Pollen competition between cultivated and wild rice species (Oryza sativa and O. rufipogon)

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.

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Preferential occurrence of diazotrophic endophytes, Azoarcus spp., in wild rice species and land races of Oryza sativa in comparison with modern races

Environmental Microbiology ◽

10.1046/j.1462-2920.2000.00078.x ◽

2000 ◽

Vol 2 (2) ◽

pp. 131-141 ◽

Cited By ~ 125

Author(s):

Margret Engelhard ◽

Thomas Hurek ◽

Barbara Reinhold-Hurek

Keyword(s):

Oryza Sativa ◽

Wild Rice ◽

Land Races ◽

Wild Rice Species ◽

Diazotrophic Endophytes

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Genetic differentiation among Sri Lankan traditional rice (Oryza sativa) varieties and wild rice species by AFLP markers

Nordic Journal of Botany ◽

10.1111/j.1756-1051.2011.00998.x ◽

2011 ◽

Vol 29 (2) ◽

pp. 238-243 ◽

Cited By ~ 1

Author(s):

Gowri Rajkumar ◽

Jagathpriya Weerasena ◽

Kumudu Fernando ◽

Athula Liyanage ◽

Rangika Silva

Keyword(s):

Oryza Sativa ◽

Genetic Differentiation ◽

Wild Rice ◽

Aflp Markers ◽

Sri Lankan ◽

Wild Rice Species ◽

Traditional Rice

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

Scientific Reports ◽

10.1038/s41598-021-88533-9 ◽

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.

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Characterization of Interspecific Hybrids Between Oryza sativa L. and Three Wild Rice Species of China by Genomic In Situ Hybridization

Journal of Integrative Plant Biology ◽

10.1111/j.1744-7909.2006.00336.x ◽

2006 ◽

Vol 48 (9) ◽

pp. 1077-1083 ◽

Cited By ~ 3

Author(s):

Guang-Xuan Tan ◽

Zhi-Yong Xiong ◽

Hua-Jun Jin ◽

Gang Li ◽

Li-Li Zhu ◽

...

Keyword(s):

Oryza Sativa ◽

In Situ Hybridization ◽

Wild Rice ◽

Interspecific Hybrids ◽

Oryza Sativa L ◽

Genomic In Situ Hybridization ◽

Wild Rice Species

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Nipponbare and wild rice species as unexpected tolerance and susceptibility sources against Schizotetranychus oryzae (Acari: Tetranychidae) mite infestation

10.1101/2020.01.22.914184 ◽

2020 ◽

Author(s):

Giseli Bufon ◽

Édina Aparecida dos Reis Blasi ◽

Thainá Inês Lamb ◽

Janete Mariza Adamski ◽

Joséli Schwambach ◽

...

Keyword(s):

Oryza Sativa ◽

Wild Rice ◽

Energy Production ◽

Leaf Damage ◽

Mite Infestation ◽

Oryza Glaberrima ◽

Primary Metabolism ◽

Wild Rice Species ◽

Related Proteins ◽

Differentially Abundant Proteins

AbstractCultivated rice (Oryza sativa L.) is frequently exposed to multiple stresses, including Schizotetranychus oryzae mite infestation. Rice domestication has narrowed the genetic diversity of the species, reducing the stress resistance and leading to a wide susceptibility. Therefore, wild rice species present an alternative to search for this lost variability. Aiming to observe the response of two wild rice species (Oryza barthii and Oryza glaberrima) and two Oryza sativa genotypes (cv. Nipponbare and O. sativa f. spontanea) to S. oryzae infestation, we used agronomic, physiological and molecular analyses. Surprisingly, analyses of leaf damage, histochemistry, chlorophyll concentration and chlorophyll fluorescence showed that the wild species present higher level of leaf damage, increased accumulation of H2O2 and lower photosynthetic capacity when compared to O. sativa genotypes under infested conditions. Infestation did not affect plant height, but decreased tiller number, except in cv. Nipponbare, whose development was not affected. Infestation also caused the death of wild plants during the reproductive stage, unlike O. sativa genotypes, which were able to tolerate stress and produce seeds. While infestation did not affect the weight of 1,000 grains in both O. sativa genotypes, the number of panicles per plant was affected only in O. sativa f. spontanea, and the percentage of full seeds per panicle and seed length were increased only in cv. Nipponbare. Proteomic analysis allowed us to identify 195 differentially abundant proteins when comparing susceptible (O. barthii) and tolerant (O. sativa cv. Nipponbare) genotypes under control and infested conditions. We found that O. barthii has a less abundant antioxidant arsenal. In addition, it is unable to modulate proteins involved with general metabolism and energy production under infested condition. In Nipponbare we found high abundance of detoxification-related proteins, general metabolic processes and energy production, which allows us to suggest that, under infested condition, the primary metabolism is maintained more active compared to O. barthii. Also, Nipponbare presents a greater abundance of defense-related proteins, such as osmotin, ricin B-like lectin, and protease inhibitors of the Bowman Birk trypsin inhibitor family, as well as higher levels of the compatible osmolyte Proline under infested condition. Identification of these differentially abundant proteins can be used as an important biotechnological tool in breeding programs that aim increased tolerance to phytophagous mite infestation.

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Weedy Rice (Oryza spp.): What’s In a Name?

Weed Science ◽

10.1017/wsc.2021.22 ◽

2021 ◽

pp. 1-36

Author(s):

Nilda Roma-Burgos ◽

Maggie Pui San Sudo ◽

Kenneth M. Olsen ◽

Isabel Werle ◽

Beng-Kah Song

Keyword(s):

Oryza Sativa ◽

Wild Rice ◽

Weedy Rice ◽

Ganges River ◽

Cultivated Rice ◽

Wild Progenitor ◽

Wild Rice Species ◽

Proper Name ◽

Direct Seeded ◽

The Ganges

Abstract There are two species of cultivated rice in the world - Oryza sativa L. from Asia and O. glaberrima from Africa. The former was domesticated from the wild progenitor, O. rufipogon and the latter from the African wild rice species O. barthii. The first known center of rice cultivation in China generated the O. sativa subspecies japonica. The indica subspecies arose from the second center of domestication in the Ganges River plains of India. Variants of domesticated lines and the continuous hybridization between cultivated varieties and the wild progenitor(s) resulted in weedy rice types. Some weedy types resemble the wild ancestor, but the majority of weedy rices today bear close resemblance to cultivated rice. Weedy rice accompanies rice culture and has increased in occurrence with the global shift in rice establishment from transplanting to direct-seeded, or dry-drill-seeded rice. Weedy rice (Oryza spp.) is the most-difficult-weed to control in rice, causing as much as 90% yield loss or abandonment of severely infested fields. The gene flow continuum between cultivar and weedy rice or wild relative, crop dedomestication, and regionalized adaptation has resulted in a myriad of weedy rice types. The complex lineage of weedy rice has resulted in confusion of weedy rice nomenclature. Two names are generally used for weedy rice – O. sativa L. and O. sativa f. spontanea. Genomic data shows that Oryza sativa L. applies to weedy rice populations derived from cultivated O. sativa whereas spontanea applies only to weedy types that primarily descended from O. rufipogon. Neither of these names apply to African weedy rice, which are of African wild rice, or O. glaberrima lineage. Therefore, unless the lineage of the weedy population in question is known, the proper name to use is the generalized name Oryza spp.

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