Development and verification of SSR markers from drought stress-responsive miRNAs in common 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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Genome-wide identification of conserved microRNA and their response to drought stress in Dongxiang wild rice (Oryza rufipogon Griff.)

Biotechnology Letters ◽

10.1007/s10529-015-2012-0 ◽

2015 ◽

Vol 38 (4) ◽

pp. 711-721 ◽

Cited By ~ 26

Author(s):

Fantao Zhang ◽

Xiangdong Luo ◽

Yi Zhou ◽

Jiankun Xie

Keyword(s):

Drought Stress ◽

Wild Rice ◽

Oryza Rufipogon ◽

Genome Wide ◽

Oryza Rufipogon Griff ◽

Dongxiang Wild Rice

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

10.1101/2021.08.23.457289 ◽

2021 ◽

Cited By ~ 1

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.

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

Plant Genetic Resources ◽

10.1017/s1479262119000145 ◽

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.

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

Genes ◽

10.3390/genes12111831 ◽

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.

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Identification, analysis, and confirmation of seed storability-related loci in Dongxiang wild rice (Oryza rufipogon Griff.)

10.1101/2021.11.16.468766 ◽

2021 ◽

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 (BSAseq) was used to identify seed storability related loci in the DXWR and F6 population. Two main genomic regions containing 18,550,000 to 20,870,000 bp on chromosome 4 and 7,860,000 to 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.

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

Plant Genetic Resources ◽

10.1017/s1479262121000617 ◽

2022 ◽

pp. 1-4

Author(s):

Wanling Yang ◽

Yuanwei Fan ◽

Yong Chen ◽

Gumu Ding ◽

Hu Liu ◽

...

Keyword(s):

Ssr Markers ◽

Stress Responses ◽

Wild Rice ◽

Diversity Index ◽

Repeat Sequence ◽

Oryza Rufipogon ◽

Coding Sequences ◽

Genome Wide ◽

Ssr Loci ◽

Dongxiang Wild Rice

Abstract Dongxiang wild rice (Oryza rufipogon Griff.) (DXWR) is the northernmost distributed wild rice found in the world. Similar to other populations of O. rufipogon, DXWR 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 plant 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 our previous study, we obtained 1655 lncRNA transcripts from DXWR using strand-specific RNA sequencing. 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 accessions. The results showed that 42 (58.33%) pairs of primers have abundant polymorphism among these rice materials; the polymorphism information content 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.

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