151
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Plant response to butterfly eggs: inducibility, severity and success of egg-killing leaf necrosis depends on plant genotype and egg clustering. Sci Rep 2017; 7:7316. [PMID: 28779155 PMCID: PMC5544688 DOI: 10.1038/s41598-017-06704-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 06/16/2017] [Indexed: 12/29/2022] Open
Abstract
Plants employ various defences killing the insect attacker in an early stage. Oviposition by cabbage white butterflies (Pieris spp.) on brassicaceous plants, including Brassica nigra, induces a hypersensitive response (HR) - like leaf necrosis promoting desiccation of eggs. To gain a deeper insight into the arms race between butterflies and plants, we conducted field and greenhouse experiments using different B. nigra genotypes. We investigated variation in HR and consequent survival of P. brassicae egg clusters. Impact of egg density, distribution type and humidity on HR formation and egg survival was tested. HR differed among plant genotypes as well as plant individuals. Egg density per plant did not affect HR formation. Remarkably, egg survival did not depend on the formation of HR, unless butterflies were forced to lay single eggs. Larval hatching success from single eggs was lower on plants expressing HR. This may be due to increased vulnerability of single eggs to low humidity conditions at necrotic leaf sites. We conclude that effectiveness of HR-like necrosis in B. nigra varies with plant genotype, plant individual and the type of egg laying behaviour (singly or clustered). By clustering eggs, cabbage white butterflies can escape the egg-killing, direct plant defence trait.
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152
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Lee SH, Weerasinghe WMSP, van der Werf JHJ. Genotype-environment interaction on human cognitive function conditioned on the status of breastfeeding and maternal smoking around birth. Sci Rep 2017; 7:6087. [PMID: 28729621 PMCID: PMC5519601 DOI: 10.1038/s41598-017-06214-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 06/08/2017] [Indexed: 11/23/2022] Open
Abstract
We estimated genotype by environment interaction (G × E) on later cognitive performance and educational attainment across four unique environments, i.e. 1) breastfed without maternal smoking, 2) breastfed with maternal smoking, 3) non-breastfed without maternal smoking and 4) non-breastfed with maternal smoking, using a novel design and statistical approach that was facilitated by the availability of datasets with the genome-wide single nucleotide polymorphisms (SNPs). There was significant G × E for both fluid intelligence (p-value = 1.0E-03) and educational attainment (p-value = 8.3E-05) when comparing genetic effects in the group of individuals who were breastfed without maternal smoking with those not breastfed without maternal smoking. There was also significant G × E for fluid intelligence (p-value = 3.9E-05) when comparing the group of individuals who were breastfed with maternal smoking with those not breastfed without maternal smoking. Genome-wide significant SNPs were different between different environmental groups. Genomic prediction accuracies were significantly higher when using the target and discovery sample from the same environmental group than when using those from the different environmental groups. This finding demonstrates G × E has important implications for future studies on the genetic architecture, genome-wide association studies and genomic predictions.
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Affiliation(s)
- S Hong Lee
- School of Environmental and Rural Science, University of New England, Armidale, New South Wales 2351, Australia.
| | - W M Shalanee P Weerasinghe
- School of Environmental and Rural Science, University of New England, Armidale, New South Wales 2351, Australia
| | - Julius H J van der Werf
- School of Environmental and Rural Science, University of New England, Armidale, New South Wales 2351, Australia
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153
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Feldman MJ, Paul RE, Banan D, Barrett JF, Sebastian J, Yee MC, Jiang H, Lipka AE, Brutnell TP, Dinneny JR, Leakey ADB, Baxter I. Time dependent genetic analysis links field and controlled environment phenotypes in the model C4 grass Setaria. PLoS Genet 2017. [PMID: 28644860 PMCID: PMC5507400 DOI: 10.1371/journal.pgen.1006841] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Vertical growth of plants is a dynamic process that is influenced by genetic and environmental factors and has a pronounced effect on overall plant architecture and biomass composition. We have performed six controlled growth trials of an interspecific Setaria italica x Setaria viridis recombinant inbred line population to assess how the genetic architecture of plant height is influenced by developmental queues, water availability and planting density. The non-destructive nature of plant height measurements has enabled us to monitor height throughout the plant life cycle in both field and controlled environments. We find that plant height is reduced under water limitation and high density planting and affected by growth environment (field vs. growth chamber). The results support a model where plant height is a heritable, polygenic trait and that the major genetic loci that influence plant height function independent of growth environment. The identity and contribution of loci that influence height changes dynamically throughout development and the reduction of growth observed in water limited environments is a consequence of delayed progression through the genetic program which establishes plant height in Setaria. In this population, alleles inherited from the weedy S. viridis parent act to increase plant height early, whereas a larger number of small effect alleles inherited from the domesticated S. italica parent collectively act to increase plant height later in development. Growth is a dynamic process that responds to a changing environment. Most of the methods that we have for measuring are static and collecting information throughout an organisms lifecycle is labor and cost prohibitive. Advances in imaging and robotics technology have enabled novel approaches to understanding how plants adapt to the environment. Using the model grass Setaria and new methods for measuring parameters from images, we investigate the genetic architecture of plant height in response to water availability and planting density. Height is one of the most influential components of plant architecture, determining tradeoffs between competition and resource allocation and is an important trait for boosting yields. The non-destructive nature of plant height measurements has enabled us to monitor growth throughout the plant life cycle in both field and controlled environments. We identified several loci controlling height in a population derived from a wild strain of Setaria viridis and its domesticated relative Setaria italica, as well as the developmental time in which these loci act. In this population, alleles inherited from the wild parent act to increase plant height early, whereas a larger number of small effect alleles inherited from the domesticated parent collectively act to increase plant height later in development.
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Affiliation(s)
- Max J. Feldman
- Donald Danforth Plant Science Center, St. Louis, Missouri, United States of America
| | - Rachel E. Paul
- Department of Plant Biology and Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Darshi Banan
- Department of Plant Biology and Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Jennifer F. Barrett
- Donald Danforth Plant Science Center, St. Louis, Missouri, United States of America
| | - Jose Sebastian
- Carnegie Institution for Science, Department of Plant Biology, Stanford, California, United States of America
| | - Muh-Ching Yee
- Carnegie Institution for Science, Department of Plant Biology, Stanford, California, United States of America
| | - Hui Jiang
- Donald Danforth Plant Science Center, St. Louis, Missouri, United States of America
| | - Alexander E. Lipka
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Thomas P. Brutnell
- Donald Danforth Plant Science Center, St. Louis, Missouri, United States of America
| | - José R. Dinneny
- Carnegie Institution for Science, Department of Plant Biology, Stanford, California, United States of America
| | - Andrew D. B. Leakey
- Department of Plant Biology and Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Ivan Baxter
- Donald Danforth Plant Science Center, St. Louis, Missouri, United States of America
- USDA-ARS, Plant Genetics Research Unit, St. Louis, Missouri, United States of America
- * E-mail:
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154
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Des Marais DL, Guerrero RF, Lasky JR, Scarpino SV. Topological features of a gene co-expression network predict patterns of natural diversity in environmental response. Proc Biol Sci 2017; 284:20170914. [PMID: 28615505 PMCID: PMC5474086 DOI: 10.1098/rspb.2017.0914] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 05/17/2017] [Indexed: 01/26/2023] Open
Abstract
Molecular interactions affect the evolution of complex traits. For instance, adaptation may be constrained by pleiotropic or epistatic effects, both of which can be reflected in the structure of molecular interaction networks. To date, empirical studies investigating the role of molecular interactions in phenotypic evolution have been idiosyncratic, offering no clear patterns. Here, we investigated the network topology of genes putatively involved in local adaptation to two abiotic stressors-drought and cold-in Arabidopsis thaliana Our findings suggest that the gene-interaction topologies for both cold and drought stress response are non-random, with genes that show genetic variation in drought expression response (eGxE) being significantly more peripheral and cold response genes being significantly more central than genes which do not show GxE. We suggest that the observed topologies reflect different constraints on the genetic pathways involved in environmental response. The approach presented here may inform predictive models linking genetic variation in molecular signalling networks with phenotypic variation, specifically traits involved in environmental response.
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Affiliation(s)
- David L Des Marais
- Arnold Arboretum and Department of Organismic and Evolutionary Biology, Harvard University, 1300 Centre Street, Boston, MA 20131, USA
| | - Rafael F Guerrero
- Department of Biology, Indiana University, Jordan Hall 142, Bloomington, IN 47405, USA
| | - Jesse R Lasky
- Department of Biology, Pennsylvania State University, 408 Life Sciences Building, University Park, PA 16802, USA
| | - Samuel V Scarpino
- Department of Mathematics and Statistics and Vermont Complex Systems Center, University of Vermont, 210 Colchester Avenue, Burlington, VT 05405, USA
- Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM, 87501, USA
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155
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Self-Referential Encoding on Modules of Anticodon Pairs-Roots of the Biological Flow System. Life (Basel) 2017; 7:life7020016. [PMID: 28383509 PMCID: PMC5492138 DOI: 10.3390/life7020016] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Revised: 03/24/2017] [Accepted: 03/26/2017] [Indexed: 12/22/2022] Open
Abstract
The proposal that the genetic code was formed on the basis of (proto)tRNA Dimer-Directed Protein Synthesis is reviewed and updated. The tRNAs paired through the anticodon loops are an indication on the process. Dimers are considered mimics of the ribosomes-structures that hold tRNAs together and facilitate the transferase reaction, and of the translation process-anticodons are at the same time codons for each other. The primitive protein synthesis system gets stabilized when the product peptides are stable and apt to bind the producers therewith establishing a self-stimulating production cycle. The chronology of amino acid encoding starts with Glycine and Serine, indicating the metabolic support of the Glycine-Serine C1-assimilation pathway, which is also consistent with evidence on origins of bioenergetics mechanisms. Since it is not possible to reach for substrates simpler than C1 and compounds in the identified pathway are apt for generating the other central metabolic routes, it is considered that protein synthesis is the beginning and center of a succession of sink-effective mechanisms that drive the formation and evolution of the metabolic flow system. Plasticity and diversification of proteins construct the cellular system following the orientation given by the flow and implementing it. Nucleic acid monomers participate in bioenergetics and the polymers are conservative memory systems for the synthesis of proteins. Protoplasmic fission is the final sink-effective mechanism, part of cell reproduction, guaranteeing that proteins don't accumulate to saturation, which would trigger inhibition.
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156
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Des Marais DL, Lasky JR, Verslues PE, Chang TZ, Juenger TE. Interactive effects of water limitation and elevated temperature on the physiology, development and fitness of diverse accessions of Brachypodium distachyon. THE NEW PHYTOLOGIST 2017; 214:132-144. [PMID: 27864966 DOI: 10.1111/nph.14316] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 10/03/2016] [Indexed: 05/21/2023]
Abstract
An enduring question in plant physiology and evolution is how single genotypes of plants optimize performance in diverse, often highly variable, environments. We grew 35 natural accessions of the grass Brachypodium distachyon in four environments in the glasshouse, contrasting soil water deficit, elevated temperature and their interaction. We modeled treatment, genotype and interactive effects on leaf-level and whole-plant traits, including fecundity. We also assessed the relationship between glasshouse-measured traits and parameters related to climate at the place of origin. We found abundant genetic variation in both constitutive and induced traits related to plant-water relations. Most traits showed strong interaction between temperature and water availability, and we observed genotype-by-environment interaction for several traits. Notably, leaf free proline abundance showed a strong effect of genotype × temperature × water. We found strong associations between phenology, biomass and water use efficiency (WUE) with parameters describing climate of origin. Plants respond to multiple stressors in ways not directly predictable from single stressors, underscoring the complex and trait-specific mechanisms of environmental response. Climate-trait correlations support a role for WUE and phenology in local adaptation to climate in B. distachyon.
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Affiliation(s)
- David L Des Marais
- Department of Integrative Biology and Institute for Cell and Molecular Biology, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Jesse R Lasky
- Department of Biology, Pennsylvania State University, University Park, PA, 16802, USA
| | - Paul E Verslues
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Trent Z Chang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Thomas E Juenger
- Department of Integrative Biology and Institute for Cell and Molecular Biology, The University of Texas at Austin, Austin, TX, 78712, USA
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157
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Kokko H, Chaturvedi A, Croll D, Fischer MC, Guillaume F, Karrenberg S, Kerr B, Rolshausen G, Stapley J. Can Evolution Supply What Ecology Demands? Trends Ecol Evol 2017; 32:187-197. [DOI: 10.1016/j.tree.2016.12.005] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 12/09/2016] [Accepted: 12/13/2016] [Indexed: 11/26/2022]
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158
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Suneja Y, Gupta AK, Bains NS. Bread wheat progenitors: Aegilops tauschii (DD genome) and Triticum dicoccoides (AABB genome) reveal differential antioxidative response under water stress. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2017; 23:99-114. [PMID: 28250587 PMCID: PMC5313413 DOI: 10.1007/s12298-016-0409-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2016] [Revised: 12/09/2016] [Accepted: 12/23/2016] [Indexed: 05/22/2023]
Abstract
Antioxidant enzymes are known to play a significant role in scavenging reactive oxygen species and maintaining cellular homeostasis. Activity of four antioxidant enzymes viz., superoxide dismutase (SOD), catalase (CAT), ascorbate peroxidase (APX) and glutathione reductase (GR) was examined in the flag leaves of nine Aegilops tauschii and three Triticum dicoccoides accessions along with two bread wheat cultivars under irrigated and rain-fed conditions. These accessions were shortlisted from a larger set on the basis of field performance for a set of morpho-physiological traits. At anthesis, significant differences were observed in enzyme activities in two environments. A 45% elevation in average GR activity was observed under rain-fed conditions. Genotypic variation was evident within each environment as well as in terms of response to stress environment. Aegilops tauschii accession 3769 (86% increase in SOD, 41% in CAT, 72% in APX, 48% in GR activity) and acc. 14096 (37% increase in SOD, 32% CAT, 25% APX, 42% GR) showed up-regulation in the activity of all the four studied antioxidant enzymes. Aegilops tauschii accessions-9809, 14189 and 14113 also seemed to have strong induction mechanism as elevated activity of at least three enzymes was observed in them under rain-fed conditions. T. dicoccoides, on the other hand, maintained active antioxidative machinery under irrigated condition with relatively lower induction under stress. A significant positive correlation (r = 0.760) was identified between change in the activity of CAT and GR under stress. Changes in plant height, spike length and grain weight were recorded under stress and non-stress conditions on the basis of which a cumulative tolerance index was deduced and accessions were ranked for drought tolerance. Overall, Ae. tauschii accession 3769, 14096, 14113 (DD-genome) and T. dicoccoides accession 7054 (AABB-genome) may be used as donors to combine beneficial stress adaptive traits of all the three sub-genomes into a synthetic hexaploid for improving wheat for water stress conditions.
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Affiliation(s)
- Yadhu Suneja
- Department of Biochemistry, Punjab Agricultural University, Ludhiana, India
| | - Anil Kumar Gupta
- Department of Biochemistry, Punjab Agricultural University, Ludhiana, India
| | - Navtej Singh Bains
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
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159
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Fu G, Dai X, Symanzik J, Bushman S. Quantitative gene-gene and gene-environment mapping for leaf shape variation using tree-based models. THE NEW PHYTOLOGIST 2017; 213:455-469. [PMID: 27650962 DOI: 10.1111/nph.14131] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 07/01/2016] [Indexed: 05/28/2023]
Abstract
Leaf shape traits have long been a focus of many disciplines, but the complex genetic and environmental interactive mechanisms regulating leaf shape variation have not yet been investigated in detail. The question of the respective roles of genes and environment and how they interact to modulate leaf shape is a thorny evolutionary problem, and sophisticated methodology is needed to address it. In this study, we investigated a framework-level approach that inputs shape image photographs and genetic and environmental data, and then outputs the relative importance ranks of all variables after integrating shape feature extraction, dimension reduction, and tree-based statistical models. The power of the proposed framework was confirmed by simulation and a Populus szechuanica var. tibetica data set. This new methodology resulted in the detection of novel shape characteristics, and also confirmed some previous findings. The quantitative modeling of a combination of polygenetic, plastic, epistatic, and gene-environment interactive effects, as investigated in this study, will improve the discernment of quantitative leaf shape characteristics, and the methods are ready to be applied to other leaf morphology data sets. Unlike the majority of approaches in the quantitative leaf shape literature, this framework-level approach is data-driven, without assuming any pre-known shape attributes, landmarks, or model structures.
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Affiliation(s)
- Guifang Fu
- Department of Mathematics and Statistics, Utah State University, Logan, UT, 84321, USA
| | - Xiaotian Dai
- Department of Mathematics and Statistics, Utah State University, Logan, UT, 84321, USA
| | - Jürgen Symanzik
- Department of Mathematics and Statistics, Utah State University, Logan, UT, 84321, USA
| | - Shaun Bushman
- Forage and Range Research Lab, USDA-ARS, Logan, UT, 84322, USA
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160
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The Interaction of Genotype and Environment Determines Variation in the Maize Kernel Ionome. G3-GENES GENOMES GENETICS 2016; 6:4175-4183. [PMID: 27770027 PMCID: PMC5144985 DOI: 10.1534/g3.116.034827] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Plants obtain soil-resident elements that support growth and metabolism from the water-flow facilitated by transpiration and active transport processes. The availability of elements in the environment interacts with the genetic capacity of organisms to modulate element uptake through plastic adaptive responses, such as homeostasis. These interactions should cause the elemental contents of plants to vary such that the effects of genetic polymorphisms will be dramatically dependent on the environment in which the plant is grown. To investigate genotype by environment interactions underlying elemental accumulation, we analyzed levels of elements in maize kernels of the Intermated B73 × Mo17 (IBM) recombinant inbred population grown in 10 different environments, spanning a total of six locations and five different years. In analyses conducted separately for each environment, we identified a total of 79 quantitative trait loci (QTL) controlling seed elemental accumulation. While a set of these QTL was found in multiple environments, the majority were specific to a single environment, suggesting the presence of genetic by environment interactions. To specifically identify and quantify QTL by environment interactions (QEIs), we implemented two methods: linear modeling with environmental covariates, and QTL analysis on trait differences between growouts. With these approaches, we found several instances of QEI, indicating that elemental profiles are highly heritable, interrelated, and responsive to the environment.
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161
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Albert E, Segura V, Gricourt J, Bonnefoi J, Derivot L, Causse M. Association mapping reveals the genetic architecture of tomato response to water deficit: focus on major fruit quality traits. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:6413-6430. [PMID: 27856709 PMCID: PMC5181584 DOI: 10.1093/jxb/erw411] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Water scarcity constitutes a crucial constraint for agriculture productivity. High-throughput approaches in model plant species identified hundreds of genes potentially involved in survival under drought, but few having beneficial effects on quality and yield. Nonetheless, controlled water deficit may improve fruit quality through higher concentration of flavor compounds. The underlying genetic determinants are still poorly known. In this study, we phenotyped 141 highly diverse small fruit tomato accessions for 27 traits under two contrasting watering conditions. A subset of 55 accessions exhibited increased metabolite contents and maintained yield under water deficit. Using 6100 single nucleotide polymorphisms (SNPs), association mapping revealed 31, 41, and 44 quantitative trait loci (QTLs) under drought, control, and both conditions, respectively. Twenty-five additional QTLs were interactive between conditions, emphasizing the interest in accounting for QTLs by watering regime interactions in fruit quality improvement. Combining our results with the loci previously identified in a biparental progeny resulted in 11 common QTLs and contributed to a first detailed characterization of the genetic determinants of response to water deficit in tomato. Major QTLs for fruit quality traits were dissected and candidate genes were proposed using expression and polymorphism data. The outcomes provide a basis for fruit quality improvement under deficit irrigation while limiting yield losses.
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Affiliation(s)
- Elise Albert
- INRA, UR1052, Génétique et Amélioration des Fruits et Légumes, 67 Allée des Chênes, Centre de Recherche PACA, Domaine Saint Maurice, CS60094, Montfavet, 84143, France
| | - Vincent Segura
- INRA, UR0588, Amélioration, Génétique et Physiologie Forestières, 2163 Avenue de la Pomme de Pin, Centre de Recherche Val de Loire, CS 40001, Orléans, 45075, France
| | - Justine Gricourt
- INRA, UR1052, Génétique et Amélioration des Fruits et Légumes, 67 Allée des Chênes, Centre de Recherche PACA, Domaine Saint Maurice, CS60094, Montfavet, 84143, France
| | | | | | - Mathilde Causse
- INRA, UR1052, Génétique et Amélioration des Fruits et Légumes, 67 Allée des Chênes, Centre de Recherche PACA, Domaine Saint Maurice, CS60094, Montfavet, 84143, France
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162
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De Kort H, Mergeay J, Jacquemyn H, Honnay O. Transatlantic invasion routes and adaptive potential in North American populations of the invasive glossy buckthorn, Frangula alnus. ANNALS OF BOTANY 2016; 118:1089-1099. [PMID: 27539599 PMCID: PMC5091722 DOI: 10.1093/aob/mcw157] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Revised: 05/02/2016] [Accepted: 06/17/2016] [Indexed: 05/31/2023]
Abstract
BACKGROUND AND AIMS Many invasive species severely threaten native biodiversity and ecosystem functioning. One of the most prominent questions in invasion genetics is how invasive populations can overcome genetic founder effects to establish stable populations after colonization of new habitats. High native genetic diversity and multiple introductions are expected to increase genetic diversity and adaptive potential in the invasive range. Our aim was to identify the European source populations of Frangula alnus (glossy buckthorn), an ornamental and highly invasive woody species that was deliberately introduced into North America at the end of the 18th century. A second aim of this study was to assess the adaptive potential as an explanation for the invasion success of this species. METHODS Using a set of annotated single-nucleotide polymorphisms (SNPs) that were assigned a putative function based on sequence comparison with model species, a total of 38 native European and 21 invasive North American populations were subjected to distance-based structure and assignment analyses combined with population genomic tools. Genetic diversity at SNPs with ecologically relevant functions was considered as a proxy for adaptive potential. KEY RESULTS Patterns of invasion coincided with early modern transatlantic trading routes. Multiple introductions through transatlantic trade from a limited number of European port regions to American urban areas led to the establishment of bridgehead populations with high allelic richness and expected heterozygosity, allowing continuous secondary migration to natural areas. CONCLUSIONS Targeted eradication of the urban populations, where the highest genetic diversity and adaptive potential were observed, offers a promising strategy to arrest further invasion of native American prairies and forests.
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Affiliation(s)
- Hanne De Kort
- Plant Conservation and Population Biology, Biology Department, University of Leuven, Kasteelpark Arenberg 31, B-3001 Heverlee, Belgium Station d'Ecologie Théorique et Expérimentale du CNRS, Centre National de la Recherche Scientifique, 2 Route du CNRS, FR-09200 Moulis, France
| | - Joachim Mergeay
- Research Institute for Nature and Forest, Gaverstraat 4, B-9500 Geraardsbergen, Belgium
| | - Hans Jacquemyn
- Plant Conservation and Population Biology, Biology Department, University of Leuven, Kasteelpark Arenberg 31, B-3001 Heverlee, Belgium
| | - Olivier Honnay
- Plant Conservation and Population Biology, Biology Department, University of Leuven, Kasteelpark Arenberg 31, B-3001 Heverlee, Belgium
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163
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Vacher C, Hampe A, Porté AJ, Sauer U, Compant S, Morris CE. The Phyllosphere: Microbial Jungle at the Plant–Climate Interface. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2016. [DOI: 10.1146/annurev-ecolsys-121415-032238] [Citation(s) in RCA: 229] [Impact Index Per Article: 28.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
| | - Arndt Hampe
- BIOGECO, INRA, Univ. Bordeaux, 33610 Cestas, France
| | | | - Ursula Sauer
- Bioresources Unit, Department of Health and Environment, AIT Austrian Institute of Technology GmbH, 3430 Tulln, Austria
| | - Stéphane Compant
- Bioresources Unit, Department of Health and Environment, AIT Austrian Institute of Technology GmbH, 3430 Tulln, Austria
| | - Cindy E. Morris
- INRA, Unité de Recherche de Pathologie Végétale, 84143 Montfavet, France
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164
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Henning JA, Weston DJ, Pelletier DA, Timm CM, Jawdy SS, Classen AT. Root bacterial endophytes alter plant phenotype, but not physiology. PeerJ 2016; 4:e2606. [PMID: 27833797 PMCID: PMC5101591 DOI: 10.7717/peerj.2606] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 09/24/2016] [Indexed: 12/15/2022] Open
Abstract
Plant traits, such as root and leaf area, influence how plants interact with their environment and the diverse microbiota living within plants can influence plant morphology and physiology. Here, we explored how three bacterial strains isolated from the Populus root microbiome, influenced plant phenotype. We chose three bacterial strains that differed in predicted metabolic capabilities, plant hormone production and metabolism, and secondary metabolite synthesis. We inoculated each bacterial strain on a single genotype of Populus trichocarpa and measured the response of plant growth related traits (root:shoot, biomass production, root and leaf growth rates) and physiological traits (chlorophyll content, net photosynthesis, net photosynthesis at saturating light-Asat, and saturating CO2-Amax). Overall, we found that bacterial root endophyte infection increased root growth rate up to 184% and leaf growth rate up to 137% relative to non-inoculated control plants, evidence that plants respond to bacteria by modifying morphology. However, endophyte inoculation had no influence on total plant biomass and photosynthetic traits (net photosynthesis, chlorophyll content). In sum, bacterial inoculation did not significantly increase plant carbon fixation and biomass, but their presence altered where and how carbon was being allocated in the plant host.
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Affiliation(s)
- Jeremiah A. Henning
- Department of Ecology & Evolutionary Biology, University of Tennessee–Knoxville, Knoxville, Tennessee, United States
| | - David J. Weston
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Dale A. Pelletier
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Collin M. Timm
- Joint Institute for Biological Sciences, University of Tennessee, Oak Ridge, TN, United States
| | - Sara S. Jawdy
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Aimée T. Classen
- Department of Ecology & Evolutionary Biology, University of Tennessee–Knoxville, Knoxville, Tennessee, United States
- Center for Macroecology, Evolution, and Climate, The Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
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165
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Estoup A, Ravigné V, Hufbauer R, Vitalis R, Gautier M, Facon B. Is There a Genetic Paradox of Biological Invasion? ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2016. [DOI: 10.1146/annurev-ecolsys-121415-032116] [Citation(s) in RCA: 158] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Arnaud Estoup
- Unité Mixte de Recherche Centre de Biologie pour la Gestion des Populations, Institut National de la Recherche Agronomique, 34988 Montferrier sur Lez, France;
| | - Virginie Ravigné
- Unité Mixte de Recherche Peuplements Végétaux et Bioagresseurs en Milieu Tropical, Centre de Coopération Internationale en Recherche Agronomique pour le Développement, 97410 Saint-Pierre, La Réunion, France
| | - Ruth Hufbauer
- Department of Bioagricultural Science and Pest Management, Colorado State University, Fort Collins, Colorado 80523
| | - Renaud Vitalis
- Unité Mixte de Recherche Centre de Biologie pour la Gestion des Populations, Institut National de la Recherche Agronomique, 34988 Montferrier sur Lez, France;
| | - Mathieu Gautier
- Unité Mixte de Recherche Centre de Biologie pour la Gestion des Populations, Institut National de la Recherche Agronomique, 34988 Montferrier sur Lez, France;
| | - Benoit Facon
- Unité Mixte de Recherche Centre de Biologie pour la Gestion des Populations, Institut National de la Recherche Agronomique, 34988 Montferrier sur Lez, France;
- Unité Mixte de Recherche Peuplements Végétaux et Bioagresseurs en Milieu Tropical, Centre de Coopération Internationale en Recherche Agronomique pour le Développement, 97410 Saint-Pierre, La Réunion, France
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166
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Cheng B, Furtado A, Smyth HE, Henry RJ. Influence of genotype and environment on coffee quality. Trends Food Sci Technol 2016. [DOI: 10.1016/j.tifs.2016.09.003] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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167
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Des Marais DL, Razzaque S, Hernandez KM, Garvin DF, Juenger TE. Quantitative trait loci associated with natural diversity in water-use efficiency and response to soil drying in Brachypodium distachyon. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2016; 251:2-11. [PMID: 27593458 DOI: 10.1016/j.plantsci.2016.03.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Revised: 03/18/2016] [Accepted: 03/23/2016] [Indexed: 05/25/2023]
Abstract
All plants must optimize their growth with finite resources. Water use efficiency (WUE) measures the relationship between biomass acquisition and transpired water. In the present study, we performed two experiments to understand the genetic basis of WUE and other parameters of plant-water interaction under control and water-limited conditions. Our study used two inbred natural accessions of Brachypodium distachyon, a model grass species with close phylogenetic affinity to temperate forage and cereal crops. First, we identify the soil water content which causes a reduction in leaf relative water content and an increase in WUE. Second, we present results from a large phenotyping experiment utilizing a recombinant inbred line mapping population derived from these same two natural accessions. We identify QTLs associated with environmentally-insensitive genetic variation in WUE, including a pair of epistatically interacting loci. We also identify QTLs associated with constitutive differences in biomass and a QTL describing an environmentally-sensitive difference in leaf carbon content. Finally, we present a new linkage map for this mapping population based on new SNP markers as well as updated genomic positions for previously described markers. Our studies provide an initial characterization of plant-water relations in B. distachyon and identify candidate genomic regions involved in WUE.
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Affiliation(s)
- David L Des Marais
- Department of Integrative Biology and Institute for Cell and Molecular Biology, The University of Texas at Austin, United States.
| | - Samsad Razzaque
- Department of Integrative Biology and Institute for Cell and Molecular Biology, The University of Texas at Austin, United States
| | - Kyle M Hernandez
- Department of Integrative Biology and Institute for Cell and Molecular Biology, The University of Texas at Austin, United States
| | - David F Garvin
- U.S. Department of Agriculture-Agricultural Research Service, Plant Science Research Unit, St. Paul, MN, United States
| | - Thomas E Juenger
- Department of Integrative Biology and Institute for Cell and Molecular Biology, The University of Texas at Austin, United States
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168
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Herman JJ, Sultan SE. DNA methylation mediates genetic variation for adaptive transgenerational plasticity. Proc Biol Sci 2016; 283:20160988. [PMID: 27629032 PMCID: PMC5031651 DOI: 10.1098/rspb.2016.0988] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 08/24/2016] [Indexed: 12/21/2022] Open
Abstract
Environmental stresses experienced by individual parents can influence offspring phenotypes in ways that enhance survival under similar conditions. Although such adaptive transgenerational plasticity is well documented, its transmission mechanisms are generally unknown. One possible mechanism is environmentally induced DNA methylation changes. We tested this hypothesis in the annual plant Polygonum persicaria, a species known to express adaptive transgenerational plasticity in response to parental drought stress. Replicate plants of 12 genetic lines (sampled from natural populations) were grown in dry versus moist soil. Their offspring were exposed to the demethylating agent zebularine or to control conditions during germination and then grown in dry soil. Under control germination conditions, the offspring of drought-stressed parents grew longer root systems and attained greater biomass compared with offspring of well-watered parents of the same genetic lines. Demethylation removed these adaptive developmental effects of parental drought, but did not significantly alter phenotypic expression in offspring of well-watered parents. The effect of demethylation on the expression of the parental drought effect varied among genetic lines. Differential seed provisioning did not contribute to the effect of parental drought on offspring phenotypes. These results demonstrate that DNA methylation can mediate adaptive, genotype-specific effects of parental stress on offspring phenotypes.
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Affiliation(s)
- Jacob J Herman
- Biology Department, Wesleyan University, Middletown, CT 06459, USA
| | - Sonia E Sultan
- Biology Department, Wesleyan University, Middletown, CT 06459, USA
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169
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Sadras VO, Lake L, Li Y, Farquharson EA, Sutton T. Phenotypic plasticity and its genetic regulation for yield, nitrogen fixation and δ13C in chickpea crops under varying water regimes. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:4339-51. [PMID: 27296246 DOI: 10.1093/jxb/erw221] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
We measured yield components, nitrogen fixation, soil nitrogen uptake and carbon isotope composition (δ(13)C) in a collection of chickpea genotypes grown in environments where water availability was the main source of yield variation. We aimed to quantify the phenotypic plasticity of these traits using variance ratios, and to explore their genetic basis using FST genome scan. Fifty-five genes in three genomic regions were found to be under selection for plasticity of yield; 54 genes in four genomic regions for the plasticity of seeds per m(2); 48 genes in four genomic regions for the plasticity of δ(13)C; 54 genes in two genomic regions for plasticity of flowering time; 48 genes in five genomic regions for plasticity of nitrogen fixation and 49 genes in three genomic regions for plasticity of nitrogen uptake from soil. Plasticity of yield was related to plasticity of nitrogen uptake from soil, and unrelated to plasticity of nitrogen fixation, highlighting the need for closer attention to nitrogen uptake in legumes. Whereas the theoretical link between δ(13)C and transpiration efficiency is strong, the actual link with yield is erratic due to trade-offs and scaling issues. Genes associated with plasticity of δ(13)C were identified that may help to untangle the δ(13)C-yield relationship. Combining a plasticity perspective to deal with complex G×E interactions with FST genome scan may help understand and improve both crop adaptation to stress and yield potential.
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Affiliation(s)
- Victor O Sadras
- South Australian Research and Development Institute, Waite Campus, Australia
| | - Lachlan Lake
- South Australian Research and Development Institute, Waite Campus, Australia
| | - Yongle Li
- Australian Centre for Plant Functional Genomics, The University of Adelaide, Waite Campus, Australia
| | | | - Tim Sutton
- South Australian Research and Development Institute, Waite Campus, Australia
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170
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Xu Q, Zhu C, Fan Y, Song Z, Xing S, Liu W, Yan J, Sang T. Population transcriptomics uncovers the regulation of gene expression variation in adaptation to changing environment. Sci Rep 2016; 6:25536. [PMID: 27150248 PMCID: PMC4858677 DOI: 10.1038/srep25536] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 04/19/2016] [Indexed: 11/23/2022] Open
Abstract
Expression variation plays an important role in plant adaptation, but little is known about the factors impacting the expression variation when population adapts to changing environment. We used RNA-seq data from 80 individuals in 14 Miscanthus lutarioriparius populations, which were transplanted into a harsh environment from native habitat, to investigate the expression level, expression diversity and genetic diversity for genes expressed in both environments. The expression level of genes with lower expression level or without SNP tended to be more changeable in new environment, which suggested highly expressed genes experienced stronger purifying selection than those at lower level. Low proportion of genes with population effect confirmed the weak population structure and frequent gene flow in these populations. Meanwhile, the number of genes with environment effect was the most frequent compared with that with population effect. Our results showed that environment and genetic diversity were the main factors determining gene expression variation in population. This study could facilitate understanding the mechanisms of global gene expression variation when plant population adapts to changing environment.
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Affiliation(s)
- Qin Xu
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Caiyun Zhu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yangyang Fan
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhihong Song
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shilai Xing
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei Liu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Juan Yan
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei 430074, China
| | - Tao Sang
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.,State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
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171
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Lovell JT, Schwartz S, Lowry DB, Shakirov EV, Bonnette JE, Weng X, Wang M, Johnson J, Sreedasyam A, Plott C, Jenkins J, Schmutz J, Juenger TE. Drought responsive gene expression regulatory divergence between upland and lowland ecotypes of a perennial C4 grass. Genome Res 2016; 26:510-8. [PMID: 26953271 PMCID: PMC4817774 DOI: 10.1101/gr.198135.115] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 01/26/2016] [Indexed: 01/18/2023]
Abstract
Climatic adaptation is an example of a genotype-by-environment interaction (G×E) of fitness. Selection upon gene expression regulatory variation can contribute to adaptive phenotypic diversity; however, surprisingly few studies have examined how genome-wide patterns of gene expression G×E are manifested in response to environmental stress and other selective agents that cause climatic adaptation. Here, we characterize drought-responsive expression divergence between upland (drought-adapted) and lowland (mesic) ecotypes of the perennial C4 grass,Panicum hallii, in natural field conditions. Overall, we find that cis-regulatory elements contributed to gene expression divergence across 47% of genes, 7.2% of which exhibit drought-responsive G×E. While less well-represented, we observe 1294 genes (7.8%) with transeffects.Trans-by-environment interactions are weaker and much less common than cis G×E, occurring in only 0.7% oft rans-regulated genes. Finally, gene expression heterosis is highly enriched in expression phenotypes with significant G×E. As such, modes of inheritance that drive heterosis, such as dominance or overdominance, may be common among G×E genes. Interestingly, motifs specific to drought-responsive transcription factors are highly enriched in the promoters of genes exhibiting G×E and transregulation, indicating that expression G×E and heterosis may result from the evolution of transcription factors or their binding sites.P. hallii serves as the genomic model for its close relative and emerging biofuel crop, switchgrass (Panicum virgatum). Accordingly, the results here not only aid in the discovery of the genetic mechanisms that underlie local adaptation but also provide a foundation to improve switchgrass yield under water-limited conditions.
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Affiliation(s)
- John T Lovell
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas 78712, USA
| | - Scott Schwartz
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas 78712, USA
| | - David B Lowry
- Department of Plant Sciences, Michigan State University, East Lansing, Michigan 48824, USA
| | - Eugene V Shakirov
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas 78712, USA; Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 42008, Republic of Tatarstan, Russia
| | - Jason E Bonnette
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas 78712, USA
| | - Xiaoyu Weng
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas 78712, USA
| | - Mei Wang
- Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
| | - Jenifer Johnson
- Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
| | | | - Christopher Plott
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
| | - Jerry Jenkins
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
| | - Jeremy Schmutz
- Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA; HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
| | - Thomas E Juenger
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas 78712, USA
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172
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Xu Y. Envirotyping for deciphering environmental impacts on crop plants. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2016; 129:653-673. [PMID: 26932121 PMCID: PMC4799247 DOI: 10.1007/s00122-016-2691-5] [Citation(s) in RCA: 106] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Accepted: 02/08/2016] [Indexed: 05/17/2023]
Abstract
Global climate change imposes increasing impacts on our environments and crop production. To decipher environmental impacts on crop plants, the concept "envirotyping" is proposed, as a third "typing" technology, complementing with genotyping and phenotyping. Environmental factors can be collected through multiple environmental trials, geographic and soil information systems, measurement of soil and canopy properties, and evaluation of companion organisms. Envirotyping contributes to crop modeling and phenotype prediction through its functional components, including genotype-by-environment interaction (GEI), genes responsive to environmental signals, biotic and abiotic stresses, and integrative phenotyping. Envirotyping, driven by information and support systems, has a wide range of applications, including environmental characterization, GEI analysis, phenotype prediction, near-iso-environment construction, agronomic genomics, precision agriculture and breeding, and development of a four-dimensional profile of crop science involving genotype (G), phenotype (P), envirotype (E) and time (T) (developmental stage). In the future, envirotyping needs to zoom into specific experimental plots and individual plants, along with the development of high-throughput and precision envirotyping platforms, to integrate genotypic, phenotypic and envirotypic information for establishing a high-efficient precision breeding and sustainable crop production system based on deciphered environmental impacts.
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Affiliation(s)
- Yunbi Xu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, 100081, Beijing, China.
- International Maize and Wheat Improvement Center (CIMMYT), El Batan, Texcoco, CP 56130, Mexico.
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173
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Li P, Zhuang Z, Cai H, Cheng S, Soomro AA, Liu Z, Gu R, Mi G, Yuan L, Chen F. Use of genotype-environment interactions to elucidate the pattern of maize root plasticity to nitrogen deficiency. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2016; 58:242-53. [PMID: 26269087 DOI: 10.1111/jipb.12384] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2015] [Accepted: 08/10/2015] [Indexed: 05/26/2023]
Abstract
Maize (Zea mays L.) root morphology exhibits a high degree of phenotypic plasticity to nitrogen (N) deficiency, but the underlying genetic architecture remains to be investigated. Using an advanced BC4 F3 population, we investigated the root growth plasticity under two contrasted N levels and identified the quantitative trait loci (QTLs) with QTL-environment (Q × E) interaction effects. Principal components analysis (PCA) on changes of root traits to N deficiency (ΔLN-HN) showed that root length and biomass contributed for 45.8% in the same magnitude and direction on the first PC, while root traits scattered highly on PC2 and PC3. Hierarchical cluster analysis on traits for ΔLN-HN further assigned the BC4 F3 lines into six groups, in which the special phenotypic responses to N deficiency was presented. These results revealed the complicated root plasticity of maize in response to N deficiency that can be caused by genotype-environment (G × E) interactions. Furthermore, QTL mapping using a multi-environment analysis identified 35 QTLs for root traits. Nine of these QTLs exhibited significant Q × E interaction effects. Taken together, our findings contribute to understanding the phenotypic and genotypic pattern of root plasticity to N deficiency, which will be useful for developing maize tolerance cultivars to N deficiency.
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Affiliation(s)
- Pengcheng Li
- Key Lab of Plant-Soil Interaction, MOE, Center for Resources, Environment and Food Security, College Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China
| | - Zhongjuan Zhuang
- Key Lab of Plant-Soil Interaction, MOE, Center for Resources, Environment and Food Security, College Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China
- Leading Bio-agricultural Co., Ltd., Qinhuangdao, 066000, China
| | - Hongguang Cai
- Key Lab of Plant-Soil Interaction, MOE, Center for Resources, Environment and Food Security, College Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China
- Institute of Agricultural Resource and Environment, Jilin Academy of Agricultural Sciences, Changchun, 130033, China
| | - Shuai Cheng
- Key Lab of Plant-Soil Interaction, MOE, Center for Resources, Environment and Food Security, College Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China
| | - Ayaz Ali Soomro
- Key Lab of Plant-Soil Interaction, MOE, Center for Resources, Environment and Food Security, College Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China
| | - Zhigang Liu
- Key Lab of Plant-Soil Interaction, MOE, Center for Resources, Environment and Food Security, College Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China
| | - Riliang Gu
- Key Lab of Plant-Soil Interaction, MOE, Center for Resources, Environment and Food Security, College Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China
| | - Guohua Mi
- Key Lab of Plant-Soil Interaction, MOE, Center for Resources, Environment and Food Security, College Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China
| | - Lixing Yuan
- Key Lab of Plant-Soil Interaction, MOE, Center for Resources, Environment and Food Security, College Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China
| | - Fanjun Chen
- Key Lab of Plant-Soil Interaction, MOE, Center for Resources, Environment and Food Security, College Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China
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174
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Albert E, Gricourt J, Bertin N, Bonnefoi J, Pateyron S, Tamby JP, Bitton F, Causse M. Genotype by watering regime interaction in cultivated tomato: lessons from linkage mapping and gene expression. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2016; 129:395-418. [PMID: 26582510 DOI: 10.1007/s00122-015-2635-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 11/04/2015] [Indexed: 05/20/2023]
Abstract
KEY MESSAGE In tomato, genotype by watering interaction resulted from genotype re-ranking more than scale changes. Interactive QTLs according to watering regime were detected. Differentially expressed genes were identified in some intervals. ABSTRACT As a result of climate change, drought will increasingly limit crop production in the future. Studying genotype by watering regime interactions is necessary to improve plant adaptation to low water availability. In cultivated tomato (Solanum lycopersicum L.), extensively grown in dry areas, well-mastered water deficits can stimulate metabolite production, increasing plant defenses and concentration of compounds involved in fruit quality, at the same time. However, few tomato Quantitative Trait Loci (QTLs) and genes involved in response to drought are identified or only in wild species. In this study, we phenotyped a population of 119 recombinant inbred lines derived from a cross between a cherry tomato and a large fruit tomato, grown in greenhouse under two watering regimes, in two locations. A large genetic variability was measured for 19 plant and fruit traits, under the two watering treatments. Highly significant genotype by watering regime interactions were detected and resulted from re-ranking more than scale changes. The population was genotyped for 679 SNP markers to develop a genetic map. In total, 56 QTLs were identified among which 11 were interactive between watering regimes. These later mainly exhibited antagonist effects according to watering treatment. Variation in gene expression in leaves of parental accessions revealed 2259 differentially expressed genes, among which candidate genes presenting sequence polymorphisms were identified under two main interactive QTLs. Our results provide knowledge about the genetic control of genotype by watering regime interactions in cultivated tomato and the possible use of deficit irrigation to improve tomato quality.
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Affiliation(s)
- Elise Albert
- INRA, UR1052, Génétique et Amélioration des Fruits et Légumes, 67 Allée des chênes, Centre de Recherche PACA, Domaine Saint Maurice, CS60094, 84143, Montfavet, France
| | - Justine Gricourt
- INRA, UR1052, Génétique et Amélioration des Fruits et Légumes, 67 Allée des chênes, Centre de Recherche PACA, Domaine Saint Maurice, CS60094, 84143, Montfavet, France
| | - Nadia Bertin
- INRA, UR 1115, Plante et Système de cultures Horticoles, 228 Route de l'aérodrome, Centre de Recherche PACA, Domaine Saint Paul, CS40509, 84914, Avignon Cedex 9, France
| | | | - Stéphanie Pateyron
- INRA, Institut of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Rue de Noetzlin, Plateau du Moulon, 91405, Orsay, France
| | - Jean-Philippe Tamby
- INRA, Institut of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Rue de Noetzlin, Plateau du Moulon, 91405, Orsay, France
| | - Frédérique Bitton
- INRA, UR1052, Génétique et Amélioration des Fruits et Légumes, 67 Allée des chênes, Centre de Recherche PACA, Domaine Saint Maurice, CS60094, 84143, Montfavet, France
| | - Mathilde Causse
- INRA, UR1052, Génétique et Amélioration des Fruits et Légumes, 67 Allée des chênes, Centre de Recherche PACA, Domaine Saint Maurice, CS60094, 84143, Montfavet, France.
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175
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Gorter FA, Aarts MMG, Zwaan BJ, de Visser JAGM. Dynamics of Adaptation in Experimental Yeast Populations Exposed to Gradual and Abrupt Change in Heavy Metal Concentration. Am Nat 2016; 187:110-9. [DOI: 10.1086/684104] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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176
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Riordan EC, Gugger PF, Ortego J, Smith C, Gaddis K, Thompson P, Sork VL. Association of genetic and phenotypic variability with geography and climate in three southern California oaks. AMERICAN JOURNAL OF BOTANY 2016; 103:73-85. [PMID: 26758886 DOI: 10.3732/ajb.1500135] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 09/10/2015] [Indexed: 06/05/2023]
Abstract
PREMISE OF THE STUDY Geography and climate shape the distribution of organisms, their genotypes, and their phenotypes. To understand historical and future evolutionary and ecological responses to climate, we compared the association of geography and climate of three oak species (Quercus engelmannii, Quercus berberidifolia, and Quercus cornelius-mulleri) in an environmentally heterogeneous region of southern California at three organizational levels: regional species distributions, genetic variation, and phenotypic variation. METHODS We identified climatic variables influencing regional distribution patterns using species distribution models (SDMs), and then tested whether those individual variables are important in shaping genetic (microsatellite) and phenotypic (leaf morphology) variation. We estimated the relative contributions of geography and climate using multivariate redundancy analyses (RDA) with variance partitioning. KEY RESULTS The modeled distribution of each species was influenced by climate differently. Our analysis of genetic variation using RDA identified small but significant associations between genetic variation with climate and geography in Q. engelmannii and Q. cornelius-mulleri, but not in Q. berberidifolia, and climate explained more of the variation. Our analysis of phenotypic variation in Q. engelmannii indicated that climate had more impact than geography, but not in Q. berberidifolia. Throughout our analyses, we did not find a consistent pattern in effects of individual climatic variables. CONCLUSIONS Our comparative analysis illustrates that climate influences tree response at all organizational levels, but the important climate factors vary depending on the level and on the species. Because of these species-specific and level-specific responses, today's sympatric species are unlikely to have similar distributions in the future.
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Affiliation(s)
- Erin C Riordan
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Box 957239, Los Angeles, California 90095-7239 USA
| | - Paul F Gugger
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Box 957239, Los Angeles, California 90095-7239 USA
| | - Joaquín Ortego
- Department of Integrative Ecology, Estación Biológica de Doñana (EBD-CSIC), Avenida Américo Vespucio s/n 41092 Seville, Spain
| | - Carrie Smith
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Box 957239, Los Angeles, California 90095-7239 USA
| | - Keith Gaddis
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Box 957239, Los Angeles, California 90095-7239 USA
| | - Pam Thompson
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Box 957239, Los Angeles, California 90095-7239 USA
| | - Victoria L Sork
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Box 957239, Los Angeles, California 90095-7239 USA Institute of the Environment and Sustainability, University of California Los Angeles, Box 951496, Los Angeles, California 90095-1496 USA
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Pereira A. Plant Abiotic Stress Challenges from the Changing Environment. FRONTIERS IN PLANT SCIENCE 2016; 7:1123. [PMID: 27512403 PMCID: PMC4962010 DOI: 10.3389/fpls.2016.01123] [Citation(s) in RCA: 111] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 07/14/2016] [Indexed: 05/04/2023]
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178
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Parmesan C, Hanley ME. Plants and climate change: complexities and surprises. ANNALS OF BOTANY 2015; 116:849-64. [PMID: 26555281 PMCID: PMC4640131 DOI: 10.1093/aob/mcv169] [Citation(s) in RCA: 191] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Revised: 10/07/2015] [Accepted: 10/09/2015] [Indexed: 05/02/2023]
Abstract
BACKGROUND Anthropogenic climate change (ACC) will influence all aspects of plant biology over coming decades. Many changes in wild species have already been well-documented as a result of increased atmospheric CO2 concentrations, warming climate and changing precipitation regimes. A wealth of available data has allowed the use of meta-analyses to examine plant-climate interactions on more sophisticated levels than before. These analyses have revealed major differences in plant response among groups, e.g. with respect to functional traits, taxonomy, life-history and provenance. Interestingly, these meta-analyses have also exposed unexpected mismatches between theory, experimental, and observational studies. SCOPE We reviewed the literature on species' responses to ACC, finding ∼42 % of 4000 species studied globally are plants (primarily terrestrial). We review impacts on phenology, distributions, ecophysiology, regeneration biology, plant-plant and plant-herbivore interactions, and the roles of plasticity and evolution. We focused on apparent deviations from expectation, and highlighted cases where more sophisticated analyses revealed that unexpected changes were, in fact, responses to ACC. CONCLUSIONS We found that conventionally expected responses are generally well-understood, and that it is the aberrant responses that are now yielding greater insight into current and possible future impacts of ACC. We argue that inconclusive, unexpected, or counter-intuitive results should be embraced in order to understand apparent disconnects between theory, prediction, and observation. We highlight prime examples from the collection of papers in this Special Issue, as well as general literature. We found use of plant functional groupings/traits had mixed success, but that some underutilized approaches, such as Grime's C/S/R strategies, when incorporated, have improved understanding of observed responses. Despite inherent difficulties, we highlight the need for ecologists to conduct community-level experiments in systems that replicate multiple aspects of ACC. Specifically, we call for development of coordinating experiments across networks of field sites, both natural and man-made.
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Affiliation(s)
- Camille Parmesan
- School of Biological Sciences, University of Plymouth, Drake Circus, Plymouth PL4 8AA, UK
| | - Mick E Hanley
- School of Biological Sciences, University of Plymouth, Drake Circus, Plymouth PL4 8AA, UK
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179
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Sultan SE, Matesanz S. An ideal weed: plasticity and invasiveness in Polygonum cespitosum. Ann N Y Acad Sci 2015; 1360:101-19. [PMID: 26457473 DOI: 10.1111/nyas.12946] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The introduced Asian plant Polygonum cespitosum has only recently become invasive in northeastern North America, spreading into sunny as well as shaded habitats. We present findings from a multiyear case study of this ongoing species invasion, drawing on field environmental measurements, glasshouse plasticity and resurrection experiments, and molecular genetic (microsatellite) data. We focus in particular on patterns of individual phenotypic plasticity (norms of reaction), their diversity within and among populations in the species' introduced range, and their contribution to its potential to evolve even greater invasiveness. Genotypes from introduced-range P. cespitosum populations have recently evolved to express greater adaptive plasticity to full sun and/or dry conditions without any loss of fitness in shade. Evidently, this species may evolve the sort of "general-purpose genotypes" hypothesized by Herbert Baker to characterize an "ideal weed." Indeed, we identified certain genotypes capable of extremely high reproductive output across contrasting conditions, including sunny, shaded, moist, and dry. Populations containing these high-performance genotypes had consistently higher fitness in all glasshouse habitats; there was no evidence for local adaptive differentiation among populations from sunny, shaded, moist, or dry sites. Norm of reaction data may provide valuable insights to invasion biology: the presence of broadly adaptive, high-performance genotypes can promote a species' ecological spread while providing the fuel for increased invasiveness to evolve.
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Affiliation(s)
- Sonia E Sultan
- Biology Department, Wesleyan University, Middletown, Connecticut
| | - Silvia Matesanz
- Área de Biodiversidad y Conservación, Departamento de Biología y Geología, Universidad Rey Juan Carlos, c/ Tulipán s/n, Móstoles, Spain
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180
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Baker RL, Leong WF, Brock MT, Markelz RJC, Covington MF, Devisetty UK, Edwards CE, Maloof J, Welch S, Weinig C. Modeling development and quantitative trait mapping reveal independent genetic modules for leaf size and shape. THE NEW PHYTOLOGIST 2015; 208:257-68. [PMID: 26083847 DOI: 10.1111/nph.13509] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Accepted: 05/11/2015] [Indexed: 05/24/2023]
Abstract
Improved predictions of fitness and yield may be obtained by characterizing the genetic controls and environmental dependencies of organismal ontogeny. Elucidating the shape of growth curves may reveal novel genetic controls that single-time-point (STP) analyses do not because, in theory, infinite numbers of growth curves can result in the same final measurement. We measured leaf lengths and widths in Brassica rapa recombinant inbred lines (RILs) throughout ontogeny. We modeled leaf growth and allometry as function valued traits (FVT), and examined genetic correlations between these traits and aspects of phenology, physiology, circadian rhythms and fitness. We used RNA-seq to construct a SNP linkage map and mapped trait quantitative trait loci (QTL). We found genetic trade-offs between leaf size and growth rate FVT and uncovered differences in genotypic and QTL correlations involving FVT vs STPs. We identified leaf shape (allometry) as a genetic module independent of length and width and identified selection on FVT parameters of development. Leaf shape is associated with venation features that affect desiccation resistance. The genetic independence of leaf shape from other leaf traits may therefore enable crop optimization in leaf shape without negative effects on traits such as size, growth rate, duration or gas exchange.
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Affiliation(s)
- Robert L Baker
- Department of Botany, University of Wyoming, Laramie, WY, 82071, USA
| | - Wen Fung Leong
- Department of Agronomy, Kansas State University, Manhattan, KS, 66506, USA
| | - Marcus T Brock
- Department of Botany, University of Wyoming, Laramie, WY, 82071, USA
| | - R J Cody Markelz
- Department of Plant Biology, University of California, Davis, CA, 95616, USA
| | - Michael F Covington
- Department of Plant Biology, University of California, Davis, CA, 95616, USA
| | - Upendra K Devisetty
- Department of Plant Biology, University of California, Davis, CA, 95616, USA
| | - Christine E Edwards
- Center for Conservation and Sustainable Development, Missouri Botanical Garden, St Louis, MO, 63166, USA
| | - Julin Maloof
- Department of Plant Biology, University of California, Davis, CA, 95616, USA
| | - Stephen Welch
- Department of Agronomy, Kansas State University, Manhattan, KS, 66506, USA
| | - Cynthia Weinig
- Department of Botany, University of Wyoming, Laramie, WY, 82071, USA
- Department of Molecular Biology, University of Wyoming, Laramie, WY, 82071, USA
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181
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Chen Q, Liu Z, Wang B, Wang X, Lai J, Tian F. Transcriptome sequencing reveals the roles of transcription factors in modulating genotype by nitrogen interaction in maize. PLANT CELL REPORTS 2015; 34:1761-71. [PMID: 26116219 PMCID: PMC4569664 DOI: 10.1007/s00299-015-1822-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2015] [Revised: 06/06/2015] [Accepted: 06/10/2015] [Indexed: 05/07/2023]
Abstract
Global transcriptome analysis in maize revealed differential nitrogen response between genotypes and implicate a crucial role of transcription factors in driving genotype by nitrogen interactions at gene expression level. Developing nitrogen-efficient cultivars are essential for sustainable and productive agriculture. Nitrogen use efficiency of plants is highly dependent on the interaction of environmental and genetic variation and results in adaptive phenotypes. This study used transcriptome sequencing to perform a comprehensive genotype by nitrogen (G × N) interaction analysis for two elite Chinese maize inbreds grown at normal and low nitrogen levels in field conditions. We demonstrated that the two maize inbreds showed contrasting agronomic and transcriptomic responses to changes in nitrogen availability. A total of 96 genes with a significant G × N interaction were detected. After characterizing the expression patterns of G × N interaction genes, we found that the G × N interaction genes tended to show condition-specific differential expression. The functional annotations of G × N interaction genes revealed that many different kinds of genes were involved in G × N interactions, but a significant enrichment for transcription factors was detected, particularly the AP2/EREBP and WRKY family, suggesting that transcription factors might play important roles in driving G × N interaction at gene expression level for nitrogen response in maize. Taken together, these results not only provide novel insights into the mechanism of nitrogen response in maize and set important basis for further characterization but also have important implications for other genotype by stress interaction.
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Affiliation(s)
- Qiuyue Chen
- National Maize Improvement Center of China, China Agricultural University, Beijing, 100193, China
| | - Zhipeng Liu
- National Maize Improvement Center of China, China Agricultural University, Beijing, 100193, China
| | - Baobao Wang
- National Maize Improvement Center of China, China Agricultural University, Beijing, 100193, China
| | - Xufeng Wang
- National Maize Improvement Center of China, China Agricultural University, Beijing, 100193, China
| | - Jinsheng Lai
- National Maize Improvement Center of China, China Agricultural University, Beijing, 100193, China
| | - Feng Tian
- National Maize Improvement Center of China, China Agricultural University, Beijing, 100193, China.
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182
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Hernandez KM. Understanding the genetic architecture of complex traits using the function-valued approach. THE NEW PHYTOLOGIST 2015; 208:1-3. [PMID: 26311281 DOI: 10.1111/nph.13607] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Affiliation(s)
- Kyle M Hernandez
- Center for Research Informatics, Biological Sciences Division, University of Chicago, Chicago, IL, 60637, USA
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183
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Aspinwall MJ, Loik ME, Resco de Dios V, Tjoelker MG, Payton PR, Tissue DT. Utilizing intraspecific variation in phenotypic plasticity to bolster agricultural and forest productivity under climate change. PLANT, CELL & ENVIRONMENT 2015; 38:1752-64. [PMID: 25132508 DOI: 10.1111/pce.12424] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Revised: 07/21/2014] [Accepted: 07/28/2014] [Indexed: 05/15/2023]
Abstract
Climate change threatens the ability of agriculture and forestry to meet growing global demands for food, fibre and wood products. Information gathered from genotype-by-environment interactions (G × E), which demonstrate intraspecific variation in phenotypic plasticity (the ability of a genotype to alter its phenotype in response to environmental change), may prove important for bolstering agricultural and forest productivity under climate change. Nonetheless, very few studies have explicitly quantified genotype plasticity-productivity relationships in agriculture or forestry. Here, we conceptualize the importance of intraspecific variation in agricultural and forest species plasticity, and discuss the physiological and genetic factors contributing to intraspecific variation in phenotypic plasticity. Our discussion highlights the need for an integrated understanding of the mechanisms of G × E, more extensive assessments of genotypic responses to climate change under field conditions, and explicit testing of genotype plasticity-productivity relationships. Ultimately, further investigation of intraspecific variation in phenotypic plasticity in agriculture and forestry may prove important for identifying genotypes capable of increasing or sustaining productivity under more extreme climatic conditions.
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Affiliation(s)
- Michael J Aspinwall
- Hawkesbury Institute for the Environment, University of Western Sydney, Penrith, New South Wales, 2751, Australia
| | - Michael E Loik
- Department of Environmental Studies, University of California - Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Victor Resco de Dios
- Hawkesbury Institute for the Environment, University of Western Sydney, Penrith, New South Wales, 2751, Australia
- Department of Crop and Forest Sciences - AGROTECNIO Center, Universitat de Lleida, Lleida, E25198, Spain
| | - Mark G Tjoelker
- Hawkesbury Institute for the Environment, University of Western Sydney, Penrith, New South Wales, 2751, Australia
| | - Paxton R Payton
- USDA-ARS Cropping Systems Research Laboratory, Lubbock, TX, 74915, USA
| | - David T Tissue
- Hawkesbury Institute for the Environment, University of Western Sydney, Penrith, New South Wales, 2751, Australia
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184
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Baack E, Melo MC, Rieseberg LH, Ortiz-Barrientos D. The origins of reproductive isolation in plants. THE NEW PHYTOLOGIST 2015; 207:968-84. [PMID: 25944305 DOI: 10.1111/nph.13424] [Citation(s) in RCA: 192] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Accepted: 03/16/2015] [Indexed: 05/23/2023]
Abstract
Reproductive isolation in plants occurs through multiple barriers that restrict gene flow between populations, but their origins remain uncertain. Work in the past decade has shown that postpollination barriers, such as the failure to form hybrid seeds or sterility of hybrid offspring, are often less strong than prepollination barriers. Evidence implicates multiple evolutionary forces in the origins of reproductive barriers, including mutation, stochastic processes and natural selection. Although adaptation to different environments is a common element of reproductive isolation, genomic conflicts also play a role, including female meiotic drive. The genetic basis of some reproductive barriers, particularly flower colour influencing pollinator behaviour, is well understood in some species, but the genetic changes underlying many other barriers, especially pollen-stylar interactions, are largely unknown. Postpollination barriers appear to accumulate at a faster rate in annuals compared with perennials, due in part to chromosomal rearrangements. Chromosomal changes can be important isolating barriers in themselves but may also reduce the recombination of genes contributing to isolation. Important questions for the next decade include identifying the evolutionary forces responsible for chromosomal rearrangements, determining how often prezygotic barriers arise due to selection against hybrids, and establishing the relative importance of genomic conflicts in speciation.
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Affiliation(s)
- Eric Baack
- Department of Biology, Luther College, Decorah, IA, 52101, USA
| | - Maria Clara Melo
- School of Biological Sciences, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Loren H Rieseberg
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
- Department of Biology, Indiana University, Bloomington, IN, 47405, USA
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185
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Jogesh T, Stanley MC, Berenbaum MR. Evolution of tolerance in an invasive weed after reassociation with its specialist herbivore. J Evol Biol 2015; 27:2334-46. [PMID: 25417738 DOI: 10.1111/jeb.12469] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Revised: 07/30/2014] [Accepted: 08/05/2014] [Indexed: 11/26/2022]
Abstract
The interaction between the European wild parsnip Pastinaca sativa and its coevolved florivore the parsnip webworm Depressaria pastinacella, established in North America for over 150 years, has resulted in evolution of local chemical phenotype matching. The recent invasion of New Zealand by webworms, exposing parsnips there to florivore selection for the first time, provided an opportunity to assess rates of adaptive response in a real-time experiment. We planted reciprocal common gardens in the USA and NZ with seeds from (1) US populations with a long history of webworm association; (2) NZ populations that had never been infested and (3) NZ populations infested for 3 years (since 2007) or 6 years (since 2004). We measured impacts of florivory on realized fitness, reproductive effort and pollination success and measured phenotypic changes in infested NZ populations relative to uninfested NZ populations to determine whether rapid adaptive evolution in response to florivory occurred. Irrespective of country of origin or location, webworms significantly reduced plant fitness. Webworms reduced pollination success in small plants but not in larger plants. Although defence chemistry remained unchanged, plants in infested populations were larger after 3-6 years of webworm florivory. As plant size is a strong predictor of realized fitness, evolution of large size as a component of florivore tolerance may occur more rapidly than evolution of enhanced chemical defence.
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Affiliation(s)
- T Jogesh
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
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186
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Lasky JR, Upadhyaya HD, Ramu P, Deshpande S, Hash CT, Bonnette J, Juenger TE, Hyma K, Acharya C, Mitchell SE, Buckler ES, Brenton Z, Kresovich S, Morris GP. Genome-environment associations in sorghum landraces predict adaptive traits. SCIENCE ADVANCES 2015; 1:e1400218. [PMID: 26601206 PMCID: PMC4646766 DOI: 10.1126/sciadv.1400218] [Citation(s) in RCA: 152] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 04/26/2015] [Indexed: 05/15/2023]
Abstract
Improving environmental adaptation in crops is essential for food security under global change, but phenotyping adaptive traits remains a major bottleneck. If associations between single-nucleotide polymorphism (SNP) alleles and environment of origin in crop landraces reflect adaptation, then these could be used to predict phenotypic variation for adaptive traits. We tested this proposition in the global food crop Sorghum bicolor, characterizing 1943 georeferenced landraces at 404,627 SNPs and quantifying allelic associations with bioclimatic and soil gradients. Environment explained a substantial portion of SNP variation, independent of geographical distance, and genic SNPs were enriched for environmental associations. Further, environment-associated SNPs predicted genotype-by-environment interactions under experimental drought stress and aluminum toxicity. Our results suggest that genomic signatures of environmental adaptation may be useful for crop improvement, enhancing germplasm identification and marker-assisted selection. Together, genome-environment associations and phenotypic analyses may reveal the basis of environmental adaptation.
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Affiliation(s)
- Jesse R. Lasky
- Earth Institute, and Department of Ecology, Evolution, and Environmental Biology, Columbia University, New York, NY 10025, USA
| | - Hari D. Upadhyaya
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502 324, Telangana, India
- Department of Agronomy, Kansas State University, Manhattan, KS 66506, USA
- UWA Institute of Agriculture, University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Punna Ramu
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502 324, Telangana, India
- Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853, USA
| | - Santosh Deshpande
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502 324, Telangana, India
| | - C. Tom Hash
- ICRISAT Sahelian Center, BP 12404, Niamey, Niger
| | - Jason Bonnette
- Department of Integrative Biology, Institute for Cellular and Molecular Biology, and Brackenridge Field Laboratory, University of Texas at Austin, Austin, TX 78712, USA
| | - Thomas E. Juenger
- Department of Integrative Biology, Institute for Cellular and Molecular Biology, and Brackenridge Field Laboratory, University of Texas at Austin, Austin, TX 78712, USA
| | - Katie Hyma
- Genomic Diversity Facility, Institute of Biotechnology, Cornell University, Ithaca, NY 14853, USA
| | - Charlotte Acharya
- Genomic Diversity Facility, Institute of Biotechnology, Cornell University, Ithaca, NY 14853, USA
| | - Sharon E. Mitchell
- Genomic Diversity Facility, Institute of Biotechnology, Cornell University, Ithaca, NY 14853, USA
| | - Edward S. Buckler
- Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853, USA
- U.S. Department of Agriculture–Agricultural Research Service, Ithaca, NY 14853, USA
| | - Zachary Brenton
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA
| | - Stephen Kresovich
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA
| | - Geoffrey P. Morris
- Department of Agronomy, Kansas State University, Manhattan, KS 66506, USA
- Corresponding author. E-mail:
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187
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Khanal N, Moffatt BA, Gray GR. Acquisition of freezing tolerance in Arabidopsis and two contrasting ecotypes of the extremophile Eutrema salsugineum (Thellungiella salsuginea). JOURNAL OF PLANT PHYSIOLOGY 2015; 180:35-44. [PMID: 25889872 DOI: 10.1016/j.jplph.2015.03.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Revised: 03/13/2015] [Accepted: 03/13/2015] [Indexed: 05/28/2023]
Abstract
Eutrema salsugineum (Thellungiella salsuginea) is an extremophile, a close relative of Arabidopsis, but possessing much higher constitutive levels of tolerance to abiotic stress. This study aimed to characterize the freezing tolerance of Arabidopsis (Columbia ecotype) and two ecotypes of Eutrema (Yukon and Shandong) isolated from contrasting geographical locations. Under our growth conditions, maximal freezing tolerance was observed after two- and three-weeks of cold acclimation for Arabidopsis and Eutrema, respectively. The ecotypes of Eutrema and Arabidopsis do not differ in their constitutive level of freezing tolerance or short-term cold acclimation capacity. However Eutrema remarkably outperforms Arabidopsis in long-term acclimation capacity suggesting a wider phenotypic plasticity for the trait of freezing tolerance. The combination of drought treatment and one-week of cold acclimation was more effective than long-term cold acclimation in achieving maximum levels of freezing tolerance in Eutrema, but not Arabidopsis. Furthermore, it was demonstrated growth conditions, particularly irradiance, are determinates of the level of freezing tolerance attained during cold acclimation suggesting a role for photosynthetic processes in adaptive stress responses.
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Affiliation(s)
- Nityananda Khanal
- Department of Plant Sciences, University of Saskatchewan, Saskatoon SK S7N 5A8, Canada
| | - Barbara A Moffatt
- Department of Biology, University of Waterloo, Waterloo ON N2L 3G1, Canada
| | - Gordon R Gray
- Department of Plant Sciences, University of Saskatchewan, Saskatoon SK S7N 5A8, Canada; Department of Biochemistry, University of Saskatchewan, Saskatoon SK S7N 5E5, Canada.
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188
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Kooyers NJ. The evolution of drought escape and avoidance in natural herbaceous populations. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2015; 234:155-62. [PMID: 25804818 DOI: 10.1016/j.plantsci.2015.02.012] [Citation(s) in RCA: 180] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 02/04/2015] [Accepted: 02/19/2015] [Indexed: 05/03/2023]
Abstract
While the functional genetics and physiological mechanisms controlling drought resistance in crop plants have been intensely studied, less research has examined the genetic basis of adaptation to drought stress in natural populations. Drought resistance adaptations in nature reflect natural rather than human-mediated selection and may identify novel mechanisms for stress tolerance. Adaptations conferring drought resistance have historically been divided into alternative strategies including drought escape (rapid development to complete a life cycle before drought) and drought avoidance (reducing water loss to prevent dehydration). Recent studies in genetic model systems such as Arabidopsis, Mimulus, and Panicum have begun to elucidate the genes, expression profiles, and physiological changes responsible for ecologically important variation in drought resistance. Similar to most crop plants, variation in drought escape and avoidance is complex, underlain by many QTL of small effect, and pervasive gene by environment interactions. Recently identified major-effect alleles point to a significant role for genetic constraints in limiting the concurrent evolution of both drought escape and avoidance strategies, although these constraints are not universally found. This progress suggests that understanding the mechanistic basic and fitness consequences of gene by environment interactions will be critical for crop improvement and forecasting population persistence in unpredictable environments.
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Affiliation(s)
- Nicholas J Kooyers
- Department of Biology, University of Virginia, Charlottesville, VA 22904, USA.
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189
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Toräng P, Wunder J, Obeso JR, Herzog M, Coupland G, Ågren J. Large-scale adaptive differentiation in the alpine perennial herb Arabis alpina. THE NEW PHYTOLOGIST 2015; 206:459-470. [PMID: 25422098 DOI: 10.1111/nph.13176] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Accepted: 10/14/2014] [Indexed: 06/04/2023]
Abstract
Information about the incidence and magnitude of local adaptation can help to predict the response of natural populations to a changing environment, and should be of particular interest in arctic and alpine environments where the effects of climate change are expected to be severe. To quantify adaptive differentiation in the arctic-alpine perennial herb Arabis alpina, we conducted reciprocal transplant experiments for 3 yr between Spanish and Scandinavian populations. At the sites of one Spanish and one Scandinavian population, we planted seedlings representing two Spanish and four Scandinavian populations, and recorded survival, flowering propensity and fecundity. The experiment was replicated in two subsequent years. The results demonstrate strong adaptive differentiation between A. alpina populations from the two regions. At the field site in Spain, survival and fruit production of Spanish populations were higher than those of Scandinavian populations, while the opposite was true at the site in Scandinavia, and these differences were consistent across years. By comparison, fitness varied little among populations from the same region. The results suggest that the magnitude and geographical scale of local adaptation need to be considered in predictions of the effects of global change on the dynamics of arctic and alpine plant populations.
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Affiliation(s)
- Per Toräng
- Department of Plant Ecology and Evolution, EBC, Uppsala University, Norbyvägen 18D, SE-752 36, Uppsala, Sweden
| | - Jörg Wunder
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl von Linné Weg 10, 50829, Cologne, Germany
| | - José Ramón Obeso
- Research Unit of Biodivesity (UO-CSIC-PA), Universidad de Oviedo, Campus de Mieres, 33600, Mieres, Spain
| | - Michel Herzog
- LECA, Université Grenoble Alpes, F-38000, Grenoble, France
| | - George Coupland
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl von Linné Weg 10, 50829, Cologne, Germany
| | - Jon Ågren
- Department of Plant Ecology and Evolution, EBC, Uppsala University, Norbyvägen 18D, SE-752 36, Uppsala, Sweden
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190
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Xu Q, Xing S, Zhu C, Liu W, Fan Y, Wang Q, Song Z, Yang W, Luo F, Shang F, Kang L, Chen W, Yan J, Li J, Sang T. Population transcriptomics reveals a potentially positive role of expression diversity in adaptation. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2015; 57:284-99. [PMID: 25251542 DOI: 10.1111/jipb.12287] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2014] [Accepted: 09/19/2014] [Indexed: 05/27/2023]
Abstract
While it is widely accepted that genetic diversity determines the potential of adaptation, the role that gene expression variation plays in adaptation remains poorly known. Here we show that gene expression diversity could have played a positive role in the adaptation of Miscanthus lutarioriparius. RNA-seq was conducted for 80 individuals of the species, with half planted in the energy crop domestication site and the other half planted in the control site near native habitats. A leaf reference transcriptome consisting of 18,503 high-quality transcripts was obtained using a pipeline developed for de novo assembling with population RNA-seq data. The population structure and genetic diversity of M. lutarioriparius were estimated based on 30,609 genic single nucleotide polymorphisms. Population expression (Ep ) and expression diversity (Ed ) were defined to measure the average level and the magnitude of variation of a gene expression in the population, respectively. It was found that expression diversity increased while genetic diversity decreased after the species was transplanted from the native habitats to the harsh domestication site, especially for genes involved in abiotic stress resistance, histone methylation, and biomass synthesis under water limitation. The increased expression diversity could have enriched phenotypic variation directly subject to selections in the new environment.
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Affiliation(s)
- Qin Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
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191
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Des Marais DL, Skillern WD, Juenger TE. Deeply Diverged Alleles in the Arabidopsis AREB1 Transcription Factor Drive Genome-Wide Differences in Transcriptional Response to the Environment. Mol Biol Evol 2015; 32:956-69. [DOI: 10.1093/molbev/msu401] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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192
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Stillman JH, Armstrong E. Genomics Are Transforming Our Understanding of Responses to Climate Change. Bioscience 2015. [DOI: 10.1093/biosci/biu219] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
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193
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Bock DG, Caseys C, Cousens RD, Hahn MA, Heredia SM, Hübner S, Turner KG, Whitney KD, Rieseberg LH. What we still don't know about invasion genetics. Mol Ecol 2015; 24:2277-97. [PMID: 25474505 DOI: 10.1111/mec.13032] [Citation(s) in RCA: 239] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2014] [Revised: 11/27/2014] [Accepted: 11/28/2014] [Indexed: 12/12/2022]
Abstract
Publication of The Genetics of Colonizing Species in 1965 launched the field of invasion genetics and highlighted the value of biological invasions as natural ecological and evolutionary experiments. Here, we review the past 50 years of invasion genetics to assess what we have learned and what we still don't know, focusing on the genetic changes associated with invasive lineages and the evolutionary processes driving these changes. We also suggest potential studies to address still-unanswered questions. We now know, for example, that rapid adaptation of invaders is common and generally not limited by genetic variation. On the other hand, and contrary to prevailing opinion 50 years ago, the balance of evidence indicates that population bottlenecks and genetic drift typically have negative effects on invasion success, despite their potential to increase additive genetic variation and the frequency of peak shifts. Numerous unknowns remain, such as the sources of genetic variation, the role of so-called expansion load and the relative importance of propagule pressure vs. genetic diversity for successful establishment. While many such unknowns can be resolved by genomic studies, other questions may require manipulative experiments in model organisms. Such studies complement classical reciprocal transplant and field-based selection experiments, which are needed to link trait variation with components of fitness and population growth rates. We conclude by discussing the potential for studies of invasion genetics to reveal the limits to evolution and to stimulate the development of practical strategies to either minimize or maximize evolutionary responses to environmental change.
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Affiliation(s)
- Dan G Bock
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Room 3529-6270 University Blvd, Vancouver, BC, V6T 1Z4, Canada
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194
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Chown SL, Hodgins KA, Griffin PC, Oakeshott JG, Byrne M, Hoffmann AA. Biological invasions, climate change and genomics. Evol Appl 2015; 8:23-46. [PMID: 25667601 PMCID: PMC4310580 DOI: 10.1111/eva.12234] [Citation(s) in RCA: 132] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Accepted: 10/24/2014] [Indexed: 12/13/2022] Open
Abstract
The rate of biological invasions is expected to increase as the effects of climate change on biological communities become widespread. Climate change enhances habitat disturbance which facilitates the establishment of invasive species, which in turn provides opportunities for hybridization and introgression. These effects influence local biodiversity that can be tracked through genetic and genomic approaches. Metabarcoding and metagenomic approaches provide a way of monitoring some types of communities under climate change for the appearance of invasives. Introgression and hybridization can be followed by the analysis of entire genomes so that rapidly changing areas of the genome are identified and instances of genetic pollution monitored. Genomic markers enable accurate tracking of invasive species' geographic origin well beyond what was previously possible. New genomic tools are promoting fresh insights into classic questions about invading organisms under climate change, such as the role of genetic variation, local adaptation and climate pre-adaptation in successful invasions. These tools are providing managers with often more effective means to identify potential threats, improve surveillance and assess impacts on communities. We provide a framework for the application of genomic techniques within a management context and also indicate some important limitations in what can be achieved.
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Affiliation(s)
- Steven L Chown
- School of Biological Sciences, Monash UniversityClayton, Vic., Australia
| | - Kathryn A Hodgins
- School of Biological Sciences, Monash UniversityClayton, Vic., Australia
| | - Philippa C Griffin
- Department of Genetics, Bio21 Institute, The University of MelbourneParkville, Vic., Australia
| | - John G Oakeshott
- CSIRO Land and Water Flagship, Black Mountain LaboratoriesCanberra, ACT, Australia
| | - Margaret Byrne
- Science and Conservation Division, Department of Parks and Wildlife, Bentley Delivery CentreBentley, WA, Australia
| | - Ary A Hoffmann
- Departments of Zoology and Genetics, Bio21 Institute, The University of MelbourneParkville, Vic., Australia
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195
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Malcom JW, Hernandez KM, Likos R, Wayne T, Leibold MA, Juenger TE. Extensive cross-environment fitness variation lies along few axes of genetic variation in the model alga, Chlamydomonas reinhardtii. THE NEW PHYTOLOGIST 2015; 205:841-851. [PMID: 25264298 DOI: 10.1111/nph.13063] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2014] [Accepted: 08/11/2014] [Indexed: 06/03/2023]
Abstract
Variation is essential to ecological and evolutionary dynamics, but genetic variation of quantitative traits may be concentrated in a limited number of dimensions, constraining ecoevolutionary dynamics. We describe high-dimension variation in natural accessions of the model alga, Chlamydomonas reinhardtii, and test the hypothesis that extensive fitness variation across 30 environments is constrained to a small number of axes. We used high-throughput phenotyping to investigate morphological, fitness, and genotype × environment (G × E) variation in 18 natural C. reinhardtii accessions in 30 environments. The organismal phenotypes of cell cycle, cell size, and phototactic behavior exhibited substantial genetic variation between lines, and we found up to 74-fold fitness variation across accessions and environments. Approximately 47% of the extensive G × E variation is accounted for by the first two principal components (PCs) of the G-matrix corresponding to covariation in metals response, nitrogen availability, or salt and nutrient response. The natural variation of C. reinhardtii accessions supports the hypothesis that, despite abundant genetic variation across single environments, the species' adaptive response should be constrained along few major axes of selection. These results highlight the utility of natural accessions for integrating ecoevolutionary and genetic research.
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Affiliation(s)
- Jacob W Malcom
- Department of Integrative Biology, The University of Texas at Austin, 1 University Station #C0930, Austin, TX, 78712, USA
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196
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Des Marais DL, Juenger TE. Brachypodium and the Abiotic Environment. GENETICS AND GENOMICS OF BRACHYPODIUM 2015. [DOI: 10.1007/7397_2015_13] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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197
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Bhaskara GB, Yang TH, Verslues PE. Dynamic proline metabolism: importance and regulation in water limited environments. FRONTIERS IN PLANT SCIENCE 2015; 6:484. [PMID: 26161086 PMCID: PMC4479789 DOI: 10.3389/fpls.2015.00484] [Citation(s) in RCA: 106] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Accepted: 06/16/2015] [Indexed: 05/18/2023]
Abstract
Drought-induced proline accumulation observed in many plant species has led to the hypothesis that further increases in proline accumulation would promote drought tolerance. Here we discuss both previous and new data showing that proline metabolism and turnover, rather than just proline accumulation, functions to maintain growth during water limitation. Mutants of Δ (1)-Pyrroline-5-Carboxylate Synthetase1 (P5CS1) and Proline Dehydrogenase1 (PDH1), key enzymes in proline synthesis and catabolism respectively, both have similar reductions in growth during controlled soil drying. Such results are consistent with patterns of natural variation in proline accumulation and with evidence that turnover of proline can act to buffer cellular redox status during drought. Proline synthesis and catabolism are regulated by multiple cellular mechanisms, of which we know only a few. An example of this is immunoblot detection of P5CS1 and PDH1 showing that the Highly ABA-induced (HAI) protein phosphatase 2Cs (PP2Cs) have different effects on P5CS1 and PDH1 protein levels despite having similar increases in proline accumulation. Immunoblot data also indicate that both P5CS1 and PDH1 are subjected to unknown post-translational modifications.
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Affiliation(s)
| | | | - Paul E. Verslues
- *Correspondence: Paul E. Verslues, Institute of Plant and Microbial Biology, Academia Sinica, No. 128 Section 2 Academia Road, Nankang District, Taipei 11529, Taiwan,
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198
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DeHaan LR, Van Tassel DL. Useful insights from evolutionary biology for developing perennial grain crops. AMERICAN JOURNAL OF BOTANY 2014; 101:1801-1819. [PMID: 25326622 DOI: 10.3732/ajb.1400084] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Annual grain crops dominate agricultural landscapes and provide the majority of calories consumed by humanity. Perennial grain crops could potentially ameliorate the land degradation and off-site impacts associated with annual grain cropping. However, herbaceous perennial plants with constitutively high allocation to harvestable seeds are rare to absent in nature. Recent trade-off theory models suggest that rugged fitness landscapes may explain the absence of this form better than sink competition models. Artificial selection for both grain production and multiyear lifespan can lead to more rapid progress in the face of fitness and genetic trade-offs than natural selection but is likely to result in plant types that differ substantially from all current domestic crops. Perennial grain domestication is also likely to require the development of selection strategies that differ from published crop breeding methods, despite their success in improving long-domesticated crops; for this purpose, we have reviewed literature in the areas of population and evolutionary genetics, domestication, and molecular biology. Rapid domestication will likely require genes with large effect that are expected to exhibit strong pleiotropy and epistasis. Cryptic genetic variation will need to be deliberately exposed both to purge mildly deleterious alleles and to generate novel agronomic phenotypes. We predict that perennial grain domestication programs will benefit from population subdivision followed by selection for simple traits in each subpopulation, the evaluation of very large populations, high selection intensity, rapid cycling through generations, and heterosis. The latter may be particularly beneficial in the development of varieties with stable yield and tolerance to crowding.
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Affiliation(s)
- Lee R DeHaan
- The Land Institute, 2440 E. Water Well Rd., Salina, Kansas 67401 USA
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199
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Lasky JR, Des Marais DL, Lowry DB, Povolotskaya I, McKay JK, Richards JH, Keitt TH, Juenger TE. Natural variation in abiotic stress responsive gene expression and local adaptation to climate in Arabidopsis thaliana. Mol Biol Evol 2014; 31:2283-96. [PMID: 24850899 PMCID: PMC4137704 DOI: 10.1093/molbev/msu170] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Gene expression varies widely in natural populations, yet the proximate and ultimate causes of this variation are poorly known. Understanding how variation in gene expression affects abiotic stress tolerance, fitness, and adaptation is central to the field of evolutionary genetics. We tested the hypothesis that genes with natural genetic variation in their expression responses to abiotic stress are likely to be involved in local adaptation to climate in Arabidopsis thaliana. Specifically, we compared genes with consistent expression responses to environmental stress (expression stress responsive, "eSR") to genes with genetically variable responses to abiotic stress (expression genotype-by-environment interaction, "eGEI"). We found that on average genes that exhibited eGEI in response to drought or cold had greater polymorphism in promoter regions and stronger associations with climate than those of eSR genes or genomic controls. We also found that transcription factor binding sites known to respond to environmental stressors, especially abscisic acid responsive elements, showed significantly higher polymorphism in drought eGEI genes in comparison to eSR genes. By contrast, eSR genes tended to exhibit relatively greater pairwise haplotype sharing, lower promoter diversity, and fewer nonsynonymous polymorphisms, suggesting purifying selection or selective sweeps. Our results indicate that cis-regulatory evolution and genetic variation in stress responsive gene expression may be important mechanisms of local adaptation to climatic selective gradients.
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Affiliation(s)
- Jesse R Lasky
- Department of Integrative Biology, University of Texas at AustinEarth Institute and Department of Ecology, Evolution and Environmental Biology, Columbia University
| | | | - David B Lowry
- Department of Integrative Biology, University of Texas at Austin
| | - Inna Povolotskaya
- Bioinformatics and Genomics Program, Centre for Genomic Regulation, Barcelona, Spain
| | - John K McKay
- Bioagricultural Sciences and Pest Management, Colorado State University
| | | | - Timothy H Keitt
- Department of Integrative Biology, University of Texas at Austin
| | - Thomas E Juenger
- Department of Integrative Biology, University of Texas at Austin
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200
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Association mapping of germination traits in Arabidopsis thaliana under light and nutrient treatments: searching for G×E effects. G3-GENES GENOMES GENETICS 2014; 4:1465-78. [PMID: 24902604 PMCID: PMC4132177 DOI: 10.1534/g3.114.012427] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
In the natural world, genotype expression is influenced by an organism’s environment. Identifying and understanding the genes underlying phenotypes in different environments is important for making advances in fields ranging from evolution to medicine to agriculture. With the availability of genome-wide genetic-marker datasets, it is possible to look for genes that interact with the environment. Using the model organism, Arabidopsis thaliana, we looked for genes underlying phenotypes as well as genotype-by-environment interactions in four germination traits under two light and two nutrient conditions. We then performed genome-wide association tests to identify candidate genes underlying the observed phenotypes and genotype-by-environment interactions. Of the four germination traits examined, only two showed significant genotype-by-environment interactions. While genome-wide association analyses did not identify any markers or genes explicitly linked to genotype-by-environment interactions, we did identify a total of 55 markers and 71 genes associated with germination differences. Of the 71 genes, four—ZIGA4, PS1, TOR, and TT12—appear to be strong candidates for further study of germination variation under different environments.
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