Comparative genetic mapping and discovery of linkage disequilibrium across linkage groups in white clover (Trifolium repens L.)

Sachiko N. Isobe, Hiroshi Hisano, Shusei Sato, Hideki Hirakawa, Kenji Okumura, Kenta Shirasawa, Shigemi Sasamoto, Akiko Watanabe, Tsuyuko Wada, Yoshie Kishida, Hisano Tsuruoka, Tsunakazu Fujishiro, Manabu Yamada, Mistuyo Kohara, Satoshi Tabata

Research output: Contribution to journalArticle

16 Citations (Scopus)

Abstract

White clover (Trifolium repens L.) is an allotetraploid species (2n 1/4 4X 1/4 32) that is widely distributed in temperate regions and cultivated as a forage legume. In this study, we developed expressed sequence tag (EST)-derived simple sequence repeat (SSR) markers, constructed linkage maps, and performed comparative mapping with other legume species. A total of 7982 ESTs that could be assembled into 5400 contigs and 2582 singletons were generated. Using the EST sequences that were obtained, 1973 primer pairs to amplify EST-derived SSR markers were designed and used for linkage analysis of 188 F1 progenies, which were generated by a cross between two Japanese plants, '273-7' and 'T17-349,' with previously published SSR markers. An integrated linkage map was constructed by combining parentalspecific maps, which consisted of 1743 SSR loci on 16 homeologous linkage groups with a total length of 2511 cM. The primer sequences of the developed EST-SSR markers and their map positions are available on http://clovergarden.jp/. Linkage disequilibrium (LD) was observed on 9 of 16 linkage groups of a parental- specific map. The genome structures were compared among white clover, red clover (T. pratense L.), Medicago truncatula, and Lotus japonicus. Macrosynteny was observed across the four legume species. Surprisingly, the comparative genome structure between white clover and M. truncatula had a higher degree of conservation than that of the two clover species.

Original languageEnglish
Pages (from-to)607-617
Number of pages11
JournalG3: Genes, Genomes, Genetics
Volume2
Issue number5
DOIs
Publication statusPublished - May 1 2012

Keywords

  • comparative map
  • disequilibrium
  • expressed sequence
  • linkage
  • repeat
  • tag-simple sequence
  • white clover

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics
  • Genetics(clinical)

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