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

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.

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

Plants ◽

10.3390/plants8100398 ◽

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.

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Classification and relationships of rice strains with AA genome by identification of transposable elements at nine loci

Genes & Genetic Systems ◽

10.1266/ggs.68.205 ◽

1993 ◽

Vol 68 (3) ◽

pp. 205-217

Author(s):

Kayoko MOCHIZUKI ◽

Hisako OHTSUBO ◽

Hiro-Yuki HIRANO ◽

Yoshio SANO ◽

Eiichi OHTSUBO

Keyword(s):

Transposable Elements ◽

Aa Genome

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Genetic structure of three Oryza AA genome species (O. rufipogon, O. nivara and O. sativa) as assessed by SSR analysis on the Vientiane Plain of Laos

Conservation Genetics ◽

10.1007/s10592-006-9156-3 ◽

2006 ◽

Vol 8 (1) ◽

pp. 149-158 ◽

Cited By ~ 21

Author(s):

Yosuke Kuroda ◽

Yo-Ichiro Sato ◽

Chay Bounphanousay ◽

Yasuyuki Kono ◽

Koji Tanaka

Keyword(s):

Genetic Structure ◽

Genome Species ◽

Ssr Analysis ◽

Aa Genome

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Polymorphisms and evolutionary history of retrotransposon insertions in rice promoters

Genome ◽

10.1139/g11-030 ◽

2011 ◽

Vol 54 (8) ◽

pp. 629-638 ◽

Cited By ~ 7

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.

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Transposable elements in the genome of the lichen-forming fungus Umbilicaria pustulata, and their distribution in different climate zones along elevation

10.1101/2021.06.24.448634 ◽

2021 ◽

Author(s):

Francesco Dal Grande ◽

Veronique Jamilloux ◽

Nathalie Choisne ◽

Anjuli Calchera ◽

Malte Petersen ◽

...

Keyword(s):

Transposable Elements ◽

Phenotypic Diversity ◽

Elevation Gradients ◽

Climate Niche ◽

Fungal Evolution ◽

Specific Distribution ◽

Fungal Adaptation ◽

The Impact ◽

Insertion Frequency

Background: Transposable elements (TEs) are an important source of genome plasticity across the tree of life. Accumulating evidence suggests that TEs may not be randomly distributed in the genome. Drift and natural selection are important forces shaping TE distribution and accumulation, acting directly on the TE element or indirectly on the host species. Fungi, with their multifaceted phenotypic diversity and relatively small genome size, are ideal models to study the role of TEs in genome evolution and their impact on the host's ecological and life history traits. Here we present an account of all TEs found in a high-quality reference genome of the lichen-forming fungus Umbilicaria pustulata, a macrolichen species comprising two climatic ecotypes: Mediterranean and cold-temperate. We trace the occurrence of the newly identified TEs in populations along three replicated elevation gradients using a Pool-Seq approach, to identify TE insertions of potential adaptive significance. Results: We found that TEs cover 21.26 % of the 32.9 Mbp genome, with LTR Gypsy and Copia clades being the most common TEs. Out of a total of 182 TE copies we identified 28 insertions displaying consistent insertion frequency differences between the two host ecotypes across the elevation gradients. Most of the highly differentiated insertions were located near genes, indicating a putative function. Conclusions: This pioneering study into the content and climate niche-specific distribution of TEs in a lichen-forming fungus contributes to understanding the roles of TEs in fungal evolution. Particularly, it may serve as a foundation for assessing the impact of TE dynamics on fungal adaptation to the abiotic environment, and the impact of TE activity on the evolution and maintenance of a symbiotic lifestyle.

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