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Zhang H, Cao Y, Wang Z, Ye M, Wu R. Functional Mapping of Genes Modulating Plant Shade Avoidance Using Leaf Traits. PLANTS (BASEL, SWITZERLAND) 2023; 12:608. [PMID: 36771692 PMCID: PMC9920004 DOI: 10.3390/plants12030608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 01/19/2023] [Accepted: 01/23/2023] [Indexed: 06/18/2023]
Abstract
Shade avoidance syndrome (SAS) refers to a set of plant responses that increases light capture in dense stands. This process is crucial for plants in natural and agricultural environments as they compete for resources and avoid suboptimal conditions. Although the molecular, biochemical, and physiological mechanisms underlying the SAS response have been extensively studied, the genetic basis of developmental variation in leaves in regard to leaf area, petiole length, and leaf length (i.e., their allometric relationships) remains unresolved. In this study, with the recombinant inbred line (RIL) population, the developmental traits of leaves of Arabidopsis were investigated under two growth density conditions (high- and low-density plantings). The observed changes were then reconstructed digitally, and their allometric relationships were modelled. Taking the genome-wide association analysis, the SNP genotype and the dynamic phenotype of the leaf from both densities were combined to explore the allometry QTLs. Under different densities, leaf change phenotype was analyzed from two core ecological scenarios: (i) the allometric change of the leaf area with leaf length, and (ii) the change of the leaf length with petiole length. QTLs modulating these two scenarios were characterized as 'leaf shape QTLs' and 'leaf position QTLs'. With functional mapping, results showed a total of 30 and 24 significant SNPs for shapeQTLs and positionQTLs, respectively. By annotation, immune pathway genes, photosensory receptor genes, and phytohormone genes were identified to be involved in the SAS response. Interestingly, genes modulating the immune pathway and salt tolerance, i.e., systemic acquired resistance (SAR) regulatory proteins (MININ-1-related) and salt tolerance homologs (STH), were reported to mediate the SAS response. By dissecting and comparing QTL effects from low- and high-density conditions, our results elucidate the genetic control of leaf formation in the context of the SAS response. The mechanism with leaf development × density interaction can further aid the development of density-tolerant crop varieties for agricultural practices.
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Affiliation(s)
- Han Zhang
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing 100083, China
| | - Yige Cao
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing 100083, China
| | - Zijian Wang
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing 100083, China
| | - Meixia Ye
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing 100083, China
| | - Rongling Wu
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing 100083, China
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Schneider HM. Characterization, costs, cues and future perspectives of phenotypic plasticity. ANNALS OF BOTANY 2022; 130:131-148. [PMID: 35771883 PMCID: PMC9445595 DOI: 10.1093/aob/mcac087] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 06/28/2022] [Indexed: 06/09/2023]
Abstract
BACKGROUND Plastic responses of plants to the environment are ubiquitous. Phenotypic plasticity occurs in many forms and at many biological scales, and its adaptive value depends on the specific environment and interactions with other plant traits and organisms. Even though plasticity is the norm rather than the exception, its complex nature has been a challenge in characterizing the expression of plasticity, its adaptive value for fitness and the environmental cues that regulate its expression. SCOPE This review discusses the characterization and costs of plasticity and approaches, considerations, and promising research directions in studying plasticity. Phenotypic plasticity is genetically controlled and heritable; however, little is known about how organisms perceive, interpret and respond to environmental cues, and the genes and pathways associated with plasticity. Not every genotype is plastic for every trait, and plasticity is not infinite, suggesting trade-offs, costs and limits to expression of plasticity. The timing, specificity and duration of plasticity are critical to their adaptive value for plant fitness. CONCLUSIONS There are many research opportunities to advance our understanding of plant phenotypic plasticity. New methodology and technological breakthroughs enable the study of phenotypic responses across biological scales and in multiple environments. Understanding the mechanisms of plasticity and how the expression of specific phenotypes influences fitness in many environmental ranges would benefit many areas of plant science ranging from basic research to applied breeding for crop improvement.
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Feng L, Dong T, Jiang P, Yang Z, Dong A, Xie SQ, Griffin CH, Wu R. An eco-evo-devo genetic network model of stress response. HORTICULTURE RESEARCH 2022; 9:uhac135. [PMID: 36061617 PMCID: PMC9433980 DOI: 10.1093/hr/uhac135] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 06/04/2022] [Indexed: 05/23/2023]
Abstract
The capacity of plants to resist abiotic stresses is of great importance to agricultural, ecological and environmental sustainability, but little is known about its genetic underpinnings. Existing genetic tools can identify individual genetic variants mediating biochemical, physiological, and cellular defenses, but fail to chart an overall genetic atlas behind stress resistance. We view stress response as an eco-evo-devo process by which plants adaptively respond to stress through complex interactions of developmental canalization, phenotypic plasticity, and phenotypic integration. As such, we define and quantify stress response as the developmental change of adaptive traits from stress-free to stress-exposed environments. We integrate composite functional mapping and evolutionary game theory to reconstruct omnigenic, information-flow interaction networks for stress response. Using desert-adapted Euphrates poplar as an example, we infer salt resistance-related genome-wide interactome networks and trace the roadmap of how each SNP acts and interacts with any other possible SNPs to mediate salt resistance. We characterize the previously unknown regulatory mechanisms driving trait variation; i.e. the significance of a SNP may be due to the promotion of positive regulators, whereas the insignificance of a SNP may result from the inhibition of negative regulators. The regulator-regulatee interactions detected are not only experimentally validated by two complementary experiments, but also biologically interpreted by their encoded protein-protein interactions. Our eco-evo-devo model of genetic interactome networks provides an approach to interrogate the genetic architecture of stress response and informs precise gene editing for improving plants' capacity to live in stress environments.
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Affiliation(s)
| | | | | | - Zhenyu Yang
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Ang Dong
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Shang-Qian Xie
- Key Laboratory of Ministry of Education for Genetics and Germplasm Innovation of Tropical Special Trees and Ornamental Plants, College of Forestry, Hainan University, Haikou 570228, China
| | - Christopher H Griffin
- Applied Research Laboratory, The Pennsylvania State University, University Park, PA 16802, USA
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Yang D, Zheng X, Jiang L, Ye M, He X, Jin Y, Wu R. Functional Mapping of Phenotypic Plasticity of Staphylococcus aureus Under Vancomycin Pressure. Front Microbiol 2021; 12:696730. [PMID: 34566908 PMCID: PMC8458881 DOI: 10.3389/fmicb.2021.696730] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Accepted: 08/23/2021] [Indexed: 11/17/2022] Open
Abstract
Phenotypic plasticity is the exhibition of various phenotypic traits produced by a single genotype in response to environmental changes, enabling organisms to adapt to environmental changes by maintaining growth and reproduction. Despite its significance in evolutionary studies, we still know little about the genetic control of phenotypic plasticity. In this study, we designed and conducted a genome-wide association study (GWAS) to reveal genetic architecture of how Staphylococcus aureus strains respond to increasing concentrations of vancomycin (0, 2, 4, and 6 μg/mL) in a time course. We implemented functional mapping, a dynamic model for genetic mapping using longitudinal data, to map specific loci that mediate the growth trajectories of abundance of vancomycin-exposed S. aureus strains. 78 significant single nucleotide polymorphisms were identified following analysis of the whole growth and development process, and seven genes might play a pivotal role in governing phenotypic plasticity to the pressure of vancomycin. These seven genes, SAOUHSC_00020 (walR), SAOUHSC_00176, SAOUHSC_00544 (sdrC), SAOUHSC_02998, SAOUHSC_00025, SAOUHSC_00169, and SAOUHSC_02023, were found to help S. aureus regulate antibiotic pressure. Our dynamic gene mapping technique provides a tool for dissecting the phenotypic plasticity mechanisms of S. aureus under vancomycin pressure, emphasizing the feasibility and potential of functional mapping in the study of bacterial phenotypic plasticity.
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Affiliation(s)
- Dengcheng Yang
- Center for Computational Biology, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Xuyang Zheng
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Libo Jiang
- Center for Computational Biology, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China.,College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Meixia Ye
- Center for Computational Biology, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China.,College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Xiaoqing He
- Center for Computational Biology, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China.,College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Yi Jin
- Center for Computational Biology, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China.,College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Rongling Wu
- Center for Computational Biology, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China.,College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China.,Department of Public Health Sciences and Statistics, Center for Statistical Genetics, The Pennsylvania State University, Hershey, PA, United States
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Ye M, Jiang L, Chen C, Zhu X, Wang M, Wu R. np 2 QTL: networking phenotypic plasticity quantitative trait loci across heterogeneous environments. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 99:796-806. [PMID: 31009134 DOI: 10.1111/tpj.14355] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Revised: 03/29/2019] [Accepted: 04/04/2019] [Indexed: 05/18/2023]
Abstract
Despite its critical importance to our understanding of plant growth and adaptation, the question of how environment-induced plastic response is affected genetically remains elusive. Previous studies have shown that the reaction norm of an organism across environmental index obeys the allometrical scaling law of part-whole relationships. The implementation of this phenomenon into functional mapping can characterize how quantitative trait loci (QTLs) modulate the phenotypic plasticity of complex traits to heterogeneous environments. Here, we assemble functional mapping and allometry theory through Lokta-Volterra ordinary differential equations (LVODE) into an R-based computing platform, np2 QTL, aimed to map and visualize phenotypic plasticity QTLs. Based on LVODE parameters, np2 QTL constructs a bidirectional, signed and weighted network of QTL-QTL epistasis, whose emergent properties reflect the ecological mechanisms for genotype-environment interactions over any range of environmental change. The utility of np2 QTL was validated by comprehending the genetic architecture of phenotypic plasticity via the reanalysis of published plant height data involving 3502 recombinant inbred lines of maize planted in multiple discrete environments. np2 QTL also provides a tool for constructing a predictive model of phenotypic responses in extreme environments relative to the median environment.
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Affiliation(s)
- Meixia Ye
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Libo Jiang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Chixiang Chen
- Departments of Public Health Sciences and Statistics, Center for Statistical Genetics, Pennsylvania State University, Hershey, PA, 17033, USA
| | - Xuli Zhu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Ming Wang
- Departments of Public Health Sciences and Statistics, Center for Statistical Genetics, Pennsylvania State University, Hershey, PA, 17033, USA
| | - Rongling Wu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
- Departments of Public Health Sciences and Statistics, Center for Statistical Genetics, Pennsylvania State University, Hershey, PA, 17033, USA
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Sun L, Sang M, Zheng C, Wang D, Shi H, Liu K, Guo Y, Cheng T, Zhang Q, Wu R. The genetic architecture of heterochrony as a quantitative trait: lessons from a computational model. Brief Bioinform 2018; 19:1430-1439. [PMID: 28575183 DOI: 10.1093/bib/bbx056] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2017] [Indexed: 11/14/2022] Open
Abstract
Heterochrony is known as a developmental change in the timing or rate of ontogenetic events across phylogenetic lineages. It is a key concept synthesizing development into ecology and evolution to explore the mechanisms of how developmental processes impact on phenotypic novelties. A number of molecular experiments using contrasting organisms in developmental timing have identified specific genes involved in heterochronic variation. Beyond these classic approaches that can only identify single genes or pathways, quantitative models derived from current next-generation sequencing data serve as a more powerful tool to precisely capture heterochronic variation and systematically map a complete set of genes that contribute to heterochronic processes. In this opinion note, we discuss a computational framework of genetic mapping that can characterize heterochronic quantitative trait loci that determine the pattern and process of development. We propose a unifying model that charts the genetic architecture of heterochrony that perceives and responds to environmental perturbations and evolves over geologic time. The new model may potentially enhance our understanding of the adaptive value of heterochrony and its evolutionary origins, providing a useful context for designing new organisms that can best use future resources.
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Affiliation(s)
- Lidan Sun
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture at Beijing Forestry University
| | - Mengmeng Sang
- Computational Genetics in the Center for Computational Biology at Beijing Forestry University
| | - Chenfei Zheng
- Computational Genetics in the Center for Computational Biology at Beijing Forestry University
| | - Dongyang Wang
- Computational Biology Center for Computational Biology at Beijing Forestry University
| | - Hexin Shi
- Computational Biology Center for Computational Biology at Beijing Forestry University
| | - Kaiyue Liu
- Computational Biology Center for Computational Biology at Beijing Forestry University
| | - Yanfang Guo
- Computational Biology Center for Computational Biology at Beijing Forestry University
| | - Tangren Cheng
- National Engineering Research Center for Floriculture at Beijing Forestry University
| | - Qixiang Zhang
- National Engineering Research Center for Floriculture at Beijing Forestry University
| | - Rongling Wu
- Center for Computational Biology at Beijing Forestry University
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Wang Z, Wang N, Wu R, Wang Z. fGWAS: An R package for genome-wide association analysis with longitudinal phenotypes. J Genet Genomics 2018; 45:411-413. [PMID: 30049619 PMCID: PMC6179436 DOI: 10.1016/j.jgg.2018.06.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 06/18/2018] [Accepted: 06/27/2018] [Indexed: 10/28/2022]
Affiliation(s)
- Zhong Wang
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China; Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY 14850, USA.
| | - Nating Wang
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Rongling Wu
- Center for Computational Biology, Beijing Forestry University, Beijing 100083, China; Center for Statistical Genetics, Department of Public Health Sciences, Pennsylvania State College of Medicine, Hershey, PA 17033, USA
| | - Zuoheng Wang
- Department of Biostatistics, Yale School of Public Health, New Haven, CT 06510, USA.
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8
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Harney E, Paterson S, Plaistow SJ. Offspring development and life‐history variation in a water flea depends upon clone‐specific integration of genetic, non‐genetic and environmental cues. Funct Ecol 2017. [DOI: 10.1111/1365-2435.12887] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ewan Harney
- Ifremer UMR CNRS 6539 (CNRS/UBO/IRD/Ifremer) Laboratoire des Sciences de l'Environnement Marin (LEMAR) ZI de la Pointe du Diable CS 10070 Plouzané29280 France
| | - Steve Paterson
- Institute of Integrative Biology University of Liverpool Biosciences Building Crown Street LiverpoolL69 7ZB UK
| | - Stewart J. Plaistow
- Institute of Integrative Biology University of Liverpool Biosciences Building Crown Street LiverpoolL69 7ZB UK
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9
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Sun L, Wang J, Zhu X, Jiang L, Gosik K, Sang M, Sun F, Cheng T, Zhang Q, Wu R. HpQTL: a geometric morphometric platform to compute the genetic architecture of heterophylly. Brief Bioinform 2017; 19:603-612. [DOI: 10.1093/bib/bbx011] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Indexed: 01/19/2023] Open
Affiliation(s)
- Lidan Sun
- Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Forestry University, Beijing, China
| | - Jing Wang
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Xuli Zhu
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Libo Jiang
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Kirk Gosik
- Statistical Genetics, Department of Public Health Sciences, Pennsylvania State University, Pennsylvania, USA
| | - Mengmeng Sang
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Fengsuo Sun
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Tangren Cheng
- Ornamental Genetics, National Engineering Research, Center for Floriculture, Beijing Forestry University Beijing, China
| | - Qixiang Zhang
- Ornamental Genetics, National Engineering Research, Center for Floriculture, Beijing Forestry University Beijing, China
| | - Rongling Wu
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Center for Statistical Genetics, Pennsylvania State University, Pennsylvania, PA, USA
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Li Z, Sillanpää MJ. Dynamic Quantitative Trait Locus Analysis of Plant Phenomic Data. TRENDS IN PLANT SCIENCE 2015; 20:822-833. [PMID: 26482958 DOI: 10.1016/j.tplants.2015.08.012] [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: 03/18/2015] [Revised: 08/12/2015] [Accepted: 08/26/2015] [Indexed: 05/27/2023]
Abstract
Advanced platforms have recently become available for automatic and systematic quantification of plant growth and development. These new techniques can efficiently produce multiple measurements of phenotypes over time, and introduce time as an extra dimension to quantitative trait locus (QTL) studies. Functional mapping utilizes a class of statistical models for identifying QTLs associated with the growth characteristics of interest. A major benefit of functional mapping is that it integrates information over multiple timepoints, and therefore could increase the statistical power for QTL detection. We review the current development of computationally efficient functional mapping methods which provide invaluable tools for analyzing large-scale timecourse data that are readily available in our post-genome era.
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Affiliation(s)
- Zitong Li
- Biocenter Oulu, Oulu, Finland; Department of Mathematical Sciences and Department of Biology, University of Oulu, 90014 Oulu, Finland
| | - Mikko J Sillanpää
- Biocenter Oulu, Oulu, Finland; Department of Mathematical Sciences and Department of Biology, University of Oulu, 90014 Oulu, Finland.
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11
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Martin TE. Age-related mortality explains life history strategies of tropical and temperate songbirds. Science 2015; 349:966-70. [DOI: 10.1126/science.aad1173] [Citation(s) in RCA: 129] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Yen JDL, Thomson JR, Paganin DM, Keith JM, Mac Nally R. Function regression in ecology and evolution: FREE. Methods Ecol Evol 2014. [DOI: 10.1111/2041-210x.12290] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Jian D. L. Yen
- School of Physics; Monash University; Clayton Vic 3800 Australia
| | - James R. Thomson
- Institute for Applied Ecology; The University of Canberra; Bruce ACT 2617 Australia
| | - David M. Paganin
- School of Physics; Monash University; Clayton Vic 3800 Australia
| | - Jonathan M. Keith
- School of Mathematical Sciences; Monash University; Clayton Vic 3800 Australia
| | - Ralph Mac Nally
- Institute for Applied Ecology; The University of Canberra; Bruce ACT 2617 Australia
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Küttner E, Parsons KJ, Easton AA, Skúlason S, Danzmann RG, Ferguson MM. Hidden genetic variation evolves with ecological specialization: the genetic basis of phenotypic plasticity in Arctic charr ecomorphs. Evol Dev 2014; 16:247-57. [PMID: 24920458 DOI: 10.1111/ede.12087] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The genetic variance that determines phenotypic variation can change across environments through developmental plasticity and in turn play a strong role in evolution. Induced changes in genotype-phenotype relationships should strongly influence adaptation by exposing different sets of heritable variation to selection under some conditions, while also hiding variation. Therefore, the heritable variation exposed or hidden from selection is likely to differ among habitats. We used ecomorphs from two divergent populations of Arctic charr (Salvelinus alpinus) to test the prediction that genotype-phenotype relationships would change in relation to environment. If present over several generations this should lead to divergence in genotype-phenotype relationships under common conditions, and to changes in the amount and type of hidden genetic variance that can evolve. We performed a common garden experiment whereby two ecomorphs from each of two Icelandic lakes were reared under conditions that mimicked benthic and limnetic prey to induce responses in craniofacial traits. Using microsatellite based genetic maps, we subsequently detected QTL related to these craniofacial traits. We found substantial changes in the number and type of QTL between diet treatments and evidence that novel diet treatments can in some cases provide a higher number of QTL. These findings suggest that selection on phenotypic variation, which is both genetically and environmentally determined, has shaped the genetic architecture of adaptive divergence in Arctic charr. However, while adaptive changes are occurring in the genome there also appears to be an accumulation of hidden genetic variation for loci not expressed in the contemporary environment.
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Affiliation(s)
- Eva Küttner
- Department of Integrative Biology, University of Guelph, Guelph, 50 Stone Road West, ON, Canada, N1G 2W1
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