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Exploitation of pepper EST–SSRs and an SSR-based linkage map

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Abstract

As genome and cDNA sequencing projects progress, a tremendous amount of sequence information is becoming publicly available. These sequence resources can be exploited for gene discovery and marker development. Simple sequence repeat (SSR) markers are among the most useful because of their great variability, abundance, and ease of analysis. By in silico analysis of 10,232 non-redundant expressed sequence tags (ESTs) in pepper as a source of SSR markers, 1,201 SSRs were found, corresponding to one SSR in every 3.8 kb of the ESTs. Eighteen percent of the SSR–ESTs were dinucleotide repeats, 66.0% were trinucleotide, 7.7% tetranucleotide, and 8.2% pentanucleotide; AAG (14%) and AG (12.4%) motifs were the most abundant repeat types. Based on the flanking sequences of these 1,201 SSRs, 812 primer pairs that satisfied melting temperature conditions and PCR product sizes were designed. 513 SSRs (63.1%) were successfully amplified and 150 of them (29.2%) showed polymorphism between Capsicum annuum ‘TF68’ and C. chinense ‘Habanero’. Dinucleotide SSRs and EST–SSR markers containing AC-motifs were the most polymorphic. Polymorphism increased with repeat length and repeat number. The polymorphic EST–SSRs were mapped onto the previously generated pepper linkage map, using 107 F2 individuals from an interspecific cross of TF68  ×  Habanero. One-hundred and thirtynine EST–SSRs were located on the linkage map in addition to 41 previous SSRs and 63 RFLP markers, forming 14 linkage groups (LGs) and spanning 2,201.5 cM. The EST–SSR markers were distributed over all the LGs. This SSR-based map will be useful as a reference map in Capsicum and should facilitate the use of molecular markers in pepper breeding.

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Acknowledgements

This work was supported by grants from the Agricultural R & D Promotion Center (ARPC), and from the Center for Plant Molecular Genetics and Breeding Research (CPMGBR) through the Korea Science and Engineering Foundation (KOSEF) and the Korea Ministry of Science and Technology (MOST).

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  1. Doil Choi

    Present address: Department of Plant Science, College of Agriculture and Life Sciences and Center for Plant Molecular Genetics and Breeding Research, Seoul National University, Seoul, 151-921, Korea

Authors and Affiliations

  1. Department of Plant Science, College of Agriculture and Life Sciences and Center for Plant Molecular Genetics and Breeding Research, Seoul National University, Seoul, 151-921, South Korea

    Gibum Yi, Je Min Lee & Byung-Dong Kim

  2. Plant Genomics Laboratory, Genome Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejon, 305-333, South Korea

    Sanghyeob Lee & Doil Choi

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  1. Gibum Yi
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  2. Je Min Lee
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Correspondence to Byung-Dong Kim.

Additional information

Communicated by I. Paran.

Gibum Yi and Je Min Lee equally contributed to this work.

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Yi, G., Lee, J.M., Lee, S. et al. Exploitation of pepper EST–SSRs and an SSR-based linkage map. Theor Appl Genet 114, 113–130 (2006). https://doi.org/10.1007/s00122-006-0415-y

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