A survey of the Sli gene in wild and cultivated potato

Authors: Ames Sevillano, Mercedes; Hamernik, Andy; BEHLING, WILLIAM - Michigan State University; DOUCHES, DAVID - Michigan State University; Halterman, Dennis; Bethke, Paul

Submitted to: Plant Direct
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/18/2024
Publication Date: 5/17/2024
Citation: Ames Sevillano, M.I., Hamernik, A.J., Behling, W., Douches, D., Halterman, D.A., Bethke, P.C. 2024. A survey of the Sli gene in wild and cultivated potato. Plant Direct. https://doi.org/10.1002/pld3.589.
DOI: https://doi.org/10.1002/pld3.589

Interpretive Summary: Breeding of diploid potatoes would benefit greatly from breeding lines that are self-fertile. One way of introducing self-fertility is to introduce the S-locus inhibitor gene. To learn more about S-locus inhibitor gene diversity and function in wild species relatives of cultivated potato, we obtained S-locus inhibitor gene DNA sequences from 22 wild species relatives of potato and cultivated potato. Sequence comparisons show that there are two highly conserved groups of sequences. One group contain a 533 base pair insertion upstream of the start codon and the other group lacks the insertion. Seven individuals of wild species collected from geographically disjointed localities contained the gene with the insertion. For most of the wild species examined, however, S-locus inhibitor gene did not have the insertion. Further analysis indicated that the S-locus inhibitor gene sequences with the insertion trace back to a single origin. Although the S-locus inhibitor gene with the insertion confers self-compatibility in cultivated potato, the presence of this allele is not a guarantee of self-compatibility in wild potato species.

Technical Abstract: Inbred-hybrid breeding of diploid potatoes necessitates breeding lines that are self-compatible. One way of incorporating self-compatibility into incompatible potato germplasm is to introduce the S-locus inhibitor gene (Sli), which functions as a dominant inhibitor of gametophytic self-incompatibility. To learn more about Sli diversity and function in wild species relatives of cultivated potato (Solanum tuberosum), we obtained Sli gene sequences that extended from the 5’UTR to the 3’UTR from 133 individuals from 22 wild species relatives of potato and eight diverse cultivated potato clones. Sequence alignment and phylogenetic trees based on DNA and protein sequences show that there are two highly conserved groups of Sli sequences. DNA sequences in one group contain the 533 bp insertion upstream of the start codon that was identified previously in self-compatible potato. The second group lacks the insertion. Three diploid and four polyploid individuals of wild species collected from geographically disjointed localities contained Sli with the 533 bp insertion. For most of the wild species clones examined, however, Sli did not have the insertion. Phylogenetic analysis indicates that Sli sequences with the insertion, in wild species and in cultivated clones, trace back to a single origin. Some diploid wild potatoes that have Sli with the insertion were self-incompatible and some wild potatoes that lack the insertion were self-compatible. Although there is evidence of positive selection for some codon positions in Sli, there is no evidence of diversifying selection at the gene level. In-silico analysis of Sli protein structure did not support the hypothesis that amino acid changes from wild-type (no insertion) to insertion-type account for changes in protein function.