Combining genome composition and differential gene expression analyses reveals that SmPGH1 contributes to bacterial wilt resistance in somatic hybrids

Key message Clarification of the genome composition of the potato + eggplant somatic hybrids cooperated with transcriptome analysis efficiently identified the eggplant geneSmPGH1that contributes to bacterial wilt resistance. The cultivated potato is susceptible and lacks resistance to bacterial wilt (BW), a soil-borne disease caused byRalstonia solanacearum.It also has interspecies incompatibility withinSolanaceaeplants. Previously, we have successfully conducted the protoplast fusion of potato and eggplant and regenerated somatic hybrids that showing resistance to eggplant BW. For efficient use of these novel germplasm and improve BW resistance of cultivated potato, it is essential to dissect the genetic basis of the resistance to BW obtained from eggplant. The strategy of combining genome composition and transcriptome analysis was established to explore the gene that confers BW resistance to the hybrids. Genome composition of the 90 somatic hybrids was studied using genomic in situ hybridization coupled with 44 selected eggplant-specific SSRs (smSSRs). The analysis revealed a diverse set of genome combinations among the hybrids and showed a possibility of integration of alien genes along with the detection of 7 smSSRs linked to BW resistance (BW-linked SSRs) in the hybrids. Transcriptome comparison between the resistant and susceptible gene pools identified a BW resistance associated gene,smPGH1,which was significantly induced byR. solanacearumin the resistant pool. Remarkably,smPGH1was co-localized with the BW-linked SSR emh01E15 on eggplant chromosome 9, which was further confirmed thatsmPGH1was activated byR. solanacearumonly in the resistant hybrids. Taken together, the identified genesmPGH1and BW-linked SSRs have provided novel genetic resources that will aid in potato breeding for BW resistance.