scholarly journals Wild rice harbors more root endophytic fungi than cultivated rice in the F1 offspring after crossbreeding

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Lei Tian ◽  
Enze Wang ◽  
Xiaolong Lin ◽  
Li Ji ◽  
Jingjing Chang ◽  
...  
Keyword(s):  
Endophytic Fungi ◽  
Wild Rice ◽  
High Throughput Sequencing ◽  
Sequencing Data ◽  
Cultivated Rice ◽  
The Core ◽  
Bacterial Genus ◽  
Wild Rice Species ◽  
Root Endophytic Fungi ◽  
Bacteria And Fungi

Abstract Background Rice, which serves as a staple food for more than half of the world’s population, is grown worldwide. The hybridization of wild and cultivated rice has enabled the incorporation of resistance to varying environmental conditions. Endophytic microbiota are known to be transferred with their host plants. Although some studies have reported on the endophytic microbiota of wild and cultivated rice, the inheritance from wild and cultivated rice accessions in next generations, in terms of endophytic microbiota, has not been examined. Results In the present study, the endophytic microbial community structures of Asian and African wild and cultivated rice species were compared with those of their F1 offspring. High-throughput sequencing data of bacterial 16S rDNA and fungal internal transcribed spacer regions were used to classify the endophytic microbiota of collected samples of rice. Results indicated that when either African or Asian wild rice species were crossed with cultivated rice accessions, the first generation harbored a greater number of root endophytic fungi than the cultivated parent used to make the crosses. Network analysis of the bacterial and fungal operational taxonomic units revealed that Asian and African wild rice species clustered together and exhibited a greater number of significant correlations between fungal taxa than cultivated rice. The core bacterial genus Acidovorax and the core fungal order Pleosporales, and genera Myrothecium and Bullera connected African and Asian wild rice accessions together, and both the wild rice accessions with their F1 offspring. On the other hand, the core bacterial genus Bradyrhizobium and the core fungal genera Dendroclathra linked the African and Asian cultivated rice accessions together. Conclusions This study has theoretical significance for understanding the effect of breeding on the inheritance of endophytic microbiota of rice and identifying beneficial endophytic bacteria and fungi among wild and cultivated rice species, and their F1 offspring.

Wild rice controls more root endophytic fungi than cultivated rice in the F1 offsprings after the crossbreeding

2020 ◽  
Author(s):  
Lei Tian ◽  
Xiaolong Lin ◽  
Li Ji ◽  
Jingjing Chang ◽  
Xiujun Li ◽  
...  
Keyword(s):  
Endophytic Fungi ◽  
Wild Rice ◽  
Endophytic Bacteria ◽  
Bacterial Species ◽  
Fungal Species ◽  
Cultivated Rice ◽  
The Core ◽  
Wild Rice Species ◽  
Root Endophytic Fungi ◽  
Bacteria And Fungi

Abstract Background: Rice, which serves as a staple food for more than half of the world’s population, has been planted all over the world. The hybridization of wild and cultivated rice has helped rice gain resistance to variable environmental conditions. Endophytic microbiomes have been known to be transferred along with the plants. However, the endophytic bacteria or fungi for the wild and cultivated rice, and their first crossbred generation have not been illustrated until now. Results: In this study, we systematically compared the endophytic microbial community structures of Asian and African wild and cultivated rice species with their F1 offsprings. Results showed that both African and Asian wild rice controls more root endophytic fungi than cultivated rice in their first generation after crossbreeding. Furthermore, network analysis of the bacterial and fungal operational taxonomic units showed that Asian and African wild rice species can cluster and have more significant correlations than cultivated rice fungal species. The core bacterial species that connected wild rice with its F1 offsprings was Acidovorax, wherea the core bacterial species that linked cultivated rice to its F1 offsprings was Bradyrhizobium; and the core fungal species that can connect in wild rice and the F1 offsprings were Pleosporales, Myrothecium and Bullera, while the core fungal species that can connect in cultivated rice was those belonging to the Dendroclathra genus.Conclusions: This study may provide the theoretical significance of the endophytic bacteria and fungi for wild and cultivated rice along with their F1 offsprings.

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 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 High-throughput sequencing reveals the core gut microbiota of the mud crab (Scylla paramamosain) in different coastal regions of southern China

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Hongling Wei ◽  
Huan Wang ◽  
Lei Tang ◽  
Changkao Mu ◽  
Chunyu Ye ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
High Throughput Sequencing ◽  
Southern China ◽  
Scylla Paramamosain ◽  
Mud Crab ◽  
Sequencing Data ◽  
Coastal Regions ◽  
Female Crab ◽  
The Core ◽  
Commercially Important

Abstract Background Scylla paramamosain is a commercially important mud crab. The microbiota is a community that inhabits the crab intestine, and is important for physiological functional and host health. Results Proteobacteria, Firmicutes, Bacteroidetes, Tenericutes, Spirochaetae and Fusobacteria were the dominant phyla of the 36 representative phyla. Eleven genera of the 820 representative genera were considered as core gut microbiota and were distributed in the five dominant phyla. The core genus of the Proteobacteria included Arcobacter, Photobacterium, Vibrio, Shewanella and Desulfovibrio. The other four phyla contained one or two genera. Male and female crab samples had two different core genera, (male samples: Psychrilyobacter & Lactococcus; female samples: Clostridium_sensu_stricto_11 and Candidatus_Bacilloplasma). Conclusions This is the first time core intestinal microbiota have been identified in crab from nine coastal regions of southern China. This study provides sequencing data related to the gut microbiota of S. paramamosain, and may contribute to probiotic development for S. paramamosain aquaculture industries.

scholarly journals The Root Endophytic Fungi Community Structure of Pennisetum sinese from Four Representative Provinces in China

2019 ◽  
Vol 7 (9) ◽  
pp. 332
Author(s):  
Zhen-Shan Deng ◽  
Xiao-Dong Liu ◽  
Bao-Cheng Zhang ◽  
Shuo Jiao ◽  
Xiang-Ying Qi ◽  
...  
Keyword(s):  
Biomass Production ◽  
Endophytic Fungi ◽  
High Throughput Sequencing ◽  
The Other ◽  
Its Sequences ◽  
Total Carbon ◽  
Shaanxi Province ◽  
Maturity Stage ◽  
Annual Average ◽  
Root Endophytic Fungi

Pennisetum sinese is a good forage grass with high biomass production and crude proteins. However, little is known about the endophytic fungi diversity of P. sinese, which might play an important role in the plant’s growth and biomass production. Here, we used high throughput sequencing of the Internal Transcribed Spacer (ITS) sequences based on primers ITS5-1737 and ITS2-2043R to investigate the endophytic fungi diversity of P. sinese roots at the maturity stage, as collected from four provinces (Shaanxi province, SX; Fujian province, FJ; the Xinjiang Uyghur autonomous prefecture, XJ and Inner Mongolia, including sand (NS) and saline-alkali land (NY), China). The ITS sequences were processed using QIIME and R software. A total of 374,875 effective tags were obtained, and 708 operational taxonomic units (OTUs) were yielded with 97% identity in the five samples. Ascomycota and Basidiomycota were the two dominant phyla in the five samples, and the genera Khuskia and Heydenia were the most abundant in the FJ and XJ samples, respectively, while the most abundant tags in the other three samples could not be annotated at the genus level. In addition, our study revealed that the FJ sample possessed the highest OTU numbers (242) and the NS sample had the lowest (86). Moreover, only 22 OTUs were present in all samples simultaneously. The beta diversity analysis suggested a division of two endophytic fungi groups: the FJ sample from the south of China and the other four samples from north or northwest China. Correlation analysis between the environmental factors and endophytic fungi at the class level revealed that Sordariomycetes and Pucciniomycetes had extremely significant positive correlations with the total carbon, annual average precipitation, and annual average temperature, while Leotiomycetes showed an extremely significant negative correlation with quick acting potassium. The results revealed significant differences in the root endophytic fungi diversity of P. sinese in different provinces and might be useful for growth promotion and biomass production in the future.

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.

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