1
|
Wang L, Liu L, Zhao J, Li C, Wu H, Zhao H, Wu Q. Granule-bound starch synthase in plants: Towards an understanding of their evolution, regulatory mechanisms, applications, and perspectives. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 336:111843. [PMID: 37648115 DOI: 10.1016/j.plantsci.2023.111843] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 08/22/2023] [Accepted: 08/23/2023] [Indexed: 09/01/2023]
Abstract
Amylose content (AC) is a significant quality trait in starchy crops, affecting their processing and application by the food and non-food industries. Therefore, fine-tuning AC in these crops has become a focus for breeders. Granule-bound starch synthase (GBSS) is the core enzyme that directly determines the AC levels. Several excellent reviews have summarized key progress in various aspects of GBSS research in recent years, but they mostly focus on cereals. Herein, we provide an in-depth review of GBSS research in monocots and dicots, focusing on the molecular characteristics, evolutionary relationships, expression patterns, molecular regulation mechanisms, and applications. We also discuss future challenges and directions for controlling AC in starchy crops, and found simultaneously increasing both the PTST and GBSS gene expression levels may be an effective strategy to increase amylose content.
Collapse
Affiliation(s)
- Lei Wang
- College of Life Science, Sichuan Agricultural University, No. 46, Xinkang Road, Ya'an 625014, China
| | - Linling Liu
- College of Life Science, Sichuan Agricultural University, No. 46, Xinkang Road, Ya'an 625014, China
| | - Jiali Zhao
- College of Life Science, Sichuan Agricultural University, No. 46, Xinkang Road, Ya'an 625014, China
| | - Chenglei Li
- College of Life Science, Sichuan Agricultural University, No. 46, Xinkang Road, Ya'an 625014, China
| | - Huala Wu
- College of Life Science, Sichuan Agricultural University, No. 46, Xinkang Road, Ya'an 625014, China
| | - Haixia Zhao
- College of Life Science, Sichuan Agricultural University, No. 46, Xinkang Road, Ya'an 625014, China
| | - Qi Wu
- College of Life Science, Sichuan Agricultural University, No. 46, Xinkang Road, Ya'an 625014, China.
| |
Collapse
|
2
|
Zhuo J, Vasupalli N, Wang Y, Zhou G, Gao H, Zheng Y, Li B, Hou D, Lin X. Molecular identification of Bambusa changningensis is the natural bamboo hybrid of B. rigida × Dendrocalamus farinosus. FRONTIERS IN PLANT SCIENCE 2023; 14:1231940. [PMID: 37727859 PMCID: PMC10505617 DOI: 10.3389/fpls.2023.1231940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 08/09/2023] [Indexed: 09/21/2023]
Abstract
Bamboo is one of the fastest-growing plants commonly used in food, fibre, paper, biofuel, ornamental and medicinal industries. Natural hybridization in bamboo is rare due to its long vegetative period followed by gregarious flowering and death of the entire population. In the current study, a new bamboo species, Bambusa changningensis, shows intermediate characteristics of Dendrocalamus farinosus and B. rigida morphologically, but it is unknown whether B. changningensis is a natural hybrid. Moreover, B. changningensis has been identified as a superior variety of Sichuan Province with high pulping yield, fibre length and width. Therefore, we analyzed the morphological characteristics, DNA markers, DNA barcoding and chloroplast genomes to identify the hybrid origin of B. changningensis and possible maternal parent. We have developed the transcriptomic data for B. changningensis and mined the SSR loci. The putative parental lines and hybrid were screened for 64 SSR makers and identified that SSR14, SSR28, SSR31 and SSR34 markers showed both alleles of the parental species in B. changningensis, proving heterozygosity. Sequencing nuclear gene GBSSI partial regions and phylogenetic analysis also confirm the hybrid nature of B. changningensis. Further, we have generated the complete chloroplast genome sequence (139505 bp) of B. changningensis. By analyzing the cp genomes of both parents and B. changningensis, we identified that B. rigida might be the female parent. In conclusion, our study identified that B. changningensis is a natural hybrid, providing evidence for bamboo's natural hybridization. This is the first report on confirming a natural bamboo hybrid and its parents through SSR and chloroplast genome sequence.
Collapse
Affiliation(s)
- Juan Zhuo
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Lin’An, Zhejiang, China
| | - Naresh Vasupalli
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Lin’An, Zhejiang, China
| | - Yong Wang
- Forest and Bamboo Resources Conservation and Cultivation Institute, Yibin Forestry and Bamboo Industry Research Institute, Yibin, Sichuan, China
| | - Guoqiang Zhou
- Forest and Bamboo Resources Conservation and Cultivation Institute, Yibin Forestry and Bamboo Industry Research Institute, Yibin, Sichuan, China
| | - Huibin Gao
- Forest and Bamboo Resources Conservation and Cultivation Institute, Yibin Forestry and Bamboo Industry Research Institute, Yibin, Sichuan, China
| | - Ying Zheng
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Lin’An, Zhejiang, China
| | - Benxiang Li
- Sichuan Changning Century Bamboo Garden, Yibin, Sichuan, China
| | - Dan Hou
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Lin’An, Zhejiang, China
| | - Xinchun Lin
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Lin’An, Zhejiang, China
| |
Collapse
|
3
|
Fenstemaker S, Sim L, Cooperstone J, Francis D. Solanum galapagense-derived purple tomato fruit color is conferred by novel alleles of the anthocyanin fruit and atroviolacium loci. PLANT DIRECT 2022; 6:e394. [PMID: 35449754 PMCID: PMC9014491 DOI: 10.1002/pld3.394] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 03/07/2022] [Accepted: 03/16/2022] [Indexed: 06/14/2023]
Abstract
One hypothesis for the origin of endemic species of tomato on the Galápagos islands postulates a hybridization of Solanum pimpinellifolium and Solanum habrochaites. Solanum galapagense accession LA1141 has purple fruit pigmentation, previously described in green-fruited wild tomatoes such as S. habrochaites or Solanum chilense. Characterization of LA1141 derived purple pigmentation provides a test of the hybridization hypothesis. Purple pigmentation was recovered in progenies derived from LA1141, and the anthocyanins malvidin 3(coumaroyl)rutinoside-5-glucoside, petunidin 3-(coumaroyl) rutinoside-5-glucoside, and petunidin 3-(caffeoyl)rutinoside-5-glucoside were abundant. Fruit color was evaluated in an introgression population, and three quantitative trait loci (QTLs) were mapped and validated in subsequent populations. The loci atroviolacium on chromosome 7, Anthocyanin fruit on chromosome 10, and uniform ripening also on chromosome 10 underly these QTLs. Sequence analysis suggested that the LA1141 alleles of Aft and atv are unique relative to those previously described from S. chilense accession LA0458 and Solanum cheesmaniae accession LA0434, respectively. Phylogenetic analysis of the LA1141 Aft genomic sequence did not support a green-fruited origin, and the locus clustered with members of the red-fruited tomato clade. The LA1141 allele of Aft is not the result of an ancient introgression from the green-fruited clade and underlies a gain of anthocyanin pigmentation in the red-fruited clade.
Collapse
Affiliation(s)
- Sean Fenstemaker
- Department of Horticulture and Crop ScienceThe Ohio State UniversityWoosterOhioUSA
| | - Leah Sim
- Department of Horticulture and Crop ScienceThe Ohio State UniversityWoosterOhioUSA
| | - Jessica Cooperstone
- Department of Food Science and TechnologyThe Ohio State UniversityColumbusOhioUSA
- Department of Horticulture and Crop ScienceThe Ohio State UniversityColumbusOhioUSA
| | - David Francis
- Department of Horticulture and Crop ScienceThe Ohio State UniversityWoosterOhioUSA
| |
Collapse
|
4
|
Alaria A, Chau JH, Olmstead RG, Peralta IE. Relationships among Calibrachoa, Fabiana and Petunia (Petunieae tribe, Solanaceae) and a new generic placement of Argentinean endemic Petuniapatagonica. PHYTOKEYS 2022; 194:75-93. [PMID: 35586321 PMCID: PMC9033757 DOI: 10.3897/phytokeys.194.68404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 01/03/2022] [Indexed: 05/13/2023]
Abstract
Calibrachoa Cerv., Fabiana Ruiz & Pav., and Petunia Juss. form a clade within tribe Petunieae (Solanaceae). Phylogenetic studies of Petunieae, either as part of a family-wide analysis or focusing on the genera Calibrachoa and Petunia, have either left Fabiana unsampled or included only a single species. These studies have found conflicting relationships among the three genera with all three possible topologies obtained. Petuniapatagonica (Speg.) Millán, originally described in the genus Nierembergia Ruiz & Pav., is morphologically distinct within Petunia and geographically disjunct from other members of the genus. For the first time, in this study we include multiple species of Fabiana, Calibrachoa, and Petunia, including P.patagonica. Using three chloroplast DNA regions and the nuclear gene GBSSI, or "waxy," our results provide strong support for a sister group relationship between Calibrachoa and Fabiana and for the placement of P.patagonica within Fabiana. Since there is already a species Fabianapatagonica Speg., we provide the new name Fabianaaustralis Alaria nom. nov. to replace Petuniapatagonica.
Collapse
Affiliation(s)
- Alejandrina Alaria
- Agronomy Faculty, National University of Cuyo, Alte. Brown 500, Luján de Cuyo, Mendoza, ArgentinaNational University of CuyoMendozaArgentina
| | - John H. Chau
- Department of Biology, University of Washington, Seattle, Washington, 98195, USAUniversity of WashingtonSeattleUnited States of America
- Centre for Ecological Genomics and Wildlife Conservation, Department of Zoology, University of Johannesburg, Auckland Park 2006, South AfricaUniversity of JohannesburgJohannesburgSouth Africa
| | - Richard G. Olmstead
- Department of Biology, University of Washington, Seattle, Washington, 98195, USAUniversity of WashingtonSeattleUnited States of America
| | - Iris E. Peralta
- Agronomy Faculty, National University of Cuyo, Alte. Brown 500, Luján de Cuyo, Mendoza, ArgentinaNational University of CuyoMendozaArgentina
- IADIZA CCT CONICET, Adrián Ruiz Leal s/n Parque general San Martín, Mendoza, ArgentinaIADIZA CCT CONICETMendozaArgentina
| |
Collapse
|
5
|
Fruit Colour and Novel Mechanisms of Genetic Regulation of Pigment Production in Tomato Fruits. HORTICULTURAE 2021. [DOI: 10.3390/horticulturae7080259] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Fruit colour represents a genetic trait with ecological and nutritional value. Plants mainly use colour to attract animals and favour seed dispersion. Thus, in many species, fruit colour coevolved with frugivories and their preferences. Environmental factors, however, represented other adaptive forces and further diversification was driven by domestication. All these factors cooperated in the evolution of tomato fruit, one of the most important in human nutrition. Tomato phylogenetic history showed two main steps in colour evolution: the change from green-chlorophyll to red-carotenoid pericarp, and the loss of the anthocyanic pigmentation. These events likely occurred with the onset of domestication. Then spontaneous mutations repeatedly occurred in carotenoid and phenylpropanoid pathways, leading to colour variants which often were propagated. Introgression breeding further enriched the panel of pigmentation patterns. In recent decades, the genetic determinants underneath tomato colours were identified. Novel evidence indicates that key regulatory and biosynthetic genes undergo mechanisms of gene expression regulation that are much more complex than what was imagined before: post-transcriptional mechanisms, with RNA splicing among the most common, indeed play crucial roles to fine-tune the expression of this trait in fruits and offer new substrate for the rise of genetic variables, thus providing further evolutionary flexibility to the character.
Collapse
|
6
|
Climatic Diversity and Ecological Descriptors of Wild Tomato Species ( Solanum sect . Lycopersicon) and Close Related Species ( Solanum sect . Juglandifolia y sect. Lycopersicoides) in Latin America. PLANTS 2021; 10:plants10050855. [PMID: 33922706 PMCID: PMC8145878 DOI: 10.3390/plants10050855] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 04/16/2021] [Accepted: 04/19/2021] [Indexed: 11/21/2022]
Abstract
Conservation and sustainable use of species diversity require a description of the environment where they develop. The objectives were to determine ecological descriptors and climatic diversity of areas along the distribution range of 12 species of wild tomatoes (Solanum sect. Lycopersicon) and four wild species of phylogenetically related groups (Solanum sect. Juglandifolia and sect. Lycopersicoides), as well as their ecological similarity in Latin America. With 4228 selected tomato accessions and an environmental information system (EIS) composed of 21 climatic variables, diversity patterns of the distribution areas were identified for each species, as well as ecological descriptors through the use of geographic information systems (GIS). The contribution of climatic variables to the species geographical distribution was identified by principal component analysis (PCA), and similarity in species distribution as a function of the variables identified with cluster analysis (CA). Climatic characteristics and the environmental amplitude of wild tomatoes and related species along their distributional range were satisfactorily determined by ecological descriptors. Eleven climate types were identified, predominantly BSk (arid, steppe, cold), BWh (arid, desert, hot), and Cfb (temperate, no dry season, warm summer). PCA determined 10 most important variables were the most important for the geographical distribution. Six groups of species were identified according to CA and climatic distribution similarity. This approach has shown promissory applications for biodiversity conservation of valuable genetic resources for tomato crop breeding.
Collapse
|
7
|
Tamburino R, Sannino L, Cafasso D, Cantarella C, Orrù L, Cardi T, Cozzolino S, D’Agostino N, Scotti N. Cultivated Tomato ( Solanum lycopersicum L.) Suffered a Severe Cytoplasmic Bottleneck during Domestication: Implications from Chloroplast Genomes. PLANTS 2020; 9:plants9111443. [PMID: 33114641 PMCID: PMC7692331 DOI: 10.3390/plants9111443] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 10/21/2020] [Accepted: 10/22/2020] [Indexed: 12/13/2022]
Abstract
In various crops, genetic bottlenecks occurring through domestication can limit crop resilience to biotic and abiotic stresses. In the present study, we investigated nucleotide diversity in tomato chloroplast genome through sequencing seven plastomes of cultivated accessions from the Campania region (Southern Italy) and two wild species among the closest (Solanum pimpinellifolium) and most distantly related (S. neorickii) species to cultivated tomatoes. Comparative analyses among the chloroplast genomes sequenced in this work and those available in GenBank allowed evaluating the variability of plastomes and defining phylogenetic relationships. A dramatic reduction in genetic diversity was detected in cultivated tomatoes, nonetheless, a few de novo mutations, which still differentiated the cultivated tomatoes from the closest wild relative S. pimpinellifolium, were detected and are potentially utilizable as diagnostic markers. Phylogenetic analyses confirmed that S. pimpinellifolium is the closest ancestor of all cultivated tomatoes. Local accessions all clustered together and were strictly related with other cultivated tomatoes (S. lycopersicum group). Noteworthy, S. lycopersicum var. cerasiforme resulted in a mixture of both cultivated and wild tomato genotypes since one of the two analyzed accessions clustered with cultivated tomato, whereas the other with S. pimpinellifolium. Overall, our results revealed a very reduced cytoplasmic variability in cultivated tomatoes and suggest the occurrence of a cytoplasmic bottleneck during their domestication.
Collapse
Affiliation(s)
- Rachele Tamburino
- CNR-IBBR, National Research Council of Italy, Institute of Biosciences and BioResources, Via Università 133, 80055 Portici (NA), Italy; (R.T.); (L.S.)
| | - Lorenza Sannino
- CNR-IBBR, National Research Council of Italy, Institute of Biosciences and BioResources, Via Università 133, 80055 Portici (NA), Italy; (R.T.); (L.S.)
| | - Donata Cafasso
- Department of Biology, University of Naples Federico II, Via Cinthia, 80126 Naples, Italy; (D.C.); (S.C.)
| | - Concita Cantarella
- CREA Research Centre for Vegetable and Ornamental Crops, Via dei Cavalleggeri 25, 84098 Pontecagnano Faiano (SA), Italy; (C.C.); (T.C.); (N.D.)
| | - Luigi Orrù
- CREA Research Centre for Genomics and Bioinformatics, via S. Protaso 302, 29017 Fiorenzuola d’Arda (PC), Italy;
| | - Teodoro Cardi
- CREA Research Centre for Vegetable and Ornamental Crops, Via dei Cavalleggeri 25, 84098 Pontecagnano Faiano (SA), Italy; (C.C.); (T.C.); (N.D.)
| | - Salvatore Cozzolino
- Department of Biology, University of Naples Federico II, Via Cinthia, 80126 Naples, Italy; (D.C.); (S.C.)
| | - Nunzio D’Agostino
- CREA Research Centre for Vegetable and Ornamental Crops, Via dei Cavalleggeri 25, 84098 Pontecagnano Faiano (SA), Italy; (C.C.); (T.C.); (N.D.)
- Department of Agricultural Sciences, University of Naples Federico II, Via Università 133, 80055 Portici (NA), Italy
| | - Nunzia Scotti
- CNR-IBBR, National Research Council of Italy, Institute of Biosciences and BioResources, Via Università 133, 80055 Portici (NA), Italy; (R.T.); (L.S.)
- Correspondence: ; Tel.: +39-0812-53-9482
| |
Collapse
|
8
|
Ferrero V, Baeten L, Blanco-Sánchez L, Planelló R, Díaz-Pendón JA, Rodríguez-Echeverría S, Haegeman A, de la Peña E. Complex patterns in tolerance and resistance to pests and diseases underpin the domestication of tomato. THE NEW PHYTOLOGIST 2020; 226:254-266. [PMID: 31793000 DOI: 10.1111/nph.16353] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 11/19/2019] [Indexed: 05/26/2023]
Abstract
A frequent hypothesis explaining the high susceptibility of many crops to pests and diseases is that, in the process of domestication, crops have lost defensive genes and traits against pests and diseases. Ecological theory predicts trade-offs whereby resistance and tolerance go at the cost of each other. We used wild relatives, early domesticated varieties, traditional local landraces and cultivars of tomato (Solanum lycopersicum) to test whether resistance and tolerance trade-offs were phylogenetically structured or varied according to degree of domestication. We exposed tomato genotypes to the aphid Macrosiphum euphorbiae, the cotton leafworm Spodoptera littoralis, the root knot nematode Meloidogyne incognita and two common insect-transmitted plant viruses, and reconstructed their phylogenetic relationships using Genotyping-by-Sequencing. We found differences in the performance and effect of pest and diseases but such differences were not related with domestication degree nor genetic relatedness, which probably underlie a complex genetic basis for resistance and indicate that resistance traits appeared at different stages and in unrelated genetic lineages. Still, wild and early domesticated accessions showed greater resistance to aphids and tolerance to caterpillars, nematodes and diseases than modern cultivars. Our findings help to understand how domestication affects plant-pest interactions and underline the importance of tolerance in crop breeding.
Collapse
Affiliation(s)
- Victoria Ferrero
- Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, 3000-456, Coimbra, Portugal
- Institute for Subtropical and Mediterranean Horticulture, Spanish National Research Council (IHSM-UMA-CSIC), Finca Experimental La Mayora, Algarrobo-Costa, 29750, Málaga, Spain
| | - Lander Baeten
- Department of Environment, Forest & Nature Lab, Ghent University, BE-9090, Melle-Gontrode, Belgium
| | - Lidia Blanco-Sánchez
- Institute for Subtropical and Mediterranean Horticulture, Spanish National Research Council (IHSM-UMA-CSIC), Finca Experimental La Mayora, Algarrobo-Costa, 29750, Málaga, Spain
| | - Rosario Planelló
- Grupo de Biología y Toxicología Ambiental, Facultad de Ciencias, Universidad Nacional de Educación a Distancia, UNED, Paseo de la Senda del Rey 9, 28040, Madrid, Spain
| | - Juan Antonio Díaz-Pendón
- Institute for Subtropical and Mediterranean Horticulture, Spanish National Research Council (IHSM-UMA-CSIC), Finca Experimental La Mayora, Algarrobo-Costa, 29750, Málaga, Spain
| | - Susana Rodríguez-Echeverría
- Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, 3000-456, Coimbra, Portugal
| | - Annelies Haegeman
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Caritasstraat 39, B-9090, Melle, Belgium
| | - Eduardo de la Peña
- Institute for Subtropical and Mediterranean Horticulture, Spanish National Research Council (IHSM-UMA-CSIC), Finca Experimental La Mayora, Algarrobo-Costa, 29750, Málaga, Spain
- Department of Biology, Faculty of Sciences, Ghent University, K.L. Ledeganckstraat 35, B-9000, Gent, Belgium
| |
Collapse
|
9
|
Slugina MA, Shchennikova AV, Kochieva EZ. The expression pattern of the Pho1a genes encoding plastidic starch phosphorylase correlates with the degradation of starch during fruit ripening in green-fruited and red-fruited tomato species. FUNCTIONAL PLANT BIOLOGY : FPB 2019; 46:1146-1157. [PMID: 31615619 DOI: 10.1071/fp18317] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 07/17/2019] [Indexed: 06/10/2023]
Abstract
Genes encoding plastidic starch phosphorylase Pho1a were identified in 10 tomato species (Solanum section Lycopersicon). Pho1a genes showed higher variability in green-fruited than in red-fruited tomato species, but had an extremely low polymorphism level compared with other carbohydrate metabolism genes and an unusually low ratio of intron to exon single nucleotide polymorphisms (SNPs). In red-fruited species, Pho1a was expressed in all analysed tissues, including fruit at different developmental stages, with the highest level in mature green fruit, which is strong sink organ importing sucrose and accumulating starch. In green-fruited species Solanum peruvianum and Solanum arcanum, the Pho1a expression level was similar in mature green and ripe fruit, whereas in Solanum chmielewskii, it was higher in ripe fruit, and in Solanum habrochaites, the dynamics of fruit-specific Pho1a expression was similar to that in red-fruited tomatoes. During fruit development, in red-fruited Solanum lycopersicum, sucrose level was low, the monosaccharide content increased; in green-fruited S. peruvianum, the sucrose concentration increased and those of monosaccharides decreased. In both species, the starch content and Pho1a expression were downregulated. The evolutionary topology based on Pho1a sequences was consistent with the current division of tomatoes into red-fruited and green-fruited species, except for S. habrochaites.
Collapse
Affiliation(s)
- Maria A Slugina
- Institute of Bioengineering, Research Centre of Biotechnology of the Russian Academy of Sciences, Leninsky prospect. 33, bld. 2, Moscow 119071, Russia; and Corresponding author.
| | - Anna V Shchennikova
- Institute of Bioengineering, Research Centre of Biotechnology of the Russian Academy of Sciences, Leninsky prospect. 33, bld. 2, Moscow 119071, Russia
| | - Elena Z Kochieva
- Institute of Bioengineering, Research Centre of Biotechnology of the Russian Academy of Sciences, Leninsky prospect. 33, bld. 2, Moscow 119071, Russia; and Lomonosov Moscow State University, GSP-1, Leninskie Gory, Moscow 119991, Russia
| |
Collapse
|
10
|
Dupin J, Smith SD. Integrating historical biogeography and environmental niche evolution to understand the geographic distribution of Datureae. AMERICAN JOURNAL OF BOTANY 2019; 106:667-678. [PMID: 31059141 DOI: 10.1002/ajb2.1281] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 03/11/2019] [Indexed: 06/09/2023]
Abstract
PREMISE The distributions of plant clades are shaped by abiotic and biotic factors as well as historical aspects such as center of origin. Dispersals between distant areas may lead to niche evolution when lineages are established in new environments. Alternatively, dispersing lineages may exhibit niche conservatism, moving between areas with similar environmental conditions. Here we test these contrasting hypotheses in the Datureae clade (Solanaceae). METHODS We used maximum likelihood methods to estimate the ancestral range of Datureae along with the history of biogeographic events. We then characterized the niche of each taxon using climatic and soil variables and tested for shifts in environmental niche optima. Finally, we examined how these shifts relate to the niche breadth of taxa and clades within Datureae and the degree of overlap between them. RESULTS Datureae originated in the Andes and subsequently expanded its range to North America and non-Andean regions of South America. The ancestral niche, and that of most Datura and Trompettia species, is dry, while Brugmansia species likely shifted toward a more mesic environment. Nonetheless, most Datureae present moderate to high overlap in niche breadth today. CONCLUSIONS The expansion of Datureae into North America was associated with niche conservatism, with dispersal into similarly dry areas as occupied by the ancestral lineage. Subsequent niche evolution, including the apparent shift to a mesic niche in Brugmansia, diversified the range of habitats occupied by species in the tribe Datureae but also led to significant niche overlap among the three genera.
Collapse
Affiliation(s)
- Julia Dupin
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, 1800 Colorado Avenue, Boulder, Colorado, 80309, USA
| | - Stacey D Smith
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, 1800 Colorado Avenue, Boulder, Colorado, 80309, USA
| |
Collapse
|
11
|
Deanna R, Orejuela A, Barboza GE. An updated phylogeny of Deprea (Solanaceae) with a new species from Colombia: interspecific relationships, conservation assessment, and a key for Colombian species. SYST BIODIVERS 2018. [DOI: 10.1080/14772000.2018.1483976] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Rocío Deanna
- Instituto Multidisciplinario de Biología Vegetal (IMBIV), CONICET and Universidad Nacional de Córdoba, CC 495, CP 5000, Córdoba, Argentina
- Departamento de Ciencias Farmacéuticas, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba. Haya de la Torre y Medina Allende, Córdoba, Argentina
| | - Andrés Orejuela
- Tropical Diversity Section, Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh EH3 5LR, UK
- University of Edinburgh, King's Buildings, Edinburgh, UK
| | - Gloria Estela Barboza
- Instituto Multidisciplinario de Biología Vegetal (IMBIV), CONICET and Universidad Nacional de Córdoba, CC 495, CP 5000, Córdoba, Argentina
- Departamento de Ciencias Farmacéuticas, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba. Haya de la Torre y Medina Allende, Córdoba, Argentina
| |
Collapse
|
12
|
Böndel KB, Nosenko T, Stephan W. Signatures of natural selection in abiotic stress-responsive genes of Solanum chilense. ROYAL SOCIETY OPEN SCIENCE 2018; 5:171198. [PMID: 29410831 PMCID: PMC5792908 DOI: 10.1098/rsos.171198] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 12/04/2017] [Indexed: 06/01/2023]
Abstract
Environmental conditions are strong selective forces, which may influence adaptation and speciation. The wild tomato species Solanum chilense, native to South America, is exposed to a range of abiotic stress factors. To identify signatures of natural selection and local adaptation, we analysed 16 genes involved in the abiotic stress response and compared the results to a set of reference genes in 23 populations across the entire species range. The abiotic stress-responsive genes are characterized by elevated nonsynonymous nucleotide diversity and divergence. We detected signatures of positive selection in several abiotic stress-responsive genes on both the population and species levels. Local adaptation to abiotic stresses is particularly apparent at the boundary of the species distribution in populations from coastal low-altitude and mountainous high-altitude regions.
Collapse
|
13
|
Phylogenetic relationships of Deprea: New insights into the evolutionary history of physaloid groups. Mol Phylogenet Evol 2017; 119:71-80. [PMID: 29108936 DOI: 10.1016/j.ympev.2017.11.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 10/31/2017] [Accepted: 11/01/2017] [Indexed: 01/29/2023]
Abstract
Deprea is the genus with the second highest species richness in tribe Physalideae (Solanaceae) and comprises 50 species that are mainly distributed in the Andes of South America. The taxonomy of Deprea has been unstable after controversial hypotheses about its position and circumscription. Additionally, biogeographical inferences are only based on observations of the restricted area of distribution of some species and no ancestral area estimation have been performed. Here, we present a phylogenetic analysis and an ancestral area reconstruction of Deprea in order to establish its circumscription, resolve its position within Physalideae, and reconstruct its biogeographical history. Phylogenetic analyses were conducted using Maximum Likelihood and Bayesian approaches. Forty-three Deprea species and 26 related taxa were sampled for three DNA markers (psbA-trnH, ITS, and waxy). A Bayesian binary MCMC model was applied in order to infer ancestral areas. Deprea is resolved as a strongly supported monophyletic group according to its current circumscription and is placed within subtribe Withaninae of Physalideae. The phylogenetic relationships enabled us to solve taxonomic problems including the rejection and acceptance of previous synonyms. The most probable ancestral area for Deprea is the Northern Andes of South America and the Amotape-Huancabamba zone. Our phylogeny provides increased resolution and support for the current position and circumscription of Deprea. Better resolution of interspecific relationships was also obtained, although some affinities remain unclear. The phylogenetic and ancestral area reconstructions provide a framework for addressing taxonomic problems and investigating new evolutionary questions.
Collapse
|
14
|
Slugina MA, Shchennikova AV, Kochieva EZ. TAI vacuolar invertase orthologs: the interspecific variability in tomato plants (Solanum section Lycopersicon). Mol Genet Genomics 2017. [PMID: 28634826 DOI: 10.1007/s00438-017-1336-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Understanding the genetic mechanisms underlying carbohydrate metabolism can promote the development of biotechnological advances in fruit plants. The flesh tomato fruit represents an ideal system for examining the role of sucrose cleavage enzymes in fruit development, and wild tomato species differing in storage sugars serve as an excellent research material for this purpose. Plant vacuolar invertase is a key enzyme of sucrose metabolism in the sink organs. In the present study, we identified complete gene sequences encoding the TAI vacuolar invertase in 11 wild and one cultivated tomato accessions of the Solanum section Lycopersicon. The average level of interspecific polymorphism in TAI genes was 8.58%; however, in the green-fruited tomatoes, the TAI genes contained 100 times more SNPs than those in the red-fruited accessions. The TAI proteins demonstrated 8% variability, whereas the red-fruited species had none. A TAI-based phylogenetic tree revealed two main clusters containing self-compatible and self-incompatible species, which concurs with the previous crossability-based division and demonstrates that the TAI genes reflect the evolutionary relationships between the red- and green-fruited tomatoes. Furthermore, we detected differential expression patterns of the TAI genes in the fruits of wild and cultivated tomatoes, which corresponded to sugar composition. The polymorphism analysis of the TAI acid invertases of Solanum section Lycopersicon species will contribute to the understanding of the genetic potential of TAI genes to impact tomato breeding through genetic engineering of the carbohydrate composition in the fruit.
Collapse
Affiliation(s)
- M A Slugina
- Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, Moscow, 119071, Russia. .,Lomonosov Moscow State University, GSP-1, Leninskie Gory, Moscow, 119991, Russia.
| | - A V Shchennikova
- Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, Moscow, 119071, Russia
| | - E Z Kochieva
- Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, Moscow, 119071, Russia.,Lomonosov Moscow State University, GSP-1, Leninskie Gory, Moscow, 119991, Russia
| |
Collapse
|
15
|
Pailles Y, Ho S, Pires IS, Tester M, Negrão S, Schmöckel SM. Genetic Diversity and Population Structure of Two Tomato Species from the Galapagos Islands. FRONTIERS IN PLANT SCIENCE 2017; 8:138. [PMID: 28261227 PMCID: PMC5309213 DOI: 10.3389/fpls.2017.00138] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 01/23/2017] [Indexed: 05/19/2023]
Abstract
Endemic flora of the Galapagos Islands has adapted to thrive in harsh environmental conditions. The wild tomato species from the Galapagos Islands, Solanum cheesmaniae and S. galapagense, are tolerant to various stresses, and can be crossed with cultivated tomato. However, information about genetic diversity and relationships within and between populations is necessary to use these resources efficiently in plant breeding. In this study, we analyzed 3,974 polymorphic SNP markers, obtained through the genotyping-by-sequencing technique, DArTseq, to elucidate the genetic diversity and population structure of 67 accessions of Galapagos tomatoes (compared to two S. lycopersicum varieties and one S. pimpinellifolium accession). Two clustering methods, Principal Component Analysis and STRUCTURE, showed clear distinction between the two species and a subdivision in the S. cheesmaniae group corresponding to geographical origin and age of the islands. High genetic variation among the accessions within each species was suggested by the AMOVA. High diversity in the S. cheesmaniae group and its correlation with the islands of origin were also suggested. This indicates a possible influence of the movement of the islands, from west to east, on the gene flow. Additionally, the absence of S. galapagense populations in the eastern islands points to the species divergence occurring after the eastern islands became isolated. Based on these results, it can be concluded that the population structure of the Galapagos tomatoes collection partially explains the evolutionary history of both species, knowledge that facilitates exploitation of their genetic potential for the identification of novel alleles contributing to stress tolerance.
Collapse
Affiliation(s)
- Yveline Pailles
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and TechnologyThuwal, Saudi Arabia
| | - Shwen Ho
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and TechnologyThuwal, Saudi Arabia
| | - Inês S. Pires
- Genomics of Plants Stress Unit, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa and Instituto de Biologia Experimental e TecnológicaOeiras, Portugal
- Department of Biology and Center for Genomics and Systems Biology, New York UniversityNew York, NY, USA
| | - Mark Tester
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and TechnologyThuwal, Saudi Arabia
- *Correspondence: Mark Tester,
| | - Sónia Negrão
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and TechnologyThuwal, Saudi Arabia
| | - Sandra M. Schmöckel
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and TechnologyThuwal, Saudi Arabia
| |
Collapse
|
16
|
Haliński ŁP, Stepnowski P. Cuticular hydrocarbons and sucrose esters as chemotaxonomic markers of wild and cultivated tomato species (Solanum section Lycopersicon). PHYTOCHEMISTRY 2016; 132:57-67. [PMID: 27717501 DOI: 10.1016/j.phytochem.2016.09.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 09/01/2016] [Accepted: 09/29/2016] [Indexed: 06/06/2023]
Abstract
The tomato (Solanum lycopersicum L.) is one of the most important vegetables worldwide. Due to the limited genetic variability, wild related species are considered as potential gene pool for breeding cultivated plants with enriched genetic basis. Taxonomic relations between tomato species at the level of single groups and taxa still remain, however, not fully resolved. Hence, in addition to already reported classification based on the morphology of the plants and molecular markers, we proposed chemotaxonomic approach to unveil some aspects of tomato taxonomy. Cuticular hydrocarbons and surface sucrose esters (SEs) were used as chemotaxonomic markers. Classification based on the cuticular hydrocarbon profile was in good agreement with other taxonomic studies as long as between-species differences were taken into account. Clear separation of the common tomato and closely related species from the majority of S. pennellii accessions was obtained. In the same time, however, S. pennellii revealed broad variation: based on the results, three highly distinct types of these plants were proposed, among them one type was very similar to cultivated tomato and its relatives. Addition of SEs profiles to the dataset did not impair the classification, but clarified the position of S. pennellii. The results suggest possible hybrid origin of some of S. pennellii and wild S. lycopersicum accessions, and the approach proposed has a potential to identify such hybrid plant lines.
Collapse
Affiliation(s)
- Łukasz P Haliński
- Department of Environmental Analysis, Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland.
| | - Piotr Stepnowski
- Department of Environmental Analysis, Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
| |
Collapse
|
17
|
Zhao P, Wang M, Zhao L. Dissecting stylar responses to self-pollination in wild tomato self-compatible and self-incompatible species using comparative proteomics. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2016; 106:177-186. [PMID: 27163628 DOI: 10.1016/j.plaphy.2016.05.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Revised: 04/30/2016] [Accepted: 05/01/2016] [Indexed: 06/05/2023]
Abstract
Self-incompatibility (SI), a phenomenon that is widespread among flowering plants (angiosperms), promotes outbreeding, resulting in increased genetic diversity and species survival. SI is also important in establishing intra- or interspecies reproductive barriers, such as those that are evident in the tomato clade, Solanum section Lycopersicon, where they limit the use of wild species inbreeding programs to improve cultivated tomato. However, the molecular mechanisms underlying SI are poorly understood in the tomato clade. In this study, an SI (Solanum chilense, LA0130) and a self-compatible (SC, Solanum pimpinellifolium, LA1585) tomato species were chosen to dissect the mechanism of SI formation using a comparative proteomics approach. A total of 635 and 627 protein spots were detected in two-dimensional electrophoresis (2-DE) maps of proteins from the SI and SC species, respectively. In the SC species, 22 differently expressed proteins (DEPs) were detected in SCP versus SCUP (self-pollination versus non-pollination in SC species). Of these, 3 and 18 showed an up-or down-regulated expression in the SCP protein sample, respectively, while only one DEP (MSRA, Solyc03g111720) was exclusively expressed in the SCP sample. In the SI species, 14 DEPs were found between SIP/SIUP, and 5 of these showed higher expression in SIP, whereas two DEPs (MLP-like protein 423-like, gene ID, 460386008 and (ATP synthase subunit alpha, gene ID, Solyc00g042130) were exclusively expressed in SIP or SIUP, respectively. Finally, two S-RNases (gene IDs, 313247946 and 157377662) were exclusively expressed in the SI species. Sequence homology analysis and a gene ontology tool were used to assign the DEPs to the 'metabolism', 'energy', 'cytoskeleton dynamics', 'protein degradation', 'signal transduction', 'defence/stress responses', 'self-incompatibility' and 'unknown' protein categories. We discuss the putative functions of the DEPs in different biological processes and how these might be associated with the regulation of SI formation in the tomato clade.
Collapse
Affiliation(s)
- Panfeng Zhao
- Joint Tomato Research Institute, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China; Plant Biotechnology Research Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Meng Wang
- Department of Environment Resource, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Lingxia Zhao
- Joint Tomato Research Institute, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China; Plant Biotechnology Research Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China.
| |
Collapse
|
18
|
Herraiz FJ, Blanca J, Ziarsolo P, Gramazio P, Plazas M, Anderson GJ, Prohens J, Vilanova S. The first de novo transcriptome of pepino (Solanum muricatum): assembly, comprehensive analysis and comparison with the closely related species S. caripense, potato and tomato. BMC Genomics 2016; 17:321. [PMID: 27142449 PMCID: PMC4855764 DOI: 10.1186/s12864-016-2656-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 04/25/2016] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Solanum sect. Basarthrum is phylogenetically very close to potatoes (Solanum sect. Petota) and tomatoes (Solanum sect. Lycopersicon), two groups with great economic importance, and for which Solanum sect. Basarthrum represents a tertiary gene pool for breeding. This section includes the important regional cultigen, the pepino (Solanum muricatum), and several wild species. Among the wild species, S. caripense is prominent due to its major involvement in the origin of pepino and its wide geographical distribution. Despite the value of the pepino as an emerging crop, and the potential for gene transfer from both the pepino and S. caripense to potatoes and tomatoes, there has been virtually no genomic study of these species. RESULTS Using Illumina HiSeq 2000, RNA-Seq was performed with a pool of three tissues (young leaf, flowers in pre-anthesis and mature fruits) from S. muricatum and S. caripense, generating almost 111,000,000 reads among the two species. A high quality de novo transcriptome was assembled from S. muricatum clean reads resulting in 75,832 unigenes with an average length of 704 bp. These unigenes were functionally annotated based on similarity of public databases. We used Blast2GO, to conduct an exhaustive study of the gene ontology, including GO terms, EC numbers and KEGG pathways. Pepino unigenes were compared to both potato and tomato genomes in order to determine their estimated relative position, and to infer gene prediction models. Candidate genes related to traits of interest in other Solanaceae were evaluated by presence or absence and compared with S. caripense transcripts. In addition, by studying five genes, the phylogeny of pepino and five other members of the family, Solanaceae, were studied. The comparison of S. caripense reads against S. muricatum assembled transcripts resulted in thousands of intra- and interspecific nucleotide-level variants. In addition, more than 1000 SSRs were identified in the pepino transcriptome. CONCLUSIONS This study represents the first genomic resource for the pepino. We suggest that the data will be useful not only for improvement of the pepino, but also for potato and tomato breeding and gene transfer. The high quality of the transcriptome presented here also facilitates comparative studies in the genus Solanum. The accurate transcript annotation will enable us to figure out the gene function of particular traits of interest. The high number of markers (SSR and nucleotide-level variants) obtained will be useful for breeding programs, as well as studies of synteny, diversity evolution, and phylogeny.
Collapse
Affiliation(s)
- Francisco J. Herraiz
- />Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, 46022 Valencia Spain
| | - José Blanca
- />Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, 46022 Valencia Spain
| | - Pello Ziarsolo
- />Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, 46022 Valencia Spain
| | - Pietro Gramazio
- />Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, 46022 Valencia Spain
| | - Mariola Plazas
- />Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, 46022 Valencia Spain
| | - Gregory J. Anderson
- />Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06268-3043 USA
| | - Jaime Prohens
- />Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, 46022 Valencia Spain
| | - Santiago Vilanova
- />Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, 46022 Valencia Spain
| |
Collapse
|
19
|
The Tomato (Solanum lycopersicum L., Solanaceae) and Its Botanical Relatives. COMPENDIUM OF PLANT GENOMES 2016. [DOI: 10.1007/978-3-662-53389-5_2] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
|
20
|
Effects of low temperature on mRNA and small RNA transcriptomes in Solanum lycopersicoides leaf revealed by RNA-Seq. Biochem Biophys Res Commun 2015; 464:768-73. [DOI: 10.1016/j.bbrc.2015.07.029] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2015] [Accepted: 07/06/2015] [Indexed: 11/17/2022]
|
21
|
Machida-Hirano R. Diversity of potato genetic resources. BREEDING SCIENCE 2015; 65:26-40. [PMID: 25931978 PMCID: PMC4374561 DOI: 10.1270/jsbbs.65.26] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Accepted: 02/03/2015] [Indexed: 05/05/2023]
Abstract
A considerable number of highly diverse species exist in genus Solanum. Because they can adapt to a broad range of habitats, potato wild relatives are promising sources of desirable agricultural traits. Potato taxonomy is quite complex because of introgression, interspecific hybridization, auto- and allopolyploidy, sexual compatibility among many species, a mixture of sexual and asexual reproduction, possible recent species divergence, phenotypic plasticity, and the consequent high morphological similarity among species. Recent researchers using molecular tools have contributed to the identification of genes controlling several types of resistance as well as to the revision of taxonomical relationships among potato species. Historically, primitive forms of cultivated potato and its wild relatives have been used in breeding programs and there is still an enormous and unimaginable potential for discovering desirable characteristics, particularly in wild species Different methods have been developed to incorporate useful alleles from these wild species into the improved cultivars. Potato germplasm comprising of useful alleles for different breeding objectives is preserved in various gene banks worldwide. These materials, with their invaluable information, are accessible for research and breeding purposes. Precise identification of species base on the new taxonomy is essential for effective use of the germplasm collection.
Collapse
Affiliation(s)
- Ryoko Machida-Hirano
- Gene Research Center, University of Tsukuba,
1-1-1, Tennodai, Tsukuba, Ibaraki 305-3572,
Japan
| |
Collapse
|
22
|
Wang L, Li J, Zhao J, He C. Evolutionary developmental genetics of fruit morphological variation within the Solanaceae. FRONTIERS IN PLANT SCIENCE 2015; 6:248. [PMID: 25918515 PMCID: PMC4394660 DOI: 10.3389/fpls.2015.00248] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 03/27/2015] [Indexed: 05/20/2023]
Abstract
Morphological variations of fruits such as shape and size, and color are a result of adaptive evolution. The evolution of morphological novelties is particularly intriguing. An understanding of these evolutionary processes calls for the elucidation of the developmental and genetic mechanisms that result in particular fruit morphological characteristics, which determine seed dispersal. The genetic and developmental basis for fruit morphological variation was established at a microevolutionary time scale. Here, we summarize the progress on the evolutionary developmental genetics of fruit size, shape and color in the Solanaceae. Studies suggest that the recruitment of a pre-existing gene and subsequent modification of its interaction and regulatory networks are frequently involved in the evolution of morphological diversity. The basic mechanisms underlying changes in plant morphology are alterations in gene expression and/or gene function. We also deliberate on the future direction in evolutionary developmental genetics of fruit morphological variation such as fruit type. These studies will provide insights into plant developmental processes and will help to improve the productivity and fruit quality of crops.
Collapse
Affiliation(s)
- Li Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany – Chinese Academy of Sciences, BeijingChina
| | - Jing Li
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany – Chinese Academy of Sciences, BeijingChina
- Graduate University of Chinese Academy of Sciences, BeijingChina
| | - Jing Zhao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany – Chinese Academy of Sciences, BeijingChina
- Graduate University of Chinese Academy of Sciences, BeijingChina
| | - Chaoying He
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany – Chinese Academy of Sciences, BeijingChina
- *Correspondence: Chaoying He, State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany – Chinese Academy of Sciences, Nanxincun 20, Xiangshan, 100093 Beijing, China
| |
Collapse
|
23
|
Morales Palacio MN, Espinosa López G, Morales Astudillo ÁR, Sánchez Masache BR, Jiménez Castillo ÁM, Milián-García Y. Caracterización morfológica y evaluación de resistencia a Fusarium oxysporum en especies silvestres del género Solanum sección Lycopersicon. REVISTA COLOMBIANA DE BIOTECNOLOGÍA 2014. [DOI: 10.15446/rev.colomb.biote.v16n1.38259] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
|
24
|
Labate JA, Robertson LD, Strickler SR, Mueller LA. Genetic structure of the four wild tomato species in the Solanum peruvianum s.l. species complex. Genome 2014; 57:169-80. [PMID: 24884691 DOI: 10.1139/gen-2014-0003] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The most diverse wild tomato species Solanum peruvianum sensu lato (s.l.) has been reclassified into four separate species: Solanum peruvianum sensu stricto (s.s.), Solanum corneliomuelleri, Solanum huaylasense, and Solanum arcanum. However, reproductive barriers among the species are incomplete and this can lead to discrepancies regarding genetic identity of germplasm. We used genotyping by sequencing (GBS) of S. peruvianum s.l., Solanum neorickii, and Solanum chmielewskii to develop tens of thousands of mapped single nucleotide polymorphisms (SNPs) to analyze genetic relationships within and among species. The data set was condensed to 14,043 SNPs with no missing data across 46 sampled plants. Origins of accessions were mapped using geographical information systems (GIS). Isolation by distance, pairwise genetic distances, and number of clusters were estimated using population genetics approaches. Isolation by distance was strongly supported, especially between interspecific pairs. Eriopersicon (S. peruvianum s.s., S. corneliomuelleri, S. huaylasense) and Arcanum (S. arcanum, S. neorickii, S. chmielewskii) species groups were genetically distinct, except for S. huaylasense which showed 50% membership proportions in each group. Solanum peruvianum and S. corneliomuelleri were not significantly differentiated from each other. Many thousands of SNP markers were identified that could potentially be used to distinguish pairs of species, including S. peruvianum versus S. corneliomuelleri, if they are verified on larger numbers of samples. Diagnostic markers will be valuable for delimiting morphologically similar and interfertile species in germplasm management. Approximately 12% of the SNPs rejected a genome-wide test of selective neutrality based on differentiation among species of S. peruvianum s.l. These are candidates for more comprehensive studies of microevolutionary processes within this species complex.
Collapse
Affiliation(s)
- Joanne A Labate
- a Plant Genetic Resources Unit, US Department of Agriculture, Agricultural Research Service, 630 W. North Street, Geneva, NY 14456, USA
| | | | | | | |
Collapse
|
25
|
Bergougnoux V. The history of tomato: From domestication to biopharming. Biotechnol Adv 2014; 32:170-89. [DOI: 10.1016/j.biotechadv.2013.11.003] [Citation(s) in RCA: 169] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Revised: 10/24/2013] [Accepted: 11/03/2013] [Indexed: 11/28/2022]
|
26
|
González RM, Ricardi MM, Iusem ND. Epigenetic marks in an adaptive water stress-responsive gene in tomato roots under normal and drought conditions. Epigenetics 2013; 8:864-72. [PMID: 23807313 PMCID: PMC3883789 DOI: 10.4161/epi.25524] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Tolerance to water deficits was evolutionarily relevant to the conquest of land by primitive plants. In this context, epigenetic events may have played important roles in the establishment of drought stress responses. We decided to inspect epigenetic marks in the plant organ that is crucial in the sensing of drought stress: the root. Using tomato as a crop model plant, we detected the methylated epialleles of Asr2, a protein-coding gene widespread in the plant kingdom and thought to alleviate restricted water availability. We found 3 contexts (CG, CNG, and CNN) of methylated cytosines in the regulatory region of Solanum lycopersicum Asr2 but only one context (CG) in the gene body. To test the hypothesis of a link between epigenetics marks and the adaptation of plants to drought, we explored the cytosine methylation status of Asr2 in the root resulting from water-deficit stress conditions. We found that a brief exposure to simulated drought conditions caused the removal of methyl marks in the regulatory region at 77 of the 142 CNN sites. In addition, the study of histone modifications around this model gene in the roots revealed that the distal regulatory region was rich in H3K27me3 but that its abundance did not change as a consequence of stress. Additionally, under normal conditions, both the regulatory and coding regions contained the typically repressive H3K9me2 mark, which was lost after 30 min of water deprivation. As analogously conjectured for the paralogous gene Asr1, rapidly acquired new Asr2 epialleles in somatic cells due to desiccation might be stable enough and heritable through the germ line across generations, thereby efficiently contributing to constitutive, adaptive gene expression during the evolution of desiccation-tolerant populations or species.
Collapse
Affiliation(s)
- Rodrigo M González
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIByNE); CONICET; Buenos Aires, Argentina
| | | | | |
Collapse
|
27
|
Zimmer EA, Wen J. Reprint of: using nuclear gene data for plant phylogenetics: progress and prospects. Mol Phylogenet Evol 2013; 66:539-50. [PMID: 23375140 DOI: 10.1016/j.ympev.2013.01.005] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2011] [Revised: 06/14/2012] [Accepted: 07/16/2012] [Indexed: 12/25/2022]
Abstract
The paper reviews the current state of low and single copy nuclear markers that have been applied successfully in plant phylogenetics to date, and discusses case studies highlighting the potential of massively parallel high throughput or next-generation sequencing (NGS) approaches for molecular phylogenetic and evolutionary investigations. The current state, prospects and challenges of specific single- or low-copy plant nuclear markers as well as phylogenomic case studies are presented and evaluated.
Collapse
Affiliation(s)
- Elizabeth A Zimmer
- Department of Botany, National Museum of Natural History, MRC 166, Smithsonian Institution, Washington, DC 20013-7012, USA.
| | | |
Collapse
|
28
|
Zimmer EA, Wen J. Using nuclear gene data for plant phylogenetics: Progress and prospects. Mol Phylogenet Evol 2012; 65:774-85. [DOI: 10.1016/j.ympev.2012.07.015] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2011] [Revised: 06/14/2012] [Accepted: 07/16/2012] [Indexed: 10/28/2022]
|
29
|
Blanca J, Cañizares J, Cordero L, Pascual L, Diez MJ, Nuez F. Variation revealed by SNP genotyping and morphology provides insight into the origin of the tomato. PLoS One 2012; 7:e48198. [PMID: 23118951 PMCID: PMC3485194 DOI: 10.1371/journal.pone.0048198] [Citation(s) in RCA: 124] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2012] [Accepted: 09/21/2012] [Indexed: 11/28/2022] Open
Abstract
Tomato, Solanum lycopersicum, is divided into two widely distributed varieties: the cultivated S. lycopersicum var. lycopersicum, and the weedy S. lycopersicum var. cerasiforme. Solanum pimpinellifolium is the most closely related wild species of tomato. The roles of S. pimpinellifolium and S. l. cerasiforme during the domestication of tomato are still under debate. Some authors consider S. l. cerasiforme to be the ancestor, whereas others think that S. l. cerasiforme is an admixture of S. pimpinellifolium and the cultivated S. l. lycopersicum. It is also not clear whether the domestication occurred in the Andean region or in Mesoamerica. We characterized 272 accessions (63 S. pimpinellifolium, 106 S. l. cerasiforme, 95 S. l. lycopersicum and 8 derived from hybridization processes) were morphologically and genetically using the SolCap platform (7,414 SNPs). The two species were distinguished in a PCA analysis and displayed a rich geographic structure. Solanum lycopersicum var. cerasiforme and S. l. lycopersicum were also differentiated in the PCA and Structure analyses, which supports maintaining them as different varieties. Solanum pimpinellifolium and the Andean S. l. cerasiforme were more diverse than the non-Andean S. lycopersicum. Solanum lycopersicum var. cerasiforme was morphologically and molecularly intermediate between S. pimpinellifolium and tomato. Solanum lycopersicum var. cerasiforme, with the exception of several Ecuadorian and Mexican accessions, is composed of the products of admixture processes according to the Structure analysis. The non-admixtured S. l. cerasiforme might be similar to the ancestral cultivars from which the cultivated tomato originated, and presents remarkable morphological diversity, including fruits of up to 6 cm in diameter. The data obtained would fit a model in which a pre-domestication took place in the Andean region, with the domestication being completed in Mesoamerica. Subsequently, the Spaniards took plants from Mesoamerica to Spain and from there they were exported to the rest of the world.
Collapse
Affiliation(s)
- Jose Blanca
- Institute for the Conservation and Improvement of Agricultural Biodiversity, Polytechnic University of Valencia, Camino de Vera, Valencia, Spain
| | - Joaquín Cañizares
- Institute for the Conservation and Improvement of Agricultural Biodiversity, Polytechnic University of Valencia, Camino de Vera, Valencia, Spain
- * E-mail:
| | - Laura Cordero
- Institute for the Conservation and Improvement of Agricultural Biodiversity, Polytechnic University of Valencia, Camino de Vera, Valencia, Spain
| | - Laura Pascual
- Institute for the Conservation and Improvement of Agricultural Biodiversity, Polytechnic University of Valencia, Camino de Vera, Valencia, Spain
| | - María José Diez
- Institute for the Conservation and Improvement of Agricultural Biodiversity, Polytechnic University of Valencia, Camino de Vera, Valencia, Spain
| | - Fernando Nuez
- Institute for the Conservation and Improvement of Agricultural Biodiversity, Polytechnic University of Valencia, Camino de Vera, Valencia, Spain
| |
Collapse
|
30
|
Using multiple analytical methods to improve phylogenetic hypotheses in Minaria (Apocynaceae). Mol Phylogenet Evol 2012; 65:915-25. [PMID: 22982434 DOI: 10.1016/j.ympev.2012.08.019] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2011] [Revised: 07/25/2012] [Accepted: 08/17/2012] [Indexed: 11/23/2022]
Abstract
Metastelmatinae is a neotropical subtribe of Asclepiadoideae (Apocynaceae), comprising 13 genera and around 260 species whose phylogenetic relationships are often unresolved or incongruent between plastid and nuclear datasets. The genus Minaria is one of the first lineages to emerge in the Metastelmatinae and is highly supported based on plastid markers. It comprises 21 species, most of which are endemic to small areas with open vegetation in the Espinhaço Range, Brazil. In the work presented here, we use plastid (rps16, trnH-psbA, trnS-trnG, and trnD-trnT) and nuclear (ITS and ETS) datasets to investigate the relationships within Minaria. We show that the three methods mostly used in phylogenetic studies, namely, maximum parsimony, maximum likelihood, and Bayesian Inference, have different performances and that a pluralistic analytical approach combining results from them can increase tree resolution and clade confidence, providing valuable phylogenetic information.
Collapse
|
31
|
Szinay D, Wijnker E, van den Berg R, Visser RGF, de Jong H, Bai Y. Chromosome evolution in Solanum traced by cross-species BAC-FISH. THE NEW PHYTOLOGIST 2012; 195:688-698. [PMID: 22686400 DOI: 10.1111/j.1469-8137.2012.04195.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Chromosomal rearrangements are relatively rare evolutionary events and can be used as markers to study karyotype evolution. This research aims to use such rearrangements to study chromosome evolution in Solanum. Chromosomal rearrangements between Solanum crops and several related wild species were investigated using tomato and potato bacterial artificial chromosomes (BACs) in a multicolour fluorescent in situ hybridization (FISH). The BACs selected are evenly distributed over seven chromosomal arms containing inversions described in previous studies. The presence/absence of these inversions among the studied Solanum species were determined and the order of the BAC-FISH signals was used to construct phylogenetic trees.Compared with earlier studies, data from this study provide support for the current grouping of species into different sections within Solanum; however, there are a few notable exceptions, such as the tree positions of S. etuberosum (closer to the tomato group than to the potato group) and S. lycopersicoides (sister to S. pennellii). These apparent contradictions might be explained by interspecific hybridization events and/or incomplete lineage sorting. This cross-species BAC painting technique provides unique information on genome organization, evolution and phylogenetic relationships in a wide variety of species. Such information is very helpful for introgressive breeding.
Collapse
Affiliation(s)
- Dóra Szinay
- Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands
| | - Erik Wijnker
- Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands
| | - Ronald van den Berg
- Biosystematics Group, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands
| | - Richard G F Visser
- Wageningen UR Plant Breeding, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands
| | - Hans de Jong
- Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands
| | - Yuling Bai
- Wageningen UR Plant Breeding, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands
| |
Collapse
|
32
|
Genetic structure of the endangered Leucomeris decora (Asteraceae) in China inferred from chloroplast and nuclear DNA markers. CONSERV GENET 2011. [DOI: 10.1007/s10592-011-0281-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
|
33
|
Fischer I, Camus-Kulandaivelu L, Allal F, Stephan W. Adaptation to drought in two wild tomato species: the evolution of the Asr gene family. THE NEW PHYTOLOGIST 2011; 190:1032-1044. [PMID: 21323928 DOI: 10.1111/j.1469-8137.2011.03648.x] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Wild tomato species are a valuable system in which to study local adaptation to drought: they grow in diverse environments ranging from mesic to extremely arid conditions. Here, we investigate the evolution of members of the Asr (ABA/water stress/ripening induced) gene family, which have been reported to be involved in the water stress response. We analysed molecular variation in the Asr gene family in populations of two closely related species, Solanum chilense and Solanum peruvianum. We concluded that Asr1 has evolved under strong purifying selection. In contrast to previous reports, we did not detect evidence for positive selection at Asr2. However, Asr4 shows patterns consistent with local adaptation in an S. chilense population that lives in an extremely dry environment. We also discovered a new member of the gene family, Asr5. Our results show that the Asr genes constitute a dynamic gene family and provide an excellent example of tandemly arrayed genes that are of importance in adaptation. Taking the potential distribution of the species into account, it appears that S. peruvianum can cope with a great variety of environmental conditions without undergoing local adaptation, whereas S. chilense undergoes local adaptation more frequently.
Collapse
Affiliation(s)
- Iris Fischer
- Section of Evolutionary Biology, Department of Biology II, University of Munich (LMU), Grosshaderner Strasse 2, 82152 Planegg-Martinsried, Germany
| | - Létizia Camus-Kulandaivelu
- CIRAD, Biological System Department - Research Unit 39 'Genetic Diversity and Breeding of Forest Tree Species', Campus international de Baillarguet TA A-39/C, 34398 Montpellier Cedex 5, France
| | - François Allal
- CIRAD, Biological System Department - Research Unit 39 'Genetic Diversity and Breeding of Forest Tree Species', Campus international de Baillarguet TA A-39/C, 34398 Montpellier Cedex 5, France
| | - Wolfgang Stephan
- Section of Evolutionary Biology, Department of Biology II, University of Munich (LMU), Grosshaderner Strasse 2, 82152 Planegg-Martinsried, Germany
| |
Collapse
|
34
|
González RM, Ricardi MM, Iusem ND. Atypical epigenetic mark in an atypical location: cytosine methylation at asymmetric (CNN) sites within the body of a non-repetitive tomato gene. BMC PLANT BIOLOGY 2011; 11:94. [PMID: 21599976 PMCID: PMC3117769 DOI: 10.1186/1471-2229-11-94] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2011] [Accepted: 05/20/2011] [Indexed: 05/20/2023]
Abstract
BACKGROUND Eukaryotic DNA methylation is one of the most studied epigenetic processes, as it results in a direct and heritable covalent modification triggered by external stimuli. In contrast to mammals, plant DNA methylation, which is stimulated by external cues exemplified by various abiotic types of stress, is often found not only at CG sites but also at CNG (N denoting A, C or T) and CNN (asymmetric) sites. A genome-wide analysis of DNA methylation in Arabidopsis has shown that CNN methylation is preferentially concentrated in transposon genes and non-coding repetitive elements. We are particularly interested in investigating the epigenetics of plant species with larger and more complex genomes than Arabidopsis, particularly with regards to the associated alterations elicited by abiotic stress. RESULTS We describe the existence of CNN-methylated epialleles that span Asr1, a non-transposon, protein-coding gene from tomato plants that lacks an orthologous counterpart in Arabidopsis. In addition, to test the hypothesis of a link between epigenetics modifications and the adaptation of crop plants to abiotic stress, we exhaustively explored the cytosine methylation status in leaf Asr1 DNA, a model gene in our system, resulting from water-deficit stress conditions imposed on tomato plants. We found that drought conditions brought about removal of methyl marks at approximately 75 of the 110 asymmetric (CNN) sites analysed, concomitantly with a decrease of the repressive H3K27me3 epigenetic mark and a large induction of expression at the RNA level. When pinpointing those sites, we observed that demethylation occurred mostly in the intronic region. CONCLUSIONS These results demonstrate a novel genomic distribution of CNN methylation, namely in the transcribed region of a protein-coding, non-repetitive gene, and the changes in those epigenetic marks that are caused by water stress. These findings may represent a general mechanism for the acquisition of new epialleles in somatic cells, which are pivotal for regulating gene expression in plants.
Collapse
Affiliation(s)
- Rodrigo M González
- Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires e IFIByNE-CONICET, Buenos Aires, Argentina
| | - Martiniano M Ricardi
- Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires e IFIByNE-CONICET, Buenos Aires, Argentina
| | - Norberto D Iusem
- Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires e IFIByNE-CONICET, Buenos Aires, Argentina
| |
Collapse
|
35
|
McDowell ET, Kapteyn J, Schmidt A, Li C, Kang JH, Descour A, Shi F, Larson M, Schilmiller A, An L, Jones AD, Pichersky E, Soderlund CA, Gang DR. Comparative functional genomic analysis of Solanum glandular trichome types. PLANT PHYSIOLOGY 2011; 155:524-39. [PMID: 21098679 PMCID: PMC3075747 DOI: 10.1104/pp.110.167114] [Citation(s) in RCA: 119] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2010] [Accepted: 11/18/2010] [Indexed: 05/19/2023]
Abstract
Glandular trichomes play important roles in protecting plants from biotic attack by producing defensive compounds. We investigated the metabolic profiles and transcriptomes to characterize the differences between different glandular trichome types in several domesticated and wild Solanum species: Solanum lycopersicum (glandular trichome types 1, 6, and 7), Solanum habrochaites (types 1, 4, and 6), Solanum pennellii (types 4 and 6), Solanum arcanum (type 6), and Solanum pimpinellifolium (type 6). Substantial chemical differences in and between Solanum species and glandular trichome types are likely determined by the regulation of metabolism at several levels. Comparison of S. habrochaites type 1 and 4 glandular trichomes revealed few differences in chemical content or transcript abundance, leading to the conclusion that these two glandular trichome types are the same and differ perhaps only in stalk length. The observation that all of the other species examined here contain either type 1 or 4 trichomes (not both) supports the conclusion that these two trichome types are the same. Most differences in metabolites between type 1 and 4 glands on the one hand and type 6 glands on the other hand are quantitative but not qualitative. Several glandular trichome types express genes associated with photosynthesis and carbon fixation, indicating that some carbon destined for specialized metabolism is likely fixed within the trichome secretory cells. Finally, Solanum type 7 glandular trichomes do not appear to be involved in the biosynthesis and storage of specialized metabolites and thus likely serve another unknown function, perhaps as the site of the synthesis of protease inhibitors.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | - David R. Gang
- Bio5 Institute (E.T.M., J.K., A.D., C.A.S., D.R.G.) and Department of Agricultural and Biosystems Engineering (L.A.), University of Arizona, Tucson, Arizona 85721; Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109–1048 (A.S., E.P.); Department of Chemistry (C.L., F.S., A.D.J.), Department of Energy-Plant Research Laboratory (J.-H.K.), and Department of Biochemistry and Molecular Biology (M.L., A.S., A.D.J.), Michigan State University, East Lansing, Michigan 48824–1319; Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164–6340 (D.R.G.)
| |
Collapse
|
36
|
Miller JS, Kostyun JL. Functional gametophytic self-incompatibility in a peripheral population of Solanum peruvianum (Solanaceae). Heredity (Edinb) 2010; 107:30-9. [PMID: 21119705 DOI: 10.1038/hdy.2010.151] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
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.
Collapse
Affiliation(s)
- J S Miller
- Department of Biology, Amherst College, MA, USA.
| | | |
Collapse
|
37
|
Rodríguez F, Ghislain M, Clausen AM, Jansky SH, Spooner DM. Hybrid origins of cultivated potatoes. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2010; 121:1187-1198. [PMID: 20734187 DOI: 10.1007/s00122-010-1422-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2010] [Accepted: 07/30/2010] [Indexed: 05/26/2023]
Abstract
Solanum section Petota is taxonomically difficult, partly because of interspecific hybridization at both the diploid and polyploid levels. The taxonomy of cultivated potatoes is particularly controversial. Using DNA sequence data of the waxy gene, we here infer relationships among the four species of cultivated potatoes accepted in the latest taxonomic treatment (S. ajanhuiri, S. curtilobum, S. juzepczukii and S. tuberosum, the latter divided into the Andigenum and Chilotanum Cultivar Groups). The data support prior ideas of hybrid origins of S. ajanhuiri from the S. tuberosum Andigenum Group (2x = S. stenotomum) × S. megistacrolobum; S. juzepczukii from the S. tuberosum Andigenum Group (2x = S. stenotomum) × S. acaule; and S. curtilobum from the S. tuberosum Andigenum Group (4x = S. tuberosum subsp. andigenum) × S. juzepczukii. For the tetraploid cultivar-groups of S. tuberosum, hybrid origins are suggested entirely within much more closely related species, except for two of three examined accessions of the S. tuberosum Chilotanum Group that appear to have hybridized with the wild species S. maglia. Hybrid origins of the crop/weed species S. sucrense are more difficult to support and S. vernei is not supported as a wild species progenitor of the S. tuberosum Andigenum Group.
Collapse
Affiliation(s)
- Flor Rodríguez
- USDA, Agricultural Research Service, Department of Horticulture, University of Wisconsin, 1575 Linden Drive, Madison, WI 53706-1590, USA
| | | | | | | | | |
Collapse
|
38
|
Robertson K, Goldberg EE, Igić B. Comparative evidence for the correlated evolution of polyploidy and self-compatibility in Solanaceae. Evolution 2010; 65:139-55. [PMID: 20722729 DOI: 10.1111/j.1558-5646.2010.01099.x] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Breakdown of self-incompatibility occurs repeatedly in flowering plants with important evolutionary consequences. In plant families in which self-incompatibility is mediated by S-RNases, previous evidence suggests that polyploidy may often directly cause self-compatibility through the formation of diploid pollen grains. We use three approaches to examine relationships between self-incompatibility and ploidy. First, we test whether evolution of self-compatibility and polyploidy is correlated in the nightshade family (Solanaceae), and find the expected close association between polyploidy and self-compatibility. Second, we compare the rate of breakdown of self-incompatibility in the absence of polyploidy against the rate of breakdown that arises as a byproduct of polyploidization, and we find the former to be greater. Third, we apply a novel extension to these methods to show that the relative magnitudes of the macroevolutionary pathways leading to self-compatible polyploids are time dependent. Over small time intervals, the direct pathway from self-incompatible diploids is dominant, whereas the pathway through self-compatible diploids prevails over longer time scales. This pathway analysis is broadly applicable to models of character evolution in which sequential combinations of rates are compared. Finally, given the strong evidence for both irreversibility of the loss of self-incompatibility in the family and the significant association between self-compatibility and polyploidy, we argue that ancient polyploidy is highly unlikely to have occurred within the Solanaceae, contrary to previous claims based on genomic analyses.
Collapse
Affiliation(s)
- Kelly Robertson
- Department of Biological Sciences, 840 West Taylor St., M/C 067, University of Illinois at Chicago, Chicago, Illinois 60607, USA.
| | | | | |
Collapse
|
39
|
Moyle LC, Muir CD. Reciprocal insights into adaptation from agricultural and evolutionary studies in tomato. Evol Appl 2010; 3:409-21. [PMID: 25567935 PMCID: PMC3352507 DOI: 10.1111/j.1752-4571.2010.00143.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2010] [Accepted: 05/13/2010] [Indexed: 02/05/2023] Open
Abstract
Although traditionally separated by different aims and methodologies, research on agricultural and evolutionary problems shares a common goal of understanding the mechanisms underlying functionally important traits. As such, research in both fields offers potential complementary and reciprocal insights. Here, we discuss adaptive stress responses (specifically to water stress) as an example of potentially fruitful research reciprocity, where agricultural research has clearly produced advances that could benefit evolutionary studies, while evolutionary studies offer approaches and insights underexplored in crop studies. We focus on research on Solanum species that include the domesticated tomato and its wild relatives. Integrated approaches to understanding ecological adaptation are particularly attractive in tomato and its wild relatives: many presumptively adaptive phenotypic differences characterize wild species, and the physiological and mechanistic basis of many relevant traits and environmental responses has already been examined in the context of cultivated tomato and some wild species. We highlight four specific instances where these reciprocal insights can be combined to better address questions that are fundamental both to agriculture and evolution.
Collapse
Affiliation(s)
- Leonie C Moyle
- Department of Biology, Indiana University Bloomington, IN, USA
| | | |
Collapse
|
40
|
Nakazato T, Warren DL, Moyle LC. Ecological and geographic modes of species divergence in wild tomatoes. AMERICAN JOURNAL OF BOTANY 2010; 97:680-93. [PMID: 21622430 DOI: 10.3732/ajb.0900216] [Citation(s) in RCA: 112] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Understanding the role of geography and ecology in species divergence is central to the study of evolutionary diversification. We used climatic, geographic, and biological data from nine wild Andean tomato species to describe each species' ecological niche and to evaluate the likely ecological and geographical modes of speciation in this clade. Using data from >1000 wild accessions and publicly available data derived from geographic information systems for various environmental variables, we found most species pairs were significantly differentiated for one or more environmental variables. By comparing species' predicted niches generated by species distribution modeling (SDM), we found significant niche differentiation among three of four sister-species pairs, suggesting ecological divergence is consistently associated with recent divergence. In comparison, based on age-range correlation (ARC) analysis, there was no evidence for a predominant geographical (allopatric vs. sympatric) context for speciation in this group. Overall, our results suggest an important role for environmentally mediated differentiation, rather than simply geographical isolation, in species divergence.
Collapse
Affiliation(s)
- Takuya Nakazato
- Department of Biology, The University of Memphis, Memphis, Tennessee 38152 USA
| | | | | |
Collapse
|
41
|
Tank DC, Olmstead RG. The evolutionary origin of a second radiation of annual Castilleja (Orobanchaceae) species in South America: The role of long distance dispersal and allopolyploidy. AMERICAN JOURNAL OF BOTANY 2009; 96:1907-1921. [PMID: 21622312 DOI: 10.3732/ajb.0800416] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Considerable attention has been directed toward understanding the wide gaps in range that are common among many groups of closely related organisms. By placing their biology and geography in a phylogenetic context, we may gain a broader knowledge of the series of historical events that have led to present species distributions. In addition to the North American annuals, a second radiation of annual Castilleja species is in Andean Peru and central Chile. Phylogenetic analyses of chloroplast and nuclear DNA regions revealed a complex history for the origin and diversification of annual Castilleja species in South America. In addition to at least three independent long-distance dispersal events from North America, allopolyploidy has played a significant role in this disjunct radiation. Only C. attenuata occurs in both California and South America, and these results support its recent arrival to central Chile. Two Peruvian species are inferred to be allopolyploids; hybridization between annual lineages derived from independent long-distance dispersal events from North America gave rise to C. profunda, and hybridization between South American annual and perennial species gave rise to C. cerroana. The relative importance these events are discussed with reference to the observed morphological, ecological, and distributional patterns.
Collapse
Affiliation(s)
- David C Tank
- Department of Forest Resources & Stillinger Herbarium, College of Natural Resources, University of Idaho, P.O. Box 441133, Moscow, Idaho 83844-1133 USA
| | | |
Collapse
|
42
|
Rodriguez F, Wu F, Ané C, Tanksley S, Spooner DM. Do potatoes and tomatoes have a single evolutionary history, and what proportion of the genome supports this history? BMC Evol Biol 2009; 9:191. [PMID: 19664206 PMCID: PMC3087518 DOI: 10.1186/1471-2148-9-191] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2009] [Accepted: 08/07/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Phylogenies reconstructed with only one or a few independently inherited loci may be unresolved or incongruent due to taxon and gene sampling, horizontal gene transfer, or differential selection and lineage sorting at individual loci. In an effort to remedy this situation, we examined the utility of conserved orthologous set (COSII) nuclear loci to elucidate the phylogenetic relationships among 29 diploid Solanum species in the sister clades that include tomato and potato, and in Datura inoxia as a far outgroup. We screened 40 COSII markers with intron content over 60% that are mapped in different chromosomes; selected a subset of 19 by the presence of single band amplification of size mostly between 600 and 1200 bp; sequenced these 19 COSII markers, and performed phylogenetic analyses with individual and concatenated datasets. The present study attempts to provide a fully resolved phylogeny among the main clades in potato and tomato that can help to identify the appropriate markers for future studies using additional species. RESULTS Among potatoes, when total evidence is invoked, one single predominant history is highlighted with complete resolution within and among the three main clades. It also supports the hypothesis of the North and Central American B-genome origin of the tuber-bearing members of Solanum sect. Petota and shows a clear division between A genomes in clades 3 and 4, and B genomes in clade 1+2. On the other hand, when a prior agreement approach is invoked other potato evolutionary histories are revealed but with less support. These alternative histories could be explained by past hybridization, or fast rates of speciation. In the case of tomato, the analyses with all sequence data completely resolved 19 of 21 clades, for the first time revealed the monophyly of five clades, and gave further support for the recent segregation of new species from the former Solanum peruvianum. Concordance analyses revealed and summarized the extensive discordance among COSII markers. Some potential reasons for discordance could be methodological, to include systematic errors due to using a wrong model of sequence evolution, coupled with long branches, or mixtures of branch lengths within COSII, or undetected paralogy or alignment bias. Other reasons could be biological processes such as hybridization or lineage sorting. CONCLUSION This study confirms and quantifies the utility of using DNA sequences from different parts of the genome in phylogenetic studies to avoid possible bias in the sampling. It shows that 11-18 loci are enough to get the dominant history in this group of Solanum, but more loci would be needed to discern the distribution of gene genealogies in more depth, and thus detect which mechanism most likely shaped the discordance.
Collapse
Affiliation(s)
- Flor Rodriguez
- USDA, Agricultural Research Service; Department of Horticulture, 1575 Linden Drive, University of Wisconsin-Madison, Madison, Wisconsin 53706-1590, USA
| | - Feinan Wu
- Department of Plant Breeding and Genetics, Department of Plant Biology, 248 Emerson Hall, Cornell University, Ithaca, New York 14853, USA
| | - Cécile Ané
- Department of Statistics, Department of Botany, 1300 University Ave., University of Wisconsin-Madison, Madison, Wisconsin 53706-1590, USA
| | - Steve Tanksley
- Department of Plant Breeding and Genetics, Department of Plant Biology, 248 Emerson Hall, Cornell University, Ithaca, New York 14853, USA
| | - David M Spooner
- USDA, Agricultural Research Service; Department of Horticulture, 1575 Linden Drive, University of Wisconsin-Madison, Madison, Wisconsin 53706-1590, USA
| |
Collapse
|
43
|
Muir CD, Moyle LC. Antagonistic epistasis for ecophysiological trait differences between Solanum species. THE NEW PHYTOLOGIST 2009; 183:789-802. [PMID: 19659589 DOI: 10.1111/j.1469-8137.2009.02949.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Epistasis, the nonadditive interaction between loci, is thought to play a role in many fundamental evolutionary processes, including adaptive differentiation and speciation. Focusing on species differences in ecophysiological traits, we examined the strength and direction of pairwise epistatic interactions between target chromosomal regions from one species, when co-introgressed into the genetic background of a foreign species. A full diallel cross was performed using 15 near-isogenic lines (NILs) constructed between two tomato species (Solanum habrochaites and Solanum lycopersicum) to compare the phenotypic effects of each chromosomal region singly and in combination with each other region. We detected main effect quantitative trait loci (QTLs) for two of our three focal traits. Epistatic effects accounted for c. 25% of detected effects on trait means, depending on the trait. Strikingly, all but two interactions were antagonistic, with the combined effect of chromosomal regions acting in the opposite direction from that of one or both individual chromosomal regions. Our study is one of the few to systematically examine pairwise epistatic effects in a nonmicrobial system. Our results suggest that epistatic interactions can contribute substantially to the genetic basis of traits involved in adaptive species differentiation, especially highly complex, multivariate traits.
Collapse
Affiliation(s)
- Christopher D Muir
- Department of Biology, Indiana University, 1001 East Third Street, Bloomington, IN 47401, USA
| | - Leonie C Moyle
- Department of Biology, Indiana University, 1001 East Third Street, Bloomington, IN 47401, USA
| |
Collapse
|
44
|
Easlon HM, Richards JH. Drought response in self-compatible species of tomato (Solanaceae). AMERICAN JOURNAL OF BOTANY 2009; 96:605-11. [PMID: 21628216 DOI: 10.3732/ajb.0800189] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Wild tomatoes occur in habitats from the extremely dry Atacama Desert to moist areas in the Andean highlands, which may have resulted in adaptation of populations or species to differences in soil moisture availability. However, when two accessions representing extremes in habitat water availability from each of the five self-compatible species were grown in a common garden, we observed no differences in leaf physiological responses to soil drought within or between species. All five species had drought avoidance characteristics with the same threshold soil moisture availability for decline of assimilation, stomatal conductance, and leaf water potential (Ψ(l)) in response to slowly decreasing soil moisture. After rewatering, all species rapidly recovered to near predrought Ψ(l), but bulk leaf solute potential after recovery did not indicate any osmotic adjustment. The lack of variation in shoot physiological traits during soil drought is unexpected as water deficit is commonly thought to have imposed selective pressure in the evolution of plant physiology. However, species did differ in assimilation under nonstressed conditions, which may contribute to differential soil water conservation and growth or survival during drought.
Collapse
Affiliation(s)
- Hsien Ming Easlon
- Department of Land, Air, & Water Resources, University of California, One Shields Avenue, Davis, California 95616 USA
| | | |
Collapse
|
45
|
Albrecht E, Chetelat RT. Comparative genetic linkage map of Solanum sect. Juglandifolia: evidence of chromosomal rearrangements and overall synteny with the tomatoes and related nightshades. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2009; 118:831-847. [PMID: 19099284 DOI: 10.1007/s00122-008-0943-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2008] [Accepted: 11/21/2008] [Indexed: 05/27/2023]
Abstract
The two nightshades Solanum ochranthum and S. juglandifolium show genetic and morphological similarities to the tomatoes (Solanum sect. Lycopersicon), but are isolated from them by strong reproductive barriers. Their genetic relationships to tomato and other Solanum species were investigated using comparative genetic linkage maps obtained from an interspecific F(2) S. ochranthum x S. juglandifolium population. Sixty-six plants were screened using a total of 132 markers--CAPs, RFLPs and SSRs--previously mapped in tomato. Twelve linkage groups were identified, generally corresponding to the expected (syntenic) tomato chromosomes, with two exceptions. Chromosome 1 was composed of two linkage groups and chromosomes 8 and 12 were connected in one large linkage group, indicating a likely reciprocal translocation differentiating the two parental genomes. The total map length comprised 790 cM, representing a 42% reduction in recombination rate relative to the tomato reference map. Transmission ratio distortion affected one-third of the genome, with 13 putative TRD loci identified on 9 out of 12 chromosomes. Most regions were collinear with the tomato reference maps, including the long arm of chromosome 10, which is inverted relative to two other tomato-like nightshades, S. lycopersicoides and S. sitiens. The results support the status of S. ochranthum and S. juglandifolium as the nearest outgroup to the tomatoes and imply they are more closely related to cultivated tomato than predicted from crossing relationships, thus encouraging further attempts at hybridization and introgression between them.
Collapse
Affiliation(s)
- Elena Albrecht
- Department of Plant Sciences, University of California, One Shields Avenue, Davis, CA 95616, USA.
| | | |
Collapse
|
46
|
Levin RA, Blanton J, Miller JS. Phylogenetic utility of nuclear nitrate reductase: A multi-locus comparison of nuclear and chloroplast sequence data for inference of relationships among American Lycieae (Solanaceae). Mol Phylogenet Evol 2009; 50:608-17. [DOI: 10.1016/j.ympev.2008.12.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2008] [Revised: 11/13/2008] [Accepted: 12/04/2008] [Indexed: 11/27/2022]
|
47
|
Orsi CH, Tanksley SD. Natural variation in an ABC transporter gene associated with seed size evolution in tomato species. PLoS Genet 2009; 5:e1000347. [PMID: 19165318 PMCID: PMC2617763 DOI: 10.1371/journal.pgen.1000347] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2008] [Accepted: 12/17/2008] [Indexed: 01/23/2023] Open
Abstract
Seed size is a key determinant of evolutionary fitness in plants and is a trait that often undergoes tremendous changes during crop domestication. Seed size is most often quantitatively inherited, and it has been shown that Sw4.1 is one of the most significant quantitative trait loci (QTLs) underlying the evolution of seed size in the genus Solanum—especially in species related to the cultivated tomato. Using a combination of genetic, developmental, molecular, and transgenic techniques, we have pinpointed the cause of the Sw4.1 QTL to a gene encoding an ABC transporter gene. This gene exerts its control on seed size, not through the maternal plant, but rather via gene expression in the developing zygote. Phenotypic effects of allelic variation at Sw4.1 are manifested early in seed development at stages corresponding to the rapid deposition of starch and lipids into the endospermic cells. Through synteny, we have identified the Arabidopsis Sw4.1 ortholog. Mutagenesis has revealed that this ortholog is associated with seed length variation and fatty acid deposition in seeds, raising the possibility that the ABC transporter may modulate seed size variation in other species. Transcription studies show that the ABC transporter gene is expressed not only in seeds, but also in other tissues (leaves and roots) and, thus, may perform functions in parts of the plants other than developing seeds. Cloning and characterization of the Sw4.1 QTL gives new insight into how plants change seed during evolution and may open future opportunities for modulating seed size in crop plants for human purposes. Given fixed resources, plants have a choice whether to produce many small seeds or a few large seeds. In terms of reproductive fitness, there are costs and benefits to both strategies. As a result, plant species vary more than 100,000-fold in both seed size and seed output. The current study focuses on understanding the molecular and developmental basis of a single genetic locus (or quantitative trait locus) that determines seed size between the cultivated tomato and its wild relatives. We show that the cause of size variation can be traced to a gene encoding an ABC transporter protein. The gene apparently exercises its control on seed size through expression in the developing seeds and not the mother plant that nurtures those seeds. A comparison with the model plant Arabidopsis thaliana suggests that the ABC transporter identified in tomato may also control seed size in other plants, opening research opportunities for understanding plant adaptation and for potentially modulating seed size in crop plants for human purposes.
Collapse
Affiliation(s)
- Cintia Hotta Orsi
- Department of Plant Breeding and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Steven D. Tanksley
- Department of Plant Breeding and Genetics, Cornell University, Ithaca, New York, United States of America
- Department of Plant Biology, Cornell University, Ithaca, New York, United States of America
- * E-mail:
| |
Collapse
|
48
|
Moyle LC. Ecological and evolutionary genomics in the wild tomatoes (Solanum sect. Lycopersicon). Evolution 2008; 62:2995-3013. [PMID: 18752600 DOI: 10.1111/j.1558-5646.2008.00487.x] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The plant group Solanum section Lycopersicon (the clade containing the domesticated tomato and its wild relatives) is ideal for integrating genomic tools and approaches into ecological and evolutionary research. Wild species within Lycopersicon span broad morphological, physiological, life history, mating system, and biochemical variation, and are separated by substantial, but incomplete postmating reproductive barriers, making this an ideal system for genetic analyses of these traits. This ecological and evolutionary diversity is matched by many logistical advantages, including extensive historical occurrence records for all species in the group, publicly available germplasm for hundreds of known wild accessions, demonstrated experimental tractability, and extensive genetic, genomic, and functional tools and information from the tomato research community. Here I introduce the numerous advantages of this system for Ecological and Evolutionary Functional Genomics (EEFG), and outline several ecological and evolutionary phenotypes and questions that can be fruitfully tackled in this system. These include biotic and abiotic adaptation, reproductive trait evolution, and the genetic basis of speciation. With the modest enhancement of some research strengths, this system is poised to join the best of our currently available model EEFG systems.
Collapse
Affiliation(s)
- Leonie C Moyle
- Department of Biology, Indiana University, Bloomington, Indiana 474051, USA.
| |
Collapse
|
49
|
Tu T, Dillon MO, Sun H, Wen J. Phylogeny of Nolana (Solanaceae) of the Atacama and Peruvian deserts inferred from sequences of four plastid markers and the nuclear LEAFY second intron. Mol Phylogenet Evol 2008; 49:561-73. [PMID: 18722540 DOI: 10.1016/j.ympev.2008.07.018] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2008] [Revised: 07/01/2008] [Accepted: 07/26/2008] [Indexed: 10/21/2022]
Abstract
The phylogeny of Nolana (Solanaceae), a genus primarily distributed in the coastal Atacama and Peruvian deserts with a few species in the Andes and one species endemic to the Galápagos Islands, was reconstructed using sequences of four plastid regions (ndhF, psbA-trnH, rps16-trnK and trnC-psbM) and the nuclear LEAFY second intron. The monophyly of Nolana was strongly supported by all molecular data. The LEAFY data suggested that the Chilean species, including Nolana sessiliflora, the N. acuminata group and at least some members of the Alona group, are basally diverged, supporting the Chilean origin of the genus. Three well-supported clades in the LEAFY tree were corroborated by the SINE (short interspersed elements) or SINE-like insertions. Taxa from Peru are grouped roughly into two clades. Nolana galapagensis from the Galápagos Island is most likely to have derived from a Peruvian ancestor. The monophyly of the morphologically well-diagnosed Nolana acuminata group (N. acuminata, N. baccata, N. paradoxa, N. parviflora, N. pterocarpa, N. rupicola and N. elegans) was supported by both plastid and LEAFY data. Incongruence between the plastid and the LEAFY data was detected concerning primarily the positions of N. sessiliflora, N. galapagensis, taxa of the Alona group and the two Peruvian clades. Such incongruence may be due to reticulate evolution or in some cases lineage sorting of plastid DNA. Incongruence between our previous GBSSI trees and the plastid-LEAFY trees was also detected concerning two well-supported major clades in the GBSSI tree. Duplication of the GBSSI gene may have contributed to this incongruence.
Collapse
Affiliation(s)
- Tieyao Tu
- Key Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650204, PR China
| | | | | | | |
Collapse
|
50
|
Nucleotide polymorphism in the drought responsive gene Asr2 in wild populations of tomato. Genetica 2008; 136:13-25. [PMID: 18636230 DOI: 10.1007/s10709-008-9295-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2007] [Accepted: 07/05/2008] [Indexed: 10/21/2022]
Abstract
The Asr gene family (named after abscicic acid [ABA], stress, ripening), exclusively present in plant genomes, is involved in transcriptional regulation. Its members are up-regulated in roots and leaves of water- or salt-stressed plants. In previous work, evidence of adaptive evolution (as inferred from synonymous and nonsynonymous divergence rates) has been reported for Asr2 in Solanum chilense and S. arcanum, two species dwelling in habitats with different precipitation regimes. In this paper we investigate patterns of intraspecific nucleotide variation in Asr2 and the unlinked locus CT114 in S. chilense and S. arcanum. The extent of nucleotide diversity in Asr2 differed between species in more than one order of magnitude. In both species we detected evidence of non-neutral evolution, which may be ascribed to different selective regimes, potentially associated to unique climatic features, or, alternatively, to demographic events. The results are discussed in the light of demographic and selective hypotheses.
Collapse
|