Identification of S-locus F-box Protein Sequences in Diploid Potato, <em>Solanum okadae</em>, via Degenerate PCR

In many plant species, self-incompatibility (SI) is a mechanism that inhibits inbreeding. SI is gametophytic in the Solanaceae, with specificity determined by S-ribonucleases (S-RNases) in the pistil and S-locus F-box proteins (SLFs) in the pollen. The role of these proteins has been studied extensively in the Solanaceae, often using <i>Petunia</i> as a model. Using degenerate PCR and Sanger sequencing, this protocol identified three SLF sequences from self-incompatible diploid potato (<i>Solanum okadae</i>). While SLFs are well-characterized in model species like <i>Petunia</i>, there is limited sequence data and no standardized protocols for identifying SLFs in non-model species such as <i>S. okadae</i>, hindering broader insights into SI across the Solanaceae. This protocol fills that gap by using degenerate PCR and Sanger sequencing with primers designed from conserved <i>Petunia</i> SLF regions to identify SLF sequences in <i>S. okadae</i>. SLF sequences from 10 distinct Solanaceae members sharing maximum identity with the S2-haplotype of <i>Petunia</i> were used to design two pairs of primers targeting different regions of the target sequence. PCR amplification using designed degenerate primers yielded amplicons that were directly sequenced and joined together to get the partial SLF sequence. It was observed that the <i>S. okadae</i> shared an orthologous relation with the <i>Petunia</i> SLF according to the phylogenetic analysis. These SLFs could be used in future SI breakdown experiments via the competitive interaction route. This protocol, including the primer design, is novel for detecting SLF sequences in <i>S. okadae</i>. Key features • This protocol is applicable when the exact nucleotide sequence of the target DNA is not known but can be deduced from an amino acid sequence. • Straightforward, cost-effective, and can be used to find "new" genes or gene families. • Guidelines and a systematic approach for designing degenerate primers, along with a framework for annotating and comparing SLF genes within the Solanaceae family.