1
|
Bruxaux J, Zhao W, Hall D, Curtu AL, Androsiuk P, Drouzas AD, Gailing O, Konrad H, Sullivan AR, Semerikov V, Wang XR. Scots pine - panmixia and the elusive signal of genetic adaptation. THE NEW PHYTOLOGIST 2024; 243:1231-1246. [PMID: 38308133 DOI: 10.1111/nph.19563] [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: 11/15/2023] [Accepted: 01/14/2024] [Indexed: 02/04/2024]
Abstract
Scots pine is the foundation species of diverse forested ecosystems across Eurasia and displays remarkable ecological breadth, occurring in environments ranging from temperate rainforests to arid tundra margins. Such expansive distributions can be favored by various demographic and adaptive processes and the interactions between them. To understand the impact of neutral and selective forces on genetic structure in Scots pine, we conducted range-wide population genetic analyses on 2321 trees from 202 populations using genotyping-by-sequencing, reconstructed the recent demography of the species and examined signals of genetic adaptation. We found a high and uniform genetic diversity across the entire range (global FST 0.048), no increased genetic load in expanding populations and minor impact of the last glacial maximum on historical population sizes. Genetic-environmental associations identified only a handful of single-nucleotide polymorphisms significantly linked to environmental gradients. The results suggest that extensive gene flow is predominantly responsible for the observed genetic patterns in Scots pine. The apparent missing signal of genetic adaptation is likely attributed to the intricate genetic architecture controlling adaptation to multi-dimensional environments. The panmixia metapopulation of Scots pine offers a good study system for further exploration into how genetic adaptation and plasticity evolve under gene flow and changing environment.
Collapse
Affiliation(s)
- Jade Bruxaux
- Department of Ecology and Environmental Science, Umeå Plant Science Center, Umeå University, 901 87, Umeå, Sweden
| | - Wei Zhao
- Department of Ecology and Environmental Science, Umeå Plant Science Center, Umeå University, 901 87, Umeå, Sweden
| | - David Hall
- Department of Ecology and Environmental Science, Umeå Plant Science Center, Umeå University, 901 87, Umeå, Sweden
- Forestry Research Institute of Sweden (Skogforsk), 918 21, Sävar, Sweden
| | | | - Piotr Androsiuk
- Department of Plant Physiology, Genetics and Biotechnology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, 10-719, Olsztyn, Poland
| | - Andreas D Drouzas
- Laboratory of Systematic Botany and Phytogeography, School of Biology, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Oliver Gailing
- Department of Forest Genetics and Forest Tree Breeding, University of Göttingen, 37077, Göttingen, Germany
| | - Heino Konrad
- Department of Forest Biodiversity and Nature Conservation, Unit of Ecological Genetics, Austrian Research Centre for Forests (BFW), 1140, Vienna, Austria
| | - Alexis R Sullivan
- Department of Ecology and Environmental Science, Umeå Plant Science Center, Umeå University, 901 87, Umeå, Sweden
| | - Vladimir Semerikov
- Institute of Plant and Animal Ecology, Ural Division of Russian Academy of Sciences, 620144, Ekaterinburg, Russia
| | - Xiao-Ru Wang
- Department of Ecology and Environmental Science, Umeå Plant Science Center, Umeå University, 901 87, Umeå, Sweden
| |
Collapse
|
2
|
Teyssier C, Rogier O, Claverol S, Gautier F, Lelu-Walter MA, Duruflé H. Comprehensive Organ-Specific Profiling of Douglas Fir ( Pseudotsuga menziesii) Proteome. Biomolecules 2023; 13:1400. [PMID: 37759800 PMCID: PMC10526743 DOI: 10.3390/biom13091400] [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: 08/08/2023] [Revised: 09/13/2023] [Accepted: 09/14/2023] [Indexed: 09/29/2023] Open
Abstract
The Douglas fir (Pseudotsuga menziesii) is a conifer native to North America that has become increasingly popular in plantations in France due to its many advantages as timber: rapid growth, quality wood, and good adaptation to climate change. Tree genetic improvement programs require knowledge of a species' genetic structure and history and the development of genetic markers. The very slow progress in this field, for Douglas fir as well as the entire genus Pinus, can be explained using the very large size of their genomes, as well as by the presence of numerous highly repeated sequences. Proteomics, therefore, provides a powerful way to access genomic information of otherwise challenging species. Here, we present the first Douglas fir proteomes acquired using nLC-MS/MS from 12 different plant organs or tissues. We identified 3975 different proteins and quantified 3462 of them, then examined the distribution of specific proteins across plant organs/tissues and their implications in various molecular processes. As the first large proteomic study of a resinous tree species with organ-specific profiling, this short note provides an important foundation for future genomic annotations of conifers and other trees.
Collapse
Affiliation(s)
| | - Odile Rogier
- INRAE, ONF, BioForA, UMR 0588, 45075 Orleans, France
| | - Stéphane Claverol
- Plateforme de Protéomique, Université de Bordeaux, 33405 Bordeaux, France
| | | | | | | |
Collapse
|
3
|
Mostert‐O'Neill MM, Tate H, Reynolds SM, Mphahlele MM, van den Berg G, Verryn SD, Acosta JJ, Borevitz JO, Myburg AA. Genomic consequences of artificial selection during early domestication of a wood fibre crop. THE NEW PHYTOLOGIST 2022; 235:1944-1956. [PMID: 35657639 PMCID: PMC9541791 DOI: 10.1111/nph.18297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 05/20/2022] [Indexed: 06/15/2023]
Abstract
From its origins in Australia, Eucalyptus grandis has spread to every continent, except Antarctica, as a wood crop. It has been cultivated and bred for over 100 yr in places such as South Africa. Unlike most annual crops and fruit trees, domestication of E. grandis is still in its infancy, representing a unique opportunity to interrogate the genomic consequences of artificial selection early in the domestication process. To determine how a century of artificial selection has changed the genome of E. grandis, we generated single nucleotide polymorphism genotypes for 1080 individuals from three advanced South African breeding programmes using the EUChip60K chip, and investigated population structure and genome-wide differentiation patterns relative to wild progenitors. Breeding and wild populations appeared genetically distinct. We found genomic evidence of evolutionary processes known to have occurred in other plant domesticates, including interspecific introgression and intraspecific infusion from wild material. Furthermore, we found genomic regions with increased linkage disequilibrium and genetic differentiation, putatively representing early soft sweeps of selection. This is, to our knowledge, the first study of genomic signatures of domestication in a timber species looking beyond the first few generations of cultivation. Our findings highlight the importance of intra- and interspecific hybridization during early domestication.
Collapse
Affiliation(s)
- Marja M. Mostert‐O'Neill
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI)University of PretoriaPrivate Bag X20Pretoria0028South Africa
| | - Hannah Tate
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI)University of PretoriaPrivate Bag X20Pretoria0028South Africa
| | - S. Melissa Reynolds
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI)University of PretoriaPrivate Bag X20Pretoria0028South Africa
| | - Makobatjatji M. Mphahlele
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI)University of PretoriaPrivate Bag X20Pretoria0028South Africa
- Mondi Forests, Tree Improvement Technology Programme, Trahar Technology Centre – TTCMountain Home Estate, Off Dennis Shepstone Dr.Hilton3245South Africa
| | - Gert van den Berg
- Sappi Forests Research, Shaw Research CentrePO Box 473Howick3290South Africa
| | - Steve D. Verryn
- Creation Breeding Innovations75 Kafue St.Lynnwood Glen0081South Africa
| | - Juan J. Acosta
- Camcore, Department of Forestry and Environmental ResourcesNorth Carolina State UniversityPO Box 7626RaleighNC27695USA
| | - Justin O. Borevitz
- Research School of Biology and Centre for Biodiversity Analysis, ARC Centre of Excellence in Plant Energy BiologyAustralian National UniversityCanberraACT0200Australia
| | - Alexander A. Myburg
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI)University of PretoriaPrivate Bag X20Pretoria0028South Africa
| |
Collapse
|
4
|
Development and Validation of a 36K SNP Array for Radiata Pine (Pinus radiata D.Don). FORESTS 2022. [DOI: 10.3390/f13020176] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Radiata pine (Pinus radiata D.Don) is one of the world’s most domesticated pines and a key economic species in New Zealand. Thus, the development of genomic resources for radiata pine has been a high priority for both research and commercial breeding. Leveraging off a previously developed exome capture panel, we tested the performance of 438,744 single nucleotide polymorphisms (SNPs) on a screening array (NZPRAD01) and then selected 36,285 SNPs for a final genotyping array (NZPRAD02). These SNPs aligned to 15,372 scaffolds from the Pinus taeda L. v. 1.01e assembly, and 20,039 contigs from the radiata pine transcriptome assembly. The genotyping array was tested on more than 8000 samples, including material from archival progenitors, current breeding trials, nursery material, clonal lines, and material from Australia. Our analyses indicate that the array is performing well, with sample call rates greater than 98% and a sample reproducibility of 99.9%. Genotyping in two linkage mapping families indicated that the SNPs are well distributed across the 12 linkage groups. Using genotypic data from this array, we were also able to differentiate representatives of the five recognized provenances of radiata pine, Año Nuevo, Monterey, Cambria, Cedros and Guadalupe. Furthermore, principal component analysis of genotyped trees revealed clear patterns of population structure, with the primary axis of variation driven by provenance ancestry and the secondary axis reflecting breeding activities. This represents the first commercial use of genomics in a radiata pine breeding program.
Collapse
|
5
|
Jahner JP, Parchman TL, Matocq MD. Multigenerational backcrossing and introgression between two woodrat species at an abrupt ecological transition. Mol Ecol 2021; 30:4245-4258. [PMID: 34219316 DOI: 10.1111/mec.16056] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 06/28/2021] [Indexed: 12/27/2022]
Abstract
When organisms experience secondary contact after allopatric divergence, genomic regions can introgress differentially depending on their relationships with adaptation, reproductive isolation, recombination, and drift. Analyses of genome-wide patterns of divergence and introgression could provide insight into the outcomes of hybridization and the potential relationship between allopatric divergence and reproductive isolation. Here, we generate population genetic data (26,262 SNPs; 353 individuals) using a reduced-representation sequencing approach to quantify patterns of ancestry, differentiation, and introgression between a pair of ecologically distinct mammals-the desert woodrat (N. lepida) and Bryant's woodrat (N. bryanti)-that hybridize at a sharp ecotone in southern California. Individual ancestry estimates confirmed that hybrids were rare in this bimodal hybrid zone, and entirely consisted of a few F1 individuals and a broad range of multigenerational backcrosses. Genomic cline analyses indicated more than half of loci had elevated introgression from one genomic background into the other. However, introgression was not associated with relative or absolute measures of divergence, and loci with extreme values for both were not typically found near detoxification enzymes previously implicated in dietary specialization for woodrats. The decoupling of differentiation and introgression suggests that processes other than adaptation, such as drift, may underlie the extreme clines at this contact zone.
Collapse
Affiliation(s)
- Joshua P Jahner
- Department of Biology, University of Nevada, Reno, Nevada, USA.,Department of Botany, University of Wyoming, Laramie, Wyoming, USA
| | - Thomas L Parchman
- Department of Biology, University of Nevada, Reno, Nevada, USA.,Program in Ecology, Evolution, and Conservation Biology, University of Nevada, Reno, Nevada, USA
| | - Marjorie D Matocq
- Program in Ecology, Evolution, and Conservation Biology, University of Nevada, Reno, Nevada, USA.,Department of Natural Resources and Environmental Science, University of Nevada, Reno, Nevada, USA
| |
Collapse
|
6
|
Caballero M, Lauer E, Bennett J, Zaman S, McEvoy S, Acosta J, Jackson C, Townsend L, Eckert A, Whetten RW, Loopstra C, Holliday J, Mandal M, Wegrzyn JL, Isik F. Toward genomic selection in Pinus taeda: Integrating resources to support array design in a complex conifer genome. APPLICATIONS IN PLANT SCIENCES 2021; 9:e11439. [PMID: 34268018 PMCID: PMC8272584 DOI: 10.1002/aps3.11439] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 05/21/2021] [Indexed: 05/13/2023]
Abstract
PREMISE An informatics approach was used for the construction of an Axiom genotyping array from heterogeneous, high-throughput sequence data to assess the complex genome of loblolly pine (Pinus taeda). METHODS High-throughput sequence data, sourced from exome capture and whole genome reduced-representation approaches from 2698 trees across five sequence populations, were analyzed with the improved genome assembly and annotation for the loblolly pine. A variant detection, filtering, and probe design pipeline was developed to detect true variants across and within populations. From 8.27 million variants, a total of 642,275 were evaluated and 423,695 of those were screened across a range-wide population. RESULTS The final informatics and screening approach delivered an Axiom array representing 46,439 high-confidence variants to the forest tree breeding and genetics community. Based on the annotated reference genome, 34% were located in or directly upstream or downstream of genic regions. DISCUSSION The Pita50K array represents a genome-wide resource developed from sequence data for an economically important conifer, loblolly pine. It uniquely integrates independent projects that assessed trees sampled across the native range. The challenges associated with the large and repetitive genome are addressed in the development of this resource.
Collapse
Affiliation(s)
- Madison Caballero
- Department of Ecology and Evolutionary BiologyUniversity of ConnecticutStorrsConnecticut06269USA
| | - Edwin Lauer
- Department of Forestry and Environmental ResourcesNorth Carolina State UniversityRaleighNorth Carolina27695USA
| | - Jeremy Bennett
- Department of Ecology and Evolutionary BiologyUniversity of ConnecticutStorrsConnecticut06269USA
| | - Sumaira Zaman
- Department of Ecology and Evolutionary BiologyUniversity of ConnecticutStorrsConnecticut06269USA
| | - Susan McEvoy
- Department of Ecology and Evolutionary BiologyUniversity of ConnecticutStorrsConnecticut06269USA
| | - Juan Acosta
- Department of Forestry and Environmental ResourcesNorth Carolina State UniversityRaleighNorth Carolina27695USA
| | - Colin Jackson
- Department of Forestry and Environmental ResourcesNorth Carolina State UniversityRaleighNorth Carolina27695USA
| | - Laura Townsend
- Department of Forestry and Environmental ResourcesNorth Carolina State UniversityRaleighNorth Carolina27695USA
| | - Andrew Eckert
- Department of BiologyVirginia Commonwealth UniversityRichmondVirginia23284USA
| | - Ross W. Whetten
- Department of Forestry and Environmental ResourcesNorth Carolina State UniversityRaleighNorth Carolina27695USA
| | - Carol Loopstra
- Department of Ecology and Conservation BiologyTexas A&M UniversityCollege StationTexas77843USA
| | - Jason Holliday
- Department of Forest Resources and Environmental ConservationVirginia Polytechnic Institute and State UniversityBlacksburgVirginia24061USA
| | - Mihir Mandal
- Department of BiologyClaflin UniversityOrangeburgSouth Carolina29115USA
| | - Jill L. Wegrzyn
- Department of Ecology and Evolutionary BiologyUniversity of ConnecticutStorrsConnecticut06269USA
| | - Fikret Isik
- Department of Forestry and Environmental ResourcesNorth Carolina State UniversityRaleighNorth Carolina27695USA
| |
Collapse
|
7
|
Matallana-Ramirez LP, Whetten RW, Sanchez GM, Payn KG. Breeding for Climate Change Resilience: A Case Study of Loblolly Pine ( Pinus taeda L.) in North America. FRONTIERS IN PLANT SCIENCE 2021; 12:606908. [PMID: 33995428 PMCID: PMC8119900 DOI: 10.3389/fpls.2021.606908] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 04/08/2021] [Indexed: 05/25/2023]
Abstract
Earth's atmosphere is warming and the effects of climate change are becoming evident. A key observation is that both the average levels and the variability of temperature and precipitation are changing. Information and data from new technologies are developing in parallel to provide multidisciplinary opportunities to address and overcome the consequences of these changes in forest ecosystems. Changes in temperature and water availability impose multidimensional environmental constraints that trigger changes from the molecular to the forest stand level. These can represent a threat for the normal development of the tree from early seedling recruitment to adulthood both through direct mortality, and by increasing susceptibility to pathogens, insect attack, and fire damage. This review summarizes the strengths and shortcomings of previous work in the areas of genetic variation related to cold and drought stress in forest species with particular emphasis on loblolly pine (Pinus taeda L.), the most-planted tree species in North America. We describe and discuss the implementation of management and breeding strategies to increase resilience and adaptation, and discuss how new technologies in the areas of engineering and genomics are shaping the future of phenotype-genotype studies. Lessons learned from the study of species important in intensively-managed forest ecosystems may also prove to be of value in helping less-intensively managed forest ecosystems adapt to climate change, thereby increasing the sustainability and resilience of forestlands for the future.
Collapse
Affiliation(s)
- Lilian P. Matallana-Ramirez
- Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, Raleigh, NC, United States
| | - Ross W. Whetten
- Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, Raleigh, NC, United States
| | - Georgina M. Sanchez
- Center for Geospatial Analytics, North Carolina State University, Raleigh, Raleigh, NC, United States
| | - Kitt G. Payn
- Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, Raleigh, NC, United States
| |
Collapse
|
8
|
Zhang Y, Luan Q, Jiang J, Li Y. Prediction and Utilization of Malondialdehyde in Exotic Pine Under Drought Stress Using Near-Infrared Spectroscopy. FRONTIERS IN PLANT SCIENCE 2021; 12:735275. [PMID: 34733301 PMCID: PMC8558207 DOI: 10.3389/fpls.2021.735275] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 09/17/2021] [Indexed: 05/10/2023]
Abstract
Drought is a major abiotic stress that adversely affects the growth and productivity of plants. Malondialdehyde (MDA), a substance produced by membrane lipids in response to reactive oxygen species (ROS), can be used as a drought indicator to evaluate the degree of plasma membrane damage and the ability of plants to drought stress tolerance. Still measuring MDA is usually a labor- and time-consuming task. In this study, near-infrared (NIR) spectroscopy combined with partial least squares (PLS) was used to obtain rapid and high-throughput measurements of MDA, and the application of this technique to plant drought stress experiments was also investigated. Two exotic conifer tree species, namely, slash pine (Pinus elliottii) and loblolly pine (Pinus taeda), were used as plant material exposed to drought stress; different types of spectral preprocessing methods and important feature-selection algorithms were applied to the PLS model to calibrate it and obtain the best MDA-predicting model. The results show that the best PLS model is established via the combined treatment of detrended variable-significant multivariate correlation algorithm (DET-sMC), where latent variables (LVs) were 6. This model has a respectable predictive capability, with a correlation coefficient (R 2) of 0.66, a root mean square error (RMSE) of 2.28%, and a residual prediction deviation (RPD) of 1.51, and it was successfully implemented in drought stress experiments as a reliable and non-destructive method to detect the MDA content in real time.
Collapse
|
9
|
Chang CYY, Bräutigam K, Hüner NPA, Ensminger I. Champions of winter survival: cold acclimation and molecular regulation of cold hardiness in evergreen conifers. THE NEW PHYTOLOGIST 2021; 229:675-691. [PMID: 32869329 DOI: 10.1111/nph.16904] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 07/31/2020] [Indexed: 06/11/2023]
Abstract
Evergreen conifers are champions of winter survival, based on their remarkable ability to acclimate to cold and develop cold hardiness. Counterintuitively, autumn cold acclimation is triggered not only by exposure to low temperature, but also by a combination of decreasing temperature, decreasing photoperiod and changes in light quality. These environmental cues control a network of signaling pathways that coordinate cold acclimation and cold hardiness in overwintering conifers, leading to cessation of growth, bud dormancy, freezing tolerance and changes in energy metabolism. Advances in genomic, transcriptomic and metabolomic tools for conifers have improved our understanding of how trees sense and respond to changes in temperature and light during cold acclimation and the development of cold hardiness, but there remain considerable gaps deserving further research in conifers. In the first section of this review, we focus on the physiological mechanisms used by evergreen conifers to adjust metabolism seasonally and to protect overwintering tissues against winter stresses. In the second section, we review how perception of low temperature and photoperiod regulate the induction of cold acclimation. Finally, we explore the evolutionary context of cold acclimation in conifers and evaluate challenges imposed on them by changing climate and discuss emerging areas of research in the field.
Collapse
Affiliation(s)
- Christine Yao-Yun Chang
- Soil and Crop Sciences Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Katharina Bräutigam
- Department of Biology, University of Toronto, Mississauga, ON, L5L1C6, Canada
- Graduate Department of Cell and Systems Biology, University of Toronto, Toronto, ON, M5S 3G5, Canada
| | - Norman P A Hüner
- Department of Biology and The Biotron Experimental Climate Change Research Centre, Western University, London, ON, N6A5B7, Canada
| | - Ingo Ensminger
- Department of Biology, University of Toronto, Mississauga, ON, L5L1C6, Canada
- Graduate Department of Cell and Systems Biology, University of Toronto, Toronto, ON, M5S 3G5, Canada
- Graduate Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, M5S 3B2, Canada
| |
Collapse
|
10
|
Wang X, Bernhardsson C, Ingvarsson PK. Demography and Natural Selection Have Shaped Genetic Variation in the Widely Distributed Conifer Norway Spruce (Picea abies). Genome Biol Evol 2020; 12:3803-3817. [PMID: 31958121 PMCID: PMC7046165 DOI: 10.1093/gbe/evaa005] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/14/2020] [Indexed: 12/13/2022] Open
Abstract
Under the neutral theory, species with larger effective population size are expected to harbor higher genetic diversity. However, across a wide variety of organisms, the range of genetic diversity is orders of magnitude more narrow than the range of effective population size. This observation has become known as Lewontin’s paradox and although aspects of this phenomenon have been extensively studied, the underlying causes for the paradox remain unclear. Norway spruce (Picea abies) is a widely distributed conifer species across the northern hemisphere, and it consequently plays a major role in European forestry. Here, we use whole-genome resequencing data from 35 individuals to perform population genomic analyses in P. abies in an effort to understand what drives genome-wide patterns of variation in this species. Despite having a very wide geographic distribution and an corresponding enormous current population size, our analyses find that genetic diversity of P. abies is low across a number of populations (π = 0.0049 in Central-Europe, π = 0.0063 in Sweden-Norway, π = 0.0063 in Finland). To assess the reasons for the low levels of genetic diversity, we infer the demographic history of the species and find that it is characterized by several reoccurring bottlenecks with concomitant decreases in effective population size can, at least partly, provide an explanation for low polymorphism we observe in P. abies. Further analyses suggest that recurrent natural selection, both purifying and positive selection, can also contribute to the loss of genetic diversity in Norway spruce by reducing genetic diversity at linked sites. Finally, the overall low mutation rates seen in conifers can also help explain the low genetic diversity maintained in Norway spruce.
Collapse
Affiliation(s)
- Xi Wang
- Umeå Plant Science Centre, Department of Ecology and Environmental Science, Umeå University, Sweden.,Linnean Centre for Plant Biology, Department of Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Carolina Bernhardsson
- Umeå Plant Science Centre, Department of Ecology and Environmental Science, Umeå University, Sweden.,Linnean Centre for Plant Biology, Department of Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden.,Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Pär K Ingvarsson
- Linnean Centre for Plant Biology, Department of Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| |
Collapse
|
11
|
Genomics of Clinal Local Adaptation in Pinus sylvestris Under Continuous Environmental and Spatial Genetic Setting. G3-GENES GENOMES GENETICS 2020; 10:2683-2696. [PMID: 32546502 PMCID: PMC7407466 DOI: 10.1534/g3.120.401285] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Understanding the consequences of local adaptation at the genomic diversity is a central goal in evolutionary genetics of natural populations. In species with large continuous geographical distributions the phenotypic signal of local adaptation is frequently clear, but the genetic basis often remains elusive. We examined the patterns of genetic diversity in Pinus sylvestris, a keystone species in many Eurasian ecosystems with a huge distribution range and decades of forestry research showing that it is locally adapted to the vast range of environmental conditions. Making P. sylvestris an even more attractive subject of local adaptation study, population structure has been shown to be weak previously and in this study. However, little is known about the molecular genetic basis of adaptation, as the massive size of gymnosperm genomes has prevented large scale genomic surveys. We generated a both geographically and genomically extensive dataset using a targeted sequencing approach. By applying divergence-based and landscape genomics methods we identified several loci contributing to local adaptation, but only few with large allele frequency changes across latitude. We also discovered a very large (ca. 300 Mbp) putative inversion potentially under selection, which to our knowledge is the first such discovery in conifers. Our results call for more detailed analysis of structural variation in relation to genomic basis of local adaptation, emphasize the lack of large effect loci contributing to local adaptation in the coding regions and thus point out the need for more attention toward multi-locus analysis of polygenic adaptation.
Collapse
|
12
|
Pyhäjärvi T, Kujala ST, Savolainen O. 275 years of forestry meets genomics in Pinus sylvestris. Evol Appl 2020; 13:11-30. [PMID: 31988655 PMCID: PMC6966708 DOI: 10.1111/eva.12809] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 04/05/2019] [Accepted: 04/24/2019] [Indexed: 12/12/2022] Open
Abstract
Pinus sylvestris has a long history of basic and applied research that is relevant for both forestry and evolutionary studies. Its patterns of adaptive variation and role in forest economic and ecological systems have been studied extensively for nearly 275 years, detailed demography for a 100 years and mating system more than 50 years. However, its reference genome sequence is not yet available and genomic studies have been lagging compared to, for example, Pinus taeda and Picea abies, two other economically important conifers. Despite the lack of reference genome, many modern genomic methods are applicable for a more detailed look at its biological characteristics. For example, RNA-seq has revealed a complex transcriptional landscape and targeted DNA sequencing displays an excess of rare variants and geographically homogenously distributed molecular genetic diversity. Current DNA and RNA resources can be used as a reference for gene expression studies, SNP discovery, and further targeted sequencing. In the future, specific consequences of the large genome size, such as functional effects of regulatory open chromatin regions and transposable elements, should be investigated more carefully. For forest breeding and long-term management purposes, genomic data can help in assessing the genetic basis of inbreeding depression and the application of genomic tools for genomic prediction and relatedness estimates. Given the challenges of breeding (long generation time, no easy vegetative propagation) and the economic importance, application of genomic tools has a potential to have a considerable impact. Here, we explore how genomic characteristics of P. sylvestris, such as rare alleles and the low extent of linkage disequilibrium, impact the applicability and power of the tools.
Collapse
Affiliation(s)
- Tanja Pyhäjärvi
- Department of Ecology and GeneticsUniversity of OuluOuluFinland
- Biocenter OuluUniversity of OuluOuluFinland
| | | | - Outi Savolainen
- Department of Ecology and GeneticsUniversity of OuluOuluFinland
- Biocenter OuluUniversity of OuluOuluFinland
| |
Collapse
|
13
|
A Complete Transcriptional Landscape Analysis of Pinus elliottii Engelm. Using Third-Generation Sequencing and Comparative Analysis in the Pinus Phylogeny. FORESTS 2019. [DOI: 10.3390/f10110942] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The planting of Pinus elliottii Engelm. has now reached close to three million ha in China. Molecular breeding as part of the improvement program for P. elliottii in southern China has been carried out in recent years. Third-generation sequencing (Pacbio sequencing technology, TGS) was used to obtain the exome of P. elliottii for molecular breeding. A total of 35.8 Gb clean reads were generated using TGS. After removing the redundant reads, we obtained 80,339 high-accuracy transcripts. Significantly, a total of 76,411 transcripts (95.1%) were blasted to public annotation databases. We predicted 65,062 intact coding sequences (CDSs), 8916 alternative splicing events, 1937 long non-coding RNAs, and 22,109 simple sequence repeats (SSRs) based on these obtained transcripts. Using the public databases and the data obtained above, 23 orthologous single-copy genes were identified to analyze the phylogenetic relationships for Pinus firstly including P. elliottii. Many positive selection genes involved in important biological processes and metabolism pathways were identified between P. elliottii and other pines. These positive selection genes could be candidate genes to be researched on the genetic basis of superior performance. Our study is the first to reveal the full-length and well-annotated transcripts of P. elliottii, which could provide reference for short transcriptome sequences in the research of genetics, phylogenetics, and genetic improvement for the non-reference genome species.
Collapse
|
14
|
Lu M, Hodgins KA, Degner JC, Yeaman S. Purifying selection does not drive signatures of convergent local adaptation of lodgepole pine and interior spruce. BMC Evol Biol 2019; 19:110. [PMID: 31138118 PMCID: PMC6537219 DOI: 10.1186/s12862-019-1438-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 05/15/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Lodgepole pine (Pinus contorta) and interior spruce (Picea glauca, Picea engelmannii, and their hybrids) are distantly related conifer species. Previous studies identified 47 genes containing variants associated with environmental variables in both species, providing evidence of convergent local adaptation. However, if the intensity of purifying selection varies with the environment, clines in nucleotide diversity could evolve through linked (background) selection that would yield allele frequency-environment signatures resembling local adaptation. If similar geographic patterns in the strength of purifying selection occur in these species, this could result in the convergent signatures of local adaptation, especially if the landscape of recombination is conserved. In the present study, we investigated whether spatially/environmentally varying purifying selection could give rise to the convergent signatures of local adaptation that had previously reported. RESULTS We analyzed 86 lodgepole pine and 50 interior spruce natural populations spanning heterogeneous environments in western Canada where previous analyses had found signatures of convergent local adaptation. We estimated nucleotide diversity and Tajima's D for each gene within each population and calculated the strength of correlations between nucleotide diversity and environmental variables. Overall, these estimates in the genes with previously identified convergent local adaptation signatures had no similar pattern between pine and spruce. Clines in nucleotide diversity along environmental variables were found for interior spruce, but not for lodgepole pine. In spruce, genes with convergent adaption signatures showed a higher strength of correlations than genes without convergent adaption signatures, but there was no such disparity in pine, which suggests the pattern in spruce may have arisen due to a combination of selection and hybridization. CONCLUSIONS The results rule out purifying/background selection as a driver of convergent local adaption signatures in lodgepole pine and interior spruce.
Collapse
Affiliation(s)
- Mengmeng Lu
- Department of Biological Sciences, University of Calgary, 507 Campus Drive NW, Calgary, T2N 4S8, Canada.
| | - Kathryn A Hodgins
- School of Biological Sciences, Monash University - Clayton Campus, Building 17, Wellington Road, Melbourne, 3800, Australia
| | - Jon C Degner
- Department of Forest and Conservation Sciences, Forest Sciences Centre 3041, University of British Columbia, 2424 Main Mall, Vancouver, V6T 1Z4, Canada
| | - Sam Yeaman
- Department of Biological Sciences, University of Calgary, 507 Campus Drive NW, Calgary, T2N 4S8, Canada
| |
Collapse
|