Genetic diversity analysis of some species in Brassicaceae family with ISSR markers

Abstract

Brassicaceae is one of the biggest family which have thousands of species all around the world. In order to use wild mustard in a breeding process, their genetic kinship levels must be defined. Inter simple sequence repeats (ISSRs) are one of the common markers to evaluate genetic diversity. Here, 28 mustard genotypes representing four taxa, 17 of Brassica juncea, 2 of B. nigra, 2 of B. rapa, and 7 of B. arvensis, were investigated with seven ISSR primers. Totally, 160 bands were scored out of which 88.75% showed polymorphism. The polymorphism information content (PIC) varied from 0.25 to 0.40. The average heterozygosity (Hav), multiplex ratio (MR), marker index (MI), and resolving power (Rp) were calculated as 0.33, 9.07, 2.99, and 8.29, respectively. STRUCTURE (v. 2.3.4) analysis unraveled two subpopulations (K=2). The dendrogram, constructed based on Jaccard similarity coefficient using the Unweighted Pair Group Average (UPGMA), in which, the first branch consisted of B. juncea, B. nigra and B. rapa, and the second branch consisted of B. arvensis, supported the results of STRUCTURE analysis. Additionally, principal component analysis (PCA) analysis supported the dendrogram and clearly separated the four taxa. This study showed that ISSRs would be useful to determine the genetic diversity in the Brassicaceae family.

Keywords

• Brassica cultivars
• Molecular markers
• Genetic diversity
• STRUCTURE

References

1. Abdelmigid, H. M. (2012). “Efficiency of Random Amplified Polymorphic DNA (RAPD) and Inter-Simple Sequence Repeats (ISSR) Markers for Genotype Fingerprinting and Genetic Diversity Studies in Canola.” African Journal of Biotechnology, 11 (24): 6409–19.
2. Afonso, S. D. J., Moreira, R. F. C., de Silva, C. A. L., Ferreira, C. F., da Silva Santos, V., & Muondo, P. A. (2019). Genetic structure of cassava populations (Manihot esculenta Crantz) from Angola assessed through (ISSR) markers. African Journal of Biotechnology, 18(7), 144–154.
3. Ahmed, M. Z. S., Masoud, I. M., & Zedan, S. Z. A. (2019). Molecular Characterization and Genetic Relationships of Cultivated Flax (Linum usitatissimum L.) Genotypes Using ISSR Markers. Middle East Journal of Agriculture Research, 8(3), 898–908.
4. Akçali-Giachino, R. R. (2020). Investigation of the genetic variation of anise (Pimpinella anisum L.) using RAPD and ISSR markers. Genetic Resources and Crop Evolution, 67, 763–780.
5. Baker, R. L., Yarkhunova, Y., Vidal, K., Ewers, B. E., & Weinig, C. (2017). Polyploidy and the relationship between leaf structure and function: Implications for correlated evolution of anatomy, morphology, and physiology in Brassica. BMC Plant Biology, 17(1), 3.
6. Banuelos, G., Dhillon, K., & Banga, S. (2013). Oilseed brassicas. In B. P. Singh (Eds.), Biofuel Crops: Production, Physiology and Genetics (1st ed., pp. 339–368). Wallingford, UK:CAB International.
7. Baruah, J., Pandey, S. K., Begum, T., Sarma, N., Paw, M., & Lal, M. (2019). Molecular diversity assessed amongst high dry rhizome recovery Ginger germplasm (Zingiber officinale Roscoe) from NE-India using RAPD and ISSR markers. Industrial Crops and Products, 129, 463–471.
8. Chen, H., Guo, A., Wang, J., Gao, J., Zhang, S., Zheng, J., Huang, X., Xi, J., & Yi, K. (2020). Evaluation of genetic diversity within asparagus germplasm based on morphological traits and ISSR markers. Physiol Mol Biol Plants, 26(2), 305–315.

9. Ciancaleoni, S., Raggi, L., & Negri, V. (2018). Assessment of spatial–temporal variation in natural populations of Brassica incana in south Italy: Implications for conservation. Plant Systematics and Evolution, 304, 731–745.
10. Contreras, R., Figueiras, M., Gallego, F. J., Benavente, E., Manzaneda, A. J., & Benito, C. (2017). Neutral molecular markers support common origin of aluminium tolerance in three congeneric grass species growing in acidic soils. AoB PLANTS, 9(6), plx060.
11. Earl, D. A., & vonHoldt, B. M. (2012). STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conservation Genetic Resources, 4, 359–361.
12. El-Esawi, M. A., Germaine, K., Bourke, P., & Malone, R. (2016). Genetic diversity and population structure of Brassica oleracea germplasm in Ireland using SSR markers. Comptes Rendus Biologies, 339(3), 133–140.
13. El-Sherbeny, G. A. R., Omara, M. K., Farrage, A. A., & Khaled, A. G. A. (2020). Associations between ISSR Markers and Quantitative Traits in Bread Wheat Genotypes. Asian Journal Research in Biosciences, 2(1), 1–8.
14. Evanno, G., Regnaut, S., & Goudet, J. (2005). Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Molecular Ecology, 14(8), 2611–2620.
15. FAOSTAT. (2018). Production quantities of Cabbages and other brassicas by country. http://www.fao.org/faostat
16. Frankham, R., Ballou, J. D., & Briscoe, D. (2010). Introduction to conservation genetics. Cambridge University Press.
17. Gupta, N., Zargar, S. M., Gupta, M., & Gupta, S. K. (2014). Assessment of Genetic Variation in Indian Mustard ( Brassica juncea L.) Using PCR Based Markers. Molecular Plant Breeding, 5(3), 10–17.
18. Jiang, J., Wang, Y., Zhu, B., Fang, T., Fang, Y., & Wang, Y. (2015). Digital gene expression analysis of gene expression differences within Brassica diploids and allopolyploids. BMC Plant Biology, 15(22), 1–13.
19. Kalia, P., Saha, P., & Ray, S. (2017). Development of RAPD and ISSR derived SCAR markers linked to Xca1Bo gene conferring resistance to black rot disease in cauliflower (Brassica oleracea var. Botrytis L.). Euphytica, 213(232).
20. Kalita, M. C., Mohapatra, T., Dhandapani, A., Yadava, D. K., Srinivasan, K., Mukherjee, A. K., & Sharma, R. P. (2007). Comparative Evaluation of RAPD, ISSR and Anchored-SSR Markers in the Assessment of Genetic Diversity and Fingerprinting of Oilseed Brassica Genotypes. J. Plant Biochemistry & Biotechnology, 16(1), 41–48.
21. Karl, R., & Koch, M. A. (2013). A world-wide perspective on crucifer speciation and evolution: Phylogenetics, biogeography and trait evolution in tribe Arabideae. Annals of Botany, 112(6), 983–1001.
22. Kaur, P., Banga, S., Kumar, N., Gupta, S., Akhatar, J., & Banga, S. S. (2014). Polyphyletic origin of Brassica juncea with B. rapa and B. nigra (Brassicaceae) participating as cytoplasm donor parents in independent hybridization events. American Journal of Botany, 101(7), 1157–1166.
23. Khalil, R. M. A., & El-Zayat, M. A. S. (2019). Molecular characterization of some Brassica species. Adv Plants Agric Res, 9, 112–119.
24. Koch, M. A., Karl, R., & German, D. A. (2017). Underexplored biodiversity of Eastern Mediterranean biota: Systematics and evolutionary history of the genus Aubrieta (Brassicaceae). Annals of Botany, 119(1), 39–57.
25. Kong, F., Mao, S. J., Jiang, J. J., Wang, J., Fang, X. P., & Wang, Y. P. (2011). Proteomic changes in newly synthesized Brassica napus allotetraploids and their early generations. Plant Mol Biol Rep, 29. https://doi.org/10.1007/s11105-011-0301-x
26. Kumar, A., Mishra, P., Singh, S. C., & Sundaresan, V. (2014). Efficiency of ISSR and RAPD markers in genetic divergence analysis and conservation management of Justicia adhatoda L., a medicinal plant. Plant Syst Evol, 300, 1409–1420.
27. Lara-Fioreze, A. C. C., Tomaz, C. A., Fioreze, S. L., Pilon, C., & Zanotto, M. D. (2013). Genetic diversity among progenies of Crambe abyssinica Hochst for seed traits. Industrial Crops and Products, 50, 771–775.
28. Mantel, N. (1967). The detection of disease clustering and a generalized regression approach. Cancer Research, 27(2), 209–220.
29. Moghaddam, M., Mohammmadi, S. B., Mohebalipour, N., Toorchi, M., Aharizad, S., & Javidfar, J. (2009). Assessment of genetic diversity in rapeseed cultivars as revealed by RAPD and microsatellite markers. African Journal of Biotechnology, 8(14), 3160–3167.
30. Mohammadin, S., Peterse, K., Kerke, S. J., Chatrou, L. W., Dönmez, A. A., Mummenhoff, K., Pires, J. C., Edger, P. P., Al-Shehbaz, I. A., & Schranz, M. E. (2017). Anatolian origins and diversification of Aethionema, the sister lineage of the core Brassicaceae. American Journal of Botany, 104(7), 1042–1054.
31. Nasim, N., Sandeep, I. S., Sahoo, A., Das, S., Panda, M. K., Acharya, L., RamaRao, V. V., Nayak, S., & Mohanty, S. (2020). Population genetic structure and diversity analysis in economically important Pandanus odorifer (Forssk.) Kuntze accessions employing ISSR and SSR markers. Industrial Crops and Products, 143, 111894.
32. Pankin, A. A., & Khavkin, E. E. (2011). Genome-specific SCAR markers help solve taxonomy issues: A case study with Sinapis arvensis (Brassiceae, Brassicaceae). American Journal of Botany, 98(3), e54–e57.
33. Powell, W., Morgante, M., Andre, C., Hanafey, M., Vogel, J., Tingey, S., & Rafalski, A. (1996). The comparison of RFLP, RAPD, AFLP and SSR (microsatellite) markers for germplasm analysis. Molecular Breeding, 2(3), 225–238.
34. Pradeep Reddy, M., Sarla, N., & Siddiq, E. A. (2002). Inter simple sequence repeat (ISSR) polymorphism and its application in plant breeding. Euphytica, 128(1), 9–17.
35. Prakash, S., Bhat, S. R., Quiros, C. F., Kirti, P. B., & Chopra, V. L. (2009). Brassica and Its Close Allies: Cytogenetics and Evolution. In Plant Breeding Reviews vol 31 (pp. 21–187). John Wiley & Sons, Inc.