Development and validation of new IRAP markers for common bean

Authors

DOI:

https://doi.org/10.5902/2179460X72380

Keywords:

Phaseolus vulgaris L, Genetic variability, PIC

Abstract

Molecular markers are powerful tools for detecting genetic variation at the DNA level, offering a direct, reliable, and efficient approach for the characterization, conservation, management, and utilization of plant germplasm. Among these, Inter-Retrotransposon Amplified Polymorphism (IRAP) markers target the genomic regions between retrotransposon insertions, revealing polymorphisms based on insertion patterns. This study aimed to develop and validate new IRAP markers for the genetic characterization of common bean (Phaseolus vulgaris) genotypes. Twelve IRAP primers were designed based on LTR retrotransposon sequences identified in the P. vulgaris genome database and tested in a panel of 22 genotypes, including 11 landraces, 10 commercial cultivars, and one F₂ individual derived from a cross between cultivars IPR Andorinha and BRS Estilo. Genomic DNA was extracted from young leaves using a modified CTAB protocol, and PCR amplifications were performed using the newly designed primers. The average polymorphism rate among the markers was 90.67%, and the mean genetic similarity among the genotypes was 0.557. The polymorphic information content (PIC) values ranged from 0.086 (Pv_IRAP_8) to 0.500 (Pv_IRAP_10), with the most informative primers being Pv_IRAP_4, Pv_IRAP_6, Pv_IRAP_7, Pv_IRAP_9, and Pv_IRAP_10. High genetic similarity was observed between some landraces and commercial cultivars, suggesting redundancy within the germplasm collection and highlighting the importance of molecular tools in optimizing genetic resource management in common bean breeding programs.

Downloads

Download data is not yet available.

Author Biographies

Patrícia Pagnoncelli Borba, Universidade Tecnológica Federal do Paraná

Agronomy student at the Federal Technological University of Paraná - Pato Branco Campus. Scientific Initiation Scholarship (PIBIC) from the Araucária Foundation. Experienced in molecular biology and plant breeding, he focuses on the physiological and molecular responses of beans (Phaseolus vulgaris L.) to water deficiency.

Leomar Guilherme Woyann, Instituto Água e Terra, Pato Branco, PR

He holds a degree in Agricultural Engineering from the Federal University of Pelotas (2012), a Master's degree in Agronomy (Area of ​​Concentration: Plant Genetic Improvement) from the Federal University of Pelotas (2014), and a PhD in Agronomy (Area of ​​Concentration: Plant Genetic Improvement) from the Federal University of Technology of Paraná (UTFPR)-Pato Branco Campus (2018). He worked as a Postdoctoral Fellow and Substitute Professor at (UTFPR)-Pato Branco Campus. He has experience in Agronomy, with an emphasis on Plant Genetic Improvement, where he worked with crops such as wheat, irrigated rice, and white oats. He is currently a Professional Agent at the Water and Land Institute (IAT) - PR, Pato Branco Regional Office (ERPAB), working in the areas of licensing and environmental inspection.

Emanueli Pereira da Silva, Universidade Tecnológica Federal do Paraná

PhD student in the Postgraduate Program in Agronomy with an emphasis on Plant Production, at the Federal University of Technology of Paraná, Pato Branco Campus. Master in Agronomy from the Federal University of Technology of Paraná. Bachelor in Biological Sciences from the Universidade Paranaense (Unipar) - Francisco Beltrão University Unit. She was a Scientific Initiation Student (2014, 2015, 2016 and 2017). Currently working with research involving Molecular Biology and in vitro cultivation of the arracacia (Arracacia xhanthorizza).

Giovani Benin, Universidade Tecnológica Federal do Paraná

Giovani Benin is a Professor at the Federal Technological University of Paraná (UTFPR), Pato Branco Campus, where he has worked since 2006. He completed his PhD (2004) and Post-doctorate (2005) in Agronomy (Concentration Area: Phytoimprovement) at UFPel. Currently, he is responsible for the disciplines of Crop Cultures 2, Crop Culture 02 (divided) in the Undergraduate Course in Agronomy and Plant Genetic Improvement, Selection Theory and Soybean Culture, in the Graduate Program in Agronomy (PPGAG) at UTFPR. He has been a CNPq Research Productivity Scholar since 2007. His research areas are Plant Genetic Improvement, Quantitative and Biometric Genetics, Molecular Markers and Cultural Management and Treatments, with an emphasis on wheat and soybean crops.

Paulo Henrique de Oliveira, Universidade Tecnológica Federal do Paraná

Full Professor (since 2020) at the Federal University of Technology of Paraná since 1994. He holds a degree in Agronomy from the Federal University of Santa Maria (1990), a master's degree in Agronomy from the Federal University of Santa Maria (1994), and a PhD in Plant Science from the Federal University of Rio Grande do Sul (2002). He has experience in Agronomy, with an emphasis on Genetics and Plant Breeding and Agricultural Experimentation, working mainly on the following topics: plant genetic improvement, oats, beans, and statistical analysis. He has worked as a professor in the Postgraduate Program in Regional Development at UTFPR Pato Branco since 2015.

Taciane Finatto, Universidade Tecnológica Federal do Paraná

Bachelor of Biological Sciences (UFPel), Master of Science in Plant Genetic Resources (UFSC), PhD in Agronomy (co-tutoring UFPel/UPVD). Associate Professor at the Federal University of Technology of Paraná, Pato Branco, PR. She teaches plant physiology and biotechnology applied to genetic improvement in the undergraduate and graduate programs in Agronomy (PPGAG). She advises undergraduate research, final projects, internships, master's and doctoral programs. She coordinates research, extension, and innovation projects. She is a reviewer of scientific articles in the area of ​​plant production and biology. She is responsible for the disciplines of Physiology of Cultivated Plants 2, Agricultural Biotechnology, Biotechnology Applied to Plant Production, and Molecular Genetics Applied to Plant Production. She coordinates the Plant Biotechnology laboratory, is a member of the NDE of the undergraduate program in Agronomy, the departmental council of Agricultural Sciences, and is currently the coordinator of the PPGAG.

References

Alikhani, L., Rahmani, M.-S., Shabanian, N., Badakhshan, H., & Khadivi-Khub, A. (2014). Genetic variability and structure of Quercus brantii assessed by ISSR, IRAP and SCoT markers. Gene, 552(1), 176–183. https://doi.org/10.1016/j.gene.2014.09.034

Alsayied, N. F., Fernández, J. A., Schwarzacher, T., & Heslop-Harrison, J. S. (2016). Diversity and relationships of Crocus sativus and its relatives analysed by inter-retroelement amplified polymorphism (IRAP). Annals of Botany, 116(3), 359–368. https://doi.org/10.1093/aob/mcv103

Boronnikova, S. V., & Kalendar, R. N. (2010). Using IRAP markers for analysis of genetic variability in populations of resource and rare species of plants. Genetika, 46, 36–42. https://doi.org/10.1134/S1022795410010060

Carvalho, A., Guedes-Pinto, H., Martins-Lopes, P., & Lima-Brito, J. (2010). Genetic variability of Old Portuguese bread wheat cultivars assayed by IRAP and REMAP markers. Annals of Applied Biology, 156, 337–345. https://doi.org/10.1111/j.1744-7348.2010.00390.x

Chédiak, G. L. C., Brondani, P. V. B., Peloso, M. J. D., Melo, L. C., & Brondani, C. (2007). Análise de pureza genética de sementes de feijoeiro comum utilizando marcadores microssatélites em sistema de genotipagem multiplex. Boletim de Pesquisa e Desenvolvimento, 28, 1–20. Embrapa.

Dice, L. R. (1945). Measures of the amount of ecological association between species. Ecology, 26, 297–302. https://doi.org/10.2307/1932409

Doyle, J. J., & Doyle, J. L. (1987). A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochemical Bulletin, 19, 11–15.

Fatmawati, Y., Setiaawan, A. B., Purwantoro, A., Respatie, D. W., & Teo, C. H. (2021). Analysis of genetic variability in F2 interspecific hybrids of mung bean (Vigna radiata) using inter-retrotransposon amplified polymorphism marker system. Biodiversitas Journal of Biological Diversity, 22(11), 4880–4889. https://doi.org/10.13057/biodiv/d221121

Franklin, C. J., Mohammed, S., Thomas, G., & Varghese, G. (2009). Genetic diversity and conservation of common bean (Phaseolus vulgaris L., Fabaceae) landraces in Nilgiris. Current Science, 97, 227–235.

Gonçalves, D. L., Barelli, M. A. A. B., dos Santos, P. R. J. S., Oliveira, T. C., da Silva, C. R., Neves, G. L., Poletine, J. P., & da Luz, P. B. (2016). Variabilidade genética de germoplasma tradicional de feijoeiro comum na região de Cáceres-MT. Ciência Rural, 46, 100–107. https://doi.org/10.1590/0103-8478cr20150357

Goodstein, D. M., Shu, S., Howson, R., Neupane, R., Hayes, R. D., Fazo, J., Mitros, T., Dirks, W., Hellsten, U., Putnam, N., & Rokhsar, D. S. (2012). Phytozome: A comparative platform for green plant genomics. Nucleic Acids Research, 40(Database issue), D1178–D1186. https://doi.org/10.1093/nar/gkr944

Haliloğlu, K., Türkoğlu, A., Ozturk, H. I., Elkoca, E., & Poczai, P. (2022). PBS-retrotransposon markers in the analysis of genetic diversity among common bean (Phaseolus vulgaris L.) germplasm from Türkiye. Genes, 13(7), 1147. https://doi.org/10.3390/genes13071147

Kalendar, R., Flavell, A. J., Ellis, T. H. N., Sjakste, T., Moisy, C., & Schulman, A. H. (2011). Analysis of plant diversity with retrotransposon-based molecular markers. Heredity, 106, 520–530. https://doi.org/10.1038/hdy.2010.93

Kalendar, R., Muterko, A., & Boronnikova, S. (2020). Retrotransposable elements: DNA fingerprinting and the assessment of genetic diversity. In Molecular Plant Taxonomy (pp. 263–286). Humana. https://doi.org/10.1007/978-1-0716-0334-5_13

Kalendar, R., & Schulman, A. H. (2014). Transposon-based tagging: IRAP, REMAP, and iPBS. In Molecular Plant Taxonomy (pp. 233–255). Humana Press. https://doi.org/10.1007/978-1-62703-767-9_12

Kalendar, R., & Schulman, A. H. (2006). IRAP and REMAP for retrotransposon-based genotyping and fingerprinting. Nature Protocols, 1, 2478–2484. https://doi.org/10.1038/nprot.2006.377

Kanwar, R., Mehta, D. K., Sharma, R., & Dogra, R. K. (2020). Studies on genetic diversity of French bean (Phaseolus vulgaris L.) landraces of Himachal Pradesh based on morphological traits and molecular markers. Legume Research, 43(4), 470–479. https://doi.org/10.18805/LR-4664

Kaya, E., & Yılmaz-Gökdoğan, E. (2016). Using two retrotransposon-based marker systems (IRAP and REMAP) for molecular characterization of olive (Olea europaea L.) cultivars. Notulae Botanicae Horti Agrobotanici Cluj-Napoca, 44, 167–174. https://doi.org/10.15835/nbha44110387

Kuhn, B. C., Mangolin, C. A., Souto, E. R., Vicient, C. M., & Machado, M. F. P. S. (2016). Development of retrotransposon-based markers IRAP and REMAP for cassava (Manihot esculenta). Genetics and Molecular Research, 15(2), gmr15027149. https://doi.org/10.4238/gmr.15027149

Langarica, H. R. G., Hernández-Delgado, P., & Pérez, N. M. (2014). Morphological and molecular characterization of common bean landraces cultivated in the semiarid Mexican high plateau. Boletín de la Sociedad Argentina de Botánica, 49, 525–540.

Lefort, F., & Douglas, G. C. (1999). An efficient micro-method of DNA isolation from mature leaves of four hardwood tree species Acer, Fraxinus, Prunus and Quercus. Annals of Forest Science, 56, 259–263. https://doi.org/10.1051/forest:19990308

Lodhi, M. A., Ye, G. N., Weeden, N. F., & Reisch, B. I. (1994). A simple and efficient method for DNA extraction from grapevine cultivars, Vitis species and Ampelopsis. Plant Molecular Biology Reporter, 12, 6–13. https://doi.org/10.1007/BF02668658

Luo, Z., Brock, J. R., Dyer, D. L., Kutchan, T. M., Schachtman, D. P., Qiu, Y., Shiu, S.-H., & Benning, C. (2019). Genetic diversity and population structure of a Camelina sativa spring panel. Frontiers in Plant Science, 10, 184. https://doi.org/10.3389/fpls.2019.00184

Mantel, N. (1967). The detection of disease clustering and a generalized regression approach. Cancer Research, 27, 209–220.

Naeem, H., Haque, I., Khan, A., Liang, C., Iqbal, Z., & Wang, X. (2021). Population structure and phylogenetic relationship of peach [Prunus persica (L.) Batsch] and nectarine [Prunus persica var. nucipersica (L.) C. K. Schneid.] based on retrotransposon markers. Genetic Resources and Crop Evolution, 68(7), 3011–3023. https://doi.org/10.1007/s10722-021-01172-x

Nasri, S., Heidari, B., Paknazar, M., Sorkheh, K., Zanganeh, R., & Mardi, M. (2013). Retrotransposon insertional polymorphism in Iranian bread wheat cultivars and breeding lines revealed by IRAP and REMAP markers. Biochemical Genetics, 51, 927–943. https://doi.org/10.1007/s10528-013-9612-9

Otwe, E. P., Agyirifo, D. S., Galyuon, I. K., & Heslop-Harrison, J. S. (2017). Molecular diversity in some Ghanaian cowpea [Vigna unguiculata L. (Walp)] accessions. Tropical Plant Biology, 10(2–3), 57–67. https://doi.org/10.1007/s12042-017-9184-9

Rohlf, F. J. (2000). NTSYS-pc: Numerical taxonomy and multivariate analysis system (Version 2.1). Exeter Software.

Roldán-Ruiz, I., Dendauw, J., Van Bockstaele, E., Depicker, A., & De Loose, M. (2000). AFLP markers reveal high polymorphic rates in ryegrasses (Lolium spp.). Molecular Breeding, 6(2), 125–134. https://doi.org/10.1023/A:1009680614564

Schmutz, J., McClean, P. E., Mamidi, S., Wu, G. A., Cannon, S. B., Grimwood, J., Jenkins, J., Shu, S., Song, Q., Chavarro, C., Torres-Torres, M., Geffroy, V., Moghaddam, S. M., Gao, D., Abernathy, B., Barry, K., Blair, M. W., Brick, M. A., Chovatia, M., … Jackson, S. A. (2014). A reference genome for common bean and genome-wide analysis of dual domestications. Nature Genetics, 46(7), 707–713. https://doi.org/10.1038/ng.3008

Serrote, C. M. L., Reiniger, L. R. S., Silva, K. B., Müller, B. S. F., & Ramalho, M. A. P. (2020). Determining the polymorphism information content of a molecular marker. Gene, 726, 144175. https://doi.org/10.1016/j.gene.2019.144175

Silva, A. O., Silva, G. F., Dias, M. C., Souza, Á., Clement, C. R., & Sousa, N. R. (2012). Desenvolvimento de “inter-retrotransposon amplified polymorphism” para análise de diversidade genética em germoplasma de mandioca. In Anais do Congresso Brasileiro de Recursos Genéticos (2ª ed., Belém, PA). Embrapa.

Singh, A., & Sengar, R. S. (2015). DNA fingerprinting based decoding of indica rice (Oryza sativa L.) via molecular marker (SSR, ISSR & RAPD) in aerobic condition. Advanced Crop Science and Technology, 3, 1–8. https://doi.org/10.4172/2329-8863.1000173

Singh, S., Nandha, P. S., & Singh, J. (2017). Transposon-based genetic diversity assessment in wild and cultivated barley. The Crop Journal, 5, 296–304. https://doi.org/10.1016/j.cj.2017.01.003

Sivolap, Y. M. (2013). Molecular markers and plant breeding. Cytology and Genetics, 47, 188–195. https://doi.org/10.3103/S0095452713030090

Sokal, R. R., & Rohlf, F. J. (1962). The comparison of dendrograms by objective methods. Taxon, 11, 30–40. https://doi.org/10.2307/1217208

Tomás, D., Carneiro, V., Miguel, C., & Margarido, F. (2016). Genetic diversity assessment of Portuguese cultivated Vicia faba L. through IRAP markers. Diversity, 8(1), 1–11. https://doi.org/10.3390/d8010005

You, F. M., Huo, N., Gu, Y. Q., Luo, M.-C., Ma, Y., Hane, D., Lazo, G. R., Dvorak, J., & Anderson, O. D. (2010). RJPrimers: Unique transposable element insertion junction discovery and PCR primer design for marker development. Nucleic Acids Research, 38, 313–320. https://doi.org/10.1093/nar/gkp938

Yuan, L., Zhang, Q., Guo, D., & Luo, Z. (2012). Genetic differences among ‘Luotian-tianshi’ (Diospyros kaki Thunb.) genotypes native to China revealed by ISSR and IRAP markers. Scientia Horticulturae, 137, 75–80. https://doi.org/10.1016/j.scienta.2012.01.025

Zargar, S. M., Raatz, B., Sonah, H., Bhat, J. A., Dar, Z. A., Agrawal, G. K., & Rakwal, R. (2016). Unraveling the efficiency of RAPD and SSR markers in diversity analysis and population structure estimation in common bean. Saudi Journal of Biological Sciences, 23(1), 139–149. https://doi.org/10.1016/j.sjbs.2015.11.004

Downloads

Published

2025-11-07

How to Cite

Borba, P. P., Woyann, L. G., Silva, E. P. da, Benin, G., Oliveira, P. . H. de, & Finatto, T. (2025). Development and validation of new IRAP markers for common bean. Ciência E Natura, 47, e72380. https://doi.org/10.5902/2179460X72380

Issue

Vol. 47 (2025): Publicação contínua

Section

Biology-Genetics

License

Copyright (c) 2025 Ciência e Natura

Creative Commons License

This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.

To access the DECLARATION AND TRANSFER OF COPYRIGHT AUTHOR’S DECLARATION AND COPYRIGHT LICENSE click here.

 

Ethical Guidelines for Journal Publication

The Ciência e Natura journal is committed to ensuring ethics in publication and quality of articles. 

Conformance to standards of ethical behavior is therefore expected of all parties involved: Authors, Editors, Reviewers, and the Publisher.

In particular, 

Authors: Authors should present an objective discussion of the significance of research work as well as sufficient detail and references to permit others to replicate the experiments. Fraudulent or knowingly inaccurate statements constitute unethical behavior and are unacceptable. Review Articles should also be objective, comprehensive, and accurate accounts of the state of the art. The Authors should ensure that their work is entirely original works, and if the work and/or words of others have been used, this has been appropriately acknowledged. Plagiarism in all its forms constitutes unethical publishing behavior and is unacceptable. Submitting the same manuscript to more than one journal concurrently constitutes unethical publishing behavior and is unacceptable. Authors should not submit articles describing essentially the same research to more than one journal. The corresponding Author should ensure that there is a full consensus of all Co-authors in approving the final version of the paper and its submission for publication.

Editors: Editors should evaluate manuscripts exclusively on the basis of their academic merit. An Editor must not use unpublished information in the editor's own research without the express written consent of the Author. Editors should take reasonable responsive measures when ethical complaints have been presented concerning a submitted manuscript or published paper.

Reviewers: Any manuscripts received for review must be treated as confidential documents. Privileged information or ideas obtained through peer review must be kept confidential and not used for personal advantage. Reviewers should be conducted objectively, and observations should be formulated clearly with supporting arguments, so that Authors can use them for improving the paper. Any selected Reviewer who feels unqualified to review the research reported in a manuscript or knows that its prompt review will be impossible should notify the Editor and excuse himself from the review process. Reviewers should not consider manuscripts in which they have conflicts of interest resulting from competitive, collaborative, or other relationships or connections with any of the authors, companies, or institutions connected to the papers.