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Binaghi M, Esfeld K, Mandel T, Freitas LB, Roesti M, Kuhlemeier C. Genetic architecture of a pollinator shift and its fate in secondary hybrid zones of two Petunia species. BMC Biol 2023; 21:58. [PMID: 36941631 PMCID: PMC10029178 DOI: 10.1186/s12915-023-01561-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 03/10/2023] [Indexed: 03/23/2023] Open
Abstract
BACKGROUND Theory suggests that the genetic architecture of traits under divergent natural selection influences how easily reproductive barriers evolve and are maintained between species. Divergently selected traits with a simple genetic architecture (few loci with major phenotypic effects) should facilitate the establishment and maintenance of reproductive isolation between species that are still connected by some gene flow. While empirical support for this idea appears to be mixed, most studies test the influence of trait architectures on reproductive isolation only indirectly. Petunia plant species are, in part, reproductively isolated by their different pollinators. To investigate the genetic causes and consequences of this ecological isolation, we deciphered the genetic architecture of three floral pollination syndrome traits in naturally occurring hybrids between the widespread Petunia axillaris and the highly endemic and endangered P. exserta. RESULTS Using population genetics, Bayesian linear mixed modelling and genome-wide association studies, we found that the three pollination syndrome traits vary in genetic architecture. Few genome regions explain a majority of the variation in flavonol content (defining UV floral colour) and strongly predict the trait value in hybrids irrespective of interspecific admixture in the rest of their genomes. In contrast, variation in pistil exsertion and anthocyanin content (defining visible floral colour) is controlled by many genome-wide loci. Opposite to flavonol content, the genome-wide proportion of admixture between the two species predicts trait values in their hybrids. Finally, the genome regions strongly associated with the traits do not show extreme divergence between individuals representing the two species, suggesting that divergent selection on these genome regions is relatively weak within their contact zones. CONCLUSIONS Among the traits analysed, those with a more complex genetic architecture are best maintained in association with the species upon their secondary contact. We propose that this maintained genotype-phenotype association is a coincidental consequence of the complex genetic architectures of these traits: some of their many underlying small-effect loci are likely to be coincidentally linked with the actual barrier loci keeping these species partially isolated upon secondary contact. Hence, the genetic architecture of a trait seems to matter for the outcome of hybridization not only then when the trait itself is under selection.
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Affiliation(s)
- Marta Binaghi
- Institute of Plant Sciences, University of Bern, 3013, Bern, Switzerland
| | - Korinna Esfeld
- Institute of Plant Sciences, University of Bern, 3013, Bern, Switzerland
| | - Therese Mandel
- Institute of Plant Sciences, University of Bern, 3013, Bern, Switzerland
| | - Loreta B Freitas
- Department of Genetics, Universidade Federal Do Rio Grande Do Sul, Porto Alegre, RS, 91501-970, Brazil
| | - Marius Roesti
- Institute of Ecology and Evolution, University of Bern, 3012, Bern, Switzerland
| | - Cris Kuhlemeier
- Institute of Plant Sciences, University of Bern, 3013, Bern, Switzerland.
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Berardi AE, Esfeld K, Jäggi L, Mandel T, Cannarozzi GM, Kuhlemeier C. Complex evolution of novel red floral color in Petunia. Plant Cell 2021; 33:2273-2295. [PMID: 33871652 PMCID: PMC8364234 DOI: 10.1093/plcell/koab114] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Accepted: 04/12/2021] [Indexed: 05/20/2023]
Abstract
Red flower color has arisen multiple times and is generally associated with hummingbird pollination. The majority of evolutionary transitions to red color proceeded from purple lineages and tend to be genetically simple, almost always involving a few loss-of-function mutations of major phenotypic effect. Here we report on the complex evolution of a novel red floral color in the hummingbird-pollinated Petunia exserta (Solanaceae) from a colorless ancestor. The presence of a red color is remarkable because the genus cannot synthesize red anthocyanins and P. exserta retains a nonfunctional copy of the key MYB transcription factor AN2. We show that moderate upregulation and a shift in tissue specificity of an AN2 paralog, DEEP PURPLE, restores anthocyanin biosynthesis in P. exserta. An essential shift in anthocyanin hydroxylation occurred through rebalancing the expression of three hydroxylating genes. Furthermore, the downregulation of an acyltransferase promotes reddish hues in typically purple pigments by preventing acyl group decoration of anthocyanins. This study presents a rare case of a genetically complex evolutionary transition toward the gain of a novel red color.
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Affiliation(s)
- Andrea E. Berardi
- Institute of Plant Sciences, University of Bern, Bern 3013, Switzerland
| | - Korinna Esfeld
- Institute of Plant Sciences, University of Bern, Bern 3013, Switzerland
| | - Lea Jäggi
- Institute of Plant Sciences, University of Bern, Bern 3013, Switzerland
| | - Therese Mandel
- Institute of Plant Sciences, University of Bern, Bern 3013, Switzerland
| | | | - Cris Kuhlemeier
- Institute of Plant Sciences, University of Bern, Bern 3013, Switzerland
- Author for correspondence:
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Esfeld K, Berardi AE, Moser M, Bossolini E, Freitas L, Kuhlemeier C. Pseudogenization and Resurrection of a Speciation Gene. Curr Biol 2018; 28:3776-3786.e7. [PMID: 30472000 DOI: 10.1016/j.cub.2018.10.019] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 09/05/2018] [Accepted: 10/05/2018] [Indexed: 12/13/2022]
Abstract
A persistent question in evolutionary biology is how complex phenotypes evolve and whether phenotypic transitions are reversible. Multiple losses of floral pigmentation have been documented in the angiosperms, but color re-gain has not yet been described, supporting that re-gain is unlikely. Pollinator-mediated selection in Petunia has resulted in several color shifts comprised of both losses and gains of color. The R2R3-MYB transcription factor AN2 has been identified as a major locus responsible for shifts in pollinator preference. Whereas the loss of visible color has previously been attributed to repeated pseudogenization of AN2, here, we describe the mechanism of an independent re-gain of floral color via AN2 evolution. In P. secreta, purple color is restored through the improbable resurrection of AN2 gene function from a non-functional AN2-ancestor by a single reading-frame-restoring mutation. Thus, floral color evolution in Petunia is mechanistically dependent on AN2 functionality, highlighting its role as a hotspot in color transitions and a speciation gene for the genus.
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Affiliation(s)
- Korinna Esfeld
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, 3013 Bern, Switzerland
| | - Andrea E Berardi
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, 3013 Bern, Switzerland
| | - Michel Moser
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, 3013 Bern, Switzerland
| | - Eligio Bossolini
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, 3013 Bern, Switzerland
| | - Loreta Freitas
- Department of Genetics, University Fed Rio Grande do Sul, POB 15053, Porto Alegre, 91501970 Rio Grande do Sul, Brazil
| | - Cris Kuhlemeier
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, 3013 Bern, Switzerland.
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Jöst M, Esfeld K, Burian A, Cannarozzi G, Chanyalew S, Kuhlemeier C, Assefa K, Tadele Z. Semi-dwarfism and lodging tolerance in tef (Eragrostis tef) is linked to a mutation in the α-Tubulin 1 gene. J Exp Bot 2015; 66:933-944. [PMID: 25399019 PMCID: PMC4321551 DOI: 10.1093/jxb/eru452] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Genetic improvement of native crops is a new and promising strategy to combat hunger in the developing world. Tef is the major staple food crop for approximately 50 million people in Ethiopia. As an indigenous cereal, it is well adapted to diverse climatic and soil conditions; however, its productivity is extremely low mainly due to susceptibility to lodging. Tef has a tall and weak stem, liable to lodge (or fall over), which is aggravated by wind, rain, or application of nitrogen fertilizer. To circumvent this problem, the first semi-dwarf lodging-tolerant tef line, called kegne, was developed from an ethyl methanesulphonate (EMS)-mutagenized population. The response of kegne to microtubule-depolymerizing and -stabilizing drugs, as well as subsequent gene sequencing and segregation analysis, suggests that a defect in the α-Tubulin gene is functionally and genetically tightly linked to the kegne phenotype. In diploid species such as rice, homozygous mutations in α-Tubulin genes result in extreme dwarfism and weak stems. In the allotetraploid tef, only one homeologue is mutated, and the presence of the second intact α-Tubulin gene copy confers the agriculturally beneficial semi-dwarf and lodging-tolerant phenotype. Introgression of kegne into locally adapted and popular tef cultivars in Ethiopia will increase the lodging tolerance in the tef germplasm and, as a result, will improve the productivity of this valuable crop.
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Affiliation(s)
- Moritz Jöst
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, CH-3013 Bern, Switzerland
| | - Korinna Esfeld
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, CH-3013 Bern, Switzerland
| | - Agata Burian
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, CH-3013 Bern, Switzerland
| | - Gina Cannarozzi
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, CH-3013 Bern, Switzerland
| | - Solomon Chanyalew
- Ethiopian Institute of Agricultural Research, Debre Zeit Agricultural Research Center, PO Box 32, Debre Zeit, Ethiopia
| | - Cris Kuhlemeier
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, CH-3013 Bern, Switzerland
| | - Kebebew Assefa
- Ethiopian Institute of Agricultural Research, Debre Zeit Agricultural Research Center, PO Box 32, Debre Zeit, Ethiopia
| | - Zerihun Tadele
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, CH-3013 Bern, Switzerland
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Cannarozzi G, Plaza-Wüthrich S, Esfeld K, Larti S, Wilson YS, Girma D, de Castro E, Chanyalew S, Blösch R, Farinelli L, Lyons E, Schneider M, Falquet L, Kuhlemeier C, Assefa K, Tadele Z. Genome and transcriptome sequencing identifies breeding targets in the orphan crop tef (Eragrostis tef). BMC Genomics 2014; 15:581. [PMID: 25007843 PMCID: PMC4119204 DOI: 10.1186/1471-2164-15-581] [Citation(s) in RCA: 104] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Accepted: 07/03/2014] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Tef (Eragrostis tef), an indigenous cereal critical to food security in the Horn of Africa, is rich in minerals and protein, resistant to many biotic and abiotic stresses and safe for diabetics as well as sufferers of immune reactions to wheat gluten. We present the genome of tef, the first species in the grass subfamily Chloridoideae and the first allotetraploid assembled de novo. We sequenced the tef genome for marker-assisted breeding, to shed light on the molecular mechanisms conferring tef's desirable nutritional and agronomic properties, and to make its genome publicly available as a community resource. RESULTS The draft genome contains 672 Mbp representing 87% of the genome size estimated from flow cytometry. We also sequenced two transcriptomes, one from a normalized RNA library and another from unnormalized RNASeq data. The normalized RNA library revealed around 38000 transcripts that were then annotated by the SwissProt group. The CoGe comparative genomics platform was used to compare the tef genome to other genomes, notably sorghum. Scaffolds comprising approximately half of the genome size were ordered by syntenic alignment to sorghum producing tef pseudo-chromosomes, which were sorted into A and B genomes as well as compared to the genetic map of tef. The draft genome was used to identify novel SSR markers, investigate target genes for abiotic stress resistance studies, and understand the evolution of the prolamin family of proteins that are responsible for the immune response to gluten. CONCLUSIONS It is highly plausible that breeding targets previously identified in other cereal crops will also be valuable breeding targets in tef. The draft genome and transcriptome will be of great use for identifying these targets for genetic improvement of this orphan crop that is vital for feeding 50 million people in the Horn of Africa.
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Affiliation(s)
- Gina Cannarozzi
- />Institute of Plant Sciences, University of Bern, Altenbergrain 21, Bern, CH-3013 Switzerland
- />Swiss Institute of Bioinformatics, Vital-IT, Quartier Sorge - Batiment Genopode, Lausanne, 1015 Switzerland
| | - Sonia Plaza-Wüthrich
- />Institute of Plant Sciences, University of Bern, Altenbergrain 21, Bern, CH-3013 Switzerland
| | - Korinna Esfeld
- />Institute of Plant Sciences, University of Bern, Altenbergrain 21, Bern, CH-3013 Switzerland
| | - Stéphanie Larti
- />Institute of Plant Sciences, University of Bern, Altenbergrain 21, Bern, CH-3013 Switzerland
- />Clinic for Parodontology, University of Bern, Freiburgstrasse 7, Bern, CH-3010 Switzerland
| | - Yi Song Wilson
- />Institute of Plant Sciences, University of Bern, Altenbergrain 21, Bern, CH-3013 Switzerland
| | - Dejene Girma
- />Institute of Plant Sciences, University of Bern, Altenbergrain 21, Bern, CH-3013 Switzerland
- />Ethiopian Institute of Agricultural Research, National Biotechnology Laboratory (Holetta), P.O. Box 2003, Addis Ababa, Ethiopia
| | - Edouard de Castro
- />Swiss Institute of Bioinformatics, Rue Michel-Servet 1, 1211 Geneva 4, Switzerland
| | - Solomon Chanyalew
- />Ethiopian Institute of Agricultural Research, Debre Zeit Agricultural Research Center, P.O. Box 32, Debre Zeit, Ethiopia
| | - Regula Blösch
- />Institute of Plant Sciences, University of Bern, Altenbergrain 21, Bern, CH-3013 Switzerland
| | - Laurent Farinelli
- />Fasteris SA, Ch. du Pont-du-Centenaire 109, P.O. Box 28, Plan-les-Ouates, CH-1228 Switzerland
| | - Eric Lyons
- />School of Plant Sciences, Univerisity of Arizona, 1140 E. South Campus Drive, 303 Forbes Building, P.O. Box 210036, Tucson, AZ 85721-0036 USA
| | - Michel Schneider
- />Swiss Institute of Bioinformatics, Rue Michel-Servet 1, 1211 Geneva 4, Switzerland
| | - Laurent Falquet
- />Swiss Institute of Bioinformatics, Vital-IT, Quartier Sorge - Batiment Genopode, Lausanne, 1015 Switzerland
- />Faculty of Science, University of Fribourg, Ch. du Musée 10, Fribourg, CH-1700 Switzerland
| | - Cris Kuhlemeier
- />Institute of Plant Sciences, University of Bern, Altenbergrain 21, Bern, CH-3013 Switzerland
| | - Kebebew Assefa
- />Ethiopian Institute of Agricultural Research, Debre Zeit Agricultural Research Center, P.O. Box 32, Debre Zeit, Ethiopia
| | - Zerihun Tadele
- />Institute of Plant Sciences, University of Bern, Altenbergrain 21, Bern, CH-3013 Switzerland
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Schneeweiss GM, Pachschwöll C, Tribsch A, Schönswetter P, Barfuss MHJ, Esfeld K, Weiss-Schneeweiss H, Thiv M. Molecular phylogenetic analyses identify Alpine differentiation and dysploid chromosome number changes as major forces for the evolution of the European endemic Phyteuma (Campanulaceae). Mol Phylogenet Evol 2013; 69:634-52. [PMID: 23891952 DOI: 10.1016/j.ympev.2013.07.015] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2013] [Revised: 07/12/2013] [Accepted: 07/15/2013] [Indexed: 11/28/2022]
Abstract
Phyteuma is a chromosomally and ecologically diverse vascular plant genus and constitutes an excellent system for studying both the role of chromosomal change for species diversification and the evolution of high-mountain biota. This kind of research is, however, hampered by the lack of a sound phylogenetic framework exacerbated by the notoriously low predictive power of traditional taxonomy with respect to phylogenetic relationships in Campanulaceae. Based on a comprehensive taxon sampling and analyses of nuclear and plastid sequence and AFLP fingerprint data, Phyteuma is confirmed as a monophyletic group sister to the monotypic Physoplexis, which is in line with their peculiar flower morphologies. Within Phyteuma two clades, largely corresponding to previously recognized sections, are consistently found. The traditional circumscription of taxonomic series is largely rejected. Whereas distinctness of the currently recognized species is mostly corroborated, some interspecific relationships remain ambiguous due to incongruences between nuclear and plastid data. Major forces for diversification and evolution of Phyteuma are descending dysploidy (i.e., a decrease in chromosome base number) as well as allopatric and ecological differentiation within the Alps, the genus' center of species diversity.
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Affiliation(s)
- Gerald M Schneeweiss
- Department of Systematic and Evolutionary Botany, University of Vienna, Rennweg 14, A-1030 Vienna, Austria.
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