InDel Markers Based on 3K Whole-Genome Re-Sequencing Data Characterise the Subspecies of Rice (Oryza sativa L.)
Abstract
:1. Introduction
2. Materials and Methods
2.1. Plant Materials and Cultivation
2.2. Data Sources of 3024 Rice Genomic Sequences
2.3. PCR Primer Design
2.4. DNA Extraction and PCR Amplification
2.5. Phylogenetic Analysis
3. Results
3.1. Identification and Distribution of InDels in the 3000 Rice Genome Dataset
3.2. Application of New InDel Markers in Nipponbare
3.3. InDel Marker Could Be Applied for Accurate Identification of Varieties in Japonica Rice
3.4. InDel Markers Might Contribute to the Divergence of Varieties in Indica
3.5. InDel Markers Could Be Applied to Identify the Recombinant Inbred Lines in a Population
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
- McClung, C.R. Making hunger yield. Science 2014, 344, 699–700. [Google Scholar] [CrossRef] [PubMed]
- McCouch, S.R.; Chen, X.; Panaud, O.; Temnykh, S.; Xu, Y.; Cho, Y.G.; Huang, N.; Ishii, T.; Blair, M. Microsatellite marker development, mapping and applications in rice genetics and breeding. In Oryza: From Molecule to Plant; Springer: Berlin/Heidelberg, Germany, 1997; pp. 89–99. [Google Scholar]
- Botstein, D.; White, R.L.; Skolnick, M.; Davis, R.W. Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am. J. Hum. Genet. 1980, 32, 314. [Google Scholar]
- Kuiper, M.; Zabeau, M. AFLP: A new concept for DNA fingerprinting. Nucleic Acids 1995, 23, 4407–4414. [Google Scholar]
- Akagi, H.; Yokozeki, Y.; Inagaki, A.; Fujimura, T. Microsatellite DNA markers for rice chromosomes. Theor. Appl. Genet. 1996, 93, 1071–1077. [Google Scholar] [CrossRef] [PubMed]
- Liu, B.; Wang, Y.; Zhai, W.; Deng, J.; Wang, H.; Cui, Y.; Cheng, F.; Wang, X.; Wu, J. Development of InDel markers for Brassica rapa based on whole-genome re-sequencing. Theor. Appl. Genet. 2012, 126, 231–239. [Google Scholar] [CrossRef] [PubMed]
- Williams, J.G.; Kubelik, A.R.; Livak, K.J.; Rafalski, J.A.; Tingey, S.V. DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Res. 1990, 18, 6531–6535. [Google Scholar] [CrossRef] [Green Version]
- Lu, B.R.; Zheng, K.L.; Qian, H.R.; Zhuang, J.Y. Genetic differentiation of wild relatives of rice as assessed by RFLP analysis. Theor. Appl. Genet. 2002, 106, 101–106. [Google Scholar] [CrossRef]
- Powell, W.; Machray, G.C.; Provan, J. Polymorphism revealed by simple sequence repeats. Trends Plant Sci. 1996, 1, 215–222. [Google Scholar] [CrossRef]
- Lian, C.; Oishi, R.; Miyashita, N.; Hogetsu, T. High somatic instability of a microsatellite locus in a clonal tree, Robinia pseudoacacia. Theor. Appl. Genet. 2004, 108, 836–841. [Google Scholar] [CrossRef] [PubMed]
- Lander, E.S. The new genomics: Global views of biology. Science 1996, 274, 536–539. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Bernardo, R. Molecular Markers and Selection for Complex Traits in Plants: Learning from the Last 20 Years. Crop Sci. 2008, 48, 1649–1664. [Google Scholar] [CrossRef] [Green Version]
- Shen, Y.J.; Jiang, H.; Jin, J.P.; Zhang, Z.B.; Xi, B.; He, Y.Y.; Wang, G.; Wang, C.; Qian, L.; Li, X.; et al. Development of genome-wide DNA polymorphism database for map-based cloning of rice genes. Plant Physiol. 2004, 135, 1198–1205. [Google Scholar] [CrossRef] [Green Version]
- Moghaddam, S.M.; Song, Q.; Mamidi, S.; Schmutz, J.; Lee, R.; Cregan, P.; Osorno, J.M.; McClean, P.E. Developing market class specific InDel markers from next generation sequence data in Phaseolus vulgaris L. Front Plant Sci. 2014, 5, 185. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Das, S.; Upadhyaya, H.D.; Srivastava, R.; Bajaj, D.; Gowda, C.L.; Sharma, S.; Singh, S.; Tyagi, A.K.; Parida, S.K. Genome-wide insertion-deletion (InDel) marker discovery and genotyping for genomics-assisted breeding applications in chickpea. DNA Res. Int. J. Rapid Publ. Rep. Genes Genomes 2015, 22, 377–386. [Google Scholar] [CrossRef] [PubMed]
- Britten, R.J.; Rowen, L.; Williams, J.; Cameron, R.A. Majority of divergence between closely related DNA samples is due to indels. Proc. Natl. Acad. Sci. USA 2003, 100, 4661–4665. [Google Scholar] [CrossRef] [Green Version]
- Mills, R.E.; Luttig, C.T.; Larkins, C.E.; Beauchamp, A.; Tsui, C.; Pittard, W.S.; Devine, S.E. An initial map of insertion and deletion (INDEL) variation in the human genome. Genome Res. 2006, 16, 1182–1190. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Pan, C.-H.; Li, A.-H.; Dai, Z.-Y.; Zhang, H.-X.; Liu, G.-Q.; Wang, Z.-B.; Yin, Y.-J.; Zhang, Y.-F.; Zuo, S.-M.; Chen, Z.-X. InDel and SNP markers and their applications in map-based cloning of rice genes. Rice Sci. 2008, 15, 251–258. [Google Scholar] [CrossRef]
- Raman, H.; Raman, R.; Wood, R.; Martin, P. Repetitive Indel Markers within the ALMT1 Gene Conditioning Aluminium Tolerance in Wheat (Triticum aestivum L.). Mol. Breed. 2006, 18, 171–183. [Google Scholar] [CrossRef]
- Pacurar, D.I.; Pacurar, M.L.; Street, N.; Bussell, J.D.; Pop, T.I.; Gutierrez, L.; Bellini, C. A collection of INDEL markers for map-based cloning in seven Arabidopsis accessions. J. Exp. Bot. 2012, 63, 2491–2501. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- García-Lor, A.; Luro, F.; Navarro, L.; Ollitrault, P. Comparative use of InDel and SSR markers in deciphering the interspecific structure of cultivated citrus genetic diversity: A perspective for genetic association studies. Mol. Genet. Genom. 2011, 287, 77–94. [Google Scholar] [CrossRef] [PubMed]
- Hayashi, K.; Yoshida, H.; Ashikawa, I. Development of PCR-based allele-specific and InDel marker sets for nine rice blast resistance genes. Theor. Appl. Genet. 2006, 113, 251–260. [Google Scholar] [CrossRef]
- Subbaiyan, G.K.; Waters, D.L.; Katiyar, S.K.; Sadananda, A.R.; Vaddadi, S.; Henry, R.J. Genome-wide DNA polymorphisms in elite indica rice inbreds discovered by whole-genome sequencing. Plant Biotechnol. J. 2012, 10, 623–634. [Google Scholar] [CrossRef]
- Wang, W.; Mauleon, R.; Hu, Z.; Chebotarov, D.; Tai, S.; Wu, Z.; Li, M.; Zheng, T.; Fuentes, R.R.; Zhang, F.; et al. Genomic variation in 3010 diverse accessions of Asian cultivated rice. Nature 2018, 557, 43–49. [Google Scholar] [CrossRef] [PubMed]
- Abbai, R.; Singh, V.K.; Nachimuthu, V.V.; Sinha, P.; Selvaraj, R.; Vipparla, A.K.; Singh, A.K.; Singh, U.M.; Varshney, R.K.; Kumar, A. Haplotype analysis of key genes governing grain yield and quality traits across 3K RG panel reveals scope for the development of tailor-made rice with enhanced genetic gains. Plant Biotechnol. J. 2019, 17, 1612–1622. [Google Scholar] [CrossRef] [Green Version]
- Li, J.-Y.; Wang, J.; Zeigler, R.S. The 3000 rice genomes project: New opportunities and challenges for future rice research. Gigascience 2014, 3, 2047-217X-3-8. [Google Scholar] [CrossRef] [Green Version]
- Lv, Q.; Huang, Z.; Xu, X.; Tang, L.; Liu, H.; Wang, C.; Zhou, Z.; Xin, Y.; Xing, J.; Peng, Z.; et al. Allelic variation of the rice blast resistance gene Pid3 in cultivated rice worldwide. Sci. Rep. 2017, 7, 10362. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Yuan, J.; Wang, X.; Zhao, Y.; Khan, N.U.; Zhao, Z.; Zhang, Y.; Wen, X.; Tang, F.; Wang, F.; Li, Z. Genetic basis and identification of candidate genes for salt tolerance in rice by GWAS. Sci. Rep. 2020, 10, 9958. [Google Scholar] [CrossRef] [PubMed]
- Mansueto, L.; Fuentes, R.R.; Borja, F.N.; Detras, J.; Abriol-Santos, J.M.; Chebotarov, D.; Sanciangco, M.; Palis, K.; Copetti, D.; Poliakov, A.; et al. Rice SNP-seek database update: New SNPs, indels, and queries. Nucleic Acids Res. 2017, 45, D1075–D1081. [Google Scholar] [CrossRef]
- Kaur, V.; Yadav, S.K.; Wankhede, D.P.; Pulivendula, P.; Kumar, A.; Chinnusamy, V. Cloning and characterization of a gene encoding MIZ1, a domain of unknown function protein and its role in salt and drought stress in rice. Protoplasma 2020, 257, 475–487. [Google Scholar] [CrossRef]
- Vitte, C.; Ishii, T.; Lamy, F.; Brar, D.; Panaud, O. Genomic paleontology provides evidence for two distinct origins of Asian rice (Oryza sativa L.). Mol. Genet. Genom. MGG 2004, 272, 504–511. [Google Scholar] [CrossRef]
- Londo, J.P.; Chiang, Y.C.; Hung, K.H.; Chiang, T.Y.; Schaal, B.A. Phylogeography of Asian wild rice, Oryza rufipogon, reveals multiple independent domestications of cultivated rice, Oryza sativa. Proc. Natl. Acad. Sci. USA 2006, 103, 9578–9583. [Google Scholar] [CrossRef] [Green Version]
- Huang, X.; Kurata, N.; Wei, X.; Wang, Z.X.; Wang, A.; Zhao, Q.; Zhao, Y.; Liu, K.; Lu, H.; Li, W.; et al. A map of rice genome variation reveals the origin of cultivated rice. Nature 2012, 490, 497–501. [Google Scholar] [CrossRef] [Green Version]
- Carpentier, M.C.; Manfroi, E.; Wei, F.J.; Wu, H.P.; Lasserre, E.; Llauro, C.; Debladis, E.; Akakpo, R.; Hsing, Y.I.; Panaud, O. Retrotranspositional landscape of Asian rice revealed by 3000 genomes. Nat. Commun. 2019, 10, 24. [Google Scholar] [CrossRef]
- Fan, F.; Li, N.; Wang, J.; Liu, X.; Liu, J.; Zhu, Y.; Li, S. Molecular marker-directed development of a novel cytoplasmic male sterile line in rice. Mol. Breed. 2015, 35. [Google Scholar] [CrossRef]
- Rohlf, F.J. NTSYS-pc: Numerical Taxonomy and Multivariate Analysis System; Version 1.8; Exeter Software: Setauket, NY, USA, 1992. [Google Scholar]
- Kumar, S.; Stecher, G.; Tamura, K. MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets. Mol. Biol. Evol. 2016, 33, 1870–1874. [Google Scholar] [CrossRef] [Green Version]
- Nagaraju, J.; Kathirvel, M.; Kumar, R.R.; Siddiq, E.A.; Hasnain, S.E. Genetic analysis of traditional and evolved Basmati and non-Basmati rice varieties by using fluorescence-based ISSR-PCR and SSR markers. Proc. Natl. Acad. Sci. USA 2002, 99, 5836–5841. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Liu, J.; Li, J.; Qu, J.; Yan, S. Development of Genome-Wide Insertion and Deletion Polymorphism Markers from Next-Generation Sequencing Data in Rice. Rice 2015, 8, 1–10. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Vaughan, D.A.; Lu, B.-R.; Tomooka, N. The evolving story of rice evolution. Plant Sci. 2008, 174, 394–408. [Google Scholar] [CrossRef]
- Vaughan, D.A.; Lu, B.-R.; Tomooka, N. Was Asian Rice (Oryza sativa) Domesticated More Than Once? Rice 2008, 1, 16–24. [Google Scholar] [CrossRef] [Green Version]
- Cheng, K.; Wang, X.; Lu, Y. The synthetical research and utilization of Yunnan rice resource: The reorganization of the Asian cultivated rice classification. Acta Agron. Sin. 1984, 10, 271–279. [Google Scholar]
- Liu, P.; Cai, X.-X.; Lu, B.-R. Single-seeded InDel fingerprints in rice: An effective tool for indica-japonica rice classification and evolutionary studies. J. Syst. Evol. 2012, 50, 1–11. [Google Scholar] [CrossRef]
- Lu, B.-R.; Cai, X.; Xin, J. Efficient indica and japonica rice identification based on the InDel molecular method: Its implication in rice breeding and evolutionary research. Prog. Nat. Sci. 2009, 19, 1241–1252. [Google Scholar] [CrossRef]
- Alonso-Blanco, C.; Andrade, J.; Becker, C.; Bemm, F.; Bergelson, J.; Borgwardt, K.M.; Cao, J.; Chae, E.; Dezwaan, T.M.; Zhou, X.; et al. 1135 Genomes Reveal the Global Pattern of Polymorphism in Arabidopsis thaliana. Cell 2016, 166, 481–491. [Google Scholar] [CrossRef] [PubMed] [Green Version]
Chromosome | Number of all InDel | Density a of all InDel | Number of InDel (≥50 bp) | Density a of InDel (≥50 bp) |
---|---|---|---|---|
Chr01 | 137,443 | 3.18 | 78,935 | 1.82 |
Chr02 | 106,837 | 2.97 | 59,497 | 1.66 |
Chr03 | 101,214 | 2.78 | 54,792 | 1.50 |
Chr04 | 115,355 | 3.25 | 61,169 | 1.72 |
Chr05 | 88,164 | 2.94 | 45,278 | 1.51 |
Chr06 | 105,922 | 3.39 | 59,853 | 1.92 |
Chr07 | 101,681 | 3.42 | 58,265 | 1.96 |
Chr08 | 103,375 | 3.63 | 57,843 | 2.03 |
Chr09 | 77,000 | 3.35 | 41,752 | 1.81 |
Chr10 | 85,481 | 3.68 | 49,995 | 2.15 |
Chr11 | 118,086 | 4.07 | 68,537 | 2.36 |
Chr12 | 107,945 | 3.92 | 63,559 | 2.31 |
Total | 1,248,503 | 3.34 | 699,475 | 1.87 |
Publisher’s Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affiliations. |
© 2021 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
Share and Cite
Yuan, H.; Yang, W.; Zou, J.; Cheng, M.; Fan, F.; Liang, T.; Yu, Y.; Qiu, R.; Li, S.; Hu, J. InDel Markers Based on 3K Whole-Genome Re-Sequencing Data Characterise the Subspecies of Rice (Oryza sativa L.). Agriculture 2021, 11, 655. https://doi.org/10.3390/agriculture11070655
Yuan H, Yang W, Zou J, Cheng M, Fan F, Liang T, Yu Y, Qiu R, Li S, Hu J. InDel Markers Based on 3K Whole-Genome Re-Sequencing Data Characterise the Subspecies of Rice (Oryza sativa L.). Agriculture. 2021; 11(7):655. https://doi.org/10.3390/agriculture11070655
Chicago/Turabian StyleYuan, Huanran, Weilong Yang, Jianing Zou, Mingxing Cheng, Fengfeng Fan, Ting Liang, Yajie Yu, Ronghua Qiu, Shaoqing Li, and Jun Hu. 2021. "InDel Markers Based on 3K Whole-Genome Re-Sequencing Data Characterise the Subspecies of Rice (Oryza sativa L.)" Agriculture 11, no. 7: 655. https://doi.org/10.3390/agriculture11070655
APA StyleYuan, H., Yang, W., Zou, J., Cheng, M., Fan, F., Liang, T., Yu, Y., Qiu, R., Li, S., & Hu, J. (2021). InDel Markers Based on 3K Whole-Genome Re-Sequencing Data Characterise the Subspecies of Rice (Oryza sativa L.). Agriculture, 11(7), 655. https://doi.org/10.3390/agriculture11070655