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.

Genome-wide genic SSR marker development for the endangered Dongxiang wild rice (Oryza rufipogon)

2016 ◽  
Vol 15 (6) ◽  
pp. 566-569
Author(s):  
Jiankun Xie ◽  
Meng Zhang ◽  
Jia Sun ◽  
Fantao Zhang
Keyword(s):  
Ssr Markers ◽  
Wild Rice ◽  
Pcr Amplification ◽  
Oryza Rufipogon ◽  
Sequencing Technology ◽  
Cultivated Rice ◽  
Genic Ssr ◽  
Genome Wide ◽  
Dongxiang Wild Rice ◽  
Simple Sequence

AbstractDongxiang wild rice (Oryza rufipogon, DXWR), one of the species of common wild rice, is regarded as an important genetic resource for the improvement of cultivated rice (Oryza sativa). Molecular markers are reliable tools that can greatly accelerate the breeding process and have been widely used in various species. In the present study, a total of 3681 genic simple sequence repeat (SSR) markers were developed for DXWR based on transcriptome sequencing technology. Additionally, 25 primer pairs were randomly selected and synthesized for the verification. Among them, 18 (72%) primer pairs were successfully amplified in PCR amplification with genomic DNA of DXWR and also had abundant polymorphisms between DXWR and cultivated rice. These novel genic SSR markers will enrich current genomic resources for DXWR, and provide an effective tool for genetic study and molecular marker assisted breeding for this valuable and endangered germplasm.

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.

scholarly journals Genome-wide development of lncRNA-derived-SSR markers for Dongxiang wild rice (Oryza rufipogon Griff.)

2021 ◽  
Author(s):  
Wanling Yang ◽  
Yuanwei Fan ◽  
Yong Chen ◽  
Gumu Ding ◽  
Hu Liu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Stress Responses ◽  
Wild Rice ◽  
Diversity Index ◽  
Oryza Rufipogon ◽  
Coding Sequences ◽  
Genome Wide ◽  
Ssr Loci ◽  
Dongxiang Wild Rice

AbstractDongxiang wild rice (Oryza rufipogon Griff., DXWR) is the northernmost distributed common wild rice found in the world. It contains a large number of agronomically valuable genes, which makes it a natural gene pool for rice breeding. Molecular markers, especially simple repeat sequence (SSR) markers, play important roles in crop breeding. Although a large number of SSR markers have been developed, most of them are derived from the genome coding sequences, rarely from non-coding sequences. Meanwhile, long non-coding RNAs (lncRNAs), which are derived from the transcription of non-coding sequences, play vital roles in plant growth, development and stress responses. In this study, 1878 SSR loci were detected from the lncRNA sequences of DXWR, and 1258 lncRNA-derived-SSR markers were developed on the genome-wide scale. To verify the validity and applicability of these markers, 72 pairs of primers were randomly selected to test 44 rice materials. The results showed that 42 (58.33%) pairs of primers have abundant polymorphism among these rice materials; the polymorphism information content (PIC) values ranged from 0.04 to 0.87 with an average of 0.50; the genetic diversity index of SSR loci varied from 0.04 to 0.88 with an average of 0.56; and the number of alleles per marker ranged from 2 to 11 with an average of 4.36. Thus, we concluded that these lncRNA-derived-SSR markers are a very useful source for future basic and applied research, including genetic diversity analysis, QTL mapping, and molecular breeding programs, to make good use of the elite lncRNA genes from DXWR.

scholarly journals Diversity of Domestication Loci in Wild Rice Populations

Proceedings ◽  
2019 ◽  
Vol 36 (1) ◽  
pp. 14
Author(s):  
Hasan ◽  
Furtado ◽  
Henry
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Wild Rice ◽  
Genetic Manipulation ◽  
Starch Synthesis ◽  
Oryza Rufipogon ◽  
Whole Genome ◽  
Nucleotide Polymorphisms ◽  
Wild Populations ◽  
Cultivated Rice

Domestication syndrome, i.e. seed shattering, seed dormancy and plant architecture have been selected during the domestication of wild rice around 10,000 years ago. These traits evolved through a series of genomic modifications, including selection of nucleotide polymorphisms resulting from spontaneous mutations, recombination, and fixation of alleles and were incorporated into cultivated rice by hybridization or introgression. The Australian wild rice populations are geographically and genetically distinct and free from genetic exchange with cultivated rice unlike the wild populations in Asia. Furthermore, recent studies reveal they have numerous traits of value and unique alleles. Therefore, these populations seem to be suitable to use to investigate the genetic basis of domestication traits as well as other important traits. In this study, we aim to determine the origin and role of domestication loci using two Australian wild populations: Taxa A (like Oryza rufipogon) and Taxa B (like Oryza meridionalis) endemic near Cairns, Northern Queensland. To do so, firstly, we will analyse the variation of domestication loci in these two wild populations by the comparison with cultivated rice (Oryza sativa spp. japonica cv. Nipponbare) using the whole genome sequencing. Secondly, we will look at the gene expression of the domestication loci at different seed development stages using transcriptomics. Thirdly, we will determine the variation of starch synthesis related genes using whole genome sequencing. Next generation sequencing along with a set of bioinformatics tools will be applied. This research may enlighten our understanding about the domestication process as well as provide insights into how to domesticate these species through genetic manipulation for commercial purpose.

Application of SV markers developed from Dongxiang common wild rice in analysis of cultivated rice

2019 ◽  
Vol 17 (5) ◽  
pp. 448-451
Author(s):  
Fantao Zhang ◽  
Yuan Luo ◽  
Bin Ai ◽  
Yong Chen ◽  
Weidong Qi ◽  
...  
Keyword(s):  
Wild Rice ◽  
Oryza Rufipogon ◽  
Genomic Research ◽  
Cultivated Rice ◽  
Structural Variations ◽  
Rice Varieties ◽  
Common Wild Rice ◽  
Genome Wide ◽  
Rice Chromosomes ◽  
Molecular Marker Development

AbstractDongxiang common wild rice (Oryza rufipogon Griff., DXWR) is an important genetic resource for the improvement of cultivated rice. For the past three decades, great achievements have been made in the field of molecular marker development. Although structural variations (SVs) had been studied between DXWR and Nipponbare (Oryza sativa L. ssp. japonica), the development and application of SV markers in DXWR has not been reported. In this study, based on the genome-wide SV loci, we developed and synthesized a total of 195 SV markers that were evenly distributed across the 12 rice chromosomes. Then, these markers were tested for their stabilities and polymorphisms. Of these 195 markers, 147 (75.4%) were successfully amplified and displayed abundant polymorphisms between DXWR and Nipponbare. Meanwhile, through the genotyping of 20 rice varieties from 13 countries and areas, we concluded that these SV markers have a wide application prospect in the analysis of cultivated rice. Therefore, these molecular markers greatly enrich the number of markers available for DXWR, which will facilitate genomic research and molecular breeding for this important and endangered germplasm resource.

scholarly journals Development of Chromosome Segment Substitution Lines (CSSLs) Derived from Guangxi Wild Rice (Oryza rufipogon Griff.) under Rice (Oryza sativa L.) Background and the Identification of QTLs for Plant Architecture, Agronomic Traits and Cold Tolerance

Genes ◽  
2020 ◽  
Vol 11 (9) ◽  
pp. 980
Author(s):  
Ruizhi Yuan ◽  
Neng Zhao ◽  
Babar Usman ◽  
Liang Luo ◽  
Shanyue Liao ◽  
...  
Keyword(s):  
Oryza Sativa ◽  
Fine Mapping ◽  
Wild Rice ◽  
Oryza Rufipogon ◽  
Chromosome Segment ◽  
Substitution Lines ◽  
Chromosome Segment Substitution Lines ◽  
Genome Wide ◽  
Oryza Rufipogon Griff ◽  
Segment Substitution

Common wild rice contains valuable resources of novel alleles for rice improvement. It is well known that genetic populations provide the basis for a wide range of genetic and genomic studies. In particular, chromosome segment substitution lines (CSSLs) ais a powerful tool for fine mapping of quantitative traits, new gene discovery and marker-assisted breeding. In this study, 132 CSSLs were developed from a cultivated rice (Oryza sativa) cultivar (93-11) and common wild rice (Oryza rufipogon Griff. DP30) by selfing-crossing, backcrossing and marker-assisted selection (MAS). Based on the high-throughput sequencing of the 93-11 and DP30, 285 pairs of Insertion-deletions (InDel) markers were selected with an average distance of 1.23 Mb. The length of this DP30-CSSLs library was 536.4 cM. The coverage rate of substitution lines cumulatively overlapping the whole genome of DP30 was about 91.55%. DP30-CSSLs were used to analyze the variation for 17 traits leading to the detection of 36 quantitative trait loci (QTLs) with significant phenotypic effects. A cold-tolerant line (RZ) was selected to construct a secondary mapping F2 population, which revealed that qCT2.1 is in the 1.7 Mb region of chromosome 2. These CSSLs may, therefore, provide powerful tools for genome wide large-scale gene discovery in wild rice. This research will also facilitate fine mapping and cloning of QTLs and genome-wide study of wild rice. Moreover, these CSSLs will provide a foundation for rice variety improvement.

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
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