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Hayatgheibi H, Hallingbäck HR, Lundqvist SO, Grahn T, Scheepers G, Nordström P, Chen ZQ, Kärkkäinen K, Wu HX, García-Gil MR. Implications of accounting for marker-based population structure in the quantitative genetic evaluation of genetic parameters related to growth and wood properties in Norway spruce. BMC Genom Data 2024; 25:60. [PMID: 38877416 PMCID: PMC11177499 DOI: 10.1186/s12863-024-01241-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Accepted: 06/05/2024] [Indexed: 06/16/2024] Open
Abstract
BACKGROUND Forest geneticists typically use provenances to account for population differences in their improvement schemes; however, the historical records of the imported materials might not be very precise or well-aligned with the genetic clusters derived from advanced molecular techniques. The main objective of this study was to assess the impact of marker-based population structure on genetic parameter estimates related to growth and wood properties and their trade-offs in Norway spruce, by either incorporating it as a fixed effect (model-A) or excluding it entirely from the analysis (model-B). RESULTS Our results indicate that models incorporating population structure significantly reduce estimates of additive genetic variance, resulting in substantial reduction of narrow-sense heritability. However, these models considerably improve prediction accuracies. This was particularly significant for growth and solid-wood properties, which showed to have the highest population genetic differentiation (QST) among the studied traits. Additionally, although the pattern of correlations remained similar across the models, their magnitude was slightly lower for models that included population structure as a fixed effect. This suggests that selection, consistently performed within populations, might be less affected by unfavourable genetic correlations compared to mass selection conducted without pedigree restrictions. CONCLUSION We conclude that the results of models properly accounting for population structure are more accurate and less biased compared to those neglecting this effect. This might have practical implications for breeders and forest managers where, decisions based on imprecise selections can pose a high risk to economic efficiency.
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Affiliation(s)
- Haleh Hayatgheibi
- Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences (SLU), Umeå, Sweden.
| | | | | | | | | | | | - Zhi-Qiang Chen
- Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences (SLU), Umeå, Sweden
| | | | - Harry X Wu
- Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences (SLU), Umeå, Sweden
- Beijing Advanced Innovation Centre for Tree Breeding By Molecular Design, Beijing Forestry University, Beijing, China
- Black Mountain Laboratory, CSIRO National Collection Research Australia, Canberra, Australia
| | - M Rosario García-Gil
- Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences (SLU), Umeå, Sweden
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2
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Schrieber K, Glüsing S, Peters L, Eichert B, Althoff M, Schwarz K, Erfmeier A, Demetrowitsch T. Population divergence in heat and drought responses of a coastal plant: from metabolic phenotypes to plant morphology and growth. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:4559-4578. [PMID: 37147850 DOI: 10.1093/jxb/erad147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 05/05/2023] [Indexed: 05/07/2023]
Abstract
Studying intraspecific variation in multistress responses is central for predicting and managing the population dynamics of wild plant species under rapid global change. Yet, it remains a challenging goal in this field to integrate knowledge on the complex biochemical underpinnings for the targeted 'non-model' species. Here, we studied divergence in combined drought and heat responses among Northern and Southern European populations of the dune plant Cakile maritima, by combining comprehensive plant phenotyping with metabolic profiling via FT-ICR-MS and UPLC-TQ-MS/MS. We observed pronounced constitutive divergence in growth phenology, leaf functional traits, and defence chemistry (glucosinolates and alkaloids) among population origins. Most importantly, the magnitude of growth reduction under drought was partly weaker in southern plants and associated with divergence in plastic growth responses (leaf abscission) and the modulation of primary and specialized metabolites with known central functions not only in plant abiotic but also in biotic stress responses. Our study indicates that divergent selection has shaped the constitutive and drought-/heat-induced expression of numerous morphological and biochemical functional traits to mediate higher abiotic stress resistance in southern Cakile populations, and highlights that metabolomics can be a powerful tool to explore the underlying mechanisms of local adaptation in 'non-model' species.
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Affiliation(s)
- Karin Schrieber
- Faculty of Mathematics and Natural Sciences, Institute for Ecosystem Research, Division of Geobotany, Kiel University, D-24118 Kiel, Germany
| | - Svea Glüsing
- Faculty of Agricultural and Nutritional Sciences, Institute for Human Nutrition and Food Science, Division of Food Technology, Kiel University, D-24118 Kiel, Germany
| | - Lisa Peters
- Faculty of Mathematics and Natural Sciences, Institute for Ecosystem Research, Division of Geobotany, Kiel University, D-24118 Kiel, Germany
- Department of Agriculture, Ecotrophology and Landscape Development, Anhalt University of Applied Sciences, D-06406 Bernburg (Saale), Germany
| | - Beke Eichert
- Faculty of Mathematics and Natural Sciences, Institute for Ecosystem Research, Division of Geobotany, Kiel University, D-24118 Kiel, Germany
- Institute of Plant Science and Microbiology, University of Hamburg, D-20146 Hamburg, Germany
| | - Merle Althoff
- Faculty of Mathematics and Natural Sciences, Institute for Ecosystem Research, Division of Geobotany, Kiel University, D-24118 Kiel, Germany
| | - Karin Schwarz
- Faculty of Agricultural and Nutritional Sciences, Institute for Human Nutrition and Food Science, Division of Food Technology, Kiel University, D-24118 Kiel, Germany
| | - Alexandra Erfmeier
- Faculty of Mathematics and Natural Sciences, Institute for Ecosystem Research, Division of Geobotany, Kiel University, D-24118 Kiel, Germany
| | - Tobias Demetrowitsch
- Faculty of Agricultural and Nutritional Sciences, Institute for Human Nutrition and Food Science, Division of Food Technology, Kiel University, D-24118 Kiel, Germany
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3
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Zhai J, Li Z, Si J, Zhang S, Han X, Chen X. Structural and Functional Responses of the Heteromorphic Leaves of Different Tree Heights on Populus euphratica Oliv. to Different Soil Moisture Conditions. PLANTS 2022; 11:plants11182376. [PMID: 36145777 PMCID: PMC9505870 DOI: 10.3390/plants11182376] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 09/05/2022] [Indexed: 11/16/2022]
Abstract
Populus euphratica Oliv., a pioneer species of desert riparian forest, is characterized heterophylly. To understand the adaptation strategies of the heteromorphic leaves of P. euphratica to soil drought, we assessed the structural and functional characteristics of the heteromorphic leaves at different heights in suitable soil moisture conditions (groundwater depth 1.5 m) and drought conditions (groundwater depth 5 m), which include morphology, anatomical structure, photosynthetic capacity, water use efficiency, osmotic adjustment capacity, and endogenous hormones. These results indicate that leaf area, leaf thickness, fence tissue, palisade-to-sea ratio, main vein xylem area, vessel area, net photosynthetic rate, transpiration rate, and proline, MDA, IAA, GA3, and ZR contents showed a positive correlation with the tree height under the two soil moisture conditions, but leaf shape index, leaf water potential (LWP), and ABA content showed a decreasing trend. In addition, the main vein vascular bundle area, main vein xylem area, and contents of malondialdehyde, ABA, GA3, and IAA were significantly greater under soil drought conditions than normal soil water content. Under soil drought stress, the heteromorphic leaves of P. euphratica showed more investment in anatomical structure and greater water use efficiency, proline, and hormone contents, and synergistic changes to maintain high photosynthetic efficiency. This is an adaptation strategy to water stress caused by soil drought and tree height changes.
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Affiliation(s)
- Juntuan Zhai
- College of Life Sciences, Tarim University and Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, Xinjiang Production & Construction Corps and Research Center of Populus Euphratica, Alar 843300, China
| | - Zhijun Li
- College of Life Sciences, Tarim University and Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, Xinjiang Production & Construction Corps and Research Center of Populus Euphratica, Alar 843300, China
- Correspondence:
| | - Jianhua Si
- Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Shanhe Zhang
- College of Life Sciences, Tarim University and Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, Xinjiang Production & Construction Corps and Research Center of Populus Euphratica, Alar 843300, China
| | - Xiaoli Han
- College of Life Sciences, Tarim University and Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, Xinjiang Production & Construction Corps and Research Center of Populus Euphratica, Alar 843300, China
| | - Xiangxiang Chen
- College of Life Sciences, Tarim University and Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, Xinjiang Production & Construction Corps and Research Center of Populus Euphratica, Alar 843300, China
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Leaf Economic and Hydraulic Traits Signal Disparate Climate Adaptation Patterns in Two Co-Occurring Woodland Eucalypts. PLANTS 2022; 11:plants11141846. [PMID: 35890479 PMCID: PMC9320154 DOI: 10.3390/plants11141846] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Revised: 07/06/2022] [Accepted: 07/09/2022] [Indexed: 11/23/2022]
Abstract
With climate change impacting trees worldwide, enhancing adaptation capacity has become an important goal of provenance translocation strategies for forestry, ecological renovation, and biodiversity conservation. Given that not every species can be studied in detail, it is important to understand the extent to which climate adaptation patterns can be generalised across species, in terms of the selective agents and traits involved. We here compare patterns of genetic-based population (co)variation in leaf economic and hydraulic traits, climate–trait associations, and genomic differentiation of two widespread tree species (Eucalyptus pauciflora and E. ovata). We studied 2-year-old trees growing in a common-garden trial established with progeny from populations of both species, pair-sampled from 22 localities across their overlapping native distribution in Tasmania, Australia. Despite originating from the same climatic gradients, the species differed in their levels of population variance and trait covariance, patterns of population variation within each species were uncorrelated, and the species had different climate–trait associations. Further, the pattern of genomic differentiation among populations was uncorrelated between species, and population differentiation in leaf traits was mostly uncorrelated with genomic differentiation. We discuss hypotheses to explain this decoupling of patterns and propose that the choice of seed provenances for climate-based plantings needs to account for multiple dimensions of climate change unless species-specific information is available.
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Hietz P, Rungwattana K, Scheffknecht S, George JP. Effects of Provenance, Growing Site, and Growth on Quercus robur Wood Anatomy and Density in a 12-Year-Old Provenance Trial. FRONTIERS IN PLANT SCIENCE 2022; 13:795941. [PMID: 35574121 PMCID: PMC9100569 DOI: 10.3389/fpls.2022.795941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 03/22/2022] [Indexed: 06/15/2023]
Abstract
Vessels are responsible for an efficient and safe water transport in angiosperm xylem. Whereas large vessels efficiently conduct the bulk of water, small vessels might be important under drought stress or after winter when large vessels are embolized. Wood anatomy can adjust to the environment by plastic adaptation, but is also modified by genetic selection, which can be driven by climate or other factors. To distinguish between plastic and genetic components on wood anatomy, we used a Quercus robur trial where trees from ten Central European provenances were planted in three locations in Austria along a rainfall gradient. Because wood anatomy also adjusts to tree size and in ring-porous species, the vessel size depends on the amount of latewood and thereby ring width, we included tree size and ring width in the analysis. We found that the trees' provenance had a significant effect on average vessel area (VA), theoretical specific hydraulic conductivity (Ks), and the vessel fraction (VF), but correlations with annual rainfall of provenances were at best weak. The trial site had a strong effect on growth (ring width, RW), which increased from the driest to the wettest site and wood density (WD), which increased from wet to dry sites. Significant site x provenance interactions were seen only for WD. Surprisingly, the drier site had higher VA, higher VF, and higher Ks. This, however, is mainly a result of greater RW and thus a greater proportion of latewood in the wetter forest. The average size of vessels > 70 μm diameter increased with rainfall. We argue that Ks, which is measured per cross-sectional area, is not an ideal parameter to compare the capacity of ring-porous trees to supply leaves with water. Small vessels (<70 μm) on average contributed only 1.4% to Ks, and we found no evidence that their number or size was adaptive to aridity. RW and tree size had strong effect on all vessel parameters, likely via the greater proportion of latewood in wide rings. This should be accounted for when searching for wood anatomical adaptations to the environment.
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Affiliation(s)
- Peter Hietz
- Department of Integrative Biology and Biodiversity Research, Institute of Botany, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Kanin Rungwattana
- Department of Integrative Biology and Biodiversity Research, Institute of Botany, University of Natural Resources and Life Sciences, Vienna, Austria
- Department of Botany, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Susanne Scheffknecht
- Department of Integrative Biology and Biodiversity Research, Institute of Botany, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Jan-Peter George
- Department of Forest Genetics, Federal Research and Training Centre for Forests, Natural Hazards and Landscape, Vienna, Austria
- Faculty of Science and Technology, University of Tartu, Tartu, Estonia
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6
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Galla SJ, Brown L, Couch-Lewis Ngāi Tahu Te Hapū O Ngāti Wheke Ngāti Waewae Y, Cubrinovska I, Eason D, Gooley RM, Hamilton JA, Heath JA, Hauser SS, Latch EK, Matocq MD, Richardson A, Wold JR, Hogg CJ, Santure AW, Steeves TE. The relevance of pedigrees in the conservation genomics era. Mol Ecol 2021; 31:41-54. [PMID: 34553796 PMCID: PMC9298073 DOI: 10.1111/mec.16192] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 09/12/2021] [Accepted: 09/17/2021] [Indexed: 01/21/2023]
Abstract
Over the past 50 years conservation genetics has developed a substantive toolbox to inform species management. One of the most long‐standing tools available to manage genetics—the pedigree—has been widely used to characterize diversity and maximize evolutionary potential in threatened populations. Now, with the ability to use high throughput sequencing to estimate relatedness, inbreeding, and genome‐wide functional diversity, some have asked whether it is warranted for conservation biologists to continue collecting and collating pedigrees for species management. In this perspective, we argue that pedigrees remain a relevant tool, and when combined with genomic data, create an invaluable resource for conservation genomic management. Genomic data can address pedigree pitfalls (e.g., founder relatedness, missing data, uncertainty), and in return robust pedigrees allow for more nuanced research design, including well‐informed sampling strategies and quantitative analyses (e.g., heritability, linkage) to better inform genomic inquiry. We further contend that building and maintaining pedigrees provides an opportunity to strengthen trusted relationships among conservation researchers, practitioners, Indigenous Peoples, and Local Communities.
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Affiliation(s)
- Stephanie J Galla
- Department of Biological Sciences, Boise State University, Boise, Idaho, USA.,School of Biological Sciences, University of Canterbury, Christchurch, Canterbury, New Zealand
| | - Liz Brown
- New Zealand Department of Conservation, Twizel, Canterbury, New Zealand
| | | | - Ilina Cubrinovska
- School of Biological Sciences, University of Canterbury, Christchurch, Canterbury, New Zealand
| | - Daryl Eason
- New Zealand Department of Conservation, Invercargill, Southland, New Zealand
| | - Rebecca M Gooley
- Smithsonian-Mason School of Conservation, Front Royal, Maryland, USA.,Center for Species Survival, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, District of Columbia, USA
| | - Jill A Hamilton
- Department of Biological Sciences, North Dakota State University, Fargo, North Dakota, USA
| | - Julie A Heath
- Department of Biological Sciences, Boise State University, Boise, Idaho, USA
| | - Samantha S Hauser
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
| | - Emily K Latch
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
| | - Marjorie D Matocq
- Department of Natural Resources and Environmental Science, Program in Ecology, Evolution and Conservation Biology, University of Nevada Reno, Reno, Nevada, USA
| | - Anne Richardson
- The Isaac Conservation and Wildlife Trust, Christchurch, Canterbury, New Zealand
| | - Jana R Wold
- School of Biological Sciences, University of Canterbury, Christchurch, Canterbury, New Zealand
| | - Carolyn J Hogg
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | - Anna W Santure
- School of Biological Sciences, University of Auckland, Auckland, Auckland, New Zealand
| | - Tammy E Steeves
- School of Biological Sciences, University of Canterbury, Christchurch, Canterbury, New Zealand
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7
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Steiner KC, Graboski LE, Berkebile JL, Fei S, Leites LP. Uncertainty in the modelled mortality of two tree species (
Fraxinus
) under novel climatic regimes. DIVERS DISTRIB 2021. [DOI: 10.1111/ddi.13293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Affiliation(s)
- Kim C. Steiner
- Department of Ecosystem Science and Management The Pennsylvania State University University Park PA USA
| | - Lake E. Graboski
- Department of Ecosystem Science and Management The Pennsylvania State University University Park PA USA
| | - Jennifer L. Berkebile
- Department of Ecosystem Science and Management The Pennsylvania State University University Park PA USA
- Pennsylvania Certified Organic Spring Mills PA USA
| | - Songlin Fei
- Department of Forestry and Natural Resources Purdue University West Lafayette IN USA
| | - Laura P. Leites
- Department of Ecosystem Science and Management The Pennsylvania State University University Park PA USA
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8
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Applying targeted genotyping by sequencing with a new set of nuclear and plastid SNP and indel loci for Quercus robur and Quercus petraea. CONSERV GENET RESOUR 2021. [DOI: 10.1007/s12686-021-01207-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
AbstractWe used Double Digest Restriction site associated DNA sequencing (ddRAD) and Miseq to develop new geographically informative nuclear and plastid SNP and indel loci in Quercus robur and Q. petraea. Genotypes derived from sequence data of 95 individuals and two pools of 20 individuals each of Q. robur and Q. mongolica covering the distribution range of the species, were analysed to select geographically informative and polymorphic loci within Germany and Russia. We successfully screened a selected set of 431 nuclear single nucleotide polymorphism (nSNP), six nuclear Indel, six mitochondrial single nucleotide polymorphism (mtSNP) and ten chloroplast single nucleotide polymorphism (cpSNP) loci with a SeqSNP genotyping platform on 100 individuals Quercus petraea from 10 locations in Germany, 100 individuals Quercus robur from ten locations in Germany and 100 individuals Quercus robur from ten locations in Russia. The newly developed loci are useful for species identification and genetic studies on the genetic diversity and genetic differentiation of Quercus robur and Quercus petraea in Europe.
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