Complete chloroplast genome of Solanum jamesii and development of PCR-based markers to discriminate between S. jamesii and other Solanum species

Solanum jamesii is a wild Solanum species with a native range from northwestern Mexico to southwestern United States.It is a resource for potato breeding due to its resistance to late blight.However, S. jamesii is diploid and has an endosperm balanced number (EBN) of one, which hampers the sexual hybridization between S. jamesii and cultivated potatoes.To overcome this problem, somatic fusion can be performed.After fusion, molecular markers are necessary to select fusion products efficiently.In this study, therefore, the chloroplast genome of S. jamesii was sequenced using next-generation sequencing (NGS) technology and was compared with those of eight other Solanaceae species to develop specific markers for S. jamesii.The total length of the chloroplast genome sequence of S. jamesii is 155,576 bp.The structural organization of the chloroplast genome is almost identical to those of other Solanum species.Phylogenetic analysis with 17 other Solanaceae species showed that S. jamesii is most closely related to S. cardiophyllum.Detailed analysis of the chloroplast genome sequence of nine Solanum species identified two S. jamesiispecific InDels and 11 S. jamesii-specific SNPs.Based on these results, six S. jamesii-specific PCR-based markers were developed.The results of this study can be used to identify S. jamesii from other Solanum species and will contribute to the development of new potato varieties using S. jamesii.