Molecular diversity of three S-allele cDNAs associated with gametophytic self-incompatibility in Lycopersicon peruvianum

Population Genomics of the "Arcanum" Species Group in Wild Tomatoes: Evidence for Separate Origins of Two Self-Compatible Lineages

Given their diverse mating systems and recent divergence, wild tomatoes (Solanum section Lycopersicon) have become an attractive model system to study ecological divergence, the build-up of reproductive barriers, and the causes and consequences of the breakdown of self-incompatibility. Here we report on a lesser-studied group of species known as the "Arcanum" group, comprising the nominal species Solanum arcanum, Solanum chmielewskii, and Solanum neorickii. The latter two taxa are self-compatible but are thought to self-fertilize at different rates, given their distinct manifestations of the morphological "selfing syndrome." Based on experimental crossings and transcriptome sequencing of a total of 39 different genotypes from as many accessions representing each species' geographic range, we provide compelling evidence for deep genealogical divisions within S. arcanum; only the self-incompatible lineage known as "var. marañón" has close genealogical ties to the two self-compatible species. Moreover, there is evidence under multiple inference schemes for different geographic subsets of S. arcanum var. marañón being closest to S. chmielewskii and S. neorickii, respectively. To broadly characterize the population-genomic consequences of these recent mating-system transitions and their associated speciation events, we fit demographic models indicating strong reductions in effective population size, congruent with reduced nucleotide and S-locus diversity in the two independently derived self-compatible species.

Functional gametophytic self-incompatibility in a peripheral population of Solanum peruvianum (Solanaceae)

The transition from self-incompatibility to self-compatibility is a common transition in angiosperms often reported in populations at the edge of species range limits. Geographically distinct populations of wild tomato species (Solanum section Lycopersicon (Solanaceae)) have been described as polymorphic for mating system with both self-incompatible and self-compatible populations. Using controlled pollinations and sequencing of the S-RNase mating system gene, we test the compatibility status of a population of S. peruvianum located near its southern range limit. Pollinations among plants of known genotypes revealed strong self-incompatibility; fruit set following compatible pollinations was significantly higher than following incompatible pollinations for all tested individuals. Sequencing of the S-RNase gene in parents and progeny arrays was also as predicted under self-incompatibility. Molecular variation at the S-RNase locus revealed a diverse set of alleles, and heterozygosity in over 500 genotyped individuals. We used controlled crosses to test the specificity of sequences recovered in this study; in all cases, results were consistent with a unique allelic specificity for each tested sequence, including two alleles sharing 92% amino-acid similarity. Site-specific patterns of selection at the S-RNase gene indicate positive selection in regions of the gene associated with allelic specificity determination and purifying selection in previously characterized conserved regions. Further, there is broad convergence between the present and previous studies in specific amino-acid positions inferred to be evolving under positive selection.

Insights into the evolution of self-compatibility in Lycopersicon from a study of stylar factors

To elucidate the molecular basis of loss of self-incompatibility in Lycopersicon, S-RNases and HT-proteins were analysed in seven self-compatible (SC) and three self-incompatible (SI) taxa. No or low stylar RNase activity was a common feature in most SC taxa examined, in contrast to the uniformly high levels of activity found in all SI species. The S-RNase gene is most likely deleted in the four red-fruited SC taxa (L. esculentum, L. esculentum var. cerasiforme, L. pimpinellifolium and L. cheesmanii) because S-RNase genes could not be amplified from genomic DNA. S-RNase genes could, however, be amplified from the genomes of the three green-fruited SC taxa examined. L. chmielewskii and L. hirsutum f. glabratum show a decreased accumulation of transcripts, possibly reflecting changes in the 5' flanking regions of the S-RNase genes. The remaining green-fruited SC species, L. parviflorum, has a functional S-RNase gene in its genome that is expressed at high levels in the style, suggesting a genetic factor responsible for the low S-RNase activity. Together these results argue for several independent mutations in the S-RNase gene over the course of Lycopersicon diversification, and that loss of S-RNase function is unlikely to the primary cause of the loss of self-incompatibility. We also examined the HT-B genes that play a role in self-incompatibility. HT-B transcripts were markedly reduced in the styles of all the SC taxa examined. A scenario is described where a mutation causing reduced transcription of HT-B in an ancestral SI species was central to the loss of self-incompatibility in Lycopersicon.

Allelic diversity and gene genealogy at the self-incompatibility locus in the Solanaceae

The self-incompatibility (S) locus of flowering plants offers an example of extreme polymorphism maintained by balancing selection. Estimates of recent and long-term effective population size (Ne) were determined for two solanaceous species by examination of S-allele diversity. Estimates of recent Ne in two solanaceous species differed by an order of magnitude, consistent with differences in the species' ecology. In one species, the evidence was consistent with historical population restriction despite a large recent Ne. In the other, no severe bottleneck was indicated over millions of years. Bottlenecks are integral to founder-event speciation, and loci that are subject to balancing selection can be used to evaluate the frequency of this mode of speciation.