Analysis of random and specific sequences of nuclear and cytoplasmic DNA in diploid and tetraploid American wild rice species (Oryza spp.)

Genome ◽  
2001 ◽  
Vol 44 (3) ◽  
pp. 476-494 ◽  
Author(s):  
Glaucia Salles Cortopassi Buso ◽  
Paulo Hideo Nakano Rangel ◽  
Márcio Elias Ferreira
Keyword(s):  
Flow Cytometry ◽  
Wild Rice ◽  
Phylogenetic Trees ◽  
Rapd Markers ◽  
Diploid Species ◽  
Distinct Species ◽  
Individual Species ◽  
Genome Species ◽  
Wild Rice Species ◽  
Cladistic Analyses

A sample of American wild rice and other accessions of the genus Oryza were studied at polymorphic regions of nuclear, mitochondrial, and chloroplastic genomes. First, flow cytometry, genome-specific RAPD markers, and chromosome counting were utilized to verify the original ploidy and classification of 230 accessions studied. Based on these methods, 8% of the accessions were considered to be misclassified either taxonomically or as a result of contamination. Second, a fine resolution analysis was conducted at genomic regions sampled at random by RAPD markers and at specific sites of the chloroplast and mitochondrial DNA by cleaved amplified polymorphic sequence (CAPS) analysis. Phylogenetic trees resulting from phenetic and cladistic analyses of RAPD, cpDNA, and mtDNA polymorphisms were obtained. The results indicated that the American diploid species O. glumaepatula should be considered an individual species, distinct from O. rufipogon, and confirmed that the American tetraploid species (O. alta, O. grandiglumis, and O. latifolia) belong to the O. officinalis complex. The data indicate that these species should still be treated as a group rather than as three distinct species and that their closest relative is a CC-genome species. It was estimated that the diploid and tetraploid American species diverged from O. sativa – O. nivara (AA genome) and CC- and BBCC-genome species, respectively, 20 million years ago.Key words: RAPD, cleaved amplified polymorphic sequences, flow cytometry, Oryza glumaepatula, rice evolution.

scholarly journals The use of chloroplast genome sequences to solve phylogenetic incongruences inPolystachyaHook (Orchidaceae Juss)

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4916 ◽  
Author(s):  
Narjara Lopes de Abreu ◽  
Ruy José Válka Alves ◽  
Sérgio Ricardo Sodré Cardoso ◽  
Yann J.K. Bertrand ◽  
Filipe Sousa ◽  
...  
Keyword(s):  
Phylogenetic Trees ◽  
Plastid Genome ◽  
Diploid Species ◽  
Distinct Species ◽  
Reticulate Evolution ◽  
Model Organisms ◽  
Current Evidence ◽  
Genomic Libraries ◽  
Coding Regions ◽  
Phylogenetic Implications

BackgroundCurrent evidence suggests that for more robust estimates of species tree and divergence times, several unlinked genes are required. However, most phylogenetic trees for non-model organisms are based on single sequences or just a few regions, using traditional sequencing methods. Techniques for massive parallel sequencing or next generation sequencing (NGS) are an alternative to traditional methods that allow access to hundreds of DNA regions. Here we use this approach to resolve the phylogenetic incongruence found inPolystachyaHook. (Orchidaceae), a genus that stands out due to several interesting aspects, including cytological (polyploid and diploid species), evolutionary (reticulate evolution) and biogeographical (species widely distributed in the tropics and high endemism in Brazil). The genus has a notoriously complicated taxonomy, with several sections that are widely used but probably not monophyletic.MethodsWe generated the complete plastid genome of 40 individuals from one clade within the genus. The method consisted in construction of genomic libraries, hybridization to RNA probes designed from available sequences of a related species, and subsequent sequencing of the product. We also tested how well a smaller sample of the plastid genome would perform in phylogenetic inference in two ways: by duplicating a fast region and analyzing multiple copies of this dataset, and by sampling without replacement from all non-coding regions in our alignment. We further examined the phylogenetic implications of non-coding sequences that appear to have undergone hairpin inversions (reverse complemented sequences associated with small loops).ResultsWe retrieved 131,214 bp, including coding and non-coding regions of the plastid genome. The phylogeny was able to fully resolve the relationships among all species in the targeted clade with high support values. The first divergent species are represented by African accessions and the most recent ones are among Neotropical species.DiscussionOur results indicate that using the entire plastid genome is a better option than screening highly variable markers, especially when the expected tree is likely to contain many short branches. The phylogeny inferred is consistent with the proposed origin of the genus, showing a probable origin in Africa, with later dispersal into the Neotropics, as evidenced by a clade containing all Neotropical individuals. The multiple positions ofPolystachya concreta(Jacq.) Garay & Sweet in the phylogeny are explained by allotetraploidy.Polystachya estrellensisRchb.f. can be considered a genetically distinct species fromP. concretaandP. foliosa(Lindl.) Rchb.f., but the delimitation ofP. concretaremains uncertain. Our study shows that NGS provides a powerful tool for inferring relationships at low taxonomic levels, even in taxonomically challenging groups with short branches and intricate morphology.

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.

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

Nonreciprocal Hybridization Failure in Crosses Between Annual Wild-Rice Species (Zizania palustris x Z. aquatica: Poaceae)

1988 ◽  
Vol 13 (2) ◽  
pp. 229 ◽  
Author(s):  
Melvin R. Duvall ◽  
David D. Biesboer
Keyword(s):  
Wild Rice ◽  
Zizania Palustris ◽  
Wild Rice Species

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.

Inter- and intra-specific distribution of Stowaway transposable elements in AA-genome species of wild rice

2000 ◽  
Vol 101 (3) ◽  
pp. 327-335 ◽  
Author(s):  
A. Kanazawa ◽  
M. Akimoto ◽  
H. Morishima ◽  
Y. Shimamoto
Keyword(s):  
Transposable Elements ◽  
Wild Rice ◽  
Genome Species ◽  
Specific Distribution ◽  
Aa Genome
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