Development of EST-SSRs and Assessment of Genetic Diversity in Little Millet (Panicum sumatrense) Germplasm
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초록
Little millet (Panicum sumatrense) is well known for its salt and drought stress tolerance and high nutritional value, but very limited knowledge of genetic variation and genomic information is available. In this study, a total of 779 primer pairs were designed from the 22,961 EST sequences of switchgrass (Pancium virgatum), of which 48 EST-SSR markers were developed based on the trials of transferability of these primers in little millet. The EST-SSR amplicons showed reproducible single band polymorphism and produced a total of 160 alleles with an average of 3.3 alleles per locus in 37 accessions of little millet. The average values of expected and observed heterozygosities were 0.266 and 0.123, respectively. The polymorphic information content (PIC) values were observed in range of 0.026 to 0.549 with an average of 0.240. The genetic relatedness among the little millet accessions was evaluated by neighbor-joining dendrogram, which grouped all accessions into two distinct groups. The validation thus demonstrated the utility of the switchgrass EST-SSR markers in assessing genomic relationships in little millet. The findings from this study could be useful for designing strategies for the identification of diverse germplasm for conservation and future molecular breeding programs for little millet. Key words - EST-SSRs, Genetic diversity, Little millet
Abstract
Little millet (Panicum sumatrense) is well known for its salt and drought stress tolerance and high nutritional value, but very limited knowledge of genetic variation and genomic information is available. In this study, a total of 779 primer pairs were designed from the 22,961 EST sequences of switchgrass (Pancium virgatum), of which 48 EST-SSR markers were developed based on the trials of transferability of these primers in little millet. The EST-SSR amplicons showed reproducible single band polymorphism and produced a total of 160 alleles with an average of 3.3 alleles per locus in 37 accessions of little millet. The average values of expected and observed heterozygosities were 0.266 and 0.123, respectively. The polymorphic information content (PIC) values were observed in range of 0.026 to 0.549 with an average of 0.240. The genetic relatedness among the little millet accessions was evaluated by neighbor-joining dendrogram, which grouped all accessions into two distinct groups. The validation thus demonstrated the utility of the switchgrass EST-SSR markers in assessing genomic relationships in little millet. The findings from this study could be useful for designing strategies for the identification of diverse germplasm for conservation and future molecular breeding programs for little millet. Key words - EST-SSRs, Genetic diversity, Little millet
참고문헌 (32)
- Asjad Ali, "EST-SSR Based Genetic Diversity and Population Structure among Korean Landraces of Foxtail Millet (Setaria italica L.)", 한국자원식물학회지, 29(3), pp.322~330 (2016), 한국자원식물학회[DOI]
- Ajithkumar, I.P., "ROS scavenging system, osmotic maintenance, pigment and growth status of panicum sumatrense roth under drought stress", Cell Bio-Chem. Biophys, 68, pp.587~595 (2014)
- Manosh Kumar Biswas, "Genome Wide Characterization of Short Tandem Repeat Markers in Sweet Orange (Citrus sinensis)", PLoS ONE, 9(8), pp.e104182~ (2014), Public Library of Science (PLoS)[DOI]
- Beck, E. H., "Specific and unspecific responses of plants to cold and drought stress", J. Biosci, 32, pp.501~510 (2007)
- Bhaskaran, J., "Accelerated reactive oxygen scavenging system and membrane integrity of two panicum species varying in salt tolerance", Cell BioChem. Biophys, 67, pp.885~892 (2013)
- Burrows, C., "The RNA binding protein Larp1 regulates cell division, apoptosis and cell migration", Nucleic Acids Res, 38, pp.5542~5553 (2010)
- Casler, M.D., "Switchgrass, Green Energy and Technology", pp.29~53 (2012), Springer
- 조영일, "Development and characterization of twenty-five new polymorphic microsatellite markers in proso millet (Panicum miliaceum L.)", Genes & Genomics, 32(3), pp.267~273 (2010), 한국유전학회
- Cordeiro, G. M., "Microsatellite markers from sugarcane (Saccharum spp) EST cross transferable to erianthus and sorghum", Plant Sci, 160, pp.1115~1123 (2001)
- De Wet, J. M. J., "Systematics and domestication of Panicum sumatrense (Graminae)", J. d'agriculture Tradit. Bot. appliquée, 30, pp.159~168 (1983)
- Da Maia, L. C., "SSR locator:tool for simple sequence repeat discovery integrated with primer design and PCR simulation. Int", J. Plant Genom (2008)[DOI]
- Travis L. Goron, "Genetic diversity and genomic resources available for the small millet crops to accelerate a New Green Revolution", Frontiers in Plant Science, 6 (2015), Frontiers Media SA[DOI]
- Govindaraj, M., "Importance of genetic diversity assessment in crop plants and its recent advances: An overview of its Analytical perspectives", Genet. Res. Int (2015)[DOI]
- "Plant Cell Rep", 2012, 323~337
- S. C. Hiremath, "Genome homology and origin of Panicum sumatrense (Gramineae).", CYTOLOGIA, 55(2), pp.315~319 (1990), International Society of Cytology[DOI]
- 임착한, "큰느타리(Pleurotus eryngii) 품종 판별을 위한 초위성체유래 다중 표지 개발", 한국균학회지, 42(2), pp.159~164 (2014), 한국균학회
- Jia, X. P., "Development of EST-SSR in foxtail millet (Setaria italica)", Genet. Resour. Crop Ev, 54, pp.233~236 (2007)
- "Theor. Appl. Genet", 2009, 821~829
- Ramesh V. Kantety, "Data mining for simple sequence repeats in expressed sequence tags from barley, maize, rice, sorghum and wheat", Plant Molecular Biology, 48(5, pp.6) (2002), 501~510[DOI]
- Lin, H. S., "Genetic diversity in the foxtail millet (Setaria italica)germplasm as determined by agronomic traits and microsatellite markers", Aus. J. crop Sci, 6(2), pp.342~349 (2012)
- Liu, K., "PowerMarker: an integrated analysis environment for genetic marker analysis", Bioinformatics, 21, pp.2128~2129 (2005)
- Samantha A. McGaughey, "Roles of Aquaporins in Setaria viridis Stem Development and Sugar Storage", Frontiers in Plant Science, 7, pp.1815~ (2016), Frontiers Media SA[DOI]
- Nicot, N., "Study of simple sequence repeat (SSR) markers from wheat expressed sequence tags (ESTs)", Theor. Appl. Genet, 109(4), pp.800~805 (2004)
- Ninth annual report: 1998-99 M.S, "MSSR", Swaminathan Research Foundation, ~ (1999)
- "DNA Res", 2013, 197~207
- Peakall, R.O.D., "GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research", Molecular Ecology Notes, 6(1), pp.288~295 (2006)
- "Darwin software" (2006)[URL]
- Pradeep, S.R., "Effect of processing methods on the nutraceutical and antioxidant properties of little millet (Panicum sumatrense) extracts", Food Chem, 126, pp.1643~1647 (2011)
- Gilda Rauscher, "Development of genomic SSR markers for fingerprinting lettuce (Lactuca sativa L.) cultivars and mapping genes", BMC Plant Biology, 13(1), pp.11~ (2013), Springer Nature[DOI]
- 서동휘, "국내 수집 감 품종을 이용한 EST-SSR marker 개발과 유전적 다양성 분석", 한국자원식물학회지, 26(4), pp.491~502 (2013), 한국자원식물학회[DOI]
- Wang, Y. W., "Development of 1,030 Genomic SSR Markers in Switchgrass", Theor. Appl. Genet, 122(4), pp.677~686 (2011)
- Wang, M. L., "Transfer of simple sequence repeat (SSR) markers from major cereal crops to minor grass species for germplasm characterization and evaluation", Plant Genet. Resour, 3(1), pp.45~57 (2005)