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Müller M, Kües U, Budde KB, Gailing O. Applying molecular and genetic methods to trees and their fungal communities. Appl Microbiol Biotechnol 2023; 107:2783-2830. [PMID: 36988668 PMCID: PMC10106355 DOI: 10.1007/s00253-023-12480-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 03/05/2023] [Accepted: 03/07/2023] [Indexed: 03/30/2023]
Abstract
Forests provide invaluable economic, ecological, and social services. At the same time, they are exposed to several threats, such as fragmentation, changing climatic conditions, or increasingly destructive pests and pathogens. Trees, the inherent species of forests, cannot be viewed as isolated organisms. Manifold (micro)organisms are associated with trees playing a pivotal role in forest ecosystems. Of these organisms, fungi may have the greatest impact on the life of trees. A multitude of molecular and genetic methods are now available to investigate tree species and their associated organisms. Due to their smaller genome sizes compared to tree species, whole genomes of different fungi are routinely compared. Such studies have only recently started in forest tree species. Here, we summarize the application of molecular and genetic methods in forest conservation genetics, tree breeding, and association genetics as well as for the investigation of fungal communities and their interrelated ecological functions. These techniques provide valuable insights into the molecular basis of adaptive traits, the impacts of forest management, and changing environmental conditions on tree species and fungal communities and can enhance tree-breeding cycles due to reduced time for field testing. It becomes clear that there are multifaceted interactions among microbial species as well as between these organisms and trees. We demonstrate the versatility of the different approaches based on case studies on trees and fungi. KEY POINTS: • Current knowledge of genetic methods applied to forest trees and associated fungi. • Genomic methods are essential in conservation, breeding, management, and research. • Important role of phytobiomes for trees and their ecosystems.
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Affiliation(s)
- Markus Müller
- Forest Genetics and Forest Tree Breeding, Faculty for Forest Sciences and Forest Ecology, University of Goettingen, Büsgenweg 2, 37077, Göttingen, Germany.
- Center for Integrated Breeding Research (CiBreed), University of Goettingen, 37073, Göttingen, Germany.
| | - Ursula Kües
- Molecular Wood Biotechnology and Technical Mycology, Faculty for Forest Sciences and Forest Ecology, University of Goettingen, Büsgenweg 2, 37077, Göttingen, Germany
- Center for Molecular Biosciences (GZMB), Georg-August-University Göttingen, 37077, Göttingen, Germany
- Center of Sustainable Land Use (CBL), Georg-August-University Göttingen, 37077, Göttingen, Germany
| | - Katharina B Budde
- Forest Genetics and Forest Tree Breeding, Faculty for Forest Sciences and Forest Ecology, University of Goettingen, Büsgenweg 2, 37077, Göttingen, Germany
- Center of Sustainable Land Use (CBL), Georg-August-University Göttingen, 37077, Göttingen, Germany
| | - Oliver Gailing
- Forest Genetics and Forest Tree Breeding, Faculty for Forest Sciences and Forest Ecology, University of Goettingen, Büsgenweg 2, 37077, Göttingen, Germany
- Center for Integrated Breeding Research (CiBreed), University of Goettingen, 37073, Göttingen, Germany
- Center of Sustainable Land Use (CBL), Georg-August-University Göttingen, 37077, Göttingen, Germany
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Liu Y, Luo C, Liang R, Lan M, Yu H, Guo Y, Chen S, Lu T, Mo X, He X. Genome-wide identification of the mango CONSTANS ( CO) family and functional analysis of two MiCOL9 genes in transgenic Arabidopsis. FRONTIERS IN PLANT SCIENCE 2022; 13:1028987. [PMID: 36325546 PMCID: PMC9618732 DOI: 10.3389/fpls.2022.1028987] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 09/28/2022] [Indexed: 06/14/2023]
Abstract
CONSTANS/CONSTANS-like (CO/COL) transcription factors play a vital role in the photoperiodic flowering pathway. However, the biological functions of COL genes in mango are unclear. In this study, we identified 31 COL genes from the 'Jin Huang' mango genome and divided them into three groups according to the specific gene structure and protein domain characteristics. These 31 MiCOL genes were heterogeneously distributed on 14 chromosomes. Expression pattern analysis showed that most MiCOL genes were mainly expressed in leaves and stems and during the floral induction period, followed by the floral differentiation period. The expression of COL genes was induced by drought and salt stress, but the expression patterns of different genes were different, which may suggest that MiCOL genes are involved in the abiotic stress response of mango. Under salt and drought conditions, two MiCOL9 genes can improve the resistance of Arabidopsis by improving the scavenging ability of ROS and proline accumulation and reducing the MDA content. Additionally, overexpression of MiCOL9 genes significantly inhibited flowering in transgenic Arabidopsis. This work provides an important foundation for understanding the biological roles of mango COL genes in plant growth, development and stress responses.
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Affiliation(s)
- Yuan Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, China
- Guangxi Key Laboratory for Agro-Environment and Agro-Product Safety, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, China
| | - Cong Luo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, China
- Guangxi Key Laboratory for Agro-Environment and Agro-Product Safety, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, China
| | - Rongzhen Liang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, China
- Guangxi Key Laboratory for Agro-Environment and Agro-Product Safety, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, China
| | - Moying Lan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, China
- Guangxi Key Laboratory for Agro-Environment and Agro-Product Safety, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, China
| | - Haixia Yu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, China
- Guangxi Key Laboratory for Agro-Environment and Agro-Product Safety, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, China
| | - Yihang Guo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, China
- Guangxi Key Laboratory for Agro-Environment and Agro-Product Safety, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, China
| | - Shuquan Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, China
- Guangxi Key Laboratory for Agro-Environment and Agro-Product Safety, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, China
| | - Tingting Lu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, China
- Guangxi Key Laboratory for Agro-Environment and Agro-Product Safety, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, China
| | - Xiao Mo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, China
- Guangxi Key Laboratory for Agro-Environment and Agro-Product Safety, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, China
| | - Xinhua He
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, China
- Guangxi Key Laboratory for Agro-Environment and Agro-Product Safety, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, China
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Götz J, Rajora OP, Gailing O. Genetic Structure of Natural Northern Range-Margin Mainland, Peninsular, and Island Populations of Northern Red Oak (Quercus rubra L.). Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.907414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Plant populations at the leading edge of the species’ native range often exhibit genetic structure as a result of genetic drift and adaptation to harsh environmental conditions. Hence, they are likely to harbour rare genetic adaptations to local environmental conditions and therefore are of particular interest to understand climate adaptation. We examined genetic structure of nine northern marginal mainland, peninsular and isolated island natural populations of northern red oak (Quercus rubraL.), a valuable long-lived North American hardwood tree species, covering a wide climatic range, using 17 nuclear microsatellites. We found pronounced genetic differentiation of a disjunct isolated island population from all mainland and peninsular populations. Furthermore, we observed remarkably strong fine-scale spatial genetic structure (SGS) in all investigated populations. Such high SGS values are uncommon and were previously solely observed in extreme range-edge marginal oak populations in one other study. We found a significant correlation between major climate parameters and SGS formation in northern range-edge red oak populations, with more pronounced SGS in colder and drier regions. Most likely, the harsh environment in leading edge populations influences the density of reproducing trees within the populations and therefore leads to restricted overlapping of seed shadows when compared to more central populations. Accordingly, SGS was negatively correlated with effective population size and increased with latitude of the population locations. The significant positive association between genetic distances and precipitation differences between populations may be indicative of isolation by adaptation in the observed range-edge populations. However, this association was not confirmed by a multiple regression analysis including geographic distances and precipitation distances, simultaneously. Our study provides new insights in the genetic structure of long-lived tree species at their leading distribution edge.
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Zumwalde BA, Fredlock B, Beckman E, Duckett D, McCauley RA, Spence ES, Hoban S. Assessing ex situ genetic and ecogeographic conservation in a threatened but widespread oak after range‐wide collecting effort. Evol Appl 2022; 15:1002-1017. [PMID: 35782011 PMCID: PMC9234636 DOI: 10.1111/eva.13391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 04/11/2022] [Accepted: 04/12/2022] [Indexed: 11/04/2022] Open
Affiliation(s)
- Bethany A. Zumwalde
- The Morton Arboretum Center for Tree Science 4100 Illinois 53 Lisle IL 60532 USA
- Department of Biology University of Florida Gainesville FL 32611 USA
| | - Bailie Fredlock
- The Morton Arboretum Center for Tree Science 4100 Illinois 53 Lisle IL 60532 USA
| | - Emily Beckman
- The Morton Arboretum Center for Tree Science 4100 Illinois 53 Lisle IL 60532 USA
| | - Drew Duckett
- The Morton Arboretum Center for Tree Science 4100 Illinois 53 Lisle IL 60532 USA
- Department of Evolution, Ecology and Organismal Biology The Ohio State University 1315 Kinnear Rd Columbus OH 43212 USA
| | - Ross A. McCauley
- Department of Biology Fort Lewis College 1000 Rim Drive Durango CO 81301 USA
| | - Emma Suzuki Spence
- The Morton Arboretum Center for Tree Science 4100 Illinois 53 Lisle IL 60532 USA
| | - Sean Hoban
- The Morton Arboretum Center for Tree Science 4100 Illinois 53 Lisle IL 60532 USA
- The Field Museum Chicago IL USA
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Li S, Wang Z, Su Y, Wang T. EST-SSR-based landscape genetics of Pseudotaxus chienii, a tertiary relict conifer endemic to China. Ecol Evol 2021; 11:9498-9515. [PMID: 34306638 PMCID: PMC8293779 DOI: 10.1002/ece3.7769] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 05/04/2021] [Accepted: 05/19/2021] [Indexed: 12/12/2022] Open
Abstract
Pseudotaxus chienii, belonging to the monotypic genus Pseudotaxus (Taxaceae), is a relict conifer endemic to China. Its populations are usually small and patchily distributed, having a low capacity of natural regeneration. To gain a clearer understanding of how landscape variables affect the local adaptation of P. chienii, we applied EST-SSR markers in conjunction with landscape genetics methods: (a) to examine the population genetic pattern and spatial genetic structure; (b) to perform genome scan and selection scan to identify outlier loci and the associated landscape variables; and (c) to model the ecological niche under climate change. As a result, P. chienii was found to have a moderate level of genetic variation and a high level of genetic differentiation. Its populations displayed a significant positive relationship between the genetic and geographical distance (i.e., "isolation by distance" pattern) and a strong fine-scale spatial genetic structure within 2 km. A putatively adaptive locus EMS6 (functionally annotated to cellulose synthase A catalytic subunit 7) was identified, which was found significantly associated with soil Cu, K, and Pb content and the combined effects of temperature and precipitation. Moreover, P. chienii was predicted to experience significant range contractions in future climate change scenarios. Our results highlight the potential of specific soil metal content and climate variables as the driving force of adaptive genetic differentiation in P. chienii. The data would also be useful to develop a conservation action plan for P. chienii.
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Affiliation(s)
- Shufeng Li
- School of Life SciencesSun Yat‐sen UniversityGuangzhouChina
| | - Zhen Wang
- School of Life SciencesSun Yat‐sen UniversityGuangzhouChina
| | - Yingjuan Su
- School of Life SciencesSun Yat‐sen UniversityGuangzhouChina
- Research Institute of Sun Yat‐sen University in ShenzhenShenzhenChina
| | - Ting Wang
- Research Institute of Sun Yat‐sen University in ShenzhenShenzhenChina
- College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
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An Updated Infrageneric Classification of the North American Oaks (Quercus Subgenus Quercus): Review of the Contribution of Phylogenomic Data to Biogeography and Species Diversity. FORESTS 2021. [DOI: 10.3390/f12060786] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The oak flora of North America north of Mexico is both phylogenetically diverse and species-rich, including 92 species placed in five sections of subgenus Quercus, the oak clade centered on the Americas. Despite phylogenetic and taxonomic progress on the genus over the past 45 years, classification of species at the subsectional level remains unchanged since the early treatments by WL Trelease, AA Camus, and CH Muller. In recent work, we used a RAD-seq based phylogeny including 250 species sampled from throughout the Americas and Eurasia to reconstruct the timing and biogeography of the North American oak radiation. This work demonstrates that the North American oak flora comprises mostly regional species radiations with limited phylogenetic affinities to Mexican clades, and two sister group connections to Eurasia. Using this framework, we describe the regional patterns of oak diversity within North America and formally classify 62 species into nine major North American subsections within sections Lobatae (the red oaks) and Quercus (the white oaks), the two largest sections of subgenus Quercus. We also distill emerging evolutionary and biogeographic patterns based on the impact of phylogenomic data on the systematics of multiple species complexes and instances of hybridization.
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7
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Chloroplast Haplotypes of Northern Red Oak (Quercus rubra L.) Stands in Germany Suggest Their Origin from Northeastern Canada. FORESTS 2020. [DOI: 10.3390/f11091025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Northern red oak (Quercus rubra L.) is one of the most important foreign tree species in Germany and considered as a major candidate for prospective sustainable forestry in the face of climate change. Therefore, Q. rubra was subject of many previous studies on its growth traits and attempts to infer the origin of various populations of this species using nuclear and chloroplast DNA markers. However, the exact geographic origin of German red oak stands has still not been identified. Its native range widely extends over North America, and the species can tolerate a broad range of environmental conditions. We genotyped individual trees in 85 populations distributed in Germany and North America using five chloroplast microsatellite and three novel chloroplast CAPS markers, resulting in the identification of 29 haplotypes. The new marker set enabled the identification of several new red oak haplotypes with restricted geographic origin. Some very rare haplotypes helped us narrow down the origin of Q. rubra stands in Germany, especially some stands from North Rhine-Westphalia, to the northern part of the species’ natural distribution area including the Peninsula of Nova Scotia, where the most similar haplotype composition was observed, compared to distinct German stands.
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Nagamitsu T, Uchiyama K, Izuno A, Shimizu H, Nakanishi A. Environment-dependent introgression from Quercus dentata to a coastal ecotype of Quercus mongolica var. crispula in northern Japan. THE NEW PHYTOLOGIST 2020; 226:1018-1028. [PMID: 31424559 PMCID: PMC7216917 DOI: 10.1111/nph.16131] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 08/09/2019] [Indexed: 05/25/2023]
Abstract
Introgression from one species in a specific environment to another may facilitate colonization of the environment by the recipient species. However, such environment-dependent introgression has been clarified in limited plant taxa. In northern Japan, there are two interfertile oak species: Quercus dentata (Qd) in coastal areas and Q. mongolica var. crispula (Qc) in inland areas. However, at higher latitudes where Qd is rare, a coastal Qc ecotype with Qd-like traits is distributed in the coastal areas. We distinguished inland Qc, coastal Qc, and coastal Qd populations based on genome-wide genotypes and multitrait phenotypes and verified introgression from coastal Qd to coastal Qc using reduced library sequencing. Genotypes and phenotypes differed among the populations, and coastal Qc was intermediate between inland Qc and coastal Qd. The ABBA-BABA test showed introgression from coastal Qd to coastal Qc. In coastal Qc, we found various stages of introgression after the first generation of backcross but detected no genomic regions where introgression was enhanced. Overall, we show evidence for introgression from a coastal species to an ecotype of an inland species, which has colonized the coastal environment. It remains unclear whether introgressed alleles are selected in the coastal environment.
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Affiliation(s)
- Teruyoshi Nagamitsu
- Hokkaido Research Center, Forestry and Forest Products Research InstituteForest Research and Management OrganizationSapporo062‐8516Japan
| | - Kentaro Uchiyama
- Department of Forest Molecular Genetics and BiotechnologyForestry and Forest Products Research InstituteForest Research and Management OrganizationTsukuba305‐8687Japan
| | - Ayako Izuno
- Department of Forest Molecular Genetics and BiotechnologyForestry and Forest Products Research InstituteForest Research and Management OrganizationTsukuba305‐8687Japan
| | - Hajime Shimizu
- Greenery Research and Information CenterForestry Research InstituteHokkaido Research OrganizationBibai079‐0198Japan
| | - Atsushi Nakanishi
- Hokkaido Research Center, Forestry and Forest Products Research InstituteForest Research and Management OrganizationSapporo062‐8516Japan
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Kremer A, Hipp AL. Oaks: an evolutionary success story. THE NEW PHYTOLOGIST 2020; 226:987-1011. [PMID: 31630400 PMCID: PMC7166131 DOI: 10.1111/nph.16274] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2019] [Accepted: 09/13/2019] [Indexed: 05/10/2023]
Abstract
The genus Quercus is among the most widespread and species-rich tree genera in the northern hemisphere. The extraordinary species diversity in America and Asia together with the continuous continental distribution of a limited number of European species raise questions about how macro- and microevolutionary processes made the genus Quercus an evolutionary success. Synthesizing conclusions reached during the past three decades by complementary approaches in phylogenetics, phylogeography, genomics, ecology, paleobotany, population biology and quantitative genetics, this review aims to illuminate evolutionary processes leading to the radiation and expansion of oaks. From opposing scales of time and geography, we converge on four overarching explanations of evolutionary success in oaks: accumulation of large reservoirs of diversity within populations and species; ability for rapid migration contributing to ecological priority effects on lineage diversification; high rates of evolutionary divergence within clades combined with convergent solutions to ecological problems across clades; and propensity for hybridization, contributing to adaptive introgression and facilitating migration. Finally, we explore potential future research avenues, emphasizing the integration of microevolutionary and macroevolutionary perspectives.
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Affiliation(s)
- Antoine Kremer
- BIOGECO, INRA, Université de Bordeaux, 69 Route
d'Arcachon, 33612 Cestas, France
| | - Andrew L. Hipp
- The Morton Arboretum, Lisle IL 60532-1293, USA
- The Field Museum, Chicago IL 60605, USA
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Müller M, Gailing O. Abiotic genetic adaptation in the Fagaceae. PLANT BIOLOGY (STUTTGART, GERMANY) 2019; 21:783-795. [PMID: 31081234 DOI: 10.1111/plb.13008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 05/09/2019] [Indexed: 06/09/2023]
Abstract
Fagaceae can be found in tropical and temperate regions and contain species of major ecological and economic importance. In times of global climate change, tree populations need to adapt to rapidly changing environmental conditions. The predicted warmer and drier conditions will potentially result in locally maladapted populations. There is evidence that major genera of the Fagaceae are already negatively affected by climate change-related factors such as drought and associated biotic stressors. Therefore, knowledge of the mechanisms underlying adaptation is of great interest. In this review, we summarise current literature related to genetic adaptation to abiotic environmental conditions. We begin with an overview of genetic diversity in Fagaceae species and then summarise current knowledge related to drought stress tolerance, bud burst timing and frost tolerance in the Fagaceae. Finally, we discuss the role of hybridisation, epigenetics and phenotypic plasticity in adaptation.
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Affiliation(s)
- M Müller
- Faculty for Forest Sciences and Forest Ecology, Forest Genetics and Forest Tree Breeding, University of Goettingen, Göttingen, Germany
| | - O Gailing
- Faculty for Forest Sciences and Forest Ecology, Forest Genetics and Forest Tree Breeding, University of Goettingen, Göttingen, Germany
- Center for Integrated Breeding Research (CiBreed), University of Goettingen, Göttingen, Germany
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A Variable Polyglutamine Repeat Affects Subcellular Localization and Regulatory Activity of a Populus ANGUSTIFOLIA Protein. G3-GENES GENOMES GENETICS 2018; 8:2631-2641. [PMID: 29884614 PMCID: PMC6071607 DOI: 10.1534/g3.118.200188] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Polyglutamine (polyQ) stretches have been reported to occur in proteins across many organisms including animals, fungi and plants. Expansion of these repeats has attracted much attention due their associations with numerous human diseases including Huntington’s and other neurological maladies. This suggests that the relative length of polyQ stretches is an important modulator of their function. Here, we report the identification of a Populus C-terminus binding protein (CtBP) ANGUSTIFOLIA (PtAN1) which contains a polyQ stretch whose functional relevance had not been established. Analysis of 917 resequenced Populus trichocarpa genotypes revealed three allelic variants at this locus encoding 11-, 13- and 15-glutamine residues. Transient expression assays using Populus leaf mesophyll protoplasts revealed that the 11Q variant exhibited strong nuclear localization whereas the 15Q variant was only found in the cytosol, with the 13Q variant exhibiting localization in both subcellular compartments. We assessed functional implications by evaluating expression changes of putative PtAN1 targets in response to overexpression of the three allelic variants and observed allele-specific differences in expression levels of putative targets. Our results provide evidence that variation in polyQ length modulates PtAN1 function by altering subcellular localization.
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12
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Grivet D, Avia K, Vaattovaara A, Eckert AJ, Neale DB, Savolainen O, González-Martínez SC. High rate of adaptive evolution in two widespread European pines. Mol Ecol 2017; 26:6857-6870. [PMID: 29110402 DOI: 10.1111/mec.14402] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Revised: 09/14/2017] [Accepted: 09/25/2017] [Indexed: 12/18/2022]
Abstract
Comparing related organisms with differing ecological requirements and evolutionary histories can shed light on the mechanisms and drivers underlying genetic adaptation. Here, by examining a common set of hundreds of loci, we compare patterns of nucleotide diversity and molecular adaptation of two European conifers (Scots pine and maritime pine) living in contrasted environments and characterized by distinct population genetic structure (low and clinal in Scots pine, high and ecotypic in maritime pine) and demographic histories. We found higher nucleotide diversity in Scots pine than in maritime pine, whereas rates of new adaptive substitutions (ωa ), as estimated from the distribution of fitness effects, were similar across species and among the highest found in plants. Sample size and population genetic structure did not appear to have resulted in significant bias in estimates of ωa . Moreover, population contraction-expansion dynamics for each species did not affect differentially the rate of adaptive substitution in these two pines. Several methodological and biological factors may underlie the unusually high rate of adaptive evolution of Scots pine and maritime pine. By providing two new case studies with contrasting evolutionary histories, we contribute to disentangling the multiple factors potentially affecting adaptive evolution in natural plant populations.
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Affiliation(s)
- Delphine Grivet
- Department of Forest Ecology and Genetics, Forest Research Centre, INIA-CIFOR, Madrid, Spain.,Sustainable Forest Management Research Institute, INIA - University of Valladolid, Palencia, Spain
| | - Komlan Avia
- Department of Ecology and Genetics and Biocenter Oulu, University of Oulu, Oulu, Finland.,Algal Genetics Group, UMR 8227, CNRS, Sorbonne Universités, UPMC, Station Biologique Roscoff, Roscoff, France.,UMI 3614 Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Universités, UPMC, Pontificia Universidad Católica de Chile, Universidad Austral de Chile, Station Biologique Roscoff, Roscoff, France
| | - Aleksia Vaattovaara
- Department of Ecology and Genetics and Biocenter Oulu, University of Oulu, Oulu, Finland.,Division of Plant Biology, Department of Biosciences, Viikki Plant Science Centre (ViPS), University of Helsinki, Helsinki, Finland
| | - Andrew J Eckert
- Department of Biology, Virginia Commonwealth University, Richmond, VA, USA
| | - David B Neale
- Department of Plant Sciences, University of California at Davis, Davis, CA, USA
| | - Outi Savolainen
- Department of Ecology and Genetics and Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Santiago C González-Martínez
- Department of Forest Ecology and Genetics, Forest Research Centre, INIA-CIFOR, Madrid, Spain.,Sustainable Forest Management Research Institute, INIA - University of Valladolid, Palencia, Spain.,BIOGECO, INRA, Univ. Bordeaux, Cestas, France
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Genetic Diversity among Age Classes of a Pinus sylvestris (L.) Population from the Białowieża Primeval Forest, Poland. FORESTS 2017. [DOI: 10.3390/f8070227] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The Białowieża Primeval Forest (BPF) is Europe’s last primeval forest and an irreplaceable area for biodiversity conservation due to its size, protection status, and substantially undisturbed nature. There is no other forest in Europe with such a large surface representing highly-advanced natural succession. This article reports on the first analysis of the genetic variability and demographic structure of a self-renewed Pinus sylvestris population located in BPF, using both chloroplast and mitochondrial DNA markers. The analysis of molecular variance (AMOVA) for chloroplast simple sequence repeats (cpSSRs) revealed a significant genetic differentiation among age classes that accounted for about 2% of the total variance, comparable to those reported among different populations of Scots pine. None of the 117 detected chloroplast haplotypes were common to all age classes. Haplotype diversity ranged from 0.370 to 0.415 for cpSSRs and from 0.320 to 0.455 for mitochondrial markers. The genetic variation of the studied age classes—represented by mitochondrial markers—strongly depicts the maternal genetic structure, indicating limited seed dispersal. Temporal genetic substructuring is maintained within a self-renewed population of Scots pine from the BPF.
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14
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Adaptive Variation and Introgression of a CONSTANS-Like Gene in North American Red Oaks. FORESTS 2016. [DOI: 10.3390/f8010003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Song Z, Zhang M, Li F, Weng Q, Zhou C, Li M, Li J, Huang H, Mo X, Gan S. Genome scans for divergent selection in natural populations of the widespread hardwood species Eucalyptus grandis (Myrtaceae) using microsatellites. Sci Rep 2016; 6:34941. [PMID: 27748400 PMCID: PMC5066178 DOI: 10.1038/srep34941] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 09/20/2016] [Indexed: 11/09/2022] Open
Abstract
Identification of loci or genes under natural selection is important for both understanding the genetic basis of local adaptation and practical applications, and genome scans provide a powerful means for such identification purposes. In this study, genome-wide simple sequence repeats markers (SSRs) were used to scan for molecular footprints of divergent selection in Eucalyptus grandis, a hardwood species occurring widely in costal areas from 32° S to 16° S in Australia. High population diversity levels and weak population structure were detected with putatively neutral genomic SSRs. Using three FST outlier detection methods, a total of 58 outlying SSRs were collectively identified as loci under divergent selection against three non-correlated climatic variables, namely, mean annual temperature, isothermality and annual precipitation. Using a spatial analysis method, nine significant associations were revealed between FST outlier allele frequencies and climatic variables, involving seven alleles from five SSR loci. Of the five significant SSRs, two (EUCeSSR1044 and Embra394) contained alleles of putative genes with known functional importance for response to climatic factors. Our study presents critical information on the population diversity and structure of the important woody species E. grandis and provides insight into the adaptive responses of perennial trees to climatic variations.
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Affiliation(s)
- Zhijiao Song
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Xiangshan Road, Beijing 100091, China
- Key Laboratory of State Forestry Administration on Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Longdong, Guangzhou 510520, China
- Baoshan University, Yuanzheng Road, Baoshan 678000, China
| | - Miaomiao Zhang
- Key Laboratory of State Forestry Administration on Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Longdong, Guangzhou 510520, China
- College of Forestry, South China Agricultural University, 284 Block, Wushan Street, Guangzhou 510642, China
| | - Fagen Li
- Key Laboratory of State Forestry Administration on Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Longdong, Guangzhou 510520, China
| | - Qijie Weng
- Key Laboratory of State Forestry Administration on Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Longdong, Guangzhou 510520, China
| | - Chanpin Zhou
- Key Laboratory of State Forestry Administration on Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Longdong, Guangzhou 510520, China
| | - Mei Li
- Key Laboratory of State Forestry Administration on Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Longdong, Guangzhou 510520, China
| | - Jie Li
- Key Laboratory of State Forestry Administration on Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Longdong, Guangzhou 510520, China
| | - Huanhua Huang
- Guangdong Academy of Forestry, Longdong, Guangzhou 510520, China
| | - Xiaoyong Mo
- College of Forestry, South China Agricultural University, 284 Block, Wushan Street, Guangzhou 510642, China
| | - Siming Gan
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Xiangshan Road, Beijing 100091, China
- Key Laboratory of State Forestry Administration on Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Longdong, Guangzhou 510520, China
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16
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Suarez-Gonzalez A, Hefer CA, Christe C, Corea O, Lexer C, Cronk QCB, Douglas CJ. Genomic and functional approaches reveal a case of adaptive introgression fromPopulus balsamifera(balsam poplar) inP. trichocarpa(black cottonwood). Mol Ecol 2016; 25:2427-42. [DOI: 10.1111/mec.13539] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Revised: 01/02/2016] [Accepted: 01/06/2016] [Indexed: 01/14/2023]
Affiliation(s)
| | - Charles A. Hefer
- Department of Botany; University of British Columbia; Vancouver BC V6T 1Z4 Canada
| | - Camille Christe
- Unit of Ecology & Evolution; Department of Biology; University of Fribourg; CH-1700 Fribourg Switzerland
| | - Oliver Corea
- Department of Biology and Centre for Forest Biology; University of Victoria; Victoria BC V8W 3N5 Canada
| | - Christian Lexer
- Unit of Ecology & Evolution; Department of Biology; University of Fribourg; CH-1700 Fribourg Switzerland
- Department of Botany and Biodiversity Research; University of Vienna; A-1030 Vienna Austria
| | - Quentin C. B. Cronk
- Department of Botany; University of British Columbia; Vancouver BC V6T 1Z4 Canada
| | - Carl J. Douglas
- Department of Botany; University of British Columbia; Vancouver BC V6T 1Z4 Canada
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