ORIGINAL PAPER Development of gene-based markers and construction of an integrated linkage map in eggplant by using Solanum orthologous (SOL) gene sets Hiroyuki Fukuoka • Koji Miyatake • Tsukasa Nunome • Satomi Negoro • Kenta Shirasawa • Sachiko Isobe • Erika Asamizu • Hirotaka Yamaguchi • Akio Ohyama Received: 15 December 2011 / Accepted: 31 January 2012 / Published online: 16 February 2012 Ó Springer-Verlag 2012 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 F 2 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 egg- plant-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 ortholo- gous 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 land- marks for the transfer of tomato’s more saturated genomic information to eggplant and will also provide compara- tive 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). Introduction The Solanaceae family is a major plant group that includes several important species of practical value, including tomato (Solanum lycopersicum L.), potato (Solanum tuberosum L.), bell pepper (Capsicum annuum L.), and eggplant (Solanum melongena L.). Except for bell pepper, these species belong to the largest genus in the Solanaceae, Solanum, which includes more than 1,000 species (D’Arcy 1991). Tomato and potato have been used as model plants for the Solanaceae and for genus Solanum, and extensive genetic and genomic information has been accumulated for these species. High-density molecular marker linkage maps (Bonierbale et al. 1988; Shirasawa et al. 2010; Tanksley Communicated by I. Paran. Electronic supplementary material The online version of this article (doi:10.1007/s00122-012-1815-9) contains supplementary material, which is available to authorized users. H. Fukuoka (&) Á K. Miyatake Á T. Nunome Á S. Negoro Á H. Yamaguchi Á A. Ohyama NARO Institute of Vegetable and Tea Science (NIVTS), National Agriculture and Food Research Organization, 360 Kusawa, Ano, Tsu, Mie 514-2392, Japan e-mail: h.fukuoka@affrc.go.jp K. Shirasawa Á S. Isobe Á E. Asamizu Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan Present Address: E. Asamizu School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan 123 Theor Appl Genet (2012) 125:47–56 DOI 10.1007/s00122-012-1815-9