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Lofgren L, Nguyen NH, Kennedy P, Pérez-Pazos E, Fletcher J, Liao HL, Wang H, Zhang K, Ruytinx J, Smith AH, Ke YH, Cotter HVT, Engwall E, Hameed KM, Vilgalys R, Branco S. Suillus: an emerging model for the study of ectomycorrhizal ecology and evolution. THE NEW PHYTOLOGIST 2024; 242:1448-1475. [PMID: 38581203 PMCID: PMC11045321 DOI: 10.1111/nph.19700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 03/07/2024] [Indexed: 04/08/2024]
Abstract
Research on mycorrhizal symbiosis has been slowed by a lack of established study systems. To address this challenge, we have been developing Suillus, a widespread ecologically and economically relevant fungal genus primarily associated with the plant family Pinaceae, into a model system for studying ectomycorrhizal (ECM) associations. Over the last decade, we have compiled extensive genomic resources, culture libraries, a phenotype database, and protocols for manipulating Suillus fungi with and without their tree partners. Our efforts have already resulted in a large number of publicly available genomes, transcriptomes, and respective annotations, as well as advances in our understanding of mycorrhizal partner specificity and host communication, fungal and plant nutrition, environmental adaptation, soil nutrient cycling, interspecific competition, and biological invasions. Here, we highlight the most significant recent findings enabled by Suillus, present a suite of protocols for working with the genus, and discuss how Suillus is emerging as an important model to elucidate the ecology and evolution of ECM interactions.
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Affiliation(s)
- Lotus Lofgren
- Department of Biology, Duke University, 130 Science Dr., Durham, NC 27708, USA
| | - Nhu H. Nguyen
- Department of Tropical Plant and Soil Sciences, University of Hawai‘i at Māno, 3190 Maile Way, Honolulu, HI 96822, USA
| | - Peter Kennedy
- Department of Plant and Microbial Biology, University of Minnesota, 1475 Gortner Ave, Saint Paul, MN 55108, USA
- Department of Ecology, Evolution and Behavior, University of Minnesota, 1475 Gortner Ave, Saint Paul, MN 55108, USA
| | - Eduardo Pérez-Pazos
- Department of Ecology, Evolution and Behavior, University of Minnesota, 1475 Gortner Ave, Saint Paul, MN 55108, USA
| | - Jessica Fletcher
- Department of Integrative Biology, University of Colorado Denver 1151 Arapahoe St, SI 2071, Denver, CO 80204, USA
| | - Hui-Ling Liao
- North Florida Research and Education Center, University of Florida, 155 Research Rd Quincy, FL 3235, USA
- Department of Soil, Water and Ecosystem Sciences, University of Florida, 1692 McCarty Dr, Room 2181, Building A, Gainesville, FL 32611, USA
| | - Haihua Wang
- North Florida Research and Education Center, University of Florida, 155 Research Rd Quincy, FL 3235, USA
- Department of Soil, Water and Ecosystem Sciences, University of Florida, 1692 McCarty Dr, Room 2181, Building A, Gainesville, FL 32611, USA
| | - Kaile Zhang
- North Florida Research and Education Center, University of Florida, 155 Research Rd Quincy, FL 3235, USA
| | - Joske Ruytinx
- Research Group of Microbiology and Plant Genetics, Department of Bioengineering Sciences, Vrije Universiteit Brussel, 1050 Brussels, Belgium, USA
| | - Alexander H. Smith
- Department of Integrative Biology, University of Colorado Denver 1151 Arapahoe St, SI 2071, Denver, CO 80204, USA
| | - Yi-Hong Ke
- Department of Ecology and Evolutionary Biology, University of Michigan, 1105 N University Ave, Ann Arbor, MI 48109, USA
| | - H. Van T. Cotter
- University of North Carolina at Chapel Hill Herbarium, 120 South Road, Chapel Hill, NC 27599, USA
| | - Eiona Engwall
- Department of Biology, University of North Carolina at Chapel Hill, 120 South Road, Chapel Hill, NC 27599, USA
| | - Khalid M. Hameed
- Department of Biology, Duke University, 130 Science Dr., Durham, NC 27708, USA
| | - Rytas Vilgalys
- Department of Biology, Duke University, 130 Science Dr., Durham, NC 27708, USA
| | - Sara Branco
- Department of Integrative Biology, University of Colorado Denver 1151 Arapahoe St, SI 2071, Denver, CO 80204, USA
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2
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Delmore K, Justen H, Kay KM, Kitano J, Moyle LC, Stelkens R, Streisfeld MA, Yamasaki YY, Ross J. Genomic Approaches Are Improving Taxonomic Representation in Genetic Studies of Speciation. Cold Spring Harb Perspect Biol 2024; 16:a041438. [PMID: 37848243 PMCID: PMC10835617 DOI: 10.1101/cshperspect.a041438] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2023]
Abstract
Until recently, our understanding of the genetics of speciation was limited to a narrow group of model species with a specific set of characteristics that made genetic analysis feasible. Rapidly advancing genomic technologies are eliminating many of the distinctions between laboratory and natural systems. In light of these genomic developments, we review the history of speciation genetics, advances that have been gleaned from model and non-model organisms, the current state of the field, and prospects for broadening the diversity of taxa included in future studies. Responses to a survey of speciation scientists across the world reveal the ongoing division between the types of questions that are addressed in model and non-model organisms. To bridge this gap, we suggest integrating genetic studies from model systems that can be reared in the laboratory or greenhouse with genomic studies in related non-models where extensive ecological knowledge exists.
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Affiliation(s)
- Kira Delmore
- Department of Biology, Texas A&M University, College Station, Texas 77843, USA
| | - Hannah Justen
- Department of Biology, Texas A&M University, College Station, Texas 77843, USA
| | - Kathleen M Kay
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, California 95060, USA
| | - Jun Kitano
- Ecological Genetics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Leonie C Moyle
- Department of Biology, Indiana University, Bloomington, Indiana 47405, USA
| | - Rike Stelkens
- Division of Population Genetics, Department of Zoology, Stockholm University, 106 91 Stockholm, Sweden
| | - Matthew A Streisfeld
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon 97403, USA
| | - Yo Y Yamasaki
- Ecological Genetics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Joseph Ross
- Department of Biology, California State University, Fresno, California 93740, USA
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3
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Escudero M, Marques A, Lucek K, Hipp AL. Genomic hotspots of chromosome rearrangements explain conserved synteny despite high rates of chromosome evolution in a holocentric lineage. Mol Ecol 2023. [PMID: 37486041 DOI: 10.1111/mec.17086] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 06/26/2023] [Accepted: 07/11/2023] [Indexed: 07/25/2023]
Abstract
Holocentric organisms, unlike typical monocentric organisms, have kinetochore activity distributed along almost the whole length of the chromosome. Because of this, chromosome rearrangements through fission and fusion are more likely to become fixed in holocentric species, which may account for the extraordinary rates of chromosome evolution that many holocentric lineages exhibit. Long blocks of genome synteny have been reported in animals with holocentric chromosomes despite high rates of chromosome rearrangements. Nothing is known from plants, however, despite the fact that holocentricity appears to have played a key role in the diversification of one of the largest angiosperm genera, Carex (Cyperaceae). In the current study, we compared genomes of Carex species and a distantly related Cyperaceae species to characterize conserved and rearranged genome regions. Our analyses span divergence times ranging between 2 and 50 million years. We also compared a C. scoparia chromosome-level genome assembly with a linkage map of the same species to study rearrangements at a population level and suppression of recombination patterns. We found longer genome synteny blocks than expected under a null model of random rearrangement breakpoints, even between very distantly related species. We also found repetitive DNA to be non-randomly associated with holocentromeres and rearranged regions of the genome. The evidence of conserved synteny in sedges despite high rates of chromosome fission and fusion suggests that conserved genomic hotspots of chromosome evolution related to repetitive DNA shape the evolution of recombination, gene order and crossability in sedges. This finding may help explain why sedges are able to maintain species cohesion even in the face of high interspecific chromosome rearrangements.
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Affiliation(s)
- Marcial Escudero
- Department of Plant Biology and Ecology, University of Seville, Sevilla, Spain
| | - André Marques
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Kay Lucek
- Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
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4
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Cutter AD. Speciation and development. Evol Dev 2023; 25:289-327. [PMID: 37545126 DOI: 10.1111/ede.12454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 06/13/2023] [Accepted: 07/20/2023] [Indexed: 08/08/2023]
Abstract
Understanding general principles about the origin of species remains one of the foundational challenges in evolutionary biology. The genomic divergence between groups of individuals can spawn hybrid inviability and hybrid sterility, which presents a tantalizing developmental problem. Divergent developmental programs may yield either conserved or divergent phenotypes relative to ancestral traits, both of which can be responsible for reproductive isolation during the speciation process. The genetic mechanisms of developmental evolution involve cis- and trans-acting gene regulatory change, protein-protein interactions, genetic network structures, dosage, and epigenetic regulation, all of which also have roots in population genetic and molecular evolutionary processes. Toward the goal of demystifying Darwin's "mystery of mysteries," this review integrates microevolutionary concepts of genetic change with principles of organismal development, establishing explicit links between population genetic process and developmental mechanisms in the production of macroevolutionary pattern. This integration aims to establish a more unified view of speciation that binds process and mechanism.
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Affiliation(s)
- Asher D Cutter
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
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5
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Morales‐Briones DF, Lin N, Huang EY, Grossenbacher DL, Sobel JM, Gilmore CD, Tank DC, Yang Y. Phylogenomic analyses in Phrymaceae reveal extensive gene tree discordance in relationships among major clades. AMERICAN JOURNAL OF BOTANY 2022; 109:1035-1046. [PMID: 35462411 PMCID: PMC9328367 DOI: 10.1002/ajb2.1860] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 04/13/2022] [Accepted: 04/14/2022] [Indexed: 06/14/2023]
Abstract
PREMISE Phylogenomic datasets using genomes and transcriptomes provide rich opportunities beyond resolving bifurcating phylogenetic relationships. Monkeyflower (Phrymaceae) is a model system for evolutionary ecology. However, it lacks a well-supported phylogeny as a basis for a stable taxonomy and for macroevolutionary comparisons. METHODS We sampled 24 genomes and transcriptomes in Phrymaceae and closely related families, including eight newly sequenced transcriptomes. We reconstructed the phylogeny using IQ-TREE and ASTRAL, evaluated gene tree discordance using PhyParts, Quartet Sampling, and a cloudogram, and carried out reticulation analyses using PhyloNet and HyDe. We searched for whole genome duplication (WGD) events using chromosome numbers, synonymous distances, and gene duplication events as evidence. RESULTS Most gene trees support the monophyly of Phrymaceae and each of its tribes. Most gene trees also support tribe Mimuleae being sister to Phrymeae + Diplaceae + Leucocarpeae, with extensive gene tree discordance among the latter three. Despite the discordance, the monophyly of Mimulus s.l. is rejected, and no individual reticulation event among the Phrymaceae tribes is well-supported. Reticulation likely occurred among Erythranthe bicolor and closely related species. No ancient WGD was detected in Phrymaceae. Instead, small-scale duplications are among potential drivers of macroevolutionary diversification of Phrymaceae. CONCLUSIONS We show that analysis of reticulate evolution is sensitive to taxon sampling and methods used. We also demonstrate that phylogenomic datasets using genomes and transcriptomes present rich opportunities to investigate gene family evolution and genome duplication events involved in lineage diversification and adaptation.
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Affiliation(s)
- Diego F. Morales‐Briones
- Department of Plant and Microbial BiologyUniversity of Minnesota‐Twin Cities1445 Gortner AvenueSt. PaulMinnesota55108‐1095USA
- Systematics, Biodiversity and Evolution of Plants, Department of Biology I, Ludwig‐Maximilians‐Universität MünchenMenzinger Strasse 6780638MunichGermany
| | - Nan Lin
- Department of Plant and Microbial BiologyUniversity of Minnesota‐Twin Cities1445 Gortner AvenueSt. PaulMinnesota55108‐1095USA
- College of Life ScienceHenan Agricultural University63 Nongye RoadZhengzhouHenan450002China
| | - Eileen Y. Huang
- Department of Plant and Microbial BiologyUniversity of Minnesota‐Twin Cities1445 Gortner AvenueSt. PaulMinnesota55108‐1095USA
| | - Dena L. Grossenbacher
- Biological Sciences DepartmentCalifornia Polytechnic State University, 1 Grand Avenue, San Luis ObispoCalifornia93407USA
| | - James M. Sobel
- Department of Biological SciencesBinghamton University (State University of New York), 4400 Vestal Parkway E, BinghamtonNew York13902USA
| | - Caroline D. Gilmore
- Department of Biological SciencesBinghamton University (State University of New York), 4400 Vestal Parkway E, BinghamtonNew York13902USA
| | - David C. Tank
- Department of Botany & Rocky Mountain HerbariumUniversity of Wyoming, 1000 E. University Avenue, LaramieWyoming82071USA
| | - Ya Yang
- Department of Plant and Microbial BiologyUniversity of Minnesota‐Twin Cities1445 Gortner AvenueSt. PaulMinnesota55108‐1095USA
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6
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Zheng X, Om K, Stanton KA, Thomas D, Cheng PA, Eggert A, Simmons E, Yuan YW, Conradi Smith GD, Puzey JR, Cooley AM. The regulatory network for petal anthocyanin pigmentation is shaped by the MYB5a/NEGAN transcription factor in Mimulus. Genetics 2021; 217:6078588. [PMID: 33724417 PMCID: PMC8045675 DOI: 10.1093/genetics/iyaa036] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 11/18/2020] [Indexed: 11/17/2022] Open
Abstract
Much of the visual diversity of angiosperms is due to the frequent evolution of novel pigmentation patterns in flowers. The gene network responsible for anthocyanin pigmentation, in particular, has become a model for investigating how genetic changes give rise to phenotypic innovation. In the monkeyflower genus Mimulus, an evolutionarily recent gain of petal lobe anthocyanin pigmentation in M. luteus var. variegatus was previously mapped to genomic region pla2. Here, we use sequence and expression analysis, followed by transgenic manipulation of gene expression, to identify MYB5a—orthologous to the NEGAN transcriptional activator from M. lewisii—as the gene responsible for the transition to anthocyanin-pigmented petals in M. l. variegatus. In other monkeyflower taxa, MYB5a/NEGAN is part of a reaction-diffusion network that produces semi-repeating spotting patterns, such as the array of spots in the nectar guides of both M. lewisii and M. guttatus. Its co-option for the evolution of an apparently non-patterned trait—the solid petal lobe pigmentation of M. l. variegatus—illustrates how reaction-diffusion can contribute to evolutionary novelty in non-obvious ways. Transcriptome sequencing of a MYB5a RNAi line of M. l. variegatus reveals that this genetically simple change, which we hypothesize to be a regulatory mutation in cis to MYB5a, has cascading effects on gene expression, not only on the enzyme-encoding genes traditionally thought of as the targets of MYB5a but also on all of its known partners in the anthocyanin regulatory network.
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Affiliation(s)
- Xingyu Zheng
- Departments of Biology and Applied Science, William & Mary, Williamsburg, VA 23185, USA.,School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Kuenzang Om
- Department of Biology, Whitman College, Walla Walla, WA 99362, USA
| | - Kimmy A Stanton
- Department of Biology, Whitman College, Walla Walla, WA 99362, USA
| | - Daniel Thomas
- Department of Biology, Whitman College, Walla Walla, WA 99362, USA
| | - Philip A Cheng
- Department of Biology, Whitman College, Walla Walla, WA 99362, USA
| | - Allison Eggert
- Department of Biology, Whitman College, Walla Walla, WA 99362, USA
| | - Emily Simmons
- Departments of Biology and Applied Science, William & Mary, Williamsburg, VA 23185, USA
| | - Yao-Wu Yuan
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA
| | | | - Joshua R Puzey
- Departments of Biology and Applied Science, William & Mary, Williamsburg, VA 23185, USA
| | - Arielle M Cooley
- Department of Biology, Whitman College, Walla Walla, WA 99362, USA
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7
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Joffard N, Silva WTAF, Twyford AD. Digest: The role of postzygotic isolation in Mimulus speciation. Evolution 2021; 75:756-758. [PMID: 33469918 DOI: 10.1111/evo.14175] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 12/30/2020] [Indexed: 01/08/2023]
Abstract
Recently diverged species often show incomplete reproductive isolation and subsequently experience hybridization and introgression. The plant genus Mimulus includes many such examples of closely related taxa that prove useful for studying incipient speciation. However, Sandstedt et al. show that in contrast to other Mimulus species, species of the M. tilingii complex are characterized by strong postzygotic isolation mediated by multiple barriers. This finding highlights the diverse speciation histories of related plant groups.
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Affiliation(s)
- Nina Joffard
- Evolutionary Biology Centre, Department of Ecology and Genetics, Plant Ecology and Evolution Program, Uppsala University, Uppsala, Sweden
| | - Willian T A F Silva
- Centre for Environmental and Climate Research, Lund University, Lund, Sweden
| | - Alex D Twyford
- Ashworth Laboratories, Institute of Evolutionary Biology, The University of Edinburgh, Edinburgh, UK.,Royal Botanic Garden Edinburgh, Edinburgh, UK
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8
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Multi-level patterns of genetic structure and isolation by distance in the widespread plant Mimulus guttatus. Heredity (Edinb) 2020; 125:227-239. [PMID: 32641721 DOI: 10.1038/s41437-020-0335-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 06/02/2020] [Accepted: 06/15/2020] [Indexed: 12/30/2022] Open
Abstract
An understanding of genetic structure is essential for answering many questions in population genetics. However, complex population dynamics and scale-dependent processes can make it difficult to detect if there are distinct genetic clusters present in natural populations. Inferring discrete population structure is particularly challenging in the presence of continuous genetic variation such as isolation by distance. Here, we use the plant species Mimulus guttatus as a case study for understanding genetic structure at three spatial scales. We use reduced-representation sequencing and marker-based genotyping to understand dispersal dynamics and to characterise genetic structure. Our results provide insight into the spatial scale of genetic structure in a widespread plant species, and demonstrate how dispersal affects spatial genetic variation at the local, regional, and range-wide scale. At a fine-spatial scale, we show dispersal is rampant with little evidence of spatial genetic structure within populations. At a regional-scale, we show continuous differentiation driven by isolation by distance over hundreds of kilometres, with broad geographic genetic clusters that span major barriers to dispersal. Across Western North America, we observe geographic genetic structure and the genetic signature of multiple postglacial recolonisation events, with historical gene flow linking isolated populations. Our genetic analyses show M. guttatus is highly dispersive and maintains large metapopulations with high intrapopulation variation. This high diversity and dispersal confounds the inference of genetic structure, with multi-level sampling and spatially-explicit analyses required to understand population history.
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9
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Tusiime FM, Gizaw A, Gussarova G, Nemomissa S, Popp M, Masao CA, Wondimu T, Abdi AA, Mirré V, Muwanika V, Eilu G, Brochmann C. Afro-alpine flagships revisited: Parallel adaptation, intermountain admixture and shallow genetic structuring in the giant senecios (Dendrosenecio). PLoS One 2020; 15:e0228979. [PMID: 32187202 PMCID: PMC7080232 DOI: 10.1371/journal.pone.0228979] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 01/27/2020] [Indexed: 11/19/2022] Open
Abstract
Distantly related lineages of the enigmatic giant rosette plants of tropical alpine environments provide classical examples of convergent adaptation. For the giant senecios (Dendrosenecio), the endemic landmarks of the East African sky islands, it has also been suggested that parallel adaptation has been important for within-lineage differentiation. To test this hypothesis and to address potential gene flow and hybridization among the isolated sky islands, we organized field expeditions to all major mountains. We sampled all currently accepted species and all but one subspecies and genotyped 460 plants representing 109 populations. We tested whether genetic structuring corresponds to geography, as predicted by a parallel adaptation hypothesis, or to altitudinal belt and habitat rather than mountains, as predicted by a hypothesis of a single origin of adaptations. Bayesian and Neighbor-Net analyses showed that the main genetic structure is shallow and largely corresponds to geography, supporting a hypothesis of recent, rapid radiation via parallel altitude/habitat adaptation on different mountains. We also found evidence for intermountain admixture, suggesting several long-distance dispersals by wind across vast areas of unsuitable habitat. The combination of parallel adaptation, secondary contact, and hybridization may explain the complex patterns of morphological variation and the contradicting taxonomic treatments of these rare enigmatic giants, supporting the use of wide taxonomic concepts. Notably, the within-population genetic diversity was very low and calls for increased conservation efforts.
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Affiliation(s)
- Felly Mugizi Tusiime
- Department of Forestry, Biodiversity and Tourism, School of Forestry, Environmental and Geographical Sciences, Makerere University, Kampala, Uganda
- Natural History Museum, University of Oslo, Blindern, Oslo, Norway
| | - Abel Gizaw
- Natural History Museum, University of Oslo, Blindern, Oslo, Norway
- Department of Plant Biology and Biodiversity Management, Addis Ababa University, Addis Ababa, Ethiopia
- * E-mail: ,
| | - Galina Gussarova
- Natural History Museum, University of Oslo, Blindern, Oslo, Norway
- Department of Botany, St Petersburg State University, St Petersburg, Russia
- UiT – The Arctic University of Norway, UMAK, The Arctic University Museum of Norway, Tromsø, Norway
| | - Sileshi Nemomissa
- Department of Plant Biology and Biodiversity Management, Addis Ababa University, Addis Ababa, Ethiopia
| | - Magnus Popp
- Natural History Museum, University of Oslo, Blindern, Oslo, Norway
| | - Catherine Aloyce Masao
- Natural History Museum, University of Oslo, Blindern, Oslo, Norway
- Department of Forest Biology, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Tigist Wondimu
- Natural History Museum, University of Oslo, Blindern, Oslo, Norway
- Department of Plant Biology and Biodiversity Management, Addis Ababa University, Addis Ababa, Ethiopia
| | - Ahmed Abdikadir Abdi
- Natural History Museum, University of Oslo, Blindern, Oslo, Norway
- Botany Department, National Museums of Kenya, Nairobi, Kenya
| | - Virginia Mirré
- Natural History Museum, University of Oslo, Blindern, Oslo, Norway
| | - Vincent Muwanika
- Department of Forestry, Biodiversity and Tourism, School of Forestry, Environmental and Geographical Sciences, Makerere University, Kampala, Uganda
| | - Gerald Eilu
- Department of Forestry, Biodiversity and Tourism, School of Forestry, Environmental and Geographical Sciences, Makerere University, Kampala, Uganda
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10
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Coughlan JM, Wilson Brown M, Willis JH. Patterns of Hybrid Seed Inviability in the Mimulus guttatus sp. Complex Reveal a Potential Role of Parental Conflict in Reproductive Isolation. Curr Biol 2020; 30:83-93.e5. [PMID: 31883810 PMCID: PMC7017923 DOI: 10.1016/j.cub.2019.11.023] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 10/01/2019] [Accepted: 11/06/2019] [Indexed: 11/19/2022]
Abstract
Genomic conflicts may play a central role in the evolution of reproductive barriers. Theory predicts that early-onset hybrid inviability may stem from conflict between parents for resource allocation to offspring. Here, we describe M. decorus: a group of cryptic species within the M. guttatus species complex that are largely reproductively isolated by hybrid seed inviability (HSI). HSI between M. guttatus and M. decorus is common and strong, but populations of M. decorus vary in the magnitude and directionality of HSI with M. guttatus. Patterns of HSI between M. guttatus and M. decorus, as well as within M. decorus, conform to the predictions of parental conflict: first, reciprocal F1s exhibit size differences and parent-of-origin-specific endosperm defects; second, the extent of asymmetry between reciprocal F1 seed size is correlated with asymmetry in HSI; and third, inferred differences in the extent of conflict predict the extent of HSI between populations. We also find that HSI is rapidly evolving, as populations that exhibit the most HSI are each others' closest relative. Lastly, although all populations appear largely outcrossing, we find that the differences in the inferred strength of conflict scale positively with π, suggesting that demographic or life history factors other than transitions to self-fertilization may influence the rate of parental-conflict-driven evolution. Overall, these patterns suggest the rapid evolution of parent-of-origin-specific resource allocation alleles coincident with HSI within and between M. guttatus and M. decorus. Parental conflict may therefore be an important evolutionary driver of reproductive isolation.
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Affiliation(s)
- Jenn M Coughlan
- Biological Sciences, Duke University, 25 Science Drive, Durham, NC 27708, USA; Biology Department, University of North Carolina, Chapel Hill, 120 South Road, Chapel Hill, NC 27599, USA.
| | - Maya Wilson Brown
- Biological Sciences, Duke University, 25 Science Drive, Durham, NC 27708, USA
| | - John H Willis
- Biological Sciences, Duke University, 25 Science Drive, Durham, NC 27708, USA
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11
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Tusso S, Nieuwenhuis BPS, Sedlazeck FJ, Davey JW, Jeffares DC, Wolf JBW. Ancestral Admixture Is the Main Determinant of Global Biodiversity in Fission Yeast. Mol Biol Evol 2019; 36:1975-1989. [PMID: 31225876 PMCID: PMC6736153 DOI: 10.1093/molbev/msz126] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Mutation and recombination are key evolutionary processes governing phenotypic variation and reproductive isolation. We here demonstrate that biodiversity within all globally known strains of Schizosaccharomyces pombe arose through admixture between two divergent ancestral lineages. Initial hybridization was inferred to have occurred ∼20-60 sexual outcrossing generations ago consistent with recent, human-induced migration at the onset of intensified transcontinental trade. Species-wide heritable phenotypic variation was explained near-exclusively by strain-specific arrangements of alternating ancestry components with evidence for transgressive segregation. Reproductive compatibility between strains was likewise predicted by the degree of shared ancestry. To assess the genetic determinants of ancestry block distribution across the genome, we characterized the type, frequency, and position of structural genomic variation using nanopore and single-molecule real-time sequencing. Despite being associated with double-strand break initiation points, over 800 segregating structural variants exerted overall little influence on the introgression landscape or on reproductive compatibility between strains. In contrast, we found strong ancestry disequilibrium consistent with negative epistatic selection shaping genomic ancestry combinations during the course of hybridization. This study provides a detailed, experimentally tractable example that genomes of natural populations are mosaics reflecting different evolutionary histories. Exploiting genome-wide heterogeneity in the history of ancestral recombination and lineage-specific mutations sheds new light on the population history of S. pombe and highlights the importance of hybridization as a creative force in generating biodiversity.
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Affiliation(s)
- Sergio Tusso
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Planegg-Martinsried, Germany
- Department of Evolutionary Biology, Science for Life Laboratories, Uppsala University, Uppsala, Sweden
| | - Bart P S Nieuwenhuis
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Planegg-Martinsried, Germany
| | - Fritz J Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
| | - John W Davey
- Bioscience Technology Facility, Department of Biology, University of York, York, United Kingdom
| | - Daniel C Jeffares
- Department of Biology, University of York, York, United Kingdom
- York Biomedical Research Institute (YBRI), University of York, York, United Kingdom
| | - Jochen B W Wolf
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Planegg-Martinsried, Germany
- Department of Evolutionary Biology, Science for Life Laboratories, Uppsala University, Uppsala, Sweden
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12
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Gould BA, Chen Y, Lowry DB. Gene regulatory divergence between locally adapted ecotypes in their native habitats. Mol Ecol 2018; 27:4174-4188. [PMID: 30168223 DOI: 10.1111/mec.14852] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 08/15/2018] [Accepted: 08/19/2018] [Indexed: 01/04/2023]
Abstract
Local adaptation is a key driver of ecological specialization and the formation of new species. Despite its importance, the evolution of gene regulatory divergence among locally adapted populations is poorly understood, especially how that divergence manifests in nature. Here, we evaluate gene expression divergence and allele-specific gene expression responses for locally adapted coastal perennial and inland annual accessions of the yellow monkeyflower, Mimulus guttatus, in a field reciprocal transplant experiment. Overall, 6765 (73%) of surveyed genes were differentially expressed between coastal and inland habitats, while 7213 (77%) were differentially expressed between the coastal perennial and inland annual accessions. Cis-regulatory variation was pervasive, affecting 79% (5532) of differentially expressed genes. We detected trans effects for 52% (3611) of differentially expressed genes. Expression plasticity of alleles across habitats (G × E interactions) appears to be relatively common (affecting 18% of transcripts) and could minimize fitness trade-offs at loci that contribute to local adaptation. We also found evidence that at least one chromosomal inversion may act as supergene by holding together haplotypes of differentially expressed genes, but this pattern depends on habitat context. Our results highlight multiple key patterns regarding the relationship between gene expression and the evolution of locally adapted populations.
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Affiliation(s)
- Billie A Gould
- Department of Plant Biology, Michigan State University, East Lansing, Michigan.,Myriad Women's Health, South San Francisco, California
| | - Yani Chen
- Department of Plant Biology, Michigan State University, East Lansing, Michigan
| | - David B Lowry
- Department of Plant Biology, Michigan State University, East Lansing, Michigan.,Program in Ecology, Evolutionary Biology and Behavior, Michigan State University, East Lansing, Michigan.,Plant Resilience Institute, Michigan State University, East Lansing, Michigan
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13
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Ravinet M. Notes from a snail island: Littorinid evolution and adaptation. Mol Ecol 2018; 27:2781-2789. [PMID: 29802775 DOI: 10.1111/mec.14730] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 05/01/2018] [Accepted: 05/06/2018] [Indexed: 12/20/2022]
Abstract
The most successful study systems are built on a foundation of decades of research on the basic biology, ecology and life history of the organisms in question. Combined with new technologies, this can provide a formidable means to address important issues in evolutionary biology and molecular ecology. Littorinid marine snails are a good example of this, with a rich literature on their taxonomy, speciation, thermal tolerance and behavioural adaptations. In August 2017, an international meeting on Littorinid evolution was held at the Tjärnö Marine Research Laboratory in Western Sweden. In this meeting review, I provide a summary of some of the exciting work on parallel evolution, sexual selection and adaptation to environmental stress presented there. I argue that newly available genomic resources present an opportunity for integrating the traditionally divergent fields of speciation and environmental adaptation in Littorinid research.
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Affiliation(s)
- Mark Ravinet
- Centre for Ecological and Evolutionary Synthesis, University of Oslo, Oslo, Norway
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14
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Twyford AD, Caola AM, Choudhary P, Raina R, Friedman J. Loss of Color Pigmentation Is Maintained at High Frequency in a Monkey Flower Population. Am Nat 2018; 191:135-145. [DOI: 10.1086/694853] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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15
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A Whole-Transcriptome Approach to Evaluating Reference Genes for Quantitative Gene Expression Studies: A Case Study in Mimulus. G3-GENES GENOMES GENETICS 2017; 7:1085-1095. [PMID: 28258113 PMCID: PMC5386857 DOI: 10.1534/g3.116.038075] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
While quantitative PCR (qPCR) is widely recognized as being among the most accurate methods for quantifying gene expression, it is highly dependent on the use of reliable, stably expressed reference genes. With the increased availability of high-throughput methods for measuring gene expression, whole-transcriptome approaches may be increasingly utilized for reference gene selection and validation. In this study, RNA-seq was used to identify a set of novel qPCR reference genes and evaluate a panel of traditional “housekeeping” reference genes in two species of the evolutionary model plant genus Mimulus. More broadly, the methods proposed in this study can be used to harness the power of transcriptomes to identify appropriate reference genes for qPCR in any study organism, including emerging and nonmodel systems. We find that RNA-seq accurately estimates gene expression means in comparison to qPCR, and that expression means are robust to moderate environmental and genetic variation. However, measures of expression variability were only in agreement with qPCR for samples obtained from a shared environment. This result, along with transcriptome-wide comparisons, suggests that environmental changes have greater impacts on expression variability than on expression means. We discuss how this issue can be addressed through experimental design, and suggest that the ever-expanding pool of published transcriptomes represents a rich and low-cost resource for developing better reference genes for qPCR.
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16
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Hendrick MF, Finseth FR, Mathiasson ME, Palmer KA, Broder EM, Breigenzer P, Fishman L. The genetics of extreme microgeographic adaptation: an integrated approach identifies a major gene underlying leaf trichome divergence in Yellowstone Mimulus guttatus. Mol Ecol 2016; 25:5647-5662. [PMID: 27393073 DOI: 10.1111/mec.13753] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 06/15/2016] [Accepted: 06/22/2016] [Indexed: 12/30/2022]
Abstract
Microgeographic adaptation provides a particularly interesting context for understanding the genetic basis of phenotypic divergence and may also present unique empirical challenges. In particular, plant adaptation to extreme soil mosaics may generate barriers to gene flow or shifts in mating system that confound simple genomic scans for adaptive loci. Here, we combine three approaches - quantitative trait locus (QTL) mapping of candidate intervals in controlled crosses, population resequencing (PoolSeq) and analyses of wild recombinant individuals - to investigate one trait associated with Mimulus guttatus (yellow monkeyflower) adaptation to geothermal soils in Yellowstone National Park. We mapped a major QTL causing dense leaf trichomes in thermally adapted plants to a <50-kb region of linkage Group 14 (Tr14) previously implicated in trichome divergence between independent M. guttatus populations. A PoolSeq scan of Tr14 region revealed a cluster of six genes, coincident with the inferred QTL peak, with high allele frequency differences sufficient to explain observed phenotypic differentiation. One of these, the R2R3 MYB transcription factor Migut.N02661, is a plausible functional candidate and was also strongly associated (r2 = 0.27) with trichome phenotype in analyses of wild-collected admixed individuals. Although functional analyses will be necessary to definitively link molecular variants in Tr14 with trichome divergence, our analyses are a major step in that direction. They point to a simple, and parallel, genetic basis for one axis of Mimulus guttatus adaptation to an extreme habitat, suggest a broadly conserved genetic basis for trichome variation across flowering plants and pave the way for further investigations of this challenging case of microgeographic incipient speciation.
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Affiliation(s)
- Margaret F Hendrick
- Division of Biological Sciences, University of Montana, 32 Campus Dr., Missoula, MT, 59812, USA.,Department of Earth and Environment, Boston University, 685 Commonwealth Ave., Boston, MA, 02215, USA
| | - Findley R Finseth
- Division of Biological Sciences, University of Montana, 32 Campus Dr., Missoula, MT, 59812, USA
| | - Minna E Mathiasson
- School of Biology and Ecology, University of Maine, 5751 Murray Hall, Orono, ME, 04469, USA
| | - Kristen A Palmer
- Department of Biology, Wheaton College, 26 E. Main St., Norton, MA, 02766, USA
| | - Emma M Broder
- Biology Department, Wesleyan University, 45 Wyllys Ave., Middletown, CT, 06259, USA
| | - Peter Breigenzer
- Division of Biological Sciences, University of Montana, 32 Campus Dr., Missoula, MT, 59812, USA
| | - Lila Fishman
- Division of Biological Sciences, University of Montana, 32 Campus Dr., Missoula, MT, 59812, USA
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17
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White OW, Doo B, Carine MA, Chapman MA. Transcriptome sequencing and simple sequence repeat marker development for three Macaronesian endemic plant species. APPLICATIONS IN PLANT SCIENCES 2016; 4:apps1600050. [PMID: 27610280 PMCID: PMC5001862 DOI: 10.3732/apps.1600050] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 07/05/2016] [Indexed: 06/06/2023]
Abstract
PREMISE OF THE STUDY Oceanic islands offer unparalleled opportunities to investigate evolutionary processes such as adaptation and speciation. However, few genomic resources are available for oceanic island endemics. In this study, we publish transcriptome sequences from three Macaronesian endemic plant species (Argyranthemum broussonetii [Asteraceae], Descurainia bourgaeana [Brassicaceae], and Echium wildpretii [Boraginaceae]) that are representative of lineages that have radiated in the region. In addition, the utility of transcriptome data for marker development is demonstrated. METHODS AND RESULTS Transcriptomes from the three plant species were sequenced, assembled, and annotated. Between 1972 and 2282 simple sequence repeats (SSRs) were identified for each taxon. Primers were designed and tested for 30 of the candidate SSRs identified in Argyranthemum, of which 12 amplified well across three species and eight were polymorphic. CONCLUSIONS We demonstrate here that a single transcriptome sequence is sufficient to identify hundreds of polymorphic SSR markers. The SSRs are applicable to a wide range of questions relating to the evolution of island lineages.
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Affiliation(s)
- Oliver W. White
- Plants Division, Natural History Museum, London SW7 5BD, United Kingdom
- Centre for Biological Sciences, University of Southampton, Southampton SO17 1BJ, United Kingdom
| | - Bethany Doo
- Centre for Biological Sciences, University of Southampton, Southampton SO17 1BJ, United Kingdom
| | - Mark A. Carine
- Plants Division, Natural History Museum, London SW7 5BD, United Kingdom
| | - Mark A. Chapman
- Centre for Biological Sciences, University of Southampton, Southampton SO17 1BJ, United Kingdom
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18
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Vallejo-Marín M, Cooley AM, Lee MY, Folmer M, McKain MR, Puzey JR. Strongly asymmetric hybridization barriers shape the origin of a new polyploid species and its hybrid ancestor. AMERICAN JOURNAL OF BOTANY 2016; 103:1272-88. [PMID: 27221281 DOI: 10.3732/ajb.1500471] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Accepted: 02/16/2016] [Indexed: 05/11/2023]
Abstract
PREMISE OF THE STUDY Hybridization between diploids and tetraploids can lead to new allopolyploid species, often via a triploid intermediate. Viable triploids are often produced asymmetrically, with greater success observed for "maternal-excess" crosses where the mother has a higher ploidy than the father. Here we investigated the evolutionary origins of Mimulus peregrinus, an allohexaploid recently derived from the triploid M. ×robertsii, to determine whether reproductive asymmetry has shaped the formation of this new species. METHODS We used reciprocal crosses between the diploid (M. guttatus) and tetraploid (M. luteus) progenitors to determine the viability of triploid M. ×robertsii hybrids resulting from paternal- vs. maternal-excess crosses. To investigate whether experimental results predict patterns seen in the field, we performed parentage analyses comparing natural populations of M. peregrinus to its diploid, tetraploid, and triploid progenitors. Organellar sequences obtained from pre-existing genomic data, supplemented with additional genotyping was used to establish the maternal ancestry of multiple M. peregrinus and M. ×robertsii populations. KEY RESULTS We found strong evidence for asymmetric origins of M. peregrinus, but opposite to the common pattern, with paternal-excess crosses significantly more successful than maternal-excess crosses. These results successfully predicted hybrid formation in nature: 111 of 114 M. ×robertsii individuals, and 27 of 27 M. peregrinus, had an M. guttatus maternal haplotype. CONCLUSION This study, which includes the first Mimulus chloroplast genome assembly, demonstrates the utility of parentage analysis through genome skimming. We highlight the benefits of complementing genomic analyses with experimental approaches to understand asymmetry in allopolyploid speciation.
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Affiliation(s)
- Mario Vallejo-Marín
- Biological and Environmental Science, School of Natural Sciences, University of Stirling, Stirling, Scotland, FK9 4LA UK
| | - Arielle M Cooley
- Biology Department, Whitman College, Walla Walla, Washington 99362 USA
| | - Michelle Yuequi Lee
- Biological and Environmental Science, School of Natural Sciences, University of Stirling, Stirling, Scotland, FK9 4LA UK
| | - Madison Folmer
- Department of Biology, College of William and Mary, Williamsburg, Virginia 23185 USA
| | - Michael R McKain
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132 USA
| | - Joshua R Puzey
- Department of Biology, College of William and Mary, Williamsburg, Virginia 23185 USA
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19
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Stanton K, Valentin CM, Wijnen ME, Stutstman S, Palacios JJ, Cooley AM. Absence of postmating barriers between a selfing vs. outcrossing Chilean Mimulus species pair. AMERICAN JOURNAL OF BOTANY 2016; 103:1030-1040. [PMID: 27283023 DOI: 10.3732/ajb.1600079] [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: 02/19/2016] [Accepted: 05/10/2016] [Indexed: 06/06/2023]
Abstract
PREMISE OF THE STUDY Reproductive isolation between sympatric species pairs may be maintained by both pre- and postmating barriers. Here we evaluate potential barriers to mating between the outcrossing Mimulus luteus and its more highly selfing sympatric congener, M. cupreus, two members of the South American luteus complex of Mimulus. METHODS Seed set was compared following autonomous self-pollination, manual pollination, conspecific outcrossing, and sympatric and allopatric hybridization, for laboratory-maintained inbred lines and wild-collected accessions. Survival and reproductive fitness of hybrids relative to parental species were examined across environments that differed with respect to temperature and soil nutrients, two factors that vary across the ranges of M. luteus and M. cupreus. KEY RESULTS Mimulus luteus was minimally capable of autonomous self-fertilization, consistent with reliance on an animal pollinator, whereas M. cupreus was a successful selfer across all tested accessions. Postmating barriers to hybridization are negligible, in both low- and high-stress environments, across multiple sympatric and allopatric populations. CONCLUSION As in the North American M. guttatus-M. nasutus species pair, postmating barriers contribute little to isolation between M. luteus and M. cupreus. This result reinforces the importance of premating barriers, specifically species differences in reliance on, and accessibility to, animal pollinators. A unique aspect of the M. luteus-M. cupreus pair is the recent gain of red floral anthocyanin pigmentation in M. cupreus. On the basis of species differences in vegetative anthocyanin production, a facultative stress-protective response, we propose a potential stress-protective role for the constitutive floral anthocyanins of M. cupreus.
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Affiliation(s)
- Kimmy Stanton
- Whitman College Biology Department, Walla Walla, Washington 99362 USA
| | - Celine M Valentin
- Whitman College Biology Department, Walla Walla, Washington 99362 USA
| | - Marijke E Wijnen
- Whitman College Biology Department, Walla Walla, Washington 99362 USA
| | - Sage Stutstman
- Whitman College Biology Department, Walla Walla, Washington 99362 USA
| | | | - Arielle M Cooley
- Whitman College Biology Department, Walla Walla, Washington 99362 USA
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20
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Comparative Transcriptomics Indicates a Role for SHORT VEGETATIVE PHASE (SVP) Genes in Mimulus guttatus Vernalization Response. G3-GENES GENOMES GENETICS 2016; 6:1239-49. [PMID: 26921300 PMCID: PMC4856076 DOI: 10.1534/g3.115.026468] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The timing of reproduction in response to variable environmental conditions is critical to plant fitness, and is a major driver of taxon differentiation. In the yellow monkey flower, Mimulus guttatus, geographically distinct North American populations vary in their photoperiod and chilling (vernalization) requirements for flowering, suggesting strong local adaptation to their surroundings. Previous analyses revealed quantitative trait loci (QTL) underlying short-day mediated vernalization responsiveness using two annual M. guttatus populations that differed in their vernalization response. To narrow down candidate genes responsible for this variation, and to reveal potential downstream genes, we conducted comparative transcriptomics and quantitative PCR (qPCR) in shoot apices of parental vernalization responsive IM62, and unresponsive LMC24 inbred lines grown under different photoperiods and temperatures. Our study identified several metabolic, hormone signaling, photosynthetic, stress response, and flowering time genes that are differentially expressed between treatments, suggesting a role for their protein products in short-day-mediated vernalization responsiveness. Only a small subset of these genes intersected with candidate genes from the previous QTL study, and, of the main candidates tested with qPCR under nonpermissive conditions, only SHORT VEGETATIVE PHASE (SVP) gene expression met predictions for a population-specific short-day-repressor of flowering that is repressed by cold.
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