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Microsatellite analysis to rationalize grape germplasm in India and development of a molecular database

Published online by Cambridge University Press:  01 May 2013

Anuradha Upadhyay ,
Lalitkumar B. Aher ,
Manisha P. Shinde ,
Kavita Y. Mundankar ,
Anuj Datre  and
G. S. Karibasappa
Anuradha Upadhyay*
Affiliation:
National Research Centre for Grapes, Manjri Farm Post, Solapur Road, Pune412 307, Maharashtra, India
Lalitkumar B. Aher
Affiliation:
National Research Centre for Grapes, Manjri Farm Post, Solapur Road, Pune412 307, Maharashtra, India
Manisha P. Shinde
Affiliation:
National Research Centre for Grapes, Manjri Farm Post, Solapur Road, Pune412 307, Maharashtra, India
Kavita Y. Mundankar
Affiliation:
National Research Centre for Grapes, Manjri Farm Post, Solapur Road, Pune412 307, Maharashtra, India
Anuj Datre
Affiliation:
National Research Centre for Grapes, Manjri Farm Post, Solapur Road, Pune412 307, Maharashtra, India
G. S. Karibasappa
Affiliation:
National Research Centre for Grapes, Manjri Farm Post, Solapur Road, Pune412 307, Maharashtra, India
*
* E-mail: anu_upadhyay@yahoo.com
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Abstract

Three hundred and seventeen grape accessions from the National Active Grape Germplasm Site in India were analysed with 25 microsatellite markers. A total of 411 alleles were detected, of which 42% were rare alleles. Unique alleles for 56 genotypes were also identified. The analysis of microsatellite data identified 63 duplicate accessions and only 254 accessions were unique genotypes. Several cases of misnomers, synonymy and homonymy were identified. Parental genotype for a few clonal selections was ascertained. Population structure analysis grouped 254 unique genotypes into four major clusters. The analysis also revealed the presence of admixtures with only 79% of pure ancestry. A core collection comprising 80 genotypes was identified, which represented all the alleles and genetic diversity. A user-friendly and interactive computer application software was developed for storage and the retrieval of molecular data. A molecular database for the 254 genotypes was created. This analysis will help in the rationalization and better management of germplasm. Information on genetic diversity and population structure will form the basis for varietal improvement programmes.

Keywords

core collectiongenetic diversitygrapemicrosatellitemolecular database

Information

Type
Research Article
Information
Plant Genetic Resources , Volume 11 , Issue 3 , December 2013 , pp. 225 - 233
Copyright
Copyright © NIAB 2013 

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References

Brown, AHD (1989) Core collections: a practical approach to genetic resources management. Genome 31: 818–824.CrossRefGoogle Scholar
Carrier, G, Le Cunff, L, Dereeper, A, Legrand, D, Sabot, F, Bouchez, O, Audeguin, L, Boursiquot, J-M and This, P (2012) Transposable elements are a major cause of somatic polymorphism in Vitis vinifera L. PLoS One 7: e32973.CrossRefGoogle Scholar
Cho, GT, Yoon, MS, Lee, J, Baek, HJ, Kang, JH, Kim, TS and Paek, NC (2008) Development of a core set of Korean soybean landraces (Glycine max (L.) Merr). Journal of Crop Sciences and Biotechnology 11: 157–162.Google Scholar
Cipriani, G, Spadotto, A, Jurman, I, Di Gaspero, G, Crespan, M, Meneghetti, S, Frare, E, Vignani, R, Cresti, M, Morgante, M, Pezzotti, M, Pe, E, Policriti, A and Testolin, R (2010) The SSR-based molecular profile of 1005 grapevine (Vitis vinifera L.) accessions uncovers new synonymy and parentages, and reveals a large admixture amongst varieties of different geographic origin. Theoretical and Applied Genetics 121: 1569–1585.Google Scholar
Crespan, M, Meneghetti, S and Cancellier, S (2009) Identification and genetic relationship of the principal rootstocks cultivated in Italy. American Journal of Enology and Viticulture 60: 349–356.CrossRefGoogle Scholar
Dangl, GS, Mendum, ML, Prins, BH, Walker, MA, Meredith, CP and Simon, CJ (2001) Simple sequence repeat analysis of a clonally propagated species: a tool for managing a grape germplasm collection. Genome 44: 432–438.Google Scholar
Dettweiler, E and Eibach, R (2003) The two Vitis databases as tools for germplasm management: Vitis international variety catalogue and European Vitis database. Acta Horticulturae (ISHS) 603: 505–509.Google Scholar
Du, Q, Wang, B, Wei, Z, Zhang, D and Li, B (2012) Genetic diversity and population structure of Chinese white poplar (Populus tomentosa) revealed by SSR markers. Journal of Heredity 103: 853–862.CrossRefGoogle ScholarPubMed
Evanno, G, Regnaut, S and Goudet, J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Molecular Ecology 14: 2611–2620.CrossRefGoogle ScholarPubMed
Falush, D, Stephens, M and Pritchard, JK (2003) Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics 164: 1567–1587.CrossRefGoogle ScholarPubMed
Frankel, OH (1984) Genetic perspective of germplasm conservation. In: Arber, W, Illmensee, K, Peacock, WJ and Starlinger, P (eds) Genetic Manipulation: Impact on Man and Society. Cambridge: Cambridge University Press, pp. 161–170.Google Scholar
Frankel, OH and Brown, AHD (1984) Current plant genetic resources – a critical appraisal. In: Chopra, VL, Joshi, BC, Sharma, RP and Bansal, HC (eds) Genetics. New Frontiers Vol. IV. New Delhi: Oxford & IBH Publishing Co., pp. 3–13.Google Scholar
Ibáñez, J, Vélez, MD, Andrés, MT and Borrego, J (2009) Molecular markers for establishing distinctness in vegetatively propagated crops: a case study in grapevine. Theoretical and Applied Genetics 119: 1213–1222.Google Scholar
Kalinowski, ST, Taper, ML and Marshall, TC (2007) Revising how the computer program CERVUS accommodates genotyping error increases success in paternity assignment. Molecular Ecology 16: 1099–1106.CrossRefGoogle ScholarPubMed
Kim, KW, Chung, HK, Cho, GT, Ma, KH, Chandrabalan, D, Gwag, JG, Kim, TS, Cho, EG and Park, YJ (2007) PowerCore: a program applying the advanced M strategy with a heuristic search for establishing allele mining sets. Bioinformatics 23: 2155–2162.CrossRefGoogle Scholar
Laucou, V, Lacombe, T, Dechesne, F, et al., (2011) High throughput analysis of grape genetic diversity as a tool for germplasm collection management. Theoretical and Applied Genetics 122: 1233–1245.Google Scholar
Le Cunff, L, Fournier-Level, A, Laucou, V, Vezzulli, S, Lacombe, T, Adam-Blondon, A-F, Boursiquot, J-M and This, P (2008) Construction of nested genetic core collections to optimize the exploitation of natural diversity in Vitis vinifera L. subsp sativa. BMC Plant Biology 8: 31.Google Scholar
Lefort, F and Roubelakis-Angelakis, KA (2000) The Greek Vitis database: a multimedia web-backed genetic database for germplasm management of Vitis resources in Greece. Journal of Wine Research 11: 233–242.CrossRefGoogle Scholar
Lin, H and Walker, MA (1998) Identifying grape rootstocks with simple sequence repeat (SSR) DNA markers. American Journal of Enology and Viticulture 49: 403–407.CrossRefGoogle Scholar
Lopez-Gartner, G, Cortina, H, McCouch, SR and Moncada, MDP (2009) Analysis of genetic structure in a sample of coffee (Coffea arabica L.) using fuorescent SSR markers. Tree Genetics and Genomes 5: 435–446.Google Scholar
Moe, KT, Gwag, J-G and Park, Y-J (2012) Efficiency of PowerCore in core set development using amplified fragment length polymorphic markers in mungbean. Plant Breeding 131: 110–117.Google Scholar
Moncada, X and Hinrichsen, P (2007) Limited genetic diversity among clones of red wine cultivar ‘Carmenère’ as revealed by microsatellite and AFLP markers. Vitis 46: 174–180.Google Scholar
Moncada, X, Pelsy, F, Merdinoglu, D and Hinrichsen, P (2006) Genetic diversity and geographical dispersal in grapevine clones revealed by microsatellite markers. Genome 49: 1459–1472.Google Scholar
Myles, S, Boyko, AR, Owens, CL, Brown, PJ, Grassi, F, Aradhya, MK, Prins, B, Reynolds, A, Jer-Ming, Chia, Ware, D, Bustamante, CD and Buckler, ES (2011) Genetic structure and domestication history of the grape. Proceedings of National Academy of Science USA 108: 3530–3535.Google Scholar
Nunez, Y, Fresno, J, Torres, V, Ponz, F and Gallego, FJ (2004) Practical use of microsatellite markers to manage Vitis vinifera germplasm: molecular identification of grapevine samples collected blindly in D.O. “El Bierzo” (Spain). Journal of Horticultural Science and Biotechnology 79(3): 437–440.Google Scholar
Patil, AV and Rane, DA (1974) A short note on a mutation of Cheema Sahebi (syn Selection 7). Vitis 13: 21–214.Google Scholar
Perrier X, Jacquemoud-Collet JP. (2006) DARwin software. Available at http://darwin.cirad.fr/darwin.Google Scholar
Pritchard, JK, Stephens, M and Donnelly, P (2000) Inference of population structure using multilocus genotype data. Genetics 155: 945–959.Google Scholar
Raina, SN, Ahuja, PS, Sharma, RK, Das, SC, Bhardwaj, P, Negi, R, Sharma, V, Singh, SS, Sud, RK, Kaur, R, Pandey, V, Banik, J, Razdan, V, Sehgal, D, Dar, TUH, Kumar, A, Bali, S, Bhat, V, Prasanna, BM, Goel, S, Negi, MS, Vijayan, P, Tripathi, SB, Bera, B, Hazarika, M, Mandal, AKA, Kumar, RR, Vijayan, D, Ramkumar, S, Chowdhury, BR and Mandi, SS (2012) Genetic structure and diversity of India hybrid tea. Genetic Resources and Crop Evolution 59: 1527–1541.Google Scholar
Regner, F, Wiedeck, E and Stadlbauer, A (2000) Differentiation and identification of White Riesling clones by genetic markers. Vitis 39: 103–107.Google Scholar
Santana, JC, Heuertz, M, Arranz, C, Rubio, JA, Martinez-Zapater, JM and Hidalgo, H (2010) Genetic structure, origins, and relationships of grapevine cultivars from the Castilian plateau of Spain. American Journal of Enology and Viticulture 61: 214–224.Google Scholar
Schoen, DJ and Brown, AHD (1993) Conservation of allelic richness in wild crop relatives is aided by assessment of genetic markers. Proceedings of National Academy of Science USA 90(10): 623–10627.Google Scholar
Sefc, K, Regner, F, Glössl, J and Steinkellner, H (1998) Genotyping of grapevine and rootstock cultivars using microsatellite markers. Vitis 37: 15–20.Google Scholar
Upadhyay, A, Kadam, US, Chacko, PM and Karibasappa, GS (2010a) Microsatellite and RAPD analysis of grape (Vitis spp.) accessions and identification of duplicates/misnomers in germplasm collection. Indian Journal of Horticulture 67: 8–15.Google Scholar
Upadhyay, A, Kadam, US, Chacko, PM, Aher, LB and Karibasappa, GS (2010b) Microsatellite analysis to differentiate clones of Thompson seedless grapevine. Indian Journal of Horticulture 67: 260–263.Google Scholar
Upadhyay, A, Aher, LB and Karibasappa, GS (2011) Detection of variation among clonal selections of grapevine (Vitis vinifera L.) cv. Kishmish Chernyi by AFLP analysis. Journal of Horticultural Science and Biotechnology 86: 230–234.CrossRefGoogle Scholar
Veloso, MM, Almandanim, MC, Baleiras-Couto, M, Pereira, HS, Carneiro, LC, Fevereiro, P and Eiras-Dias, J (2010) Microsatellite database of grapevine (Vitis vinifera L.) cultivars used for wine production in Portugal. Ciência e Técnica Vitivinicola 25: 53–61.Google Scholar
Vignani, R, Scali, M, Masi, E and Cresti, M (2002) Genomic variability in Vitis vinifera L. Sangiovese assessed by microsatellite and no radioactive AFLP test. Electron Journal of Biotechnology 5: 3–4.CrossRefGoogle Scholar
Vouillamoz, JF, Arnold, C and Frei, A (2009) Swiss Vitis microsatellite database. Acta Horticulturae 827: 477–480.Google Scholar
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