Identification of novel insertion–deletion markers for Dongxiang wild rice (Oryza rufipogon Griff.) using high-throughput sequencing technology

2015 ◽  
Vol 94 (S2) ◽  
pp. 51-55 ◽  
Author(s):  
FANTAO ZHANG ◽  
LIANGXING ZHANG ◽  
FENGLEI CUI ◽  
XIANGDONG LUO ◽  
YI ZHOU ◽  
...  
Keyword(s):  
High Throughput ◽  
Wild Rice ◽  
High Throughput Sequencing ◽  
Oryza Rufipogon ◽  
Sequencing Technology ◽  
Oryza Rufipogon Griff ◽  
Dongxiang Wild Rice

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.

scholarly journals Identification, Analysis, and Confirmation of Seed Storability-Related Loci in Dongxiang Wild Rice (Oryza rufipogon Griff.)

Genes ◽  
2021 ◽  
Vol 12 (11) ◽  
pp. 1831
Author(s):  
Minmin Zhao ◽  
Biaolin Hu ◽  
Yuanwei Fan ◽  
Gumu Ding ◽  
Wanling Yang ◽  
...  
Keyword(s):  
Wild Rice ◽  
Bulked Segregant Analysis ◽  
Oryza Rufipogon ◽  
Chromosome 9 ◽  
Rice Seed ◽  
Rice Varieties ◽  
Oryza Rufipogon Griff ◽  
Dongxiang Wild Rice ◽  
Candidate Loci ◽  
Seed Storability

Dongxiang wild rice (Oryza rufipogon Griff.) (DXWR) has strong seed storability and identifying its elite gene resources may facilitate genetic improvements in rice seed storability. In this study, we developed two backcross inbred lines (BILs) populations, with DXWR as a common donor parent and two rice varieties (F6 and R974) as recipient parents. Bulked segregant analysis via whole genome sequencing (BSA-seq) was used to identify seed storability-related loci in the DXWR and F6 population. Two main genomic regions containing 18,550,000–20,870,000 bp on chromosome 4 and 7,860,000–9,780,000 bp on chromosome 9 were identified as candidate loci of DXWR seed storability; these overlapped partially with seed storability-related quantitative trait loci (QTLs) discovered in previous studies, suggesting that these loci may provide important regions for isolating the responsible genes. In total, 448 annotated genes were predicted within the identified regions, of which 274 and 82 had nonsynonymous and frameshift mutations, respectively. We detected extensive metabolic activities and cellular processes during seed storability and confirmed the effects of the seed storability-related candidate loci using four BILs from DXWR and R974. These results may facilitate the cloning of DXWR seed storability-related genes, thereby elucidating rice seed storability and its improvement potential.

Analysis of Quantitative Trait Loci for Resistance to Brown Planthopper in Dongxiang Wild Rice (Oryza rufipogon Griff.)

2012 ◽  
Vol 38 (2) ◽  
pp. 210-214 ◽  
Author(s):  
De-Run HUANG ◽  
Jie CHEN ◽  
Feng-Xiang LAI ◽  
Guang-Jie LIU ◽  
Jie-Yun ZHUANG
Keyword(s):  
Quantitative Trait Loci ◽  
Quantitative Trait ◽  
Wild Rice ◽  
Brown Planthopper ◽  
Oryza Rufipogon ◽  
Oryza Rufipogon Griff ◽  
Trait Loci ◽  
Dongxiang Wild Rice

scholarly journals Molecular identification of the cytoplasmic male sterile source from Dongxiang wild rice (Oryza rufipogon Griff.)

2017 ◽  
Vol 16 (8) ◽  
pp. 1669-1675 ◽  
Author(s):  
Song YAN ◽  
Shan ZHU ◽  
Ling-hua MAO ◽  
Ren-liang HUANG ◽  
Hong-liang XIONG ◽  
...  
Keyword(s):  
Molecular Identification ◽  
Wild Rice ◽  
Oryza Rufipogon ◽  
Male Sterile ◽  
Cytoplasmic Male Sterile ◽  
Oryza Rufipogon Griff ◽  
Dongxiang Wild Rice

scholarly journals Transcriptome Analysis of Salt Stress Responsiveness in the Seedlings of Dongxiang Wild Rice (Oryza rufipogon Griff.)

PLoS ONE ◽  
2016 ◽  
Vol 11 (1) ◽  
pp. e0146242 ◽  
Author(s):  
Yi Zhou ◽  
Ping Yang ◽  
Fenglei Cui ◽  
Fantao Zhang ◽  
Xiangdong Luo ◽  
...  
Keyword(s):  
Salt Stress ◽  
Transcriptome Analysis ◽  
Wild Rice ◽  
Oryza Rufipogon ◽  
Oryza Rufipogon Griff ◽  
Stress Responsiveness ◽  
Dongxiang Wild Rice

scholarly journals Development and verification of SSR markers from drought stress-responsive miRNAs in common wild rice

2021 ◽  
Author(s):  
Yong Chen ◽  
Yuanwei Fan ◽  
Wanling Yang ◽  
Gumu Ding ◽  
Minmin Zhao ◽  
...  
Keyword(s):  
Drought Stress ◽  
Ssr Markers ◽  
Wild Rice ◽  
Oryza Rufipogon ◽  
Rice Varieties ◽  
Common Wild Rice ◽  
Oryza Rufipogon Griff ◽  
Rice Chromosomes ◽  
Ssr Loci ◽  
Dongxiang Wild Rice

PREMISE: Dongxiang wild rice (Oryza rufipogon Griff., DXWR) is the northernmost common wild rice found in the world, which possesses abundant elite genetic resources. We developed a set of drought stress-responsive microRNA (miRNA)-based single sequence repeat (SSR) markers for DXWR, which will help breed drought stress-resistant rice varieties. METHODS AND RESULTS: Ninety-nine SSR markers were developed from the drought stress-responsive miRNAs of DXWR. The SSR loci were distributed in all 12 rice chromosomes and most were in chromosomes 2 and 6, with di- and trinucleotides being the most abundant repeat motifs. Nine out of ten synthesized SSR markers were displayed high levels of genetic diversity in the genomes of DXWR and 41 modern rice varieties worldwide. The number of alleles per locus ranged from 2 to 6, and the observed and expected heterozygosity ranged from 0.000 to 0.024 and 0.461 to 0.738, respectively. CONCLUSIONS: These SSR markers developed from drought stress-responsive miRNAs in DXWR could be additional tools for elite genes mapping and useful for drought stress-resistant rice breeding.

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