Development of PCR-based markers for Solanum verrucosum via comparison of the complete chloroplast genome sequence of S. verrucosum with those of other Solanum species

Solanum verrucosum is a species of wild potato originating from Mexico and is widely used for potato breeding owing to its late blight resistance.However, S. verrucosum is a diploid with an endosperm balanced number (EBN) of two; these properties differ from those of cultivated potatoes (S tuberosum).Therefore, it cannot be directly crossed with cultivated tetraploid potatoes for breeding purposes.Somatic fusion can overcome this problem; and it is important to select suitable somatic hybrids using molecular markers after somatic fusion.Therefore, we determined the complete chloroplast genome sequence of S. verrucosum using next-generation sequencing (NGS) technology, and compared it with sequences of eight other Solanum species to identify S. verrucosum-specific markers.The length of the complete chloroplast genome of S. verrucosum is 155,485 bp and its structure is almost identical to those of other Solanum species.Phylogenetic analysis of S. verrucosum compared with 16 other Solanaceae family members revealed that S. verrucosum was most closely grouped with S. demissum, S. hougasii, S. Stoloniferum and S. hjertingii.Sequence alignment of the complete chloroplast sequences of nine Solanum species including S. verrucosum identified three InDels and five SNPs specific to S. verrucosum.Based on these InDels and SNPs, four S. verrucosumspecific PCR-based markers were developed.The makers can be used to distinguish S. verrucosum from other Solanum species.Our findings will facilitate the selection of fusion products and advance potato breeding using S. verrucosum.