scholarly journals The Possibility of Gene Flow Between Cultivated and Wild Rice in Ghana, A Review

2019 ◽  
Author(s):  
Gavers Kwasi Oppong ◽  
Belinda Akomeah ◽  
Isaac Tawiah ◽  
Maxwell Darko Asante
Keyword(s):  
Gene Flow ◽  
Transgenic Rice ◽  
Wild Rice ◽  
Field Trials ◽  
Cultivated Rice ◽  
Wild Rice Species ◽  
Gm Rice ◽  
Aa Genome ◽  
Autogamous Plant ◽  
Wild Oryza Species

Several transgenic rice lines have been developed and are currently under field trials around the world. There are future plans for the commercial release of transgenic rice into the environment. Rice is an autogamous plant and therefore not perceived to be a very high candidate for pollen mediated gene flow to wild and weedy relatives. However, in a tropical environment like Ghana, where sexually compatible wild Oryza species which belongs to the AA genome are present within the ecology of cultivated rice, the possibility of gene flow to wild species cannot be overlooked. There is little evidence on gene flow and its consequences on the wild rice species should they acquire useful genes through gene flow. This review discusses the chances of cultivated to wild rice gene flow in Ghana and the biosafety considerations that should be put in place before the commercial release of genetically modified (GM) rice.

scholarly journals Exploring the Loci Responsible for Awn Development in Rice through Comparative Analysis of All AA Genome Species

Plants ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 725
Author(s):  
Kanako Bessho-Uehara ◽  
Yoshiyuki Yamagata ◽  
Tomonori Takashi ◽  
Takashi Makino ◽  
Hideshi Yasui ◽  
...  
Keyword(s):  
Wild Rice ◽  
Comparative Sequence Analysis ◽  
Loss Of Function ◽  
Cultivated Rice ◽  
Substitution Lines ◽  
Genome Species ◽  
Wild Rice Species ◽  
Aa Genome ◽  
Genome Group ◽  
Cultivated Species

Wild rice species have long awns at their seed tips, but this trait has been lost through rice domestication. Awn loss mitigates harvest and seed storage; further, awnlessness increases the grain number and, subsequently, improves grain yield in Asian cultivated rice, highlighting the contribution of the loss of awn to modern rice agriculture. Therefore, identifying the genes regulating awn development would facilitate the elucidation of a part of the domestication process in rice and increase our understanding of the complex mechanism in awn morphogenesis. To identify the novel loci regulating awn development and understand the conservation of genes in other wild rice relatives belonging to the AA genome group, we analyzed the chromosome segment substitution lines (CSSL). In this study, we compared a number of CSSL sets derived by crossing wild rice species in the AA genome group with the cultivated species Oryza sativa ssp. japonica. Two loci on chromosomes 7 and 11 were newly discovered to be responsible for awn development. We also found wild relatives that were used as donor parents of the CSSLs carrying the functional alleles responsible for awn elongation, REGULATOR OF AWN ELONGATION 1 (RAE1) and RAE2. To understand the conserveness of RAE1 and RAE2 in wild rice relatives, we analyzed RAE1 and RAE2 sequences of 175 accessions among diverse AA genome species retrieved from the sequence read archive (SRA) database. Comparative sequence analysis demonstrated that most wild rice AA genome species maintained functional RAE1 and RAE2, whereas most Asian rice cultivars have lost either or both functions. In addition, some different loss-of-function alleles of RAE1 and RAE2 were found in Asian cultivated species. These findings suggest that different combinations of dysfunctional alleles of RAE1 and RAE2 were selected after the speciation of O. sativa, and that two-step loss of function in RAE1 and RAE2 contributed to awnlessness in Asian cultivated rice.

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

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.

scholarly journals Segregation Distortion Observed in the Progeny of Crosses Between Oryza sativa and O. meridionalis Caused by Abortion During Seed Development

Plants ◽  
2019 ◽  
Vol 8 (10) ◽  
pp. 398
Author(s):  
Daiki Toyomoto ◽  
Masato Uemura ◽  
Satoru Taura ◽  
Tadashi Sato ◽  
Robert Henry ◽  
...  
Keyword(s):  
Oryza Sativa ◽  
Seed Development ◽  
Wild Rice ◽  
Lethal Gene ◽  
Chromosome 6 ◽  
Cultivated Rice ◽  
Substitution Lines ◽  
Putative Gene ◽  
Aa Genome ◽  
Recurrent Backcrossing

Wild rice relatives having the same AA genome as domesticated rice (Oryza sativa) comprise the primary gene pool for rice genetic improvement. Among them, O. meridionalis and O. rufipogon are found in the northern part of Australia. Three Australian wild rice strains, Jpn1 (O. rufipogon), Jpn2, and W1297 (O. meridionalis), and one cultivated rice cultivar Taichung 65 (T65) were used in this study. A recurrent backcrossing strategy was adopted to produce chromosomal segment substitution lines (CSSLs) carrying chromosomal segments from wild relatives and used for trait evaluation and genetic analysis. The segregation of the DNA marker RM136 locus on chromosome 6 was found to be highly distorted, and a recessive lethal gene causing abortion at the seed developmental stage was shown to be located between two DNA markers, KGC6_10.09 and KGC6_22.19 on chromosome 6 of W1297. We name this gene as SEED DEVELOPMENT 1 (gene symbol: SDV1). O. sativa is thought to share the functional dominant allele Sdv1-s (s for sativa), and O. meridionalis is thought to share the recessive abortive allele sdv1-m (m for meridionalis). Though carrying the sdv1-m allele, the O. meridionalis accessions can self-fertilize and bear seeds. We speculate that the SDV1 gene may have been duplicated before the divergence between O. meridionalis and the other AA genome Oryza species, and that O. meridionalis has lost the function of the SDV1 gene and has kept the function of another putative gene named SDV2.

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

Polymorphisms and evolutionary history of retrotransposon insertions in rice promoters

Genome ◽  
2011 ◽  
Vol 54 (8) ◽  
pp. 629-638 ◽  
Author(s):  
Z. Xu ◽  
S. Rafi ◽  
W. Ramakrishna
Keyword(s):  
Oryza Sativa ◽  
Wild Rice ◽  
Evolutionary Dynamics ◽  
Genomic Sequence ◽  
Promoter Regions ◽  
Higher Plant ◽  
Wild Rice Species ◽  
History Of ◽  
Aa Genome ◽  
Rice Genotypes

Retrotransposons are ubiquitous in higher plant genomes. The presence or absence of retrotransposons in whole genome and high throughput genomic sequence (HTGS) from cultivated and wild rice was investigated to understand the organization and evolution of retrotransposon insertions in promoter regions. Approximately half of the Oryza sativa subsp. japonica ‘Nipponbare’ promoters with retrotransposons conserved in Oryza sativa subsp. indica ‘93-11’ and four wild rice species showed higher sequence conservation in retrotransposon than nonretrotransposon regions. We further investigated, in detail, the evolutionary dynamics of five retrotransposons in the promoter regions of 95 rice genotypes. Our data suggest that four of five insertions (Rp2–Rp5) occurred in the ancestor of AA genome, while the other insertion (Rp1) predates the ancestral divergence of Oryza officinalis (CC genome). Four retrotransposons (Rp2–Rp5) were present in 52% (Rp2), 29% (Rp3), 53% (Rp4), and 43% (Rp5) of the rice genotypes with AA genome type, and the fifth retrotransposon (Rp1) was present in 95% of the rice genotypes with AA, BBCC, or CC genome types. Furthermore, most of these retrotransposons were found to evolve slower than flanking promoter regions, suggesting a role in promoter function for regulating downstream genes.

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 Genetic structure of Oryza glumaepatula wild rice populations and evidence of introgression from O. sativa in Costa Rica

2015 ◽  
Author(s):  
Eric J Fuchs ◽  
Allan Meneses Martínez ◽  
Amanda Calvo ◽  
Melania Muñoz ◽  
Griselda Arrieta-Espinoza
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Costa Rica ◽  
Genetic Structure ◽  
Wild Species ◽  
Wild Rice ◽  
Wild Rice Species ◽  
Genetic Diversity And Structure ◽  
Diversity Estimates ◽  
Oryza Glumaepatula

Wild crop relatives are an important source of genetic diversity for crop improvement. However, gene flow from cultivated species into wild species may prove detrimental. Introgression may lead to changes in wild species by incorporating alleles from domesticated species, which may increase the likelihood of extinction. The objective of the present study is to analyze how genetic diversity is distributed within and among populations of the wild rice species Oryza glumaepatula in Costa Rica. We also evaluated if there is evidence of introgression between wild rice and commercial varieties of O. sativa since it is cultivated commonly in close proximity to wild rice populations. Individuals from all known O. glumaepatula populations in Costa Rica were collected. With the aid of 455 AFLP markers, we characterized the genetic diversity and structure among seven populations in northern Costa Rica. Given the dominant nature of our markers, Bayesian estimates of genetic structure were used. We also compared genetic diversity estimates between O. glumaepatula individuals and O. sativa commercial rice. Our results show that O. glumaepatula populations in Costa Rica have moderately high levels of genetic diversity, comparable to those found in South American populations. This is likely a result of large population size. Despite the restricted distributions of this wild species, in Costa Rica most populations are composed of several thousand individuals, thus reducing the effects of drift on genetic diversity. Our results also found low but significant structure (\theta=0.03±0.001) among populations that are separated by ~10 Km within a single river. The position of the population along the river did not influence genetic diversity estimates or differences among populations. This river does not have a strong current and meadows or seeds may easily move upstream, thus homogenizing genetic diversity across populations regardless of river position. Ample gene flow through pollen, seeds or detached culms within the same river reduces genetic structure. A Bayesian structure analysis showed that individuals from two populations share a significant proportion of their genomes with O. sativa genome. These results suggest that the low levels of genetic structure found in these populations are likely the result of introgression from cultivated O. sativa populations. These results expose an important biohazard as recurrent hybridization may reduce genetic diversity of this wild rice species. Introgression may transfer commercial traits into the only populations of O. glumaepatula in Costa Rica, which in turn could alter genetic diversity and increase the likelihood of local extinction. These results have important implications for in situ conservation strategies of the only wild populations of O. glumaepatula in Costa Rica.

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>

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