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Abstract Plants regenerated from seedling explants (hypocotyls and cotyledons) of the Solanaceae family membersPhysalis grisea(groundcherry),Solanum lycopersicum(tomato), andSolanum prinophyllum(forest nightshade) were used to determine the in vitro culture parameters that contribute to the incidence in polyploidization of tissue culture-derived plants (regenerants) from these species. We examined the possible effects of zeatin concentration in the plant regeneration medium, explant source, and species. Plants were grown to maturity under greenhouse conditions, pollen was collected and germinated. Flow cytometry analysis verified the utility of the pollen germination method for determining differences in ploidy, which was based on the number of pollen tubes produced with one tube representing diploid and two indicating polyploid. As for zeatin concentration, we assessed the effect of our standard method of initiation on medium containing 2 mg/l followed by 1 mg/l 2 weeks after culture initiation in comparison with 0.25, 0.5, and 1 mg/l throughout the culture lifetime. There were no major correlations for zeatin concentration on ploidy status across the species except for plants regenerated fromS. lycopersicumhypocotyl explants where the percentage of polyploid regenerants increased with increasing concentrations. As for species and explant effects,P. griseaplants regenerated from hypocotyl explants had the highest percentage of polyploid plants at 81% compared to 43% and 35% forS. lycopersicumandS. prinophyllum, respectively. From cotyledons, 8% ofS. lycopersicumand 20% ofS. prinophyllumwere polyploid. A comparison withP. griseacould not be made because cotyledon explants do not regenerate on zeatin-containing medium. The results indicated the incidence of polyploidization cannot be generalized for zeatin concentration, however, an influence of explant type and species was observed. Effects of increased ploidy on plant morphology were primarily larger flower and seed size; however, no significant differences were observed in plant or fruit size. 

Abstract Pan-genomics and genome-editing technologies are revolutionizing breeding of global crops^1,2. A transformative opportunity lies in exchanging genotype-to-phenotype knowledge between major crops (that is, those cultivated globally) and indigenous crops (that is, those locally cultivated within a circumscribed area)^3–5to enhance our food system. However, species-specific genetic variants and their interactions with desirable natural or engineered mutations pose barriers to achieving predictable phenotypic effects, even between related crops^6,7. Here, by establishing a pan-genome of the crop-rich genusSolanum⁸and integrating functional genomics and pan-genetics, we show that gene duplication and subsequent paralogue diversification are major obstacles to genotype-to-phenotype predictability. Despite broad conservation of gene macrosynteny among chromosome-scale references for 22 species, including 13 indigenous crops, thousands of gene duplications, particularly within key domestication gene families, exhibited dynamic trajectories in sequence, expression and function. By augmenting our pan-genome with African eggplant cultivars⁹and applying quantitative genetics and genome editing, we dissected an intricate history of paralogue evolution affecting fruit size. The loss of a redundant paralogue of the classical fruit size regulatorCLAVATA3(CLV3)^10,11was compensated by a lineage-specific tandem duplication. Subsequent pseudogenization of the derived copy, followed by a large cultivar-specific deletion, created a single fusedCLV3allele that modulates fruit organ number alongside an enzymatic gene controlling the same trait. Our findings demonstrate that paralogue diversifications over short timescales are underexplored contingencies in trait evolvability. Exposing and navigating these contingencies is crucial for translating genotype-to-phenotype relationships across species. 

An enduring question in evolutionary biology concerns the degree to which episodes of convergent trait evolution depend on the same genetic programs, particularly over long timescales. In this work, we genetically dissected repeated origins and losses of prickles—sharp epidermal projections—that convergently evolved in numerous plant lineages. Mutations in a cytokinin hormone biosynthetic gene caused at least 16 independent losses of prickles in eggplants and wild relatives in the genusSolanum. Homologs underlie prickle formation across angiosperms that collectively diverged more than 150 million years ago, including rice and roses. By developing newSolanumgenetic systems, we leveraged this discovery to eliminate prickles in a wild species and an indigenously foraged berry. Our findings implicate a shared hormone activation genetic program underlying evolutionarily widespread and recurrent instances of plant morphological innovation. 

Abstract An enduring question in evolutionary biology concerns the degree to which episodes of convergent trait evolution depend on the same genetic programs, particularly over long timescales. Here we genetically dissected repeated origins and losses of prickles, sharp epidermal projections, that convergently evolved in numerous plant lineages. Mutations in a cytokinin hormone biosynthetic gene caused at least 16 independent losses of prickles in eggplants and wild relatives in the genusSolanum. Strikingly, homologs promote prickle formation across angiosperms that collectively diverged over 150 million years ago. By developing newSolanumgenetic systems, we leveraged this discovery to eliminate prickles in a wild species and an indigenously foraged berry. Our findings implicate a shared hormone-activation genetic program underlying evolutionarily widespread and recurrent instances of plant morphological innovation.