Potentiality of Wild Rice in Quality Improvement of Cultivated Rice Varieties

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.

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

Jurnal Penelitian dan Pengembangan Pertanian ◽

10.21082/jp3.v35n4.2016.p197-207 ◽

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

ABSTRACT 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 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. Keywords: Oryza spp., varietal improvement, resistance genes, biotic stresses, abiotic stressesAbstrakSpesies 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.

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Application of SV markers developed from Dongxiang common wild rice in analysis of cultivated rice

Plant Genetic Resources ◽

10.1017/s1479262119000145 ◽

2019 ◽

Vol 17 (5) ◽

pp. 448-451

Author(s):

Fantao Zhang ◽

Yuan Luo ◽

Bin Ai ◽

Yong Chen ◽

Weidong Qi ◽

...

Keyword(s):

Wild Rice ◽

Oryza Rufipogon ◽

Genomic Research ◽

Cultivated Rice ◽

Structural Variations ◽

Rice Varieties ◽

Common Wild Rice ◽

Genome Wide ◽

Rice Chromosomes ◽

Molecular Marker Development

AbstractDongxiang common wild rice (Oryza rufipogon Griff., DXWR) is an important genetic resource for the improvement of cultivated rice. For the past three decades, great achievements have been made in the field of molecular marker development. Although structural variations (SVs) had been studied between DXWR and Nipponbare (Oryza sativa L. ssp. japonica), the development and application of SV markers in DXWR has not been reported. In this study, based on the genome-wide SV loci, we developed and synthesized a total of 195 SV markers that were evenly distributed across the 12 rice chromosomes. Then, these markers were tested for their stabilities and polymorphisms. Of these 195 markers, 147 (75.4%) were successfully amplified and displayed abundant polymorphisms between DXWR and Nipponbare. Meanwhile, through the genotyping of 20 rice varieties from 13 countries and areas, we concluded that these SV markers have a wide application prospect in the analysis of cultivated rice. Therefore, these molecular markers greatly enrich the number of markers available for DXWR, which will facilitate genomic research and molecular breeding for this important and endangered germplasm resource.

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

Applied and Environmental Microbiology ◽

10.1128/aem.67.11.5285-5293.2001 ◽

2001 ◽

Vol 67 (11) ◽

pp. 5285-5293 ◽

Cited By ~ 274

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.

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

10.1101/754887 ◽

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.

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Transcriptomic and proteomic responses to herbivory in cultivated, Bt-transgenic and wild rice

10.21203/rs.3.rs-19750/v1 ◽

2020 ◽

Author(s):

Yongbo Liu ◽

Weiqing Wang ◽

Yonghua Li ◽

Fang Liu ◽

Weijuan Han ◽

...

Keyword(s):

Transgenic Rice ◽

Wild Rice ◽

Crop Production ◽

Brown Planthopper ◽

Hierarchical Cluster ◽

Nilaparvata Lugens ◽

Cultivated Rice ◽

Kegg Pathways ◽

Itraq Analysis ◽

Go Terms

Abstract Background: Strategies are still employed to decrease insect damage in crop production, including conventional breeding with wild germplasm resources and transgenic technology with the insertion of foreign genes, while the insect-resistant mechanism of these strategies remains unclear. Results: Under the feeding of brown planthopper (Nilaparvata lugens), cultivated rice (WT) showed less DEGs (568) and DAPs (4) than transgenic rice (2098 and 11) and wild rice CL (1990 and 39) and DX (1932 and 25). Hierarchical cluster of DEGs showed gene expression of CL and DX were similar, slightly distinct to GT, and clearly different from WT. DEGs assigned to the GO terms were less in WT rice than GT, CL and DX, and “Metabolic process”, “cellular process”, “response to stimulus” were dominant. Wild rice CL significantly enriched in KEGG pathways of “Metabolic pathways”, “biosynthesis of secondary metabolites”, “plant-pathogen interaction” and “plant hormone signal transduction”. The iTRAQ analysis confirmed the results of RNA-seq, which showing the least GO terms and KEGG pathways responding to herbivory in the cultivated rice. Synthesize conclusions: This study demonstrated that similarity in the transcriptomic and proteomic response to herbivory for the wild rice and Bt-transgenic rice, while cultivated rice lack of enough pathways in response to herbivory. Our results highlighted the importance of conservation of crop wild species.

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Degradome comparison between wild and cultivated rice identifies differential targeting by miRNAs

BMC Genomics ◽

10.1186/s12864-021-08288-5 ◽

2022 ◽

Vol 23 (1) ◽

Author(s):

Chenna Swetha ◽

Anushree Narjala ◽

Awadhesh Pandit ◽

Varsha Tirumalai ◽

P. V. Shivaprasad

Keyword(s):

Metabolic Pathways ◽

Wild Rice ◽

Regulation Of Gene Expression ◽

Genome Integrity ◽

Cultivated Rice ◽

Mrna Targets ◽

Ribonucleoprotein Complexes ◽

The Poor ◽

Rna Targets ◽

Secondary Wall Formation

Abstract Background Small non-coding (s)RNAs are involved in the negative regulation of gene expression, playing critical roles in genome integrity, development and metabolic pathways. Targeting of RNAs by ribonucleoprotein complexes of sRNAs bound to Argonaute (AGO) proteins results in cleaved RNAs having precise and predictable 5` ends. While tools to study sliced bits of RNAs to confirm the efficiency of sRNA-mediated regulation are available, they are sub-optimal. In this study, we provide an improvised version of a tool with better efficiency to accurately validate sRNA targets. Results Here, we improvised the CleaveLand tool to identify additional micro (mi)RNA targets that belong to the same family and also other targets within a specified free energy cut-off. These additional targets were otherwise excluded during the default run. We employed these tools to understand the sRNA targeting efficiency in wild and cultivated rice, sequenced degradome from two rice lines, O. nivara and O. sativa indica Pusa Basmati-1 and analyzed variations in sRNA targeting. Our results indicate the existence of multiple miRNA-mediated targeting differences between domesticated and wild species. For example, Os5NG4 was targeted only in wild rice that might be responsible for the poor secondary wall formation when compared to cultivated rice. We also identified differential mRNA targets of secondary sRNAs that were generated after miRNA-mediated cleavage of primary targets. Conclusions We identified many differentially targeted mRNAs between wild and domesticated rice lines. In addition to providing a step-wise guide to generate and analyze degradome datasets, we showed how domestication altered sRNA-mediated cascade silencing during the evolution of indica rice.

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Genetic Divergence in Indigenous Wild and Cultivated Rice Species of Manipur Valley

ISRN Genetics ◽

10.5402/2013/651019 ◽

2013 ◽

Vol 2013 ◽

pp. 1-6 ◽

Cited By ~ 1

Author(s):

K. Medhabati ◽

K. Rajiv Das ◽

M. Rohinikumar ◽

H. Sunitibala ◽

Th. Dikash Singh

Keyword(s):

Genetic Divergence ◽

Wild Rice ◽

Flag Leaf ◽

Cluster Formation ◽

Leaf Length ◽

Cultivated Rice ◽

And Performance ◽

Flag Leaf Length ◽

The Individual ◽

Hybridization Programme

Genetic divergence of 32 indigenous rice germplasms and five wild rice of which three from Manipur and two wild rice procured from IRRI, Philippines was investigated using Mahalanobis, D2 statistic. Based on twelve agromorphological characters, the thirty-seven germplasms both wild and cultivated were grouped into five clusters based on the relative magnitudes of D2 values following Tocher's method of cluster formation. Based on the rank totals, the characters which contributed maximum towards genetic divergence in the present studies were grain yield/plant, spikelet/panicle, 100 grain weight, grain length, days to 50% flowering, ear bearing tillers/plant, and flag leaf length. In the present study, maximum intercluster distance was estimated between cluster III and (D2=14.09) which was closed followed by clusters II and V (D2=12.50). On the basis of their greater intercluster distance, high value of cluster mean according to the character to be improved and performance of the individual germplasms for the character, the germplasms could be used in hybridization programme for improvement of different plant characters in the rice germplasms of Manipur.

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Identification of long noncoding natural antisense transcripts (lncNATs) correlated with drought stress response in wild rice (Oryza nivara)

10.21203/rs.3.rs-280217/v1 ◽

2021 ◽

Author(s):

Yong-Chao Xu ◽

Jie Zhang ◽

Dong-Yan Zhang ◽

Ying-Hui Nan ◽

Song Ge ◽

...

Keyword(s):

Drought Stress ◽

Stress Response ◽

Wild Rice ◽

Oryza Rufipogon ◽

Cultivated Rice ◽

Antisense Transcripts ◽

High Genetic Diversity ◽

Natural Antisense Transcripts ◽

Form Complex ◽

Oryza Nivara

Abstract Background Wild rice, including Oryza nivara and Oryza rufipogon, which are considered as the ancestors of Asian cultivated rice (Oryza sativa L.), possess high genetic diversity and serve as a crucial resource for breeding novel cultivars of cultivated rice. Although many rice domestication related traits, such as seed shattering and plant architecture, have been intensively studied at the phenotypic and genomic levels, further investigation is needed to understand the molecular basis of phenotypic differences between cultivated and wild rice. Drought stress is one of the most severe abiotic stresses affecting rice growth and production. Adaptation to drought stress involves a cascade of genes and regulatory factors that form complex networks. Long noncoding natural antisense transcripts (lncNATs), a class of long noncoding RNAs (lncRNAs), regulate the corresponding sense transcripts and play an important role in plant growth and development. However, the contribution of lncNATs to drought stress response in wild rice remains largely unknown. Results Here, we conducted strand-specific RNA sequencing (ssRNA-seq) analysis of Nipponbare (O. sativa ssp. japonica) and two O. nivara accessions (BJ89 and BJ278) to determine the role of lncNATs in drought stress response in wild rice. A total of 1,246 lncRNAs were identified, including 1,091 coding–noncoding NAT pairs, of which 50 were expressed only in Nipponbare, and 77 were expressed only in BJ89 and/or BJ278. Of the 1,091 coding–noncoding NAT pairs, 240 were differentially expressed between control and drought stress conditions. Among these 240 NAT pairs, 12 were detected only in Nipponbare, and 187 were detected uniquely in O. nivara. Furthermore, 10 of the 240 coding–noncoding NAT pairs were correlated with genes previously demonstrated to be involved in stress response; among these, nine pairs were uniquely found in O. nivara, and one pair was shared between O. nivara and Nipponbare. Conclusion We identified lncNATs associated with drought stress response in cultivated rice and O. nivara. These results will improve our understanding of the function of lncNATs in drought tolerance and accelerate rice breeding.

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Distribution and mapping of an active autonomous aDart element responsible for mobilizing nonautonomous nDart1 transposons in cultivated rice varieties

Theoretical and Applied Genetics ◽

10.1007/s00122-007-0677-z ◽

2007 ◽

Vol 116 (3) ◽

pp. 395-405 ◽

Cited By ~ 16

Author(s):

Hideki Nishimura ◽

Nisar Ahmed ◽

Kazuo Tsugane ◽

Shigeru Iida ◽

Masahiko Maekawa

Keyword(s):

Cultivated Rice ◽

Rice Varieties

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