The structure and allelic diversity of the self-incompatibility locus (S-locus) in diploid potatoes inferred from genome sequences and transcriptome data from styles and pollen.

Gametophytic self-incompatibility (GSI) is a reproductive strategy to prevent inbreeding and promote outcrossing. Studies to understand molecular and evolutionary aspects of the self-compatibility (SC)/self-incompatibility (SI) system in the Solanaceae have been conducted using several genera including Petunia Juss., Nicotiana L., and Solanum L. S-RNases are pistil determinants of GSI and multiple S-RNase alleles have been identified in a few potato species. S-locus F-box genes (SLFs), the pollen determinants of SI, are linked to S-RNases on chromosome 1. The S-RNase and SLFs present on each chromatid determine an individual's SC/SI haplotypes. However, the extent of SLF diversity, the number and position of SLFs in the S-locus, and their mechanism of interaction with S-RNases is unknown in potato or its wild relatives, most of which are diploid and SI. A combination of genome and transcriptome analysis from pollen and pistils of wild and cultivated diploid potatoes was used to determine the structure of the S-locus. Our analysis showed that SLF sequences are expressed in pollen but not in styles, vary in number between individuals, and are distributed across a 9-17 Mb region flanking one S-RNase gene. Preferential associations within haplotigs of specific S-RNase types and SLF types were not observed. Extensive sequence diversity was observed for S-RNases and SLFs, and phylogenetic analysis indicates that diversification of both genes predates the divergence between tomatoes and potatoes. This research sheds light on how these two pistil and pollen elements interact to determine SI or SC and may further our understanding of gene flow in wild potato species.