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

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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Development of a core collection from Sri Lankan traditional rice (Oryza sativa) varieties for phenotypic and genetic diversity

Nusantara Bioscience ◽

10.13057/nusbiosci/n130109 ◽

2021 ◽

Vol 13 (1) ◽

Author(s):

Shyama Weerakoon ◽

Seneviratne Somaratne

Keyword(s):

Genetic Diversity ◽

Oryza Sativa ◽

Sri Lanka ◽

Core Collection ◽

Morphological Characters ◽

Morphological Features ◽

Sri Lankan ◽

Rice Varieties ◽

Traditional Rice ◽

Phenotypic And Genetic Diversity

Abstract. Weerakoon SR, Somaratne S. 2021. Development of a core collection from Sri Lankan traditional rice (Oryza sativa) varieties for phenotypic and genetic diversity. Nusantara Bioscience 13: 61-67. A collection of over 2000 traditional rice varieties are conserved at Gene Bank, Plant Genetics Resource Center, Sri Lanka. Oryza sativa varieties grown in Sri Lanka from ancient times to the middle of the last century are known as traditional rice. These varieties show adaptability to biotic and abiotic stresses and, an important component of biodiversity of Sri Lanka. A detailed understanding of the diversity of traditional rice varieties is essential for effective utilization of rice genetic resources and identification of potential parents possessing valuable genetic traits for future crop improvement. Study objectives were phenotypic and molecular characterization of one-hundred traditional rice varieties and to identify a core collection for phenotypic and genetic diversity. Rice varieties were grown in a plant house following RCBD with 4 replicates and 5 plants per replicate. Thirty-two agro-morphological characters were observed/collected. Genomic DNA was extracted from 20-days-old seedlings. Thirty?three microsatellite (Simple Sequence Repeat-SSR) primer pairs were used to assay genetic variation and PCR products were subjected to fragment analysis by capillary electrophoresis. Descriptive statistics and basic inferential statistical analyses were performed to access variation of agro-morphological characters among rice varieties. Cluster analysis and Multidimensional scaling produced 07 groups which were further analyzed using Classification and Regression Analysis to extract the diagnostic agro-morphological features. Groups of rice varieties were characterized by lemma palea color, awn color at maturity, seedling height, and flag-leaf angle. Traditional varieties represent distant clusters on agro-morphological features. Molecular analyses revealed all 33 loci displayed polymorphism (66.7-96.9%) among 100 traditional rice varieties with a total of 387 alleles identified with an average of 11.72 alleles per variety. All varieties were genetically structured into fifteen well-separated groups. UPGMA analysis based on Jaccard's similarity separated varieties into 05 major clusters. Genetic diversity information is useful in the efficient use of Sri Lankan rice germplasm and managing in situ and ex situ germplasm collections in conserving traditional rice varieties.

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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 for nuclear, mitochondrial and chloroplast genomes in common wild rice (Oryza rufipogon Griff.) and cultivated rice (Oryza sativa L.)

Theoretical and Applied Genetics ◽

10.1007/s00122-002-0878-4 ◽

2002 ◽

Vol 104 (8) ◽

pp. 1335-1345 ◽

Cited By ~ 53

Author(s):

C. Sun ◽

X. Wang ◽

A. Yoshimura ◽

K. Doi

Keyword(s):

Oryza Sativa ◽

Genetic Differentiation ◽

Wild Rice ◽

Oryza Sativa L ◽

Oryza Rufipogon ◽

Cultivated Rice ◽

Common Wild Rice ◽

Chloroplast Genomes ◽

Oryza Rufipogon Griff

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

New Phytologist ◽

10.1046/j.0028-646x.2001.00319.x ◽

2002 ◽

Vol 153 (2) ◽

pp. 289-296 ◽

Cited By ~ 62

Author(s):

Zhiping Song ◽

Baorong Lu ◽

Yingguo Zhu ◽

Jiakuan Chen

Keyword(s):

Oryza Sativa ◽

Wild Rice ◽

Pollen Competition ◽

Wild Rice Species

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Genetic Structure and Geographical Differentiation of Traditional Rice (Oryza sativa L.) from Northern Vietnam

Plants ◽

10.3390/plants10102094 ◽

2021 ◽

Vol 10 (10) ◽

pp. 2094

Author(s):

Ngoc Ha Luong ◽

Le-Hung Linh ◽

Kyu-Chan Shim ◽

Cheryl Adeva ◽

Hyun-Sook Lee ◽

...

Keyword(s):

Genetic Diversity ◽

Oryza Sativa ◽

Genetic Differentiation ◽

Oryza Sativa L ◽

Crop Improvement ◽

Fixation Index ◽

Northern Vietnam ◽

Rice Landraces ◽

Geographical Regions ◽

Traditional Rice

Northern Vietnam is one of the most important centers of genetic diversity for cultivated rice. Over thousands of years of cultivation, natural and artificial selection has preserved many traditional rice landraces in northern Vietnam due to its geographic situation, climatic conditions, and many ethnic groups. These local landraces serve as a rich source of genetic variation—an important resource for future crop improvement. In this study, we determined the genetic diversity and population structure of 79 rice landraces collected from northern Vietnam and 19 rice accessions collected from different countries. In total, 98 rice accessions could be differentiated into japonica and indica with moderate genetic diversity and a polymorphism information content of 0.382. Moreover, we found that genetic differentiation was related to geographical regions with an overall PhiPT (analog of fixation index FST) value of 0.130. We also detected subspecies-specific markers to classify rice (Oryza sativa L.) into indica and japonica. Additionally, we detected five marker-trait associations and rare alleles that can be applied in future breeding programs. Our results suggest that rice landraces in northern Vietnam have a dynamic genetic system that can create different levels of genetic differentiation among regions, but also maintain a balanced genetic diversity between regions.

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