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Development and characterization of tomato SSR markers from genomic sequences of anchored BAC clones on chromosome 6

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Abstract

Simple sequence repeat motifs are abundant in plant genomes and are commonly used molecular markers in plant breeding. In tomato, currently available genetic maps possess a limited number of simple sequence repeat (SSR) markers that are not evenly distributed in the genome. This situation warrants the need for more SSRs in genomic regions lacking adequate markers. The objective of the study was to develop SSR markers pertaining to chromosome 6 from bacterial artificial chromosome (BAC) sequences available at Solanaceae Genomics Network. A total of 54 SSR primer pairs from 17 BAC clones on chromosome 6 were designed and validated. Polymorphism of these loci was evaluated in a panel of 16 genotypes comprising of Solanum lycopersicum and its wild relatives. Genetic diversity analysis based on these markers could distinguish genotypes at species level. Twenty-one SSR markers derived from 13 BAC clones were polymorphic between two closely related tomato accessions, West Virginia 700 and Hawaii 7996 and were mapped using a recombinant inbred line population derived from a cross between these two accessions. The markers were distributed throughout the chromosome spanning a total length of 117.6 cM following the order of the original BAC clones. A major QTL associated with resistance to bacterial wilt was mapped on chromosome 6 at similar location of the reported Bwr-6 locus. These chromosome 6-specific SSR markers developed in this study are useful tools for cultivar identification, genetic diversity analysis and genetic mapping in tomato.

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Acknowledgements

The authors would like to thank Drs. Kadirvel Palchamy and Robert de la Peña for providing DNA samples of the tomato genotypes used in the study, Dr. Peter Hanson for providing information on tomato accessions, and Ms. Chiou-fen Hsu for technical assistance. This study is supported by funding provided by GTZ 81070160: Deutsche Gesellshaft fur Technishe Zusammenarbeit GmbH of Germany.

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Authors and Affiliations

  1. AVRDC—The World Vegetable Center, 60 Yi-Min Liao, Shanhua, Tainan, 74151, Taiwan

    Subramaniam Geethanjali & Jaw-Fen Wang

  2. Department of Agronomy, National Taiwan University, Taipei, 10617, Taiwan

    Kai-Yi Chen

  3. Institute of Biological Sciences, University of the Philippines, Los Banõs, College, 4031, Laguna, Philippines

    Davidson V. Pastrana

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  1. Subramaniam Geethanjali
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  2. Kai-Yi Chen
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  3. Davidson V. Pastrana
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  4. Jaw-Fen Wang
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Correspondence to Jaw-Fen Wang.

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Subramaniam Geethanjali and Kai-Yi Chen contributed equally for this manuscript.

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Geethanjali, S., Chen, KY., Pastrana, D.V. et al. Development and characterization of tomato SSR markers from genomic sequences of anchored BAC clones on chromosome 6. Euphytica 173, 85–97 (2010). https://doi.org/10.1007/s10681-010-0125-z

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