Hostname: page-component-586b7cd67f-t7czq Total loading time: 0 Render date: 2024-11-22T04:23:38.576Z Has data issue: false hasContentIssue false
  • English
  • Français

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

Published online by Cambridge University Press:  10 January 2022

Wanling Yang ,
Yuanwei Fan ,
Yong Chen ,
Gumu Ding ,
Hu Liu ,
Jiankun Xie  and
Fantao Zhang Open the ORCID record for Fantao Zhang [Opens in a new window]
Wanling Yang
Affiliation:
Jiangxi Provincial Key Lab of Protection and Utilization of Subtropical Plant Resources, College of Life Sciences, Jiangxi Normal University, Nanchang 330022, China
Yuanwei Fan
Affiliation:
College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
Yong Chen
Affiliation:
Jiangxi Provincial Key Lab of Protection and Utilization of Subtropical Plant Resources, College of Life Sciences, Jiangxi Normal University, Nanchang 330022, China
Gumu Ding
Affiliation:
Jiangxi Provincial Key Lab of Protection and Utilization of Subtropical Plant Resources, College of Life Sciences, Jiangxi Normal University, Nanchang 330022, China
Hu Liu
Affiliation:
Huaian Zhuxiang Ecological Agriculture CO. LTD, Huaian 223299, Jiangsu Province, China
Jiankun Xie*
Affiliation:
Jiangxi Provincial Key Lab of Protection and Utilization of Subtropical Plant Resources, College of Life Sciences, Jiangxi Normal University, Nanchang 330022, China
Fantao Zhang*
Affiliation:
Jiangxi Provincial Key Lab of Protection and Utilization of Subtropical Plant Resources, College of Life Sciences, Jiangxi Normal University, Nanchang 330022, China
*
Author for correspondence: Fantao Zhang, E-mail: [email protected]; Jiankun Xie, E-mail: [email protected]
Author for correspondence: Fantao Zhang, E-mail: [email protected]; Jiankun Xie, E-mail: [email protected]
Get access Rights & Permissions [Opens in a new window]

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.

Keywords

Crop wild relativegenetic markergermplasm resourcelong non-coding RNAsimple repeat sequence
Type
Short Communication
Information
Plant Genetic Resources , Volume 19 , Issue 6 , December 2021 , pp. 549 - 552
Copyright
Copyright © The Author(s), 2022. Published by Cambridge University Press on behalf of NIAB

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

Footnotes

*

These authors contributed equally to this work

†

Present address: Department of Biology and Center for Engineering Mechanobiology, Washington University in St. Louis, St. Louis, MO 63130, USA

References

Akhtamov, M, Adeva, C, Shim, KC, Lee, HS, Kim, SH, Jeon, YA, Luong, NH, Kang, JW, Lee, JY and Ahn, SN (2020) Characterization of quantitative trait loci for germination and coleoptile length under low-temperature condition using introgression lines derived from an interspecific cross in rice. Genes 11, 1200.CrossRefGoogle ScholarPubMed
Bhandawat, A, Sharma, H, Pundir, N, Madhawan, A and Roy, J (2020) Genome-wide identification and characterization of novel non-coding RNA-derived SSRs in wheat. Molecular Biology Reports 47, 6111–6125.10.1007/s11033-020-05687-xCrossRefGoogle ScholarPubMed
Collard, BC and Mackill, DJ (2008) Marker-assisted selection: an approach for precision plant breeding in the twenty-first century. Philosophical Transactions of the Royal Society B: Biological Sciences 363, 557–572.CrossRefGoogle ScholarPubMed
Cook, GA, Prakash, O, Zhang, K, Shank, LP, Takeguchi, WA, Robbins, A, Gong, YX, Iwamoto, T, Schultz, BD and Tomich, JM (2004) Activity and structural comparisons of solution associating and monomeric channel-forming peptides derived from the glycine receptor m2 segment. Biophysical Journal 86, 1424–1435.10.1016/S0006-3495(04)74212-5CrossRefGoogle ScholarPubMed
Jaiswal, V, Rawoof, A, Dubey, M, Chhapekar, SS, Sharma, V and Ramchiary, N (2020) Development and characterization of non-coding RNA based simple sequence repeat markers in Capsicum species. Genomics 112, 1554–1564.10.1016/j.ygeno.2019.09.005CrossRefGoogle ScholarPubMed
Kozlowski, P, de Mezer, M and Krzyzosiak, WJ (2010) Trinucleotide repeats in human genome and exome. Nucleic Acids Research 38, 4027–4039.CrossRefGoogle ScholarPubMed
Li, Q and Wan, JM (2005) SSR hunter: development of local searching software for SSR sites. Hereditas 27, 808–810.Google Scholar
Liu, K and Muse, SV (2005) PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics 21, 2128–2129.10.1093/bioinformatics/bti282CrossRefGoogle ScholarPubMed
Mao, DH, Yu, L, Chen, DZ, Li, L, Zhu, YX, Xiao, YQ, Zhang, DC and Chen, CY (2015) Multiple cold resistance loci confer the high cold tolerance adaptation of Dongxiang wild rice (Oryza rufipogon) to its high-latitude habitat. Theoretical and Applied Genetics 128, 1359–1371.10.1007/s00122-015-2511-3CrossRefGoogle ScholarPubMed
Qi, WD, Chen, HP, Yang, ZZ, Hu, BL, Luo, XD, Ai, B, Luo, Y, Huang, Y, Xie, JK and Zhang, FT (2020) Systematic characterization of long non-coding RNAs and their responses to drought stress in Dongxiang wild rice. Rice Science 27, 21–31.Google Scholar
Quan, RD, Wang, J, Hui, J, Bai, HB, Lyu, XL, Zhu, YX, Zhang, HW, Zhang, ZJ, Li, SH and Huang, RF (2018) Improvement of salt tolerance using wild rice genes. Frontiers in Plant Science 8, 2269.10.3389/fpls.2017.02269CrossRefGoogle ScholarPubMed
Singh, AK, Chaurasia, S, Kumar, S, Singh, R, Kumari, J, Yadav, MC, Singh, N, Gaba, S and Jacob, SR (2018) Identification, analysis and development of salt responsive candidate gene based SSR markers in wheat. BMC Plant Biology 18, 249.10.1186/s12870-018-1476-1CrossRefGoogle ScholarPubMed
Untergasser, A, Cutcutache, I, Koressaar, T, Ye, J, Faircloth, BC, Remm, M and Rozen, SG (2012) Primer3 – new capabilities and interfaces. Nucleic Acids Research 40, e115.CrossRefGoogle ScholarPubMed
Xie, JK, Zhang, M, Sun, J and Zhang, FT (2017) Genome-wide genic SSR marker development for the endangered Dongxiang wild rice (Oryza rufipogon). Plant Genetic Resources 15, 566–569.CrossRefGoogle Scholar
Xu, Q, Song, ZH, Zhu, CY, Tao, CC, Kang, LF, Liu, W, He, F, Yan, J and Sang, T (2017) Systematic comparison of lncRNAs with protein coding mRNAs in population expression and their response to environmental change. BMC Plant Biology 17, 42.CrossRefGoogle ScholarPubMed
Zhang, FT, Xu, T, Mao, LY, Yan, SY, Chen, XW, Wu, ZF, Chen, R, Luo, XD, Xie, JK and Gao, S (2016) Genome-wide analysis of Dongxiang wild rice (Oryza rufipogon Griff.) to investigate lost/acquired genes during rice domestication. BMC Plant Biology 16, 103.CrossRefGoogle ScholarPubMed
Supplementary material: File

Yang et al. supplementary material

Yang et al. supplementary material

Download Yang et al. supplementary material(File)
File 165.6 KB