed up-regulation coincident with upregulation of the “hub” gene LTP (Csa6G410090) previously implicated as a major gene in the resistance response to RKN in cucumber. Results of this study suggest hypotheses regarding the elements and regulation of the resistant response as well as possible RKN resistance-enhancing strategies in cucumber and perhaps more broadly in plants.

scholarly journals Enhancement of Rice Leaf Photosynthesis by Crossing between Cultivated Rice,Oryza sativaand Wild Rice Species,Oryza rufipogon

2004 ◽  
Vol 7 (3) ◽  
pp. 252-259 ◽  
Author(s):  
Chisato Masumoto ◽  
Takashige Ishii ◽  
Sono Kataoka ◽  
Tomoko Hatanaka ◽  
Naotsugu Uchida
Keyword(s):  
Wild Rice ◽  
Oryza Rufipogon ◽  
Leaf Photosynthesis ◽  
Cultivated Rice ◽  
Rice Leaf ◽  
Wild Rice Species

scholarly journals Comparison between wild and related cultivated rice species reveals strong impacts of crop domestication on methane metabolism of the rhizomicrobiome

2020 ◽  
Author(s):  
Lei Tian ◽  
Jingjing Chang ◽  
Shaohua Shi ◽  
Li Ji ◽  
Jianfeng Zhang ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Carbon Metabolism ◽  
Methane Production ◽  
Wild Rice ◽  
Nucleotide Metabolism ◽  
Cultivated Rice ◽  
Wild Rice Species ◽  
Methane Metabolism ◽  
First Time ◽  
Rice Domestication

Abstract Background Rice root-inhabited microbial communities are seriously affected by domestication as evidenced by comparing the rhizomicrobiomes of wild and related cultivated rice species. While earlier studies focused on the structures of the rhizomicrobiomes, here, we compared the functioning of the microbial communities in the rhizosphere of wild versus that of related cultivated rice species, which were originated from Africa and Asia. Results The microbial functions involved in carbon metabolism and nucleotide metabolism were found to be enriched in wild rice species, whereas those involved in nitrogen metabolism, lipid metabolism, metabolism of cofactors and vitamins, and xenobiotic biodegradation were more enriched in cultivated rice species. Among the overall carbon metabolism, specifically, methane metabolism of the rhizomicrobiomes clearly differed between wild and cultivated rice. The key enzymes in methane production and utilization were overrepresented in wild rice species, suggesting that the rhizomicrobiome of wild rice maintained a better ecological balance for methane production and utilization than the related cultivated rice species. Conclusions For the first time, the impacts of rice domestication on the main metabolic pathways of the rhizomicrobiome were assessed, which revealed the strong impacts of rice domestication on methane metabolism that is one of the most critical functions of the microbial community of the rhizosphere of rice. The results provide important guidelines for future breeding and cultivation of rice in the framework of more sustainable rice production.

scholarly journals Spesies Padi Liar (Oryza sp.) sebagai Sumber Gen Ketahanan Cekaman Abiotik dan Biotik pada Padi Budidaya

2017 ◽  
Vol 35 (4) ◽  
pp. 197
Author(s):  
Tintin Suhartini
Keyword(s):  
Resistance Gene ◽  
Resistance Genes ◽  
Abiotic Stresses ◽  
Wild Rice ◽  
Brown Planthopper ◽  
Cultivated Rice ◽  
Biotic And Abiotic Stresses ◽  
Rice Varieties ◽  
Wild Rice Species ◽  
Oryza Meyeriana

<p>ABSTRACT<br />Wild rice species could be used  for improvement of rice varieties because they have a good character for resistance to biotic and abiotic stresses. Some of Indonesian wild rice species are Oryza meyeriana, O. granulata, O. longiglumis, O. officinalis, O. ridleyi, O. rufipogon and O. schlechteri. IRRI has a collection of 2,500 accesions of wild rice and 18 species were collected in ICABIOGRAD, Bogor. Some species of wild rice are known to have resistance genes to biotic and abiotic stresses. A number of<br />accessions of O.  officinalis contained resistance gene to brown planthopper, blast disease, bacterial leaf blight (BLB) and sheath rot. One of the species that has resistance to pests and diseases is O. minuta. The resistance to tungro virus occurs in O. punctata. Tolerance to drought, Al and Fe toxicities occurs in wild rice species of O. sativa genome AA group. Resistance genes from wild rice species can be inserted into cultivated rice through conventional techniques in combination with biotechnology, while gene transfer and gene detection from wild rice to cultivated rice can be done through cross breeding, molecular markers, backcrossing and embryo rescue. The success of introgression of resistance genes from wild rice species to cultivated rice will increase genetic diversity of rice. As an example O. minuta has been implemented in introgression of BLB resistance gene on IR64. Introgression of O. nivara gene in IRRI had improved some superior rice varieties in Indonesia, namely IR30, IR32, IR34, IR36 and IR38, which were tolerant to brown planthopper, dwarf virus and bacterial leaf blight. Oryza rufipogon wich has BLB and blast resistance gene has been used for improvement of new varieties Inpari Blas and Inpari HDB which were released in 2013.<br />Keywords: Oryza spp., varietal improvement, resistance genes, biotic stresses, abiotic stresses</p><p>Abstrak</p><p>Spesies padi liar dapat dimanfaatkan dalam perakitan varietas unggul karena memiliki gen ketahanan terhadap cekaman biotik dan abiotik. Spesies padi liar yang ada di Indonesia adalah Oryza meyeriana, O. granulata, O. longiglumis, O. officinalis, O. ridleyi, O. rufipogon, dan O. schlechteri. IRRI memiliki koleksi 2.500 aksesi padi liar dan 18 spesies dikoleksi di BB Biogen. Sejumlah aksesi O. officinalis memiliki gen ketahanan terhadap wereng coklat, penyakit blas, hawar daun bakteri (HDB), dan busuk pelepah. Salah satu spesies yang memiliki ketahanan terhadap hama-penyakit tersebut adalah O. minuta. Ketahanan terhadap virus tungro terdapat pada O. punctata. Toleransi terhadap kekeringan, keracunan Al, dan Fe terdapat pada spesies padi liar kelompok O. sativa genom AA. Gen ketahanan dari spesies padi liar dapat dimasukkan (introgresi) ke dalam padi budi daya melalui teknik konvensional yang dikombinasikan dengan bioteknologi, sementara transfer gen dapat melalui persilangan, marka molekuler, silang balik, dan penyelamatan embrio. Keberhasilan introgresi gen ketahanan dari spesies padi liar ke padi budi daya akan meningkatkan keragaman genetik tanaman. Spesies padi liar O. minuta telah dimanfaatkan dalam introgresi gen ketahanan HDB pada varietas IR64. Introgresi gen asal O. nivara di IRRI menambah varietas unggul di Indonesia, yaitu IR30, IR32, IR34, IR36, dan IR38, yang toleran terhadap wereng coklat, virus kerdil rumput, dan HDB. Spesies padi liar O. rufipogon yang memiliki gen ketahanan HDB dan blas telah digunakan dalam pembentukan varietas unggul baru Inpari HDB dan Inpari Blas yang dilepas pada 2013.<br /><br /></p>

scholarly journals Endophytic Colonization and In Planta Nitrogen Fixation by a Herbaspirillum sp. Isolated from Wild Rice Species

2001 ◽  
Vol 67 (11) ◽  
pp. 5285-5293 ◽  
Author(s):  
Adel Elbeltagy ◽  
Kiyo Nishioka ◽  
Tadashi Sato ◽  
Hisa Suzuki ◽  
Bin Ye ◽  
...  
Keyword(s):  
Nitrogen Fixation ◽  
Wild Rice ◽  
Fluorescent Protein ◽  
In Planta ◽  
Cultivated Rice ◽  
Phenotypic Properties ◽  
Rice Varieties ◽  
Bacterial Populations ◽  
Rdna Sequences ◽  
Wild Rice Species

ABSTRACT Nitrogen-fixing bacteria were isolated from the stems of wild and cultivated rice on a modified Rennie medium. Based on 16S ribosomal DNA (rDNA) sequences, the diazotrophic isolates were phylogenetically close to four genera: Herbaspirillum,Ideonella, Enterobacter, andAzospirillum. Phenotypic properties and signature sequences of 16S rDNA indicated that three isolates (B65, B501, and B512) belong to the Herbaspirillum genus. To examine whether Herbaspirillum sp. strain B501 isolated from wild rice, Oryza officinalis, endophytically colonizes rice plants, the gfp gene encoding green fluorescent protein (GFP) was introduced into the bacteria. Observations by fluorescence stereomicroscopy showed that the GFP-tagged bacteria colonized shoots and seeds of aseptically grown seedlings of the original wild rice after inoculation of the seeds. Conversely, for cultivated rice Oryza sativa, no GFP fluorescence was observed for shoots and only weak signals were observed for seeds. Observations by fluorescence and electron microscopy revealed that Herbaspirillum sp. strain B501 colonized mainly intercellular spaces in the leaves of wild rice. Colony counts of surface-sterilized rice seedlings inoculated with the GFP-tagged bacteria indicated significantly more bacterial populations inside the original wild rice than in cultivated rice varieties. Moreover, after bacterial inoculation, in planta nitrogen fixation in young seedlings of wild rice, O. officinalis, was detected by the acetylene reduction and 15N2gas incorporation assays. Therefore, we conclude thatHerbaspirillum sp. strain B501 is a diazotrophic endophyte compatible with wild rice, particularly O. officinalis.

scholarly journals Rubisco activity, electron transport rate, and leaf features drive high photosynthesis rate in the selected wild rice

2019 ◽  
Author(s):  
Jyotirmaya Mathan ◽  
Anuradha Singh ◽  
Vikram Jathar ◽  
Aashish Ranjan
Keyword(s):  
Electron Transport ◽  
Wild Rice ◽  
Electron Transport Rate ◽  
Transport Rate ◽  
Leaf Photosynthesis ◽  
Cultivated Rice ◽  
Rubisco Activity ◽  
Rice Varieties ◽  
Mesophyll Cells ◽  
Wild Rice Species

AbstractThe importance of increasing photosynthetic efficiency for sustainable crop yield increases to feed the growing world population is well recognized. The natural genetic variation for leaf photosynthesis in crop plants is largely unexploited for increasing genetic yield potential. The genus Oryza, including cultivated rice and wild relatives, offers tremendous genetic variability to explore photosynthetic differences, and underlying biochemical, photochemical, and developmental basis. We quantified leaf photosynthesis and related physiological parameters for six cultivated and three wild rice genotypes, and identified photosynthetically efficient wild rice species. Fitting A/Ci curves followed by experimental validation showed that the leaf photosynthesis in cultivated rice varieties, IR64 and Nipponbare, was limited due to Rubisco activity and electron transport rate, compared to photosynthetically efficient wild rice species, Oryza australiensis and Oryza latifolia. The selected wild rice species with high leaf photosynthesis per unit area had striking anatomical features, such as larger mesophyll cells with more chloroplasts, larger and closer veins, and fewer mesophyll cells between two consecutive veins. Our results show the existence of desirable variations in Rubisco activity, electron transport rate, and mesophyll and vein features in the rice system itself that could possibly be targeted for increasing the photosynthetic efficiency of cultivated rice varieties.HighlightDistinct leaf biochemical, photochemical, and developmental features contribute to efficient photosynthesis in the selected wild rice that could potentially be exploited for increasing rice leaf photosynthesis.

scholarly journals Some Accessions of Amazonian Wild Rice (Oryza glumaepatula) Constitutively Form a Barrier to Radial Oxygen Loss along Adventitious Roots under Aerated Conditions

Plants ◽  
2020 ◽  
Vol 9 (7) ◽  
pp. 880
Author(s):  
Masato Ejiri ◽  
Yuto Sawazaki ◽  
Katsuhiro Shiono
Keyword(s):  
Wild Rice ◽  
Periodic Acid ◽  
Genetic Regulation ◽  
Wetland Plants ◽  
Radial Oxygen Loss ◽  
Root Tips ◽  
Cultivated Rice ◽  
Oxygen Loss ◽  
Wild Rice Species ◽  
Apoplastic Tracer

A barrier to radial oxygen loss (ROL), which reduces the loss of oxygen transported via the aerenchyma to the root tips, enables the roots of wetland plants to grow into anoxic/hypoxic waterlogged soil. However, little is known about its genetic regulation. Quantitative trait loci (QTLs) mapping can help to understand the factors that regulate barrier formation. Rice (Oryza sativa) inducibly forms an ROL barrier under stagnant conditions, while a few wetland plants constitutively form one under aerated conditions. Here, we evaluated the formation of a constitutive ROL barrier in a total of four accessions from two wild rice species. Three of the accessions were wetland accessions of O. glumaepatula, and the fourth was a non-wetland species of O. rufipogon. These species have an AA type genome, which allows them to be crossed with cultivated rice. The three O. glumaepatula accessions (W2165, W2149, and W1183) formed an ROL barrier under aerated conditions. The O. rufipogon accession (W1962) did not form a constitutive ROL barrier, but it formed an inducible ROL barrier under stagnant conditions. The three O. glumaepatula accessions should be useful for QTL mapping to understand how a constitutive ROL barrier forms. The constitutive barrier of W2165 was closely associated with suberization and resistance to penetration by an apoplastic tracer (periodic acid) at the exodermis but did not include lignin at the sclerenchyma.

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