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Development of gene-based markers and construction of an integrated linkage map in eggplant by using Solanum orthologous (SOL) gene sets

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Abstract

We constructed an integrated DNA marker linkage map of eggplant (Solanum melongena L.) using DNA marker segregation data sets obtained from two independent intraspecific F2 populations. The linkage map consisted of 12 linkage groups and encompassed 1,285.5 cM in total. We mapped 952 DNA markers, including 313 genomic SSR markers developed by random sequencing of simple sequence repeat (SSR)-enriched genomic libraries, and 623 single-nucleotide polymorphisms (SNP) and insertion/deletion polymorphisms (InDels) found in eggplant-expressed sequence tags (ESTs) and related genomic sequences [introns and untranslated regions (UTRs)]. Because of their co-dominant inheritance and their highly polymorphic and multi-allelic nature, the SSR markers may be more versatile than the SNP and InDel markers for map-based genetic analysis of any traits of interest using segregating populations derived from any intraspecific crosses of practical breeding materials. However, we found that the distribution of microsatellites in the genome was biased to some extent, and therefore a considerable part of the eggplant genome was first detected when gene-derived SNP and InDel markers were mapped. Of the 623 SNP and InDel markers mapped onto the eggplant integrated map, 469 were derived from eggplant unigenes contained within Solanum orthologous (SOL) gene sets (i.e., sets of orthologous unigenes from eggplant, tomato, and potato). Out of the 469 markers, 326 could also be mapped onto the tomato map. These common markers will be informative landmarks for the transfer of tomato’s more saturated genomic information to eggplant and will also provide comparative information on the genome organization of the two solanaceous species. The data are available from the DNA marker database of vegetables, VegMarks (http://vegmarks.nivot.affrc.go.jp).

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Acknowledgments

We thank Prof. S. Tanksley (Cornell University) for kindly providing plants of the tomato mapping population and genotyping data for their markers, and Dr. T. Saito (NARO Institute of Vegetable and Tea Science, NIVTS) for providing the eggplant materials. We are also grateful to Ms. Y. Kitamura (NIVTS) for her skillful technical assistance. This work was supported by grants-in-aid from the Ministry of Agriculture, Forestry, and Fisheries of Japan (‘Genomics for Agricultural Innovation’, DD-4010/SGE-1001; ‘Development of mitigation and adaptation techniques to global warming in the sectors of agriculture, forestry, and fisheries’, C-3-1010).

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Author notes

  1. Erika Asamizu

    Present address: School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan

Authors and Affiliations

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

    Hiroyuki Fukuoka, Koji Miyatake, Tsukasa Nunome, Satomi Negoro, Hirotaka Yamaguchi & Akio Ohyama

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

    Kenta Shirasawa, Sachiko Isobe & Erika Asamizu

Authors
  1. Hiroyuki Fukuoka
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  2. Koji Miyatake
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  3. Tsukasa Nunome
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  4. Satomi Negoro
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  8. Hirotaka Yamaguchi
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  9. Akio Ohyama
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Correspondence to Hiroyuki Fukuoka.

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Communicated by I. Paran.

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Fukuoka, H., Miyatake, K., Nunome, T. et al. Development of gene-based markers and construction of an integrated linkage map in eggplant by using Solanum orthologous (SOL) gene sets. Theor Appl Genet 125, 47–56 (2012). https://doi.org/10.1007/s00122-012-1815-9

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