Construction of an integrated high density simple sequence repeat linkage map in cultivated strawberry (Fragaria × ananassa) and its applicability

Sachiko N. Isobe, Hideki Hirakawa, Shusei Sato, Fumi Maeda, Masami Ishikawa, Toshiki Mori, Yuko Yamamoto, Kenta Shirasawa, Mitsuhiro Kimura, Masanobu Fukami, Fujio Hashizume, Tomoko Tsuji, Shigemi Sasamoto, Midori Kato, Keiko Nanri, Hisano Tsuruoka, Chiharu Minami, Chika Takahashi, Tsuyuko Wada, Akiko Ono & 9 others Kumiko Kawashima, Naomi Nakazaki, Yoshie Kishida, Mitsuyo Kohara, Shinobu Nakayama, Manabu Yamada, Tsunakazu Fujishiro, Akiko Watanabe, Satoshi Tabata

Research output: Contribution to journalArticle

37 Citations (Scopus)

Abstract

The cultivated strawberry (Fragaria× ananassa) is an octoploid (2n = 8x = 56) of the Rosaceae family whose genomic architecture is still controversial. Several recent studies support the AAA′A′BBB′ B′ model, but its complexity has hindered genetic and genomic analysis of this important crop. To overcome this difficulty and to assist genome-wide analysis of F. × ananassa, we constructed an integrated linkage map by organizing a total of 4474 of simple sequence repeat (SSR) markers collected from published Fragaria sequences, including 3746 SSR markers [Fragaria vesca expressed sequence tag (EST)-derived SSR markers] derived from F. vesca ESTs, 603 markers (F. × ananassa EST-derived SSR markers) from F. × ananassa ESTs, and 125 markers (F. × ananassa transcriptome-derived SSR markers) from F. × ananassa transcripts. Along with the previously published SSR markers, these markers were mapped onto five parent-specific linkage maps derived from three mapping populations, which were then assembled into an integrated linkage map. The constructed map consists of 1856 loci in 28 linkage groups (LGs) that total 2364.1 cM in length. Macrosynteny at the chromosome level was observed between the LGs of F. × ananassa and the genome of F. vesca. Variety distinction on 129 F. × ananassa lines was demonstrated using 45 selected SSR markers.

Original languageEnglish
Pages (from-to)79-92
Number of pages14
JournalDNA Research
Volume20
Issue number1
DOIs
Publication statusPublished - Feb 2013
Externally publishedYes

Fingerprint

Fragaria
Microsatellite Repeats
Expressed Sequence Tags
Genome
Rosaceae
Transcriptome
Chromosomes
Population

Keywords

  • comparative mapping
  • Fragaria × ananassa
  • integrated linkage map
  • SSR marker

ASJC Scopus subject areas

  • Genetics
  • Molecular Biology

Cite this

Construction of an integrated high density simple sequence repeat linkage map in cultivated strawberry (Fragaria × ananassa) and its applicability. / Isobe, Sachiko N.; Hirakawa, Hideki; Sato, Shusei; Maeda, Fumi; Ishikawa, Masami; Mori, Toshiki; Yamamoto, Yuko; Shirasawa, Kenta; Kimura, Mitsuhiro; Fukami, Masanobu; Hashizume, Fujio; Tsuji, Tomoko; Sasamoto, Shigemi; Kato, Midori; Nanri, Keiko; Tsuruoka, Hisano; Minami, Chiharu; Takahashi, Chika; Wada, Tsuyuko; Ono, Akiko; Kawashima, Kumiko; Nakazaki, Naomi; Kishida, Yoshie; Kohara, Mitsuyo; Nakayama, Shinobu; Yamada, Manabu; Fujishiro, Tsunakazu; Watanabe, Akiko; Tabata, Satoshi.

In: DNA Research, Vol. 20, No. 1, 02.2013, p. 79-92.

Research output: Contribution to journalArticle

Isobe, SN, Hirakawa, H, Sato, S, Maeda, F, Ishikawa, M, Mori, T, Yamamoto, Y, Shirasawa, K, Kimura, M, Fukami, M, Hashizume, F, Tsuji, T, Sasamoto, S, Kato, M, Nanri, K, Tsuruoka, H, Minami, C, Takahashi, C, Wada, T, Ono, A, Kawashima, K, Nakazaki, N, Kishida, Y, Kohara, M, Nakayama, S, Yamada, M, Fujishiro, T, Watanabe, A & Tabata, S 2013, 'Construction of an integrated high density simple sequence repeat linkage map in cultivated strawberry (Fragaria × ananassa) and its applicability', DNA Research, vol. 20, no. 1, pp. 79-92. https://doi.org/10.1093/dnares/dss035
Isobe, Sachiko N. ; Hirakawa, Hideki ; Sato, Shusei ; Maeda, Fumi ; Ishikawa, Masami ; Mori, Toshiki ; Yamamoto, Yuko ; Shirasawa, Kenta ; Kimura, Mitsuhiro ; Fukami, Masanobu ; Hashizume, Fujio ; Tsuji, Tomoko ; Sasamoto, Shigemi ; Kato, Midori ; Nanri, Keiko ; Tsuruoka, Hisano ; Minami, Chiharu ; Takahashi, Chika ; Wada, Tsuyuko ; Ono, Akiko ; Kawashima, Kumiko ; Nakazaki, Naomi ; Kishida, Yoshie ; Kohara, Mitsuyo ; Nakayama, Shinobu ; Yamada, Manabu ; Fujishiro, Tsunakazu ; Watanabe, Akiko ; Tabata, Satoshi. / Construction of an integrated high density simple sequence repeat linkage map in cultivated strawberry (Fragaria × ananassa) and its applicability. In: DNA Research. 2013 ; Vol. 20, No. 1. pp. 79-92.
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