Characterization of the soybean genome using EST-derived microsatellite markers

Hiroshi Hisano, Shusei Sato, Sachiko Isobe, Shigemi Sasamoto, Tsuyuko Wada, Ai Matsuno, Tsunakazu Fujishiro, Manabu Yamada, Shinobu Nakayama, Yasukazu Nakamura, Satoshi Watanabe, Kyuya Harada, Satoshi Tabata

Research output: Contribution to journalArticle

99 Citations (Scopus)

Abstract

AbstractWe generated a high-density genetic linkage map of soybean using expressed sequence tag (EST)-derived microsatellite markers. A total of 6920 primer pairs (10.9) were designed to amplify simple sequence repeats (SSRs) from 63 676 publicly available non-redundant soybean ESTs. The polymorphism of two parent plants, the Japanese cultivar 'Misuzudaizu' and the Chinese line 'Moshidou Gong 503', were examined using 10 polyacrylamide gel electrophoresis. Primer pairs showing polymorphism were then used for genotyping 94 recombinant inbred lines (RILs) derived from a cross between the parents. In addition to previously reported markers, 680 EST-derived microsatellite markers were selected and subjected to linkage analysis. As a result, 935 marker loci were mapped successfully onto 20 linkage groups, which totaled 2700.3 cM in length; 693 loci were detected using the 668 EST-derived microsatellite markers developed in this study, the other 242 loci were detected with 105 RFLP markers, 136 genome-derived microsatellite markers, and one phenotypic marker. We examined allelic variation among 23 soybean cultivars/lines and a wild soybean line using 668 mapped EST-derived microsatellite markers (corresponding to 686 marker loci), in order to determine the transferability of the markers among soybean germplasms. A limited degree of macrosynteny was observed at the segmental level between the genomes of soybean and the model legume Lotus japonicus, which suggests that considerable genome shuffling occurred after separation of the species and during establishment of the paleopolyploid soybean genome.

Original languageEnglish
Pages (from-to)271-281
Number of pages11
JournalDNA Research
Volume14
Issue number6
DOIs
Publication statusPublished - Dec 2007
Externally publishedYes

Fingerprint

Expressed Sequence Tags
Soybeans
Microsatellite Repeats
Genome
Genetic Linkage
Fabaceae
Restriction Fragment Length Polymorphisms
Polyacrylamide Gel Electrophoresis

Keywords

  • Comparative map
  • Genetic linkage map
  • Microsatellite markers
  • Polymorphism information content
  • Soybean

ASJC Scopus subject areas

  • Genetics
  • Molecular Biology
  • Medicine(all)

Cite this

Hisano, H., Sato, S., Isobe, S., Sasamoto, S., Wada, T., Matsuno, A., ... Tabata, S. (2007). Characterization of the soybean genome using EST-derived microsatellite markers. DNA Research, 14(6), 271-281. https://doi.org/10.1093/dnares/dsm025

Characterization of the soybean genome using EST-derived microsatellite markers. / Hisano, Hiroshi; Sato, Shusei; Isobe, Sachiko; Sasamoto, Shigemi; Wada, Tsuyuko; Matsuno, Ai; Fujishiro, Tsunakazu; Yamada, Manabu; Nakayama, Shinobu; Nakamura, Yasukazu; Watanabe, Satoshi; Harada, Kyuya; Tabata, Satoshi.

In: DNA Research, Vol. 14, No. 6, 12.2007, p. 271-281.

Research output: Contribution to journalArticle

Hisano, H, Sato, S, Isobe, S, Sasamoto, S, Wada, T, Matsuno, A, Fujishiro, T, Yamada, M, Nakayama, S, Nakamura, Y, Watanabe, S, Harada, K & Tabata, S 2007, 'Characterization of the soybean genome using EST-derived microsatellite markers', DNA Research, vol. 14, no. 6, pp. 271-281. https://doi.org/10.1093/dnares/dsm025
Hisano, Hiroshi ; Sato, Shusei ; Isobe, Sachiko ; Sasamoto, Shigemi ; Wada, Tsuyuko ; Matsuno, Ai ; Fujishiro, Tsunakazu ; Yamada, Manabu ; Nakayama, Shinobu ; Nakamura, Yasukazu ; Watanabe, Satoshi ; Harada, Kyuya ; Tabata, Satoshi. / Characterization of the soybean genome using EST-derived microsatellite markers. In: DNA Research. 2007 ; Vol. 14, No. 6. pp. 271-281.
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AU - Sato, Shusei

AU - Isobe, Sachiko

AU - Sasamoto, Shigemi

AU - Wada, Tsuyuko

AU - Matsuno, Ai

AU - Fujishiro, Tsunakazu

AU - Yamada, Manabu

AU - Nakayama, Shinobu

AU - Nakamura, Yasukazu

AU - Watanabe, Satoshi

AU - Harada, Kyuya

AU - Tabata, Satoshi

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N2 - AbstractWe generated a high-density genetic linkage map of soybean using expressed sequence tag (EST)-derived microsatellite markers. A total of 6920 primer pairs (10.9) were designed to amplify simple sequence repeats (SSRs) from 63 676 publicly available non-redundant soybean ESTs. The polymorphism of two parent plants, the Japanese cultivar 'Misuzudaizu' and the Chinese line 'Moshidou Gong 503', were examined using 10 polyacrylamide gel electrophoresis. Primer pairs showing polymorphism were then used for genotyping 94 recombinant inbred lines (RILs) derived from a cross between the parents. In addition to previously reported markers, 680 EST-derived microsatellite markers were selected and subjected to linkage analysis. As a result, 935 marker loci were mapped successfully onto 20 linkage groups, which totaled 2700.3 cM in length; 693 loci were detected using the 668 EST-derived microsatellite markers developed in this study, the other 242 loci were detected with 105 RFLP markers, 136 genome-derived microsatellite markers, and one phenotypic marker. We examined allelic variation among 23 soybean cultivars/lines and a wild soybean line using 668 mapped EST-derived microsatellite markers (corresponding to 686 marker loci), in order to determine the transferability of the markers among soybean germplasms. A limited degree of macrosynteny was observed at the segmental level between the genomes of soybean and the model legume Lotus japonicus, which suggests that considerable genome shuffling occurred after separation of the species and during establishment of the paleopolyploid soybean genome.

AB - AbstractWe generated a high-density genetic linkage map of soybean using expressed sequence tag (EST)-derived microsatellite markers. A total of 6920 primer pairs (10.9) were designed to amplify simple sequence repeats (SSRs) from 63 676 publicly available non-redundant soybean ESTs. The polymorphism of two parent plants, the Japanese cultivar 'Misuzudaizu' and the Chinese line 'Moshidou Gong 503', were examined using 10 polyacrylamide gel electrophoresis. Primer pairs showing polymorphism were then used for genotyping 94 recombinant inbred lines (RILs) derived from a cross between the parents. In addition to previously reported markers, 680 EST-derived microsatellite markers were selected and subjected to linkage analysis. As a result, 935 marker loci were mapped successfully onto 20 linkage groups, which totaled 2700.3 cM in length; 693 loci were detected using the 668 EST-derived microsatellite markers developed in this study, the other 242 loci were detected with 105 RFLP markers, 136 genome-derived microsatellite markers, and one phenotypic marker. We examined allelic variation among 23 soybean cultivars/lines and a wild soybean line using 668 mapped EST-derived microsatellite markers (corresponding to 686 marker loci), in order to determine the transferability of the markers among soybean germplasms. A limited degree of macrosynteny was observed at the segmental level between the genomes of soybean and the model legume Lotus japonicus, which suggests that considerable genome shuffling occurred after separation of the species and during establishment of the paleopolyploid soybean genome.

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