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 2012

Fingerprint

Trifolium
Medicago
Expressed Sequence Tags
Linkage Disequilibrium
Microsatellite Repeats
Medicago truncatula
Fabaceae
Genome

Keywords

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

ASJC Scopus subject areas

  • Genetics
  • Molecular Biology
  • Genetics(clinical)

Cite this

Comparative genetic mapping and discovery of linkage disequilibrium across linkage groups in white clover (Trifolium repens L.). / Isobe, Sachiko N.; Hisano, Hiroshi; Sato, Shusei; Hirakawa, Hideki; Okumura, Kenji; Shirasawa, Kenta; Sasamoto, Shigemi; Watanabe, Akiko; Wada, Tsuyuko; Kishida, Yoshie; Tsuruoka, Hisano; Fujishiro, Tsunakazu; Yamada, Manabu; Kohara, Mistuyo; Tabata, Satoshi.

In: G3: Genes, Genomes, Genetics, Vol. 2, No. 5, 05.2012, p. 607-617.

Research output: Contribution to journalArticle

Isobe, SN, Hisano, H, Sato, S, Hirakawa, H, Okumura, K, Shirasawa, K, Sasamoto, S, Watanabe, A, Wada, T, Kishida, Y, Tsuruoka, H, Fujishiro, T, Yamada, M, Kohara, M & Tabata, S 2012, 'Comparative genetic mapping and discovery of linkage disequilibrium across linkage groups in white clover (Trifolium repens L.)', G3: Genes, Genomes, Genetics, vol. 2, no. 5, pp. 607-617. https://doi.org/10.1534/g3.112.002600
Isobe, Sachiko N. ; Hisano, Hiroshi ; Sato, Shusei ; Hirakawa, Hideki ; Okumura, Kenji ; Shirasawa, Kenta ; Sasamoto, Shigemi ; Watanabe, Akiko ; Wada, Tsuyuko ; Kishida, Yoshie ; Tsuruoka, Hisano ; Fujishiro, Tsunakazu ; Yamada, Manabu ; Kohara, Mistuyo ; Tabata, Satoshi. / Comparative genetic mapping and discovery of linkage disequilibrium across linkage groups in white clover (Trifolium repens L.). In: G3: Genes, Genomes, Genetics. 2012 ; Vol. 2, No. 5. pp. 607-617.
@article{942b10b1e9254d34976d72f54089e7d8,
title = "Comparative genetic mapping and discovery of linkage disequilibrium across linkage groups in white clover (Trifolium repens L.)",
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.",
keywords = "comparative map, disequilibrium, expressed sequence, linkage, repeat, tag-simple sequence, white clover",
author = "Isobe, {Sachiko N.} and Hiroshi Hisano and Shusei Sato and Hideki Hirakawa and Kenji Okumura and Kenta Shirasawa and Shigemi Sasamoto and Akiko Watanabe and Tsuyuko Wada and Yoshie Kishida and Hisano Tsuruoka and Tsunakazu Fujishiro and Manabu Yamada and Mistuyo Kohara and Satoshi Tabata",
year = "2012",
month = "5",
doi = "10.1534/g3.112.002600",
language = "English",
volume = "2",
pages = "607--617",
journal = "G3 (Bethesda, Md.)",
issn = "2160-1836",
publisher = "Genetics Society of America",
number = "5",

}

TY - JOUR

T1 - Comparative genetic mapping and discovery of linkage disequilibrium across linkage groups in white clover (Trifolium repens L.)

AU - Isobe, Sachiko N.

AU - Hisano, Hiroshi

AU - Sato, Shusei

AU - Hirakawa, Hideki

AU - Okumura, Kenji

AU - Shirasawa, Kenta

AU - Sasamoto, Shigemi

AU - Watanabe, Akiko

AU - Wada, Tsuyuko

AU - Kishida, Yoshie

AU - Tsuruoka, Hisano

AU - Fujishiro, Tsunakazu

AU - Yamada, Manabu

AU - Kohara, Mistuyo

AU - Tabata, Satoshi

PY - 2012/5

Y1 - 2012/5

N2 - 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.

AB - 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.

KW - comparative map

KW - disequilibrium

KW - expressed sequence

KW - linkage

KW - repeat

KW - tag-simple sequence

KW - white clover

UR - http://www.scopus.com/inward/record.url?scp=84873539800&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84873539800&partnerID=8YFLogxK

U2 - 10.1534/g3.112.002600

DO - 10.1534/g3.112.002600

M3 - Article

C2 - 22670230

AN - SCOPUS:84873539800

VL - 2

SP - 607

EP - 617

JO - G3 (Bethesda, Md.)

JF - G3 (Bethesda, Md.)

SN - 2160-1836

IS - 5

ER -