Wild Crop Relatives: Genomic and Breeding Resources

The Solanaceae is a plant family of great economic importance. Despite a wealth of phylogenetic work on individual clades and a deep knowledge of particular cultivated species such as tomato and potato, a robust evolutionary framework with a dated molecular phylogeny for the family is still lacking. Here we investigate molecular divergence times for Solanaceae using a densely-sampled species-level phylogeny. We also review the fossil record of the family to derive robust calibration points, and estimate a chronogram using an uncorrelated relaxed molecular clock. Our densely-sampled phylogeny shows strong support for all previously identified clades of Solanaceae and strongly supported relationships between the major clades, particularly within Solanum. The Tomato clade is shown to be sister to section Petota, and the Regmandra clade is the first branching member of the Potato clade. The minimum age estimates for major splits within the family provided here correspond well with results from previous studies, indicating splits between tomato & potato around 8 Million years ago (Ma) with a 95% highest posterior density (HPD) 7–10 Ma, Solanum & Capsicum c. 19 Ma (95% HPD 17–21), and Solanum & Nicotiana c. 24 Ma (95% HPD 23–26). Our large time-calibrated phylogeny provides a significant step towards completing a fully sampled species-level phylogeny for Solanaceae, and provides age estimates for the whole family. The chronogram now includes 40% of known species and all but two monotypic genera, and is one of the best sampled angiosperm family phylogenies both in terms of taxon sampling and resolution published thus far. The increased resolution in the chronogram combined with the large increase in species sampling will provide much needed data for the examination of many biological questions using Solanaceae as a model system.

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A phylogenetic framework for evolutionary study of the nightshades (Solanaceae): a dated 1000-tip tree

A phylogeny of Solanaceae is presented based on the chloroplast DNA regions ndhF and trnLF. With 89 genera and 190 species included, this represents a nearly comprehensive genus-level sampling and provides a framework phylogeny for the entire family that helps integrate many previously-published phylogenetic studies within Solanaceae. The four genera comprising the family Goetzeaceae and the monotypic families Duckeodendraceae, Nolanaceae, and Sclerophylaceae, often recognized in traditional classifications, are shown to be included in Solanaceae. The current results corroborate previous studies that identify a monophyletic subfamily Solanoideae and the more inclusive "x = 12" clade, which includes Nicotiana and the Australian tribe Anthocercideae. These results also provide greater resolution among lineages within Solanoideae, confirming Jaltomata as sister to Solanum and identifying a clade comprised primarily of tribes Capsiceae (Capsicum and Lycianthes) and Physaleae. Stronger evidence also is provided for the inclusion of Capsicum within a paraphyletic Lycianthes. Solanaceae are a predominantly New World group, with several lineages represented on other continents. Apart from events within Solanum (for which sampling in this study is inadequate for biogeographic interpretations) the Old World representatives of Solanaceae can be accounted for by eight or nine dispersal events.

http://depts.washington.edu/phylo/OlmsteadPubs/Olmstead_et_al_2008.pdf

A molecular phylogeny of the Solanaceae

Speciation events often occur in rapid bursts of diversification, but the ecological and genetic factors that promote these radiations are still much debated. Using whole transcriptomes from all 13 species in the ecologically and reproductively diverse wild tomato clade (Solanum sect. Lycopersicon), we infer the species phylogeny and patterns of genetic diversity in this group. Despite widespread phylogenetic discordance due to the sorting of ancestral variation, we date the origin of this radiation to approximately 2.5 million years ago and find evidence for at least three sources of adaptive genetic variation that fuel diversification. First, we detect introgression both historically between early-branching lineages and recently between individual populations, at specific loci whose functions indicate likely adaptive benefits. Second, we find evidence of lineage-specific de novo evolution for many genes, including loci involved in the production of red fruit color. Finally, using a “PhyloGWAS” approach, we detect environment-specific sorting of ancestral variation among populations that come from different species but share common environmental conditions. Estimated across the whole clade, small but substantial and approximately equal fractions of the euchromatic portion of the genome are inferred to contribute to each of these three sources of adaptive genetic variation. These results indicate that multiple genetic sources can promote rapid diversification and speciation in response to new ecological opportunity, in agreement with our emerging phylogenomic understanding of the complexity of both ancient and recent species radiations.

/pdf/phylogenomics-reveals-three-sources-of-adaptive-variation-2l95kyaqlt.pdf

Phylogenomics Reveals Three Sources of Adaptive Variation during a Rapid Radiation.

PREMISE OF THE STUDY Archaeological and genetic analyses of seed-propagated annual crops have greatly advanced our understanding of plant domestication and evolution. Comparatively little is known about perennial plant domestication, a relevant topic for understanding how genes and genomes evolve in long-lived species, and how perennials respond to selection pressures operating on a relatively short time scale. Here, we focus on long-lived perennial crops (mainly trees and other woody plants) grown for their fruits. KEY RESULTS We reviewed (1) the basic biology of long-lived perennials, setting the stage for perennial domestication by considering how these species evolve in nature; (2) the suite of morphological features associated with perennial fruit crops undergoing domestication; (3) the origins and evolution of domesticated perennials grown for their fruits; and (4) the genetic basis of domestication in perennial fruit crops. CONCLUSIONS Long-lived perennials have lengthy juvenile phases, extensive outcrossing, widespread hybridization, and limited population structure. Under domestication, these features, combined with clonal propagation, multiple origins, and ongoing crop-wild gene flow, contribute to mild domestication bottlenecks in perennial fruit crops. Morphological changes under domestication have many parallels to annual crops, but with key differences for mating system evolution and mode of reproduction. Quantitative trait loci associated with domestication traits in perennials are mainly of minor effect and may not be stable across years. Future studies that take advantage of genomic approaches and consider demographic history will elucidate the genetics of agriculturally and ecologically important traits in perennial fruit crops and their wild relatives.

From forest to field: Perennial fruit crop domestication

Solanum, with approximately 1,500 species, is the largest genus in the Solanaceae and includes economically important species such as the tomato, potato, and eggplant. In part due to its large size and tropical center of diversity, resolving evolutionary relationships across Solanum as a whole has been challenging. In order to identify major clades within Solanum and to gain insight into phylogenetic relationships among these clades, we sampled 102 Solanum species and seven outgroup taxa for three DNA sequence regions (chloroplast ndhF and trnT- F, and nuclear waxy) and analyzed the data using parsimony and Bayesian methods. The same major Solanum clades were identified by each data partition, and the combined analysis provided the best resolved hypothesis of relationships within the genus. Our data suggest that most traditionally recognized Solanum subgenera are not monophyletic. The Thelopodium clade is sister to the rest of Solanum, which is split into two large clades. These two large clades are further divided into at least 10 subclades, for which informal names are provided and morphological synapomorphies are proposed. The identification of these subclades provides a framework for directed sampling in further phylogenetic studies, and identifies natural groups for focused revisionary work.

https://bioone.org/journals/systematic-botany/volume-32/issue-2/036364407781179671/A-Three-Gene-Phylogeny-of-the-Genus-Solanum-Solanaceae/10.1600/036364407781179671.pdf

A Three-Gene Phylogeny of the Genus Solanum (Solanaceae)

The eggplant (Solanum melongena L.), also known as aubergine or brinjal, has been cultivated for centuries in the Old World and is currently a crop species of global importance. Despite this, hypotheses of eggplant evolution have been fraught with controversy. Previous conclusions have relied solely on morphological characters or have been based on insufficient taxonomic sampling, leading to conflicting opinions of the number of species, phylogenetic relationships, and patterns of domestication in a group of related taxa termed the S. melongena complex. The S. melongena complex shows a series of morphological intermedi ates from small-fruited spiny plants to large-fruited non-spiny plants. We use DNA sequence data to show that eggplants arose in Africa and were dispersed throughout the Middle East to Asia. Solanum linnaeanum, a wild species not previously associated with eggplant evolution, is a member of the S. melongena complex. These data provide the most comprehensive evidence to date for the evolution of the cultivated eggplant.

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Eggplant origins: out of Africa, into the orient.

The majority of species in the large genus Solanum (ca. 1500 species) have five-merous, radially symmetrical flowers with equal stamens. However, some Solanum species and groups are characterized by four-merous and/or zygomorphic flowers, unequal stamens and enantiostyly (styles deflected to one side of the flower). Previous workers have used flower and seed coat morphology in these unusual Solanum species as a guide to interpreting their evolutionary relationships. However, the phylogenetic position of the zygomorphic and heterantherous solanums is only beginning to be examined using molecular data and cladistic methodology. DNA sequence data from both the chloroplast and nuclear genomes are used to infer the phylogenetic position of Solanum taxa with variously modified flowers. Zygomorphy and heteranthery have evolved multiple times within Solanum, and most frequently within the spiny solanums (Solanum subg. Leptostemonum). The phylogenies shed light on the disparate morphologies and geographical distributions encountered in the zygomorphic and heterantherous species and pinpoint the likely relatives of these taxa among the actinomorphic Solanum species with equal stamens.

Zygomorphy and Heteranthery in Solanum in a Phylogenetic Context

The Leptostemonum clade of Solanum contains approximately 350–450 species, including the cultivated eggplant, S. melongena. This clade is characterized by the presence of prickles and apically attenuate anthers. Solanum section Androceras, the focus of this study, is a group of ca. 12 species belonging to the Leptostemonum clade. This section is unusual in the genus because of its mostly north temperate distribution and distinctive zygomorphic, heterantherous, and enantiostylous flowers. We infer phylogenetic relationships among 43 Solanum taxa, including 11 species and all varieties of sect. Androceras, using DNA sequence data from two nuclear regions (ITS and the granule-bound starch synthase gene [GBSSI or waxy]) and the chloroplast region trnT-F. The combined phylogenetic tree supports sect. Androceras as a monophyletic group sister to Solanum sect. Crinitum. Only one of the three series proposed by previous taxonomists, ser. Pacificum, is supported as monophyletic. Solanum tenuipes from the ...

/pdf/phylogenetic-relationships-in-solanum-section-androceras-57wf3yuqen.pdf

Phylogenetic Relationships in Solanum Section Androceras (Solanaceae)

The endemic and rare Solanum vespertilio and S. lidii from the Canary Islands are notable in being andromonoecious, self compatible, highly heterandrous (with short >reward= anthers and one very long >pollination= anther), and bearing strongly zygomorphic corollas. Solanum vespertilio flowers are also tetramerous, and some display enantiostyly. Given their island distribution, uncommon for solanums, and many distinctive reproductive features, the phylogenetic position is of interest. With new molecular data from the chloroplast trnT-F region and the nuclear granule-bound starch synthase gene (GBSSI or waxy), we confirm the hypothesis that these two species are phylogenetically associated with Solanum lineages from Africa, rather than with previously suggested Mexican species. The phylogeny facilitates understanding the evolution of the unique suite of reproductive characteristics in these island endemics.

/pdf/phylogeny-and-biogeography-of-the-canarian-solanum-12fjd9onb4.pdf

Terri L. Weese

Papers

A Three-Gene Phylogeny of the Genus Solanum (Solanaceae)

Eggplant origins: out of Africa, into the orient.

Zygomorphy and Heteranthery in Solanum in a Phylogenetic Context

Phylogenetic Relationships in Solanum Section Androceras (Solanaceae)

Phylogeny and biogeography of the Canarian Solanum vespertilio and S. lidii (Solanaceae)