Comparative assessment of EST-SSR, EST-SNP and AFLP markers for evaluation of genetic diversity and conservation of genetic resources using wild, cultivated and elite barleys

Varshney, R K and Chabane, K and Hendre, P S and Aggarwal, R K and Graner, A (2007) Comparative assessment of EST-SSR, EST-SNP and AFLP markers for evaluation of genetic diversity and conservation of genetic resources using wild, cultivated and elite barleys. Plant Science, 173 (6). pp. 638-649. ISSN 0168-9452

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Abstract

A set of 16 expressed sequence tag (EST)-derived simple sequence repeat (SSR) and 15 EST-derived single nucleotide polymorphism (SNP) markers together with 4 amplified fragment length polymorphism (AFLP) primer combinations were analyzed on 43 wild (Hordeum vulgare ssp. spontaneum – HS), 35 cultivated (H. vulgare ssp. vulgare – HV) and 12 elite (H. vulgare ssp. vulgare – from EU) barley lines. SSR markers were found most polymorphic with an average PIC value of 0.593 and eight alleles per marker, while AFLP markers showed the highest effective multiplex ratio (26.4) and marker index (5.042). The effective marker index (EMI) was recorded highest (0.468) for AFLP markers and lowest (0.341) for the SNP markers while the SSR markers had an intermediate EMI (0.442). Cluster analysis on combined set of SSR, SNP and AFLP genotyping data classified wild, cultivated and elite barley lines in three distinct groups. The present study suggests the SNP markers as the best class of markers for characterizing and conserving the genebank materials and the AFLP and SSR markers more suitable for diversity analysis and fingerprinting.

Item Type: Article
Divisions: UNSPECIFIED
CRP: UNSPECIFIED
Uncontrolled Keywords: AFLP, SSR, SNP, Molecular markers, Genetic diversity, Barley
Subjects: Others > Genetics and Genomics
Depositing User: Library ICRISAT
Date Deposited: 22 Oct 2011 06:06
Last Modified: 08 Nov 2011 03:18
URI: http://oar.icrisat.org/id/eprint/3004
Official URL: http://dx.doi.org/10.1016/j.plantsci.2007.08.010
Projects: UNSPECIFIED
Funders: Bundesministerium für Wirtschaftliche Zusammenarbeit und Entwicklung
Acknowledgement: We are thankful to Ulrike Beier for her excellent technical assistance and to Nils Stein for his help in various ways. Thanks are also due to Claudia Wiedow, Kalina Andreeva, Tatjana Sretenovic Rajicic for useful discussions while analyzing and interpreting results. This work in part was financially supported by a GTZ project (no. 2002.7860.6-001.00 and contract no. 1060503) sponsored by BMZ (Bundesministerium für Wirtschaftliche Zusammenarbeit und Entwicklung), Germany.
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