KOREAN JOURNAL OF CROP SCIENCE (한국작물학회지)

The Korean Society of Crop Science (한국작물학회)
권호 표지
DOI QR코드

DOI QR Code

Development of EST-SSRs and Assessment of Genetic Diversity in Germplasm of the Finger Millet, Eleusine coracana (L.) Gaertn.

  • Wang, Xiaohan (National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration) ;
  • Lee, Myung Chul (National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration) ;
  • Choi, Yu-Mi (National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration) ;
  • Kim, Seong-Hoon (National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration) ;
  • Han, Seahee (Honam National Institute of Biological Resources) ;
  • Desta, Kebede Taye (National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration) ;
  • Yoon, Hye-myeong (National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration) ;
  • Lee, Yoonjung (National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration) ;
  • Oh, Miae (National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration) ;
  • Yi, Jung Yoon (National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration) ;
  • Shin, Myoung-Jae (National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration) ;
  • Kim, Kyung-Min (School of Applied Biosciences, College of Agriculture and Life Science, Kyungpook National University)
  • Received : 2021.10.09
  • Accepted : 2021.11.17
  • Published : 2021.12.01
Download PDF
⟨ Previous Next ⟩

Abstract

Finger millet (Eleusine coracana) is widely cultivated in tropical regions worldwide owing to its high nutritional value. Finger millet is more tolerant against biotic and abiotic stresses such as pests, drought, and salt than other millet crops; therefore, it was proposed as a candidate crop to adapt to climate change in Korea. In 2019, we used expressed sequence tag simple sequence repeat (EST-SSR) markers to evaluate the genetic diversity and structure of 102 finger millet accessions from two geographical regions (Africa and South Asia) to identify appropriate accessions and enhance crop diversity in Korea. In total, 40 primers produced 116 alleles, ranging in size from 135 to 457 bp, with a mean polymorphism information content (PIC) of 0.18225. Polymorphism was detected among the 40 primers, and 13 primers were found to have PIC values > 0.3. Principal coordinate and phylogenetic analyses, based on the combined data of both markers, grouped the finger millet accessions according to their respective collection areas.Therefore, the 102 accessions were classified into two groups, one from Asia and the other from Africa. We have conducted an in-depth study on the finger millet landrace pedigree. By sorting out and using the molecular characteristics of each pedigree, it will be useful for the management and accession identification of the plant resource. The novel SSR markers developed in this study will aid in future genetic analyses of E. coracana.

Keywords

Acknowledgement

This study was supported by grant allocated to M.-J.S. from National Academy of Agricultural Sciences (Project No. PJ014242), the Rural Development Administration Korea, Republic of Korea. This study was supported by the 2021 Postdoctoral Fellowship Program (X.W.) of the National Institute of Agricultural Sciences, RDA, Republic of Korea.

References

  1. Araneda, C., C. Correa, N. Lam, E. Uribe, M. Camiruaga, and P. Iturra. 2004. Asignacion de paternidadmaternidad y parentesco en un plantel de avestruces (Struthio camelus), utilizando seis loci microsatelites polimorficos. Av. Produc. Anim 29 : 3-14.
  2. Arya, L., M. Verma, V. Gupta, and J. Karihaloo. 2009. Development of EST SSRs in finger millet (Eleusine coracana ssp coracana) and their transferability to pearl millet (Pennisetum glaucum). Journal of Plant Biochemistry and Biotechnology 18 : 97-100. https://doi.org/10.1007/BF03263303
  3. Babu, B. K., N. Senthil, S. M. Gomez, K. R. Biji, N. S. Rajendraprasad, S. S. Kumar, and R. C. Babu. 2007. Assessment of genetic diversity among finger millet (Eleusine coracana (L.) Gaertn.) accessions using molecular markers. Genetic Resources and Crop Evolution 54 : 399-404. https://doi.org/10.1007/s10722-006-0002-8
  4. Baryeh, E. A. 2002. Physical properties of millet. Journal of Food Engineering 51 : 39-46. https://doi.org/10.1016/S0260-8774(01)00035-8
  5. Bradbury, P. J., Z. Zhang, D. E. Kroon, T. M. Casstevens, Y. Ramdoss, and E. S. Buckler. 2007. TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics 23 : 2633-2635. https://doi.org/10.1093/bioinformatics/btm308
  6. Cordeiro, G. M., R. Casu, C. L. McIntyre, J. M. Manners, and R. J. Henry. 2001. Microsatellite markers from sugarcane (Saccharum spp.) ESTs cross transferable to erianthus and sorghum. Plant science 160 : 1115-1123. https://doi.org/10.1016/S0168-9452(01)00365-X
  7. Da Maia, L. C., D. A. Palmieri, V. Q. De Souza, M. M. Kopp, F. I. F. de Carvalho, and A. Costa de Oliveira. 2008. SSR locator: tool for simple sequence repeat discovery integrated with primer design and PCR simulation. International journal of plant genomics 2008.
  8. De Wet, J., K. P. Rao, D. Brink, and M. Mengesha. 1984. Systematics and evolution of Eleusine coracana (Gramineae). American journal of Botany 71 : 550-557. https://doi.org/10.1002/j.1537-2197.1984.tb12540.x
  9. Dida, M. M., S. Ramakrishnan, J. L. Bennetzen, M. D. Gale, and K. M. Devos. 2007. The genetic map of finger millet, Eleusine coracana. Theoretical and Applied Genetics 114 : 321-332. https://doi.org/10.1007/s00122-006-0435-7
  10. Dida, M. M., N. Wanyera, M. L. H. Dunn, J. L. Bennetzen, and K. M. Devos. 2008. Population structure and diversity in finger millet (Eleusine coracana) germplasm. Tropical Plant Biology 1 : 131-141. https://doi.org/10.1007/s12042-008-9012-3
  11. Evanno, G., S. Regnaut, and J. Goudet. 2005. Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Molecular ecology 14 : 2611-2620. https://doi.org/10.1111/j.1365-294X.2005.02553.x
  12. Fernandez, D. R., D. J. Vanderjagt, M. Millson, Y.-S. Huang, L.-T. Chuang, A. Pastuszyn, and R. H. Glew. 2003. Fatty acid, amino acid and trace mineral composition of Eleusine coracana (Pwana) seeds from northern Nigeria. Plant Foods for Human Nutrition 58 : 1-10.
  13. Gimode, D., D. A. Odeny, E. P. de Villiers, S. Wanyonyi, M. M. Dida, E. E. Mneney, and S. M. de Villiers. 2016. Identification of SNP and SSR markers in finger millet using next generation sequencing technologies. PloS one 11 : e0159437. https://doi.org/10.1371/journal.pone.0159437
  14. Goron, T. L. and M. N. Raizada. 2015. Genetic diversity and genomic resources available for the small millet crops to accelerate a New Green Revolution. Frontiers in plant science 6 : 157. https://doi.org/10.3389/fpls.2015.00157
  15. Govindaraj, M., M. Vetriventhan, and M. Srinivasan. 2015. Importance of genetic diversity assessment in crop plants and its recent advances: an overview of its analytical perspectives. Genetics research international 2015.
  16. Gupta, R., K. Verma, D. Joshi, D. Yadav, and M. Singh. 2010. Assessment of genetic relatedness among three varieties of finger millet with variable seed coat color using RAPD and ISSR markers. Genet Eng Biotechnol J 2 : 1-9.
  17. Hittalmani, S., H. B. Mahesh, M. D. Shirke, H. Biradar, G. Uday, Y. R. Aruna, and A. Mohanrao. 2017. Genome and transcriptome sequence of finger millet (Eleusine coracana (L.) Gaertn.) provides insights into drought tolerance and nutraceutical properties. BMC genomics 18 : 1-16. https://doi.org/10.1186/s12864-016-3406-7
  18. Kalinowski, S. T., Taper, M. L., and T. C. Marshall. 2007. Revising how the computer program CERVUS accommodates genotyping error increases success in paternity assignment. Molecular ecology 16 : 1099-1106. https://doi.org/10.1111/j.1365-294X.2007.03089.x
  19. Kumar, A., D. Sharma, A. Tiwari, J. Jaiswal, N. Singh, and S. Sood. 2016. Genotyping-by-sequencing analysis for determining population structure of finger millet germplasm of diverse origins. The plant genome 9 : 1-15.
  20. Naga, B. L. R. I., L. N. Mangamoori, and S. Subramanyam. 2012. Identification and characterization of EST-SSRs in finger millet (Eleusine coracana (L.) Gaertn.). Journal of Crop Science and Biotechnology 15 : 9-16. https://doi.org/10.1007/s12892-011-0064-9
  21. Pandey, P. and G. Kumar. 2005. Finger Millet: A flair for human nutrition in Uttaranchal. Indian Farmers Digest 38 : 28-30.
  22. Perrier, X. 2006. DARwin software. http://darwin.cirad.fr/darwin:
  23. Powell, W., G. C. Machray, and J. Provan. 1996. Polymorphism revealed by simple sequence repeats. Trends in plant science 1 : 215-222. https://doi.org/10.1016/S1360-1385(96)86898-0
  24. Pritchard, J. K., M. Stephens, and P. Donnelly. 2000. Inference of population structure using multilocus genotype data. Genetics 155 : 945-959. https://doi.org/10.1093/genetics/155.2.945
  25. Saitou, N. and M. Nei. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Molecular biology and evolution 4 : 406-425.