Tuber-bearing potato species possess several genes that can be exploited to improve the genetic background of the cultivated potato Solanum tuberosum. Among them, S. bulbocastanum and S. commersonii are well known for their strong resistance to environmental stresses. However, scant information is available for these species in terms of genome organization, gene function, and regulatory networks. Consequently, genomic tools to assist breeding are meager, and efficient exploitation of these species has been limited so far. In this paper, we employed the reference genome sequences from cultivated potato and tomato and a collection of sequences of 1,423 potato Diversity Arrays Technology (DArT) markers that show polymorphic representation across the genomes of S. bulbocastanum and/or S. commersonii genotypes. Our results highlighted microscale genome sequence heterogeneity that may play a significant role in functional and structural divergence between related species. Our analytical approach provides knowledge of genome structural and sequence variability that could not be detected by transcriptome and proteome approaches. 1. Background The subgenus Potatoe of the Solanaceae family includes approximately 188 tuber-bearing species [1]. They display large ecological adaptation encompassing several traits that are lacking in the commercial potato and useful for breeding [2]. Among wild potato species, Solanum bulbocastanum Dun. and S. commersonii Dun. ex Poir. have attracted the attention of researchers and breeders. S. bulbocastanum is a known source of resistance to late blight disease of potato, and four late blight resistance genes have been cloned from this species to date [3–7]. S. commersonii ranks first among Solanums in terms of cold tolerance and capacity to cold acclimate, and it is also a source of resistance to pathogens such as Ralstonia solanacearum and Pectobacterium carotovorum [8, 9]. S. bulbocastanum and S. commersonii are among approximately 20 diploid potato species classified as superseries Stellata by Hawkes [10]. Despite their importance as sources of genes for crop improvement, relatively few genetic and genomic resources are available for these species, and little is known on their genome organization, gene function, and regulatory networks. Recently, a Diversity Arrays Technology (DArT) array was constructed for potato [11]. The array contains markers derived from various Solanum species, including S. bulbocastanum and S. commersonii. DArT arrays offer the potential to simultaneously survey large numbers of anonymous loci
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