Extraordinarily polymorphic ribosomal DNA in wild and cultivated rice

Genome ◽  
1996 ◽  
Vol 39 (6) ◽  
pp. 1109-1116 ◽  
Author(s):  
K. D. Liu ◽  
Qifa Zhang ◽  
G. P. Yang ◽  
M. A. Saghai Maroof ◽  
S. H. Zhu ◽  
...  
Keyword(s):  
Oryza Sativa ◽  
Ribosomal Dna ◽  
Wild Rice ◽  
Indica Rice ◽  
Intergenic Spacer ◽  
Oryza Rufipogon ◽  
Japonica Rice ◽  
Cultivated Rice ◽  
Spacer Length ◽  
Origin And Evolution

A collection of 481 rice accessions was surveyed for ribosomal DNA (rDNA) intergenic spacer length polymorphism to assess the extent of genetic diversity in Chinese and Asian rice germplasm. The materials included 83 accessions of common wild rice, Oryza rufipogon, 75 of which were from China; 348 entries of cultivated rice (Oryza sativa), representing almost all the rice growing areas in China; and 50 cultivars from South and East Asia. A total of 42 spacer length variants (SLVs) were detected. The size differences between adjacent SLVs in the series were very heterogeneous, ranging from ca. 21 to 311 bp. The 42 SLVs formed 80 different rDNA phenotypic combinations. Wild rice displayed a much greater number of rDNA SLVs than cultivated rice, while cultivated rice showed a larger number of rDNA phenotypes. Indica and japonica groups of O. sativa contained about equal numbers of SLVs, but the SLV distribution was significantly differentiated: indica rice was preferentially associated with longer SLVs and japonica rice with shorter ones. The results may have significant implications regarding the origin and evolution of cultivated rice, as well as the inheritance and molecular evolution of rDNA intergenic spacers in rice. Key words : rDNA, Oryza rufipogon, Oryza sativa, germplasm diversity, evolution.

Geographic pattern of variation among Asian native rice cultivars (Oryza sativa L.) based on fifteen isozyme loci

Genome ◽  
1988 ◽  
Vol 30 (5) ◽  
pp. 782-792 ◽  
Author(s):  
J. C. Glaszmann
Keyword(s):  
Genetic Diversity ◽  
Oryza Sativa ◽  
Oryza Sativa L ◽  
Indian Subcontinent ◽  
Indica Rice ◽  
Japonica Rice ◽  
Geographic Pattern ◽  
Cultivated Rice ◽  
Rice Varieties ◽  
Himalayan Foothills

The geographic pattern of isozyme variation among rice varieties (Oryza sativa L.) in Asia is described based on an electrophoretic survey of 1688 accessions for 15 loci. The distribution patterns are strongly determined by the existence of several varietal groups that are characterized by contrasting multilocus types with dissimilar environmental and macrogeographic distributions. The two main groups correspond to the indica and japonica subspecies. Other types are frequently found in the Indian subcontinent, especially along the Himalayan foothills. These types are predominant in the Indus River basin. They are differentiated into four groups in the eastern part of the Himalayan foothills. There is variation within the groups. Non-random allele distributions are observed, such as regional clines and narrow localization of alleles. Diversity among indica rice is evenly distributed in whole tropical Asia. Variation among japonica rice shows the hilly part of continental Southeast Asia to be the region of highest genetic diversity and its probable area of origin. All this information provides a guide for further analysis aimed at elucidating the history of cultivated rice in Asia and, subsequently, in other continents.Key words: Asian rice, genetic diversity, isozymes, geographic distributions.

scholarly journals Phylogeography of Asian wild rice, Oryza rufipogon, reveals multiple independent domestications of cultivated rice, Oryza sativa

2006 ◽  
Vol 103 (25) ◽  
pp. 9578-9583 ◽  
Author(s):  
J. P. Londo ◽  
Y.-C. Chiang ◽  
K.-H. Hung ◽  
T.-Y. Chiang ◽  
B. A. Schaal
Keyword(s):  
Oryza Sativa ◽  
Wild Rice ◽  
Oryza Rufipogon ◽  
Cultivated Rice

Genome-wide SNPs detection by genomic comparison between Dongxiang wild rice (Oryza rufipogon) and cultivated rice Nipponbare (Oryza sativa ssp. japonica)

2017 ◽  
Vol 16 (4) ◽  
pp. 386-389
Author(s):  
Meng Zhang ◽  
Wenyang Huang ◽  
Zijun Xia ◽  
Jiahui Liu ◽  
Jiankun Xie ◽  
...  
Keyword(s):  
Oryza Sativa ◽  
Genetic Markers ◽  
Genome Sequencing ◽  
Wild Rice ◽  
Oryza Rufipogon ◽  
Cultivated Rice ◽  
Genomic Comparison ◽  
Germplasm Resource ◽  
Genome Wide ◽  
Dongxiang Wild Rice

AbstractDongxiang wild rice (Oryza rufipogon, DXWR) exhibits valuable agronomic traits and represents a precious germplasm resource for rice breeding. The use of genetic markers can greatly speed up the breeding process and facilitate research on genetics and genomics. In our previous study, we identified insertion–deletion polymorphisms between DXWR and cultivated rice Nipponbare (Oryza sativa ssp. japonica), using whole-genome sequencing in DXWR. In this study, to further explore the genetic variations and enrich the available genetic markers of DXWR, we identified 1,089,478 single-nucleotide polymorphisms (SNPs) (corresponding to one SNP per 0.33 kb of the genome) by genomic comparison between DXWR and Nipponbare, using the genome sequencing data and bioinformatics approaches. Furthermore, the accuracy of the identified SNPs was also validated by polymerase chain reaction amplification and Sanger sequencing. This genome-wide SNPs identification greatly increases the number of genetic markers available for DXWR and provides new opportunities to exploit this valuable and endangered germplasm resource.

Origin and evolution of aus type fragrant rice (Oryza sativa L.) : A review

2020 ◽  
Vol 57 (3) ◽  
pp. 169-180
Author(s):  
S Das ◽  
CM Khanda
Keyword(s):  
Wild Rice ◽  
Oryza Sativa L ◽  
Abiotic Stress Tolerance ◽  
Japonica Rice ◽  
Biotic And Abiotic Stress ◽  
Cultivated Rice ◽  
Significant Group ◽  
Origin And Evolution ◽  
Fragrant Rice ◽  
Wild Rice Species

Diversity in wild forms and landraces of a crop in a region is an indicator and the core tenet of determining its centre of origin. Jeypore tract of Odisha with diverse rice forms is considered as the earliest, independent rice domestication region of aus ecotype. The aus group of Asian cultivated rice is a distinct population with unique alleles for biotic and abiotic stress tolerance and high genetic diversity even in its fragrant accessions, detected at the molecular level. Annual wild rice Oryza nivara is considered as the progenitor of aus rice. The aus type fragrant rice is the original crop of Indian sub-continent, domesticated in hill areas by primitive tribes, around 4500 years ago. The Chinese japonica rice which came to India later, inherited chloroplast and nuclear genome from wild aus rice and the resulting hybrids formed the aromatic group. Loss or gain of phenotypic characters is the common feature of evolution. The aus landraces possessing characters such as black hull, red pericarp, poor panicle features, low grain yield, associated with wild rice species have evolved into cultivated forms from the intermediate stages of domestication. Considering the archeological evidences, genetic inferences and correlations of different investigations relating to aus type fragrant rice, Jeypore tract is regarded as the place of origin and evolution of this small but significant group of fragrant rice.

Variation of the intergenic spacer region of ribosomal DNA in cultivated and wild rice species

Genome ◽  
1990 ◽  
Vol 33 (2) ◽  
pp. 209-218 ◽  
Author(s):  
Y. Sano ◽  
R. Sano
Keyword(s):  
Ribosomal Dna ◽  
Intergenic Spacer ◽  
Length Variation ◽  
Cultivated Rice ◽  
Spacer Length ◽  
Intergenic Spacer Region ◽  
Wild Rice Species ◽  
Cultivated Species ◽  
Restriction Enzyme Maps ◽  
Spacer Length Variants

Spacer-length variation in ribosomal DNA (rDNA) was surveyed in two cultivated rice species and their wild relatives. Among 243 accessions observed, 18 different spacer-length variants were detected. Length heterogeneity was found within and among species as well as within individuals. Conventional genetic analysis revealed that two spacer-length variants were located at two unlinked loci. Restriction enzyme maps showed that length heterogeneity resulted from repetition of short repeated sequences in the intergenic spacer region in the Asian cultivar and its progenitor; however, the spacer region greatly differed from those of reproductively isolated taxa with respect to the length and the sequence. Furthermore, the Asian cultivated species and its progenitor were highly polymorphic for rDNA spacer-length variation and they were differentiated in frequencies of spacer-length variants as well as varietal groups within the cultivated species. Asian cultivars tended to carry homogeneous repeats of rDNA compared with their progenitor, suggesting different forms of homogenization occurring in Asian cultivars.Key words: ribosomal DNA, intergenic spacer, polymorphism, inheritance, Oryza.

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.

Sign in / Sign up

Export Citation Format

Share Document