scholarly journals The Effect of Nitrogen Application Level on Photosynthetic Traits in the AA Genome Wild Rice Species, Oryza nivara

2014 ◽  
Vol 83 (4) ◽  
pp. 333-340
Author(s):  
Norimitsu Hamaoka ◽  
Osamu Ueno
Keyword(s):  
Wild Rice ◽  
Nitrogen Application ◽  
Oryza Nivara ◽  
Wild Rice Species ◽  
Aa Genome ◽  
Photosynthetic Traits

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.

Ecogeographic Variation in the Morphology of Two Asian Wild Rice Species, Oryza nivara and Oryza rufipogon

2013 ◽  
Vol 174 (6) ◽  
pp. 896-909 ◽  
Author(s):  
Maria Celeste N. Banaticla-Hilario ◽  
Marc S. M. Sosef ◽  
Kenneth L. McNally ◽  
Nigel Ruaraidh Sackville Hamilton ◽  
Ronald G. van den Berg
Keyword(s):  
Wild Rice ◽  
Oryza Rufipogon ◽  
Oryza Nivara ◽  
Wild Rice Species

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 Development of a genome-wide InDel marker set for allele discrimination between rice (Oryza sativa) and the other seven AA-genome Oryza species

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Sherry Lou Hechanova ◽  
Kamal Bhattarai ◽  
Eliza Vie Simon ◽  
Graciana Clave ◽  
Pathmasiri Karunarathne ◽  
...  
Keyword(s):  
Oryza Sativa ◽  
Wild Rice ◽  
The Other ◽  
Sequence Alignments ◽  
Rice Varieties ◽  
Genome Species ◽  
Genome Wide ◽  
Wild Rice Species ◽  
A Genome ◽  
Aa Genome

AbstractWild relatives of rice in the genus Oryza (composed of 24 species with 11 different genome types) have been significantly contributing to the varietal improvement of rice (Oryza sativa). More than 4000 accessions of wild rice species are available and they are regarded as a “genetic reservoir” for further rice improvement. DNA markers are essential tools in genetic analysis and breeding. To date, genome-wide marker sets for wild rice species have not been well established and this is one of the major difficulties for the efficient use of wild germplasm. Here, we developed 541 genome-wide InDel markers for the discrimination of alleles between the cultivated species O. sativa and the other seven AA-genome species by positional multiple sequence alignments among five AA-genome species with four rice varieties. The newly developed markers were tested by PCR-agarose gel analysis of 24 accessions from eight AA genome species (three accessions per species) along with two representative cultivars (O. sativa subsp. indica cv. IR24 and subsp. japonica cv. Nipponbare). Marker polymorphism was validated for 475 markers. The number of polymorphic markers between IR24 and each species (three accessions) ranged from 338 (versus O. rufipogon) to 416 (versus O. longistaminata) and the values in comparison with Nipponbare ranged from 179 (versus O. glaberrima) to 323 (versus O. glumaepatula). These marker sets will be useful for genetic studies and use of the AA-genome wild rice species.

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.

Identification and diversity of functional centromere satellites in the wild rice species Oryza brachyantha

2013 ◽  
Vol 21 (8) ◽  
pp. 725-737 ◽  
Author(s):  
Chuandeng Yi ◽  
Wenli Zhang ◽  
Xibin Dai ◽  
Xing Li ◽  
Zhiyun Gong ◽  
...  
Keyword(s):  
Wild Rice ◽  
Wild Rice Species ◽  
Oryza Brachyantha ◽  
In The Wild

Isolation and Identification of a Functional Centromere Element in the Wild Rice Species Oryza granulata with the GG Genome

2015 ◽  
Vol 42 (12) ◽  
pp. 699-702 ◽  
Author(s):  
Chuandeng Yi ◽  
Mingsen Wang ◽  
Wei Jiang ◽  
Derong Wang ◽  
Yong Zhou ◽  
...  
Keyword(s):  
Wild Rice ◽  
Isolation And Identification ◽  
Wild Rice Species ◽  
In The Wild ◽  
Oryza Granulata

scholarly journals The Oryza Map Alignment Project: The Golden Path to Unlocking the Genetic Potential of Wild Rice Species

2005 ◽  
Vol 59 (1) ◽  
pp. 53-62 ◽  
Author(s):  
Rod A. Wing ◽  
Jetty S. S. Ammiraju ◽  
Meizhong Luo ◽  
HyeRan Kim ◽  
Yeisoo Yu ◽  
...  
Keyword(s):  
Wild Rice ◽  
Genetic Potential ◽  
Wild Rice Species ◽  
Map Alignment ◽  
Golden Path

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

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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