1. Large-scale development of expressed sequence tag-derived simple sequence repeat markers and diversity analysis in Arachis spp.
- Author
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Koilkonda, Padmalatha, Sato, Shusei, Tabata, Satoshi, Shirasawa, Kenta, Hirakawa, Hideki, Sakai, Hiroe, Sasamoto, Shigemi, Watanabe, Akiko, Wada, Tsuyuko, Kishida, Yoshie, Tsuruoka, Hisano, Fujishiro, Tsunakazu, Yamada, Manabu, Kohara, Mitsuyo, Suzuki, Shigeru, Hasegawa, Makoto, Kiyoshima, Hiroyuki, and Isobe, Sachiko
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GENETIC markers , *PEANUTS , *SEEDLINGS , *TRINUCLEOTIDE repeats , *GENETIC polymorphisms , *SPECIES , *GENOMES - 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. [ABSTRACT FROM AUTHOR]
- Published
- 2012
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