Interrelationships of Oryza species based on electrophoretic patterns of alcohol dehydrogenase

1992 ◽  
Vol 70 (2) ◽  
pp. 352-358 ◽  
Author(s):  
Anil Grover ◽  
Deepak Pental
Keyword(s):  
Alcohol Dehydrogenase ◽  
Oryza Rufipogon ◽  
Band Pattern ◽  
Oryza Species ◽  
Oryza Glaberrima ◽  
Cultivated Rice ◽  
Major Band ◽  
Electrophoretic Patterns ◽  
Oryza Punctata ◽  
Germinating Seeds

Nineteen different species belonging to the genus Oryza were studied for variation in electrophoretic patterns of alcohol dehydrogenase (ADH) extracted from germinating seeds. The ADH patterns were similar for aerobically and anaerobically germinating seeds of all the species. Oryza saliva accessions, both indica and japonica, revealed a five-band pattern on polyacrylamide gels. African cultivated rice, Oryza glaberrima, had an alcohol dehydrogenase pattern similar to that of O. sativa. Oryza perennis complex comprising of Oryza nivara, Oryza rufipogon in Asia, Oryza barthii, Oryza longistaminata in Africa, and some of the accessions of O. rufipogon from America had ADH patterns similar to that of O. sativa. In a few accessions of O. rufipogon from America, only three bands were visualized. Oryza minuta, Oryza officinalis, Oryza punctata, Oryza alta, Oryza grandiglumis, and Oryza latifolia had similar patterns with one major band at the same Rf value as the major band of O. sativa and two minor bands corresponding to the two bands found in O. sativa. Oryza australiensis, Oryza brachyantha, and Oryza granulata had distinct patterns. Oryza ridleyi had a six-band pattern with three major and three minor bands. The three major bands correspond to the major band of O. granulata, O. officinalis, and O. australiensis. Based on alcohol dehydrogenase data, six major groups were identified amongst Oryza species. Key words: Oryza species, alcohol dehydrogenase, phylogenetics.

The Genomics ofOryzaSpecies Provides Insights into Rice Domestication and Heterosis

2019 ◽  
Vol 70 (1) ◽  
pp. 639-665 ◽  
Author(s):  
Erwang Chen ◽  
Xuehui Huang ◽  
Zhixi Tian ◽  
Rod A. Wing ◽  
Bin Han
Keyword(s):  
Complex Traits ◽  
Oryza Rufipogon ◽  
Oryza Species ◽  
Oryza Glaberrima ◽  
Cultivated Rice ◽  
African Rice ◽  
Genome Wide ◽  
Genome Variations ◽  
Genomic Studies ◽  
Rice Domestication

Here, we review recent progress in genetic and genomic studies of the diversity of Oryza species. In recent years, unlocking the genetic diversity of Oryza species has provided insights into the genomics of rice domestication, heterosis, and complex traits. Genome sequencing and analysis of numerous wild rice ( Oryza rufipogon) and Asian cultivated rice ( Oryza sativa) accessions have enabled the identification of genome-wide signatures of rice domestication and the unlocking of the origin of Asian cultivated rice. Moreover, similar studies on genome variations of African rice ( Oryza glaberrima) cultivars and their closely related wild progenitor Oryza barthii accessions have provided strong evidence to support a theory of independent domestication in African rice. Integrated genomic approaches have efficiently investigated many heterotic loci in hybrid rice underlying yield heterosis advantages and revealed the genomic architecture of rice heterosis. We conclude that in-depth unlocking of genetic variations among Oryza species will further enhance rice breeding.

scholarly journals Evolutionary Analysis of GH3 Genes in Six Oryza Species/Subspecies and Their Expression under Salinity Stress in Oryza sativa ssp. japonica

Plants ◽  
2019 ◽  
Vol 8 (2) ◽  
pp. 30 ◽  
Author(s):  
Weilong Kong ◽  
Hua Zhong ◽  
Xiaoxiao Deng ◽  
Mayank Gautam ◽  
Ziyun Gong ◽  
...  
Keyword(s):  
Oryza Sativa ◽  
Gene Family ◽  
Salinity Stress ◽  
Common Ancestor ◽  
Oryza Rufipogon ◽  
Oryza Species ◽  
Evolutionary Analysis ◽  
Wild Rice Species ◽  
Oryza Punctata ◽  
Duplication Events

Glycoside Hydrolase 3 (GH3), a member of the Auxin-responsive gene family, is involved in plant growth, the plant developmental process, and various stress responses. The GH3 gene family has been well-studied in Arabidopsis thaliana and Zea mays. However, the evolution of the GH3 gene family in Oryza species remains unknown and the function of the GH3 gene family in Oryza sativa is not well-documented. Here, a systematic analysis was performed in six Oryza species/subspecies, including four wild rice species and two cultivated rice subspecies. A total of 13, 13, 13, 13, 12, and 12 members were identified in O. sativa ssp. japonica, O. sativa ssp. indica, Oryza rufipogon, Oryza nivara, Oryza punctata, and Oryza glumaepatula, respectively. Gene duplication events, structural features, conserved motifs, a phylogenetic analysis, chromosome locations, and Ka/Ks ratios of this important family were found to be strictly conservative across these six Oryza species/subspecies, suggesting that the expansion of the GH3 gene family in Oryza species might be attributed to duplication events, and this expansion could occur in the common ancestor of Oryza species, even in common ancestor of rice tribe (Oryzeae) (23.07~31.01 Mya). The RNA-seq results of different tissues displayed that OsGH3 genes had significantly different expression profiles. Remarkably, the qRT-PCR result after NaCl treatment indicated that the majority of OsGH3 genes play important roles in salinity stress, especially OsGH3-2 and OsGH3-8. This study provides important insights into the evolution of the GH3 gene family in Oryza species and will assist with further investigation of OsGH3 genes’ functions under salinity stress.

Application of indica–japonica single-nucleotide polymorphism markers for diversity analysis of Oryza AA genome species

2014 ◽  
Vol 12 (S1) ◽  
pp. S36-S40 ◽  
Author(s):  
Yoo-Jin Lee ◽  
Michael J. Thomson ◽  
Joong Hyoun Chin
Keyword(s):  
Genetic Relationships ◽  
Snp Markers ◽  
Oryza Rufipogon ◽  
Phylogenetic Study ◽  
Oryza Glaberrima ◽  
Nucleotide Polymorphisms ◽  
Cultivated Rice ◽  
Allele Polymorphism ◽  
Single Nucleotide ◽  
Aa Genome

High-throughput genotyping using single-nucleotide polymorphisms (SNP) is one tool that can be used to study the genetic relationships between wild rice relatives and cultivated rice. In this study, a set of 96 indica–japonica SNP markers, which can differentiate indica and japonica subspecies of rice, were used to characterize 227 Oryza accessions including 93 AA genome accessions from seven wild Oryza species. A total of 72 markers of the 96 markers were selected for the phylogenetic study and allele polymorphism survey. A subset of SNP markers were present only in Oryza sativa and evolutionarily close species, Oryza nivara and Oryza rufipogon. These markers can be used for distinguishing cultivated rice from the other species and vice versa. Eight clusters were generated through phylogenetic analysis, and Oryza meridionalis and Oryza longistaminata appeared to be the most distantly related species to cultivated rice. In this study, Oryza barthii and Oryza glaberrima accessions were found to exhibit high genetic similarity. Across the wild species, more indica-type alleles were detected for most accessions. In this study, a set of markers selected to be informative across O. sativa accessions were used, but it will be interesting to compare the results of this study with SNP data obtained through next-generation sequencing in the future.

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.

Identifying neutral allele Sb at pollen-sterility loci in cultivated rice with Oryza rufipogon origin

2009 ◽  
Vol 54 (20) ◽  
pp. 3813-3821 ◽  
Author(s):  
LeiGang Shi ◽  
XiangDong Liu ◽  
Bo Liu ◽  
XingJuan Zhao ◽  
Lan Wang ◽  
...  
Keyword(s):  
Pollen Sterility ◽  
Oryza Rufipogon ◽  
Cultivated Rice

scholarly journals Screening Oryza Species Plants for Rice Sheath Blight Resistance

Plant Disease ◽  
2002 ◽  
Vol 86 (7) ◽  
pp. 808-812 ◽  
Author(s):  
G. C. Eizenga ◽  
F. N. Lee ◽  
J. N. Rutger
Keyword(s):  
Sheath Blight ◽  
Oryza Species ◽  
Growth Chamber ◽  
Lesion Length ◽  
Cultivated Rice ◽  
Visual Rating ◽  
Leaf Lesion ◽  
Generation Progeny ◽  
Limited Scale ◽  
Moderately Resistant

Rice wild relatives, Oryza species, are one possible source of sheath blight (Rhizoctonia solani) resistance genes. However, Oryza spp. cannot be screened in the field as is done for cultivated rice (O. sativa) because the plant canopy does not favor disease development and many plants drop mature seed. Thus, a growth chamber-greenhouse method of screening Oryza spp. and their early generation progeny is needed. Primary-secondary and ratoon tillers of rice cultivars-germplasm which ranged from moderately resistant to very susceptible were evaluated first for sheath blight susceptibility. Plants were inoculated by placing R. solani-colonized toothpicks at the leaf collar, then incubating plants in a growth chamber. After 7 days, plants were visually rated for sheath blight severity, and the lesion length of each leaf was measured. Ranking of cultivar-germplasm susceptibility by visual rating of primary-secondary tillers corresponded to the ranking from field ratings. Visual ratings correlated best with combined lesion length of the second and third leaves. For ratoon tillers, visual ratings correlated best with second-leaf lesion length. Next, this method was used with ratoon tillers to evaluate sheath blight susceptibility of 21 Oryza spp. accessions and F1 progeny from crosses between 17 accessions and cultivated rice. This method proved useful on a limited scale for screening germplasm that could not be evaluated under field conditions.

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

Temperature affects the dormancy and germination of sympatric annual (Oryza meridionalis) and perennial (O. rufipogon) native Australian rices (Poaceae) and influences their emergence in introduced para grass (Urochloa mutica) swards

2015 ◽  
Vol 63 (8) ◽  
pp. 687 ◽  
Author(s):  
Sean M. Bellairs ◽  
Penelope A. S. Wurm ◽  
Beckie Kernich
Keyword(s):  
Soil Surface ◽  
Field Studies ◽  
Oryza Rufipogon ◽  
Oryza Species ◽  
Northern Australia ◽  
Seed Biology ◽  
Oryza Meridionalis ◽  
Native Grasslands ◽  
Wild Rice Species ◽  
Soil Temperatures

The seed biology of two ecologically and genetically important sympatric wild rice species from northern Australia was compared – perennial Oryza rufipogon Griff. and annual Oryza meridionalis N.Q.Ng. The aim was to determine mechanisms of dormancy exhibited at seed shed and to identify factors that trigger or inhibit germination. This information was used to investigate the ecology of in situ Oryza populations in introduced para grass swards (Urochloa mutica (Forssk.) T.Q. Nguyen) and to understand interactions between the two sympatric Oryza species. Primary dormancy in the two species is similar, namely, non-deep physiological dormancy, determined by external maternal structures and broken by warm temperature treatments equivalent to dry season soil temperatures. Light quality, smoke water, gibberellic acid and nitric acid treatments had minor influences on germination. Changes to the soil profile and aboveground biomass structure due to swards of U. mutica significantly affected emergence of O. meridionalis. Thus the influence of soil temperature explains the results of previous field studies in which biomass or litter on the soil surface prevented germination. This has implications for biodiversity management on monsoonal floodplains of northern Australia, where introduced pasture species produce greater biomass than native grasslands, reduce soil temperatures and are displacing native rices. There were differences between the Oryza species – dormancy was more quickly broken in annual O. meridionalis, reflecting the reduced need for investment in seed bank persistence for annual species in annually inundated and climatically reliable wetlands.

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