Genetic Diversity Analysis of Fodder Oats (Avena sativa L.) Germplasm by Microsatellite Markers

Authors
R. Kapoor 1
K. Choudhary 2
1 Department of Plant Breeding and Genetics, PAU, Ludhiana 141004, Punjab, India.
2 Indian Council of Agricultural Research, New Delhi, India.
Abstract
The present study was undertaken to assess the genetic diversity in the ninety six oat (Avena sativa L.) elite cultivars representing the collection from various eco-geographical regions of India. The molecular diversity analysis using 40 SSR markers clustered all the 96 cultivar into ten clusters and significant level of distinction (dissimilarity coefficient ranged from 0.12 to 0.96) was depicted among the lines indicating a high degree of divergence among these lines. Genotypic pairs having utmost genetic dissimilarity (0.96) were OL1634 and OL1688, OL1702 and OL1688, OL1705 and OL1634, UPO03-3 and OL 1688, and UPO03-3 and OL1705 that can be used as parents in purposeful hybridization programs. Polymorphic Information Content (PIC) values ranged from as low as 0.06 to as high as 0.75 (AM 7). Owing to their highest PIC values, primer pairs AM7 (0.75), AM2 (0.69) and AM10 (0.69) can be further used in association mapping studies in oat. The Un-weighted Pair Group Method with Arithmetic Mean (UPGMA) based dendrogram revealed the cluster V (19 genotypes) as the largest and cluster X (3 genotypes) as the smallest one. Thus, genotypes within clusters can be predicted as similarity pool in further oat improvement programs. The selected panel of SSR markers performed well in detection of genetic diversity patterns and can be recommended for future germplasm characterization studies in oats.

Keywords

1. Abbas, S. J., Shah, S. R. U., Rasool, G. and Munir, I. 2008. Analysis of Genetic Diversity in Genus Avena. Pak. J. Weed Sci. Res., 14: 33-41.
2. Becher, R. 2007. EST-Derived Microsatellites as a Rich Source of Molecular Markers for Oats. Plant Breed., 126: 274—278.
3. Boczkowska, M., Nowosielski, J., No wosielska, D. and Podyma, W. 2014. Assessing Genetic Diversity in 23 Early Polish Oat Cultivars Based on Molecular and Morphological Studies. Gene. Resour. Crop Evol., 61(5): 927–941.
4. FAO. 2012. Production Statistics. Food and Agriculture Organisation, Rome.
5. Fu, Y. B., Cho ng, J., Fetch, T. and Wang, M. L. 2007. Microsatellite Variation in Avena sterilis Oat Germplasm. Theor. Appl. Genet., 114: 1029–1038.
6. Gao, L. F., Tang, J. F., Li, H. W. and Jia, J. Z. 2003. Analysis of Microsatellites in Major Crops Assessed by Computational and Experimental Approaches. Mol. Breed., 12: 245-261.
7. Hanif, Z., Swati, Z.A., Khan, I., Hassan, G., Marwat, K.B., Ali, S. and Khan, M. I. 2008. RAPD and SSR Analysis of Wild Oats (Avena Species) from North West Frontier Province of Pakistan. Afr. J. Plant Sci., 11: 133–139.
8. Holland, J. B., Helland, S. J., Sharopova, N. and Rhyne, D. C. 2001. Polymorphism of PCR-Based Markers Targeting Exons, Introns, Promoter Regions, and SSRs in Maize and Introns and Repeat Sequences in Oat. Genome., 44: 1065—1076.
9. Huang, X. Q., Borner, A., Roder, M. S. and Ganal M. W. 2002. Assessing Genetic Diversity of Wheat (Triticum aestivum L.) Germplasm Using Microsatellite Markers. Theor. Appl. Genet., 105: 699–707.
10. Jannink, J. L. and Gardner, S. W. 2005. Expanding the Pool of PCR Based Markers for Oat. Crop Sci., 45: 2383–2387.
11. Li, C. D., Rossnagel, B.G. and Scoles, G. J. 2000. The Development of Oat Microsatellite Markers and their use in Identifying Relationships among Avena Species and Oat Cultivars. Theor. Appl. Genet., 101: 1259-1268.
12. Litt, M. and Luty, J. A. 1989. A Hyper Variable Microsatellite Revealed by In Vitro Amplification of a Dinucleotide Repeat within the Cardiac Muscle Actin Gene. Am. J. Hum. Genet., 44: 397–401.
13. Loskutov, I. G. 2007. Oat (Avena sativa) Distribution, Taxonomy, Evolution and Breeding Value. VIR, St. Peterberg, Russia.
14. Loskutov, I. G. and Perchuk, I. N. 2000. Evaluation of Interspecific Diversity in Avena Genus by RAPD Analysis. Oat Newslett., 46 PP.
15. Montilla-Bason, G., Sanchez-Martin, J., Rispail, N., Rubiales, D., Mur, L., Langdon, T., Griffiths, I., Howarth, and Prats, E. 2013. Genetic Diversity and Population Structure among Oat Cultivars and Landraces. Plant Mol. Biol. Res., 31: 1305—1314.
16. Morgante, M. and Olivieri, A. M. 1993. PCR-Amplified Microsatellites as Markers in Plant Genetics. Plant J., 3: 175–182.
17. O’Neill, R., Snowdon, R. J. and Kohler, W. 2003. Population Genetics Aspects of Biodiversity. Progress Bot., 64: 115-137.
18. Oliver, R. E., Obert, D. E., Hu, G., Bonman, J. M. and Jackson, E. W. 2010. Development of Oat based Markers from Barley and Wheat Microsatellites. Genome, 6:458-71.
19. Orr, W. and Stephen, J. M. 2008. Development of PCR-based SCAR and CAPS Markers Linked to β-Glucan and Protein Content QTL Regions in Oat. Genome, 51: 421-425.
20. Pal, S. 2002. Oat-Derived SSRs and RFLPs. Crop Sci., 42: 912-918. Perrier, X. and Jacquemond-Collet, J. P. 2006. DARwin Software. http://darwin.cirad.fr/darwin/.
21. Poulsen, G. B., Kahl, G. and Weising, K. 1993. Abundance and Polymorphism of Simple Repetitive DNA Sequences in Brassica napus L. Theor. Appl. Genet., 85: 994-1000.
22. Powell, W., Marchray, G. C. and Provan, J. 1996. Polymorphism Revealed by Simple Sequence Repeats. Trend. Plant Sci., 1: 215–222.
23. Queller, D. C., Strassmann J. E. and Hughes, C. R. 1993. Microsatellites and Kinship. Trend. Ecol. Evol., 8: 285–328.
24. Ruwali, Y., Singh, K., Kumar, S. and Kumar, L. 2013. Molecular Diversity Analysis in Selected Fodder and Dual Purpose Oat (Avena sativa L.) Genotypes by Using Random Amplified Polymorphic DNA (RAPD). Afr. J. Biotech., 12(22): 3425-29.
25. Tanhuanpää, P., Kalendar, R., Schulman, A. H. and Kiviharju, E. 2007. A Major Gene for Grain Cadmium Accumulation in Oat (Avena sativa L.). Genome, 50(6): 588-594.
26. Weber, J. L. and May, P. E. 1989. Abundant Classes of Human DNA Polymorphisms which Can Be Typed Using the Polymerase Chain Reaction, Am. J. Hum. Genet., 44: 388–396.
27. Wight, C. P., Yan, W., Fetch, J. M., Deyl, J. and Tinker, N. A. 2010. A Set of New Simple Sequence Repeat and Avenin DNA Markers Suitable for Mapping and Fingerprinting Studies in Oat (Avena Spp.). Crop Sci., 50:1207—1218.
28. Zhu, S. and Kaeppler, H. F. 2003. Identification of Quantitative Trait Loci for Resistance of New Sources to Crown Rust in Oat Line MAM17- 5. Crop Sci., 43: 358-366.
Journal of Agricultural Science and Technology
Volume 19, Issue 6
November and December 2017
Pages 1369-1379