Large-scale development of expressed sequence tag-derived simple sequence repeat markers and diversity analysis in Arachis spp.

Padmalatha Koilkonda, Shusei Sato, Satoshi Tabata, Kenta Shirasawa, Hideki Hirakawa, Hiroe Sakai, Shigemi Sasamoto, Akiko Watanabe, Tsuyuko Wada, Yoshie Kishida, Hisano Tsuruoka, Tsunakazu Fujishiro, Manabu Yamada, Mitsuyo Kohara, Shigeru Suzuki, Makoto Hasegawa, Hiroyuki Kiyoshima, Sachiko Isobe

Research output: Contribution to journalArticle

59 Citations (Scopus)

Abstract

Large-scale development of expressed sequence tag simple sequence repeat (EST-SSR) markers was performed in peanut (Arachis hypogaea L.) to obtain more informative genetic markers. A total of 10,102 potential non-redundant EST sequences, including 3,445 contigs and 6,657 singletons, were generated from cDNA libraries of the gynophore, roots, leaves and seedlings. A total of 3,187 primer pairs were designed on flanking regions of SSRs, some of which allowed one and two base mismatches. Among the 3,187 markers generated, 2,540 (80%) were trinucleotide repeats, 302 (9%) were dinucleotide repeats, and 345 (11%) were tetranucleotide repeats. Pre-polymorphic analyses of 24 Arachis accessions were performed using 10% polyacrylamide gels. A total of 1,571 EST-SSR markers showing clear polymorphisms were selected for further polymorphic analysis with a Fluoro-fragment Analyzer. The 16 Arachis accessions examined included cultivated peanut varieties as well as diploid species with the A or B genome. Altogether 1,281 (81. 5%) of the 1,571 markers were polymorphic among the 16 accessions, and 366 (23. 3%) were polymorphic among the 12 cultivated varieties. Diversity analysis was performed and the genotypes of all 16 Arachis accessions showed similarity coefficients ranging from 0. 37 to 0. 97.

Original languageEnglish
Pages (from-to)125-138
Number of pages14
JournalMolecular Breeding
Volume30
Issue number1
DOIs
Publication statusPublished - 2012 Jun 1
Externally publishedYes

Keywords

  • Arachis spp.
  • EST-SSR marker
  • Genetic diversity
  • Polymorphic analysis

ASJC Scopus subject areas

  • Biotechnology
  • Molecular Biology
  • Agronomy and Crop Science
  • Genetics
  • Plant Science

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  • Cite this

    Koilkonda, P., Sato, S., Tabata, S., Shirasawa, K., Hirakawa, H., Sakai, H., Sasamoto, S., Watanabe, A., Wada, T., Kishida, Y., Tsuruoka, H., Fujishiro, T., Yamada, M., Kohara, M., Suzuki, S., Hasegawa, M., Kiyoshima, H., & Isobe, S. (2012). Large-scale development of expressed sequence tag-derived simple sequence repeat markers and diversity analysis in Arachis spp. Molecular Breeding, 30(1), 125-138. https://doi.org/10.1007/s11032-011-9604-8