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

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 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).

QTL hotspots in eggplant (Solanum melongena) detected with a high resolution map and CIM analysis

“…In addition these results provide a starting point for identifying putative orthologs between eggplant and tomato based on synteny. Intraspecific populations of eggplant have also been useful for developing high-density linkage maps that explore the synteny between the tomato and eggplant genomes (Barchi et al 2012;Fukuoka et al 2012) and provide for the possibility of additional quantitative trait analyses. Such analyses, combined with the recently released tomato genome sequence (Tomato Genome Consortium 2012), should facilitate further examination of conserved gene function in the Solanaceae, an economically important family of plants.…”

Simple sequence repeat-based association analysis of fruit traits in eggplant (Solanum melongena)

“…Compared with the two Solanum model species, tomato and potato, eggplant has its unique traits with larger fruit size and different kinds of stress tolerances. Furthermore, it has a unique phylogenic aspect (Fukuoka et al, 2012). Despite the importance of this crop, studies of its molecular genetics fall behind those of tomato (S. lycopersicum L.), potato (S. tuberosum L.), and pepper (Capsicum spp L.), all of which belong to the Solanaceae family (Nunome et al, 2009;Fukuoka et al, 2012).…”

High resolution map of eggplant (Solanum melongena) reveals extensive chromosome rearrangement in domesticated members of the Solanaceae

“…The map comprises 864 markers spread across eggplant's twelve chromosomes at an average genetic interval of 1.8 cM and represents a considerable improvement of the maps previously developed for this interspecific population (Doganlar et al 2002a;Wu et al 2009). While an integrated high density map of the eggplant genome has recently been produced from two intraspecific populations (Fukuoka et al 2012), the interspecific (6) population used here offers a greater degree of morphological polymorphism that can form the basis for analyzing a wider range of quantitative traits in eggplant. The recent release of the tomato genome sequence (Tomato Genome Consortium 2012) provides a springboard for comparative genomics within the Solanaceae.…”

“…Because of the tendency of SSR markers to reside in heterochromatic regions, portions of the genome are not covered by this map. Therefore, in an effort to create a saturated intraspecific map, Fukuoka et al (2012) used two separate intraspecific F 2 mapping populations (developed from 'LS1934' 9 'WCGR112-8' and 'AE-P03' 9 'LS1934' parental crosses) to construct an integrated map containing 952 SSR, SNP, and insertion/deletion polymorphism (InDel) markers spread at an average distance of one marker every 1.4 cM over the 12 linkage groups. Over 465 of the SNP and InDel markers were derived from unigenes orthologous to eggplant, tomato, and potato.…”

“…This comparison confirmed the large-scale genomic rearrangements between the tomato and eggplant genomes. In addition, eleven of the Barchi et al (2012) linkage groups could be aligned with the Fukuoka et al (2012) map based on the position of SSR and COSII markers. The utility of the Barchi et al (2012) map for quantitative trait locus (QTL) analysis was assessed through the localization of several loci controlling anthocyanin pigmentation.…”