Journal Article

Development and Application of a Whole-Genome Simple Sequence Repeat Panel for High-Throughput Genotyping in Soybean

Takashi Sayama, Tae-Young Hwang, Kunihiko Komatsu, Yoshitake Takada, Masakazu Takahashi, Shin Kato, Hiroko Sasama, Ayako Higashi, Yumi Nakamoto, Hideyuki Funatsuki and Masao Ishimoto

in DNA Research

Published on behalf of Kazusa DNA Research Institute

Volume 18, issue 2, pages 107-115
Published in print April 2011 | ISSN: 1340-2838
Published online March 2011 | e-ISSN: 1756-1663 | DOI:

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Among commonly applied molecular markers, simple sequence repeats (SSRs, or microsatellites) possess advantages such as a high level of polymorphism and codominant pattern of inheritance at individual loci. To facilitate systematic and rapid genetic mapping in soybean, we designed a genotyping panel comprised 304 SSR markers selected for allelic diversity and chromosomal location so as to provide wide coverage. Most primer pairs for the markers in the panel were redesigned to yield amplicons of 80–600 bp in multiplex polymerase chain reaction (PCR) and fluorescence-based sequencer analysis, and they were labelled with one of four different fluorescent dyes. Multiplex PCR with sets of six to eight primer pairs per reaction generated allelic data for 283 of the 304 SSR loci in three different mapping populations, with the loci mapping to the same positions as previously determined. Four SSRs on each chromosome were analysed for allelic diversity in 87 diverse soybean germplasms with four-plex PCR. These 80 loci showed an average allele number and polymorphic information content value of 14.8 and 0.78, respectively. The high level of polymorphism, ease of analysis, and high accuracy of the SSR genotyping panel should render it widely applicable to soybean genetics and breeding.

Keywords: SSR marker; fluorescent primer; multiplex PCR; polymorphic information content; high-throughput genotyping

Journal Article.  4701 words.  Illustrated.

Subjects: Genetics and Genomics

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