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Development of transcriptome shotgun assembly-derived markers in bunching onion (Allium fistulosum)

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Abstract

Bunching onion (Allium fistulosum L.) is one of the most important vegetables in Japan. Although expressed sequence tag (EST)-derived markers for bulb onion (A. cepa L.) have been developed from medium-scale sequencing, comparable EST sequences in bunching onion are lacking. In this study, we obtained 54,903 bunching onion unigenes using transcriptome shotgun assembly (TSA) and two next-generation sequencing technologies, GS-FLX and HiSeq 2000. When bunching onion and bulb onion unigenes were compared, 10,688 were estimated as reciprocal best-hit relationships. In the bunching onion TSA sequences, we discovered 2,396 di- to pentanucleotide simple sequence repeat (SSR) motifs and 5,505 exon–intron boundary sites. Moreover, we detected 9,002 single nucleotide polymorphisms and 4,335 insertion–deletion (InDel) by comparing sequence reads obtained from two inbred lines, “F” and “A.” TSA-derived SSR, cleaved amplified polymorphic sequences, InDels and intron-spanning markers were used to develop a linkage map. The genetic map, designated the FA map, contained 17 linkage groups with 364 markers (190 bunching onion TSAs, 96 bunching onion genomic SSRs, 39 bulb onion ESTs and 4 other markers) and covered a distance of 1,150 cM.

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Abbreviations

CAPS:

Cleaved amplified polymorphic sequence

EST:

Expressed sequence tag

gSSR:

Genomic simple sequence repeat

InDel:

Insertion–deletion

NGS:

Next-generation sequencing

PCR:

Polymerase chain reaction

SNP:

Single nucleotide polymorphism

SSR:

Simple sequence repeat

TSA:

Transcriptome shotgun assembly

HRM:

High-resolution melting

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Acknowledgments

We are grateful to Mss. K. Tanaka and S. Negoro for technical assistance. This work was supported by Grants-in-Aid for Kakenhi (C) (24580014) and the Strategic Japanese-New Zealand Cooperative Program on “Functional Food” (FY2011), the Japanese Society for Promotion of Science and the “Development of Genome Information Database System for Innovation of Crop and Livestock Production,” Ministry of Agriculture, Forestry and Fisheries of Japan.

Author information

Author notes

  1. Shigenori Yaguchi

    Present address: Department of Food Science and Technology, National Fisheries University, 2-7-1 Nagata-Honmachi, Shimonoseki, 759-6595, Japan

  2. Shusei Sato

    Present address: Department of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi, 980-8577, Japan

  3. Masahiko Kumagai

    Present address: Department of Biological Sciences, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan

  4. Satoshi Mizuno

    Present address: School of Medicine, Tohoku University, 2-1 Seiryo-cho, Aoba-ku, Sendai, Miyagi, 980-8575, Japan

Authors and Affiliations

  1. NARO Institute of Vegetable and Tea Science (NIVTS), National Agriculture and Food Research Organization, 360 Ano-Kusawa, Tsu, Mie, 514-2392, Japan

    Hikaru Tsukazaki, Shigenori Yaguchi, Hiroyuki Fukuoka, Ken-ichiro Yamashita & Tadayuki Wako

  2. Japan Society for the Promotion of Science, 8 Ichibancho, Chiyoda-ku, Tokyo, Tokyo, 102-8472, Japan

    Shigenori Yaguchi

  3. Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba, 292-0818, Japan

    Shusei Sato & Hideki Hirakawa

  4. National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan

    Yuichi Katayose, Hiroyuki Kanamori, Kanako Kurita, Takeshi Itoh, Masahiko Kumagai, Satoshi Mizuno & Masao Hamada

  5. The New Zealand Institute for Plant and Food Research Limited, Private Bag 4704, Christchurch, New Zealand

    John A. McCallum

  6. Department of Biological and Environmental Science, Faculty of Agriculture, Yamaguchi University, 1677-1 Yoshida, Yamaguchi, Yamaguchi, 753-8515, Japan

    Masayoshi Shigyo

Authors
  1. Hikaru Tsukazaki
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  2. Shigenori Yaguchi
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  4. Hideki Hirakawa
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  7. Kanako Kurita
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  8. Takeshi Itoh
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  9. Masahiko Kumagai
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  10. Satoshi Mizuno
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  11. Masao Hamada
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  12. Hiroyuki Fukuoka
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  13. Ken-ichiro Yamashita
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  14. John A. McCallum
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  15. Masayoshi Shigyo
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  16. Tadayuki Wako
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Corresponding author

Correspondence to Tadayuki Wako.

Additional information

Hikaru Tsukazaki and Shigenori Yaguchi have contributed equally to this publication.

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Tsukazaki, H., Yaguchi, S., Sato, S. et al. Development of transcriptome shotgun assembly-derived markers in bunching onion (Allium fistulosum). Mol Breeding 35, 55 (2015). https://doi.org/10.1007/s11032-015-0265-x

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