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Hay NM, Windham MD, Mandáková T, Lysak MA, Hendriks KP, Mummenhoff K, Lens F, Pryer KM, Bailey CD. A Hyb-Seq phylogeny of Boechera and related genera using a combination of Angiosperms353 and Brassicaceae-specific bait sets. AMERICAN JOURNAL OF BOTANY 2023; 110:e16226. [PMID: 37561651 DOI: 10.1002/ajb2.16226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 07/21/2023] [Accepted: 07/21/2023] [Indexed: 08/12/2023]
Abstract
PREMISE Although Boechera (Boechereae, Brassicaceae) has become a plant model system for both ecological genomics and evolutionary biology, all previous phylogenetic studies have had limited success in resolving species relationships within the genus. The recent effective application of sequence data from target enrichment approaches to resolve the evolutionary relationships of several other challenging plant groups prompted us to investigate their usefulness in Boechera and Boechereae. METHODS To resolve the phylogeny of Boechera and closely related genera, we utilized the Hybpiper pipeline to analyze two combined bait sets: Angiosperms353, with broad applicability across flowering plants; and a Brassicaceae-specific bait set designed for use in the mustard family. Relationships for 101 samples representing 81 currently recognized species were inferred from a total of 1114 low-copy nuclear genes using both supermatrix and species coalescence methods. RESULTS Our analyses resulted in a well-resolved and highly supported phylogeny of the tribe Boechereae. Boechereae is divided into two major clades, one comprising all western North American species of Boechera, the other encompassing the eight other genera of the tribe. Our understanding of relationships within Boechera is enhanced by the recognition of three core clades that are further subdivided into robust regional species complexes. CONCLUSIONS This study presents the first broadly sampled, well-resolved phylogeny for most known sexual diploid Boechera. This effort provides the foundation for a new phylogenetically informed taxonomy of Boechera that is crucial for its continued use as a model system.
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Affiliation(s)
- Nikolai M Hay
- Department of Biology, Duke University, Durham, 27708, North Carolina, USA
| | - Michael D Windham
- Department of Biology, Duke University, Durham, 27708, North Carolina, USA
| | - Terezie Mandáková
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, Brno, 625 00, Czech Republic
- Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 5, Brno, 625 00, Czech Republic
| | - Martin A Lysak
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, Brno, 625 00, Czech Republic
- National Centre for Biomolecular Research (NCBR), Faculty of Science, Masaryk University, Kamenice 5, Brno, 625 00, Czech Republic
| | - Kasper P Hendriks
- Department of Biology/Botany, University of Osnabrück, Barbarastraße 11, Osnabrück, D-49076, Germany
- Naturalis Biodiversity Center, P.O. Box 9517, Leiden, 2300 RA, The Netherlands
| | - Klaus Mummenhoff
- Department of Biology/Botany, University of Osnabrück, Barbarastraße 11, Osnabrück, D-49076, Germany
| | - Frederic Lens
- Naturalis Biodiversity Center, P.O. Box 9517, Leiden, 2300 RA, The Netherlands
- Institute of Biology Leiden, Plant Sciences, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
| | - Kathleen M Pryer
- Department of Biology, Duke University, Durham, 27708, North Carolina, USA
| | - C Donovan Bailey
- Department of Biology, New Mexico State University, Las Cruces, New Mexico, USA
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2
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Wijesingha Ahchige M, Fernie AR, Alseekh S. PANTOTHENATE KINASE4, LOSS OF GDU2, and TRANSPOSON PROTEIN1 affect the canalization of tomato fruit metabolism. PLANT PHYSIOLOGY 2023; 192:442-468. [PMID: 36794426 PMCID: PMC10152668 DOI: 10.1093/plphys/kiad093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 01/24/2023] [Accepted: 01/24/2023] [Indexed: 05/03/2023]
Abstract
Most studies investigating quantitative traits focus on mean levels per genotype rather than the variation between different individuals of one genotype or the variation elicited by different environments. Consequently, the genes that govern this effect are not well understood. The concept, named canalization, which describes a lack of variation, is well known in the context of developmental processes but is poorly studied for quantitative traits such as metabolism. In this study, we selected 8 putative candidate genes from previously identified canalized metabolic quantitative trait loci and created genome-edited tomato (Solanum lycopersicum) mutants of these genes for experimental validation. Most lines showed wild-type morphology, except for an ARF-like protein mutant showing aberrant phenotypes in the form of scarred fruit cuticles. In greenhouse trials with different irrigation conditions, whole-plant traits showed a general increase of their level toward the more optimal irrigation conditions, whereas most metabolic traits showed an increase toward the other end of the gradient. Mutants of a PANTOTHENATE KINASE 4, the AIRP ubiquitin gene LOSS OF GDU2, and TRANSPOSON PROTEIN 1 grown under these conditions showed an overall improved plant performance. Additional effects, on both target and other metabolites in tomato fruits, regarding the mean level at specific conditions and, ergo, the cross-environment coefficient of variation, were observed. However, variation between individuals remained unaffected. In conclusion, this study supports the idea of distinct sets of genes regulating different types of variation.
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Affiliation(s)
- Micha Wijesingha Ahchige
- Root Biology and Symbiosis, Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm 14476, Germany
| | - Alisdair R Fernie
- Root Biology and Symbiosis, Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm 14476, Germany
- Center of Plant Systems Biology and Biotechnology, Ruski Blvd. 139, Plovdiv 4000, Bulgaria
| | - Saleh Alseekh
- Root Biology and Symbiosis, Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm 14476, Germany
- Center of Plant Systems Biology and Biotechnology, Ruski Blvd. 139, Plovdiv 4000, Bulgaria
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3
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Schilling S, Melzer R, Dowling CA, Shi J, Muldoon S, McCabe PF. A protocol for rapid generation cycling (speed breeding) of hemp (Cannabis sativa) for research and agriculture. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 113:437-445. [PMID: 36458321 PMCID: PMC10108250 DOI: 10.1111/tpj.16051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 11/16/2022] [Accepted: 11/19/2022] [Indexed: 06/17/2023]
Abstract
Hemp (Cannabis sativa) is a highly versatile crop with a multitude of applications, from textiles, biofuel and building material to high-value food products for consumer markets. Furthermore, non-hallucinogenic cannabinoids like cannabidiol (CBD), which can be extracted from female hemp flowers, are potentially valuable pharmacological compounds. In addition, hemp has high carbon sequestration potential associated with its rapid growth rate. Therefore, the hemp industry is gaining more traction and breeding hemp cultivars adapted to local climate conditions or bred for specific applications is becoming increasingly important. Here, we present a method for the rapid generation cycling (speed breeding) of hemp. The speed breeding protocol makes use of the photoperiod sensitivity of Cannabis. It encompasses vegetative growth of the plants for 2 weeks under continuous light, followed by 4 weeks under short-day conditions, during which flower induction, pollination and seed development proceed, and finally a seed ripening phase under continuous light and water stress. With the protocol described here, a generation time of under 9 weeks (61 days) from seed to seed can be achieved. Furthermore, our method synchronises the flowering time of different hemp cultivars, thus facilitating crosses between cultivars. The extremely short generation time will enable hemp researchers and breeders to perform crosses in a time-efficient way and generate new hemp cultivars with defined genetic characteristics over a short period of time.
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Affiliation(s)
- Susanne Schilling
- School of Biology and Environmental ScienceUniversity College DublinBelfieldDublinIreland
- UCD Earth InstituteUniversity College DublinBelfieldDublinIreland
| | - Rainer Melzer
- School of Biology and Environmental ScienceUniversity College DublinBelfieldDublinIreland
- UCD Earth InstituteUniversity College DublinBelfieldDublinIreland
| | - Caroline A. Dowling
- School of Biology and Environmental ScienceUniversity College DublinBelfieldDublinIreland
- UCD Earth InstituteUniversity College DublinBelfieldDublinIreland
| | - Jiaqi Shi
- School of Biology and Environmental ScienceUniversity College DublinBelfieldDublinIreland
- UCD Earth InstituteUniversity College DublinBelfieldDublinIreland
| | - Shaun Muldoon
- School of Biology and Environmental ScienceUniversity College DublinBelfieldDublinIreland
- UCD Earth InstituteUniversity College DublinBelfieldDublinIreland
| | - Paul F. McCabe
- School of Biology and Environmental ScienceUniversity College DublinBelfieldDublinIreland
- UCD Earth InstituteUniversity College DublinBelfieldDublinIreland
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Posadas-García YS, Espinosa-Soto C. Early effects of gene duplication on the robustness and phenotypic variability of gene regulatory networks. BMC Bioinformatics 2022; 23:509. [DOI: 10.1186/s12859-022-05067-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 11/18/2022] [Indexed: 11/29/2022] Open
Abstract
Abstract
Background
Research on gene duplication is abundant and comes from a wide range of approaches, from high-throughput analyses and experimental evolution to bioinformatics and theoretical models. Notwithstanding, a consensus is still lacking regarding evolutionary mechanisms involved in evolution through gene duplication as well as the conditions that affect them. We argue that a better understanding of evolution through gene duplication requires considering explicitly that genes do not act in isolation. It demands studying how the perturbation that gene duplication implies percolates through the web of gene interactions. Due to evolution’s contingent nature, the paths that lead to the final fate of duplicates must depend strongly on the early stages of gene duplication, before gene copies have accumulated distinctive changes.
Methods
Here we use a widely-known model of gene regulatory networks to study how gene duplication affects network behavior in early stages. Such networks comprise sets of genes that cross-regulate. They organize gene activity creating the gene expression patterns that give cells their phenotypic properties. We focus on how duplication affects two evolutionarily relevant properties of gene regulatory networks: mitigation of the effect of new mutations and access to new phenotypic variants through mutation.
Results
Among other observations, we find that those networks that are better at maintaining the original phenotype after duplication are usually also better at buffering the effect of single interaction mutations and that duplication tends to enhance further this ability. Moreover, the effect of mutations after duplication depends on both the kind of mutation and genes involved in it. We also found that those phenotypes that had easier access through mutation before duplication had higher chances of remaining accessible through new mutations after duplication.
Conclusion
Our results support that gene duplication often mitigates the impact of new mutations and that this effect is not merely due to changes in the number of genes. The work that we put forward helps to identify conditions under which gene duplication may enhance evolvability and robustness to mutations.
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Kinmonth-Schultz H, Lewandowska-Sabat A, Imaizumi T, Ward JK, Rognli OA, Fjellheim S. Flowering Times of Wild Arabidopsis Accessions From Across Norway Correlate With Expression Levels of FT, CO, and FLC Genes. FRONTIERS IN PLANT SCIENCE 2021; 12:747740. [PMID: 34790213 PMCID: PMC8591261 DOI: 10.3389/fpls.2021.747740] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 09/30/2021] [Indexed: 06/12/2023]
Abstract
Temperate species often require or flower most rapidly in the long daylengths, or photoperiods, experienced in summer or after prolonged periods of cold temperatures, referred to as vernalization. Yet, even within species, plants vary in the degree of responsiveness to these cues. In Arabidopsis thaliana, CONSTANS (CO) and FLOWERING LOCUS C (FLC) genes are key to photoperiod and vernalization perception and antagonistically regulate FLOWERING LOCUS T (FT) to influence the flowering time of the plants. However, it is still an open question as to how these genes vary in their interactions among wild accessions with different flowering behaviors and adapted to different microclimates, yet this knowledge could improve our ability to predict plant responses in variable natural conditions. To assess the relationships among these genes and to flowering time, we exposed 10 winter-annual Arabidopsis accessions from throughout Norway, ranging from early to late flowering, along with two summer-annual accessions to 14 weeks of vernalization and either 8- or 19-h photoperiods to mimic Norwegian climate conditions, then assessed gene expression levels 3-, 5-, and 8-days post vernalization. CO and FLC explained both FT levels and flowering time (days) but not rosette leaf number at flowering. The correlation between FT and flowering time increased over time. Although vernalization suppresses FLC, FLC was high in the late-flowering accessions. Across accessions, FT was expressed only at low FLC levels and did not respond to CO in the late-flowering accessions. We proposed that FT may only be expressed below a threshold value of FLC and demonstrated that these three genes correlated to flowering times across genetically distinct accessions of Arabidopsis.
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Affiliation(s)
- Hannah Kinmonth-Schultz
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, United States
| | | | - Takato Imaizumi
- Department of Biology, University of Washington, Seattle, WA, United States
| | - Joy K. Ward
- College of Arts and Sciences, Case Western Reserve University, Cleveland, OH, United States
| | - Odd Arne Rognli
- Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
| | - Siri Fjellheim
- Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
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6
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Yan W, Wang B, Chan E, Mitchell-Olds T. Genetic architecture and adaptation of flowering time among environments. THE NEW PHYTOLOGIST 2021; 230:1214-1227. [PMID: 33484593 PMCID: PMC8193995 DOI: 10.1111/nph.17229] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 01/07/2021] [Indexed: 05/17/2023]
Abstract
The genetic basis of flowering time changes across environments, and pleiotropy may limit adaptive evolution of populations in response to local conditions. However, little information is known about how genetic architecture changes among environments. We used genome-wide association studies (GWAS) in Boechera stricta (Graham) Al-Shehbaz, a relative of Arabidopsis, to examine flowering variation among environments and associations with climate conditions in home environments. Also, we used molecular population genetics to search for evidence of historical natural selection. GWAS found 47 significant quantitative trait loci (QTLs) that influence flowering time in one or more environments, control plastic changes in phenology between experiments, or show associations with climate in sites of origin. Genetic architecture of flowering varied substantially among environments. We found that some pairs of QTLs showed similar patterns of pleiotropy across environments. A large-effect QTL showed molecular signatures of adaptive evolution and is associated with climate in home environments. The derived allele at this locus causes later flowering and predominates in sites with greater water availability. This work shows that GWAS of climate associations and ecologically important traits across diverse environments can be combined with molecular signatures of natural selection to elucidate ecological genetics of adaptive evolution.
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Affiliation(s)
- Wenjie Yan
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
- Department of Biology, Duke University, Box 90338, Durham, NC 27708, USA
| | - Baosheng Wang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, 510650 China
| | - Emily Chan
- Department of Biology, Duke University, Box 90338, Durham, NC 27708, USA
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7
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Keith RA, Mitchell-Olds T. Antagonistic selection and pleiotropy constrain the evolution of plant chemical defenses. Evolution 2019; 73:947-960. [PMID: 30950034 PMCID: PMC6652176 DOI: 10.1111/evo.13728] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Accepted: 03/13/2019] [Indexed: 01/24/2023]
Abstract
When pleiotropy is present, genetic correlations may constrain the evolution of ecologically important traits. We used a quantitative genetics approach to investigate constraints on the evolution of secondary metabolites in a wild mustard, Boechera stricta. Much of the genetic variation in chemical composition of glucosinolates in B. stricta is controlled by a single locus, BCMA1/3. In a large-scale common garden experiment under natural conditions, we quantified fitness and glucosinolate profile in two leaf types and in fruits. We estimated genetic variances and covariances (the G-matrix) and selection on chemical profile in each tissue. Chemical composition of defenses was strongly genetically correlated between tissues. We found antagonistic selection between defense composition in leaves and fruits: compounds that were favored in leaves were disadvantageous in fruits. The positive genetic correlations and antagonistic selection led to strong constraints on the evolution of defenses in leaves and fruits. In a hypothetical population with no genetic variation at BCMA1/3, we found no evidence for genetic constraints, indicating that pleiotropy affecting chemical profile in multiple tissues drives constraints on the evolution of secondary metabolites.
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Affiliation(s)
- Rose A. Keith
- University Program in Genetics and Genomics, Duke University, Durham, North Carolina, 27708, United States
- Biology Department, Duke University, Durham, North Carolina, 27708, United States
| | - Thomas Mitchell-Olds
- University Program in Genetics and Genomics, Duke University, Durham, North Carolina, 27708, United States
- Biology Department, Duke University, Durham, North Carolina, 27708, United States
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8
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Laitinen RAE, Nikoloski Z. Genetic basis of plasticity in plants. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:739-745. [PMID: 30445526 DOI: 10.1093/jxb/ery404] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 11/06/2018] [Indexed: 05/20/2023]
Abstract
The ability of an organism to change its phenotype in response to different environments, termed plasticity, is a particularly important characteristic to enable sessile plants to adapt to rapid changes in their surroundings. Plasticity is a quantitative trait that can provide a fitness advantage and mitigate negative effects due to environmental perturbations. Yet, its genetic basis is not fully understood. Alongside technological limitations, the main challenge in studying plasticity has been the selection of suitable approaches for quantification of phenotypic plasticity. Here, we propose a categorization of the existing quantitative measures of phenotypic plasticity into nominal and relative approaches. Moreover, we highlight the recent advances in the understanding of the genetic architecture underlying phenotypic plasticity in plants. We identify four pillars for future research to uncover the genetic basis of phenotypic plasticity, with emphasis on development of computational approaches and theories. These developments will allow us to perform specific experiments to validate the causal genes for plasticity and to discover their role in plant fitness and evolution.
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Affiliation(s)
- Roosa A E Laitinen
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg, Potsdam, Germany
| | - Zoran Nikoloski
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg, Potsdam, Germany
- Bioinformatics group, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
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9
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Takahashi KH. Multiple modes of canalization: Links between genetic, environmental canalizations and developmental stability, and their trait-specificity. Semin Cell Dev Biol 2018; 88:14-20. [PMID: 29787862 DOI: 10.1016/j.semcdb.2018.05.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 03/14/2018] [Accepted: 05/15/2018] [Indexed: 10/16/2022]
Abstract
The robustness of biological systems against mutational and environmental perturbations is termed canalization. Because reducing phenotypic variability under environmental and genetic perturbations can be adaptive and facilitated by natural selection, it has been suggested that once canalization mechanisms have evolved to buffer the effects of environmental perturbations, they may act to buffer any and all sources of variation. Although whether canalization mechanisms are general or specific to the types of perturbation or phenotypic traits that they buffer is often addressed, the links between different canalization mechanisms remain unclear. In this review, three major sources of phenotypic variation, associated canalization concepts and indicators of the degree of canalization are first outlined. Then, the molecular bases of canalization mechanisms based on recent empirical studies are overviewed. Finally, the links between the underlying processes of different canalization mechanisms are explored.
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Affiliation(s)
- Kazuo H Takahashi
- Graduate School of Environmental and Life Science, Okayama University, 1-1-1 Tsushima-naka, Kita-ku, Okayama-si, Okayama-ken, 700-8530, Japan.
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10
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Yadav A, Dhole K, Sinha H. Differential Regulation of Cryptic Genetic Variation Shapes the Genetic Interactome Underlying Complex Traits. Genome Biol Evol 2018; 8:3559-3573. [PMID: 28172852 PMCID: PMC5381507 DOI: 10.1093/gbe/evw258] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/21/2016] [Indexed: 12/21/2022] Open
Abstract
Cryptic genetic variation (CGV) refers to genetic variants whose effects are buffered in most conditions but manifest phenotypically upon specific genetic and environmental perturbations. Despite having a central role in adaptation, contribution of CGV to regulation of quantitative traits is unclear. Instead, a relatively simplistic architecture of additive genetic loci is known to regulate phenotypic variation in most traits. In this paper, we investigate the regulation of CGV and its implication on the genetic architecture of quantitative traits at a genome-wide level. We use a previously published dataset of biparental recombinant population of Saccharomyces cerevisiae phenotyped in 34 diverse environments to perform single locus, two-locus, and covariance mapping. We identify loci that have independent additive effects as well as those which regulate the phenotypic manifestation of other genetic variants (variance QTL). We find that whereas additive genetic variance is predominant, a higher order genetic interaction network regulates variation in certain environments. Despite containing pleiotropic loci, with effects across environments, these genetic networks are highly environment specific. CGV is buffered under most allelic combinations of these networks and perturbed only in rare combinations resulting in high phenotypic variance. The presence of such environment specific genetic networks is the underlying cause of abundant gene–environment interactions. We demonstrate that overlaying identified molecular networks on such genetic networks can identify potential candidate genes and underlying mechanisms regulating phenotypic variation. Such an integrated approach applied to human disease datasets has the potential to improve the ability to predict disease predisposition and identify specific therapeutic targets.
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Affiliation(s)
- Anupama Yadav
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | - Kaustubh Dhole
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | - Himanshu Sinha
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, India.,Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, India.,Initiative for Biological Systems Engineering, Indian Institute of Technology Madras, Chennai, India
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11
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Lee CR, Hsieh JW, Schranz ME, Mitchell-Olds T. The Functional Change and Deletion of FLC Homologs Contribute to the Evolution of Rapid Flowering in Boechera stricta. FRONTIERS IN PLANT SCIENCE 2018; 9:1078. [PMID: 30108602 PMCID: PMC6080596 DOI: 10.3389/fpls.2018.01078] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 07/03/2018] [Indexed: 05/04/2023]
Abstract
Differences in the timing of vegetative-to-reproductive phase transition have evolved independently and repeatedly in different plant species. Due to their specific biological functions and positions in pathways, some genes are important targets of repeated evolution - independent mutations on these genes caused the evolution of similar phenotypes in distantly related organisms. While many studies have investigated these genes, it remains unclear how gene duplications influence repeated phenotypic evolution. Here we characterized the genetic architecture underlying a novel rapid-flowering phenotype in Boechera stricta and investigated the candidate genes BsFLC1 and BsFLC2. The expression patterns of BsFLC1 suggested its function in flowering time suppression, and the deletion of BsFLC1 is associated with rapid flowering and loss of vernalization requirement. In contrast, BsFLC2 did not appear to be associated with flowering and had accumulated multiple amino acid substitutions in the relatively short evolutionary timeframe after gene duplication. These non-synonymous substitutions greatly changed the physicochemical properties of the original amino acids, concentrated non-randomly near a protein-interacting domain, and had greater substitution rate than synonymous changes. Here we suggested that, after recent gene duplication of the FLC gene, the evolution of rapid phenology was made possible by the change of BsFLC2 expression pattern or protein sequences and the deletion of BsFLC1.
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Affiliation(s)
- Cheng-Ruei Lee
- Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei, Taiwan
- Institute of Plant Biology, National Taiwan University, Taipei, Taiwan
- Genome and Systems Biology Degree Program, National Taiwan University, Taipei, Taiwan
- *Correspondence: Cheng-Ruei Lee,
| | - Jo-Wei Hsieh
- Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei, Taiwan
| | - M. E. Schranz
- Biosystematics Group, Wageningen University & Research, Wageningen, Netherlands
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12
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Brown KE, Kelly JK. Antagonistic pleiotropy can maintain fitness variation in annual plants. J Evol Biol 2017; 31:46-56. [DOI: 10.1111/jeb.13192] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 10/09/2017] [Indexed: 01/24/2023]
Affiliation(s)
- K. E. Brown
- Department of Ecology and Evolutionary Biology; University of Kansas; Lawrence KS USA
| | - J. K. Kelly
- Department of Ecology and Evolutionary Biology; University of Kansas; Lawrence KS USA
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13
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Alseekh S, Tong H, Scossa F, Brotman Y, Vigroux F, Tohge T, Ofner I, Zamir D, Nikoloski Z, Fernie AR. Canalization of Tomato Fruit Metabolism. THE PLANT CELL 2017; 29:2753-2765. [PMID: 29093214 PMCID: PMC5728129 DOI: 10.1105/tpc.17.00367] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Revised: 10/10/2017] [Accepted: 10/31/2017] [Indexed: 05/23/2023]
Abstract
To explore the genetic robustness (canalization) of metabolism, we examined the levels of fruit metabolites in multiple harvests of a tomato introgression line (IL) population. The IL partitions the whole genome of the wild species Solanum pennellii in the background of the cultivated tomato (Solanum lycopersicum). We identified several metabolite quantitative trait loci that reduce variability for both primary and secondary metabolites, which we named canalization metabolite quantitative trait loci (cmQTL). We validated nine cmQTL using an independent population of backcross inbred lines, derived from the same parents, which allows increased resolution in mapping the QTL previously identified in the ILs. These cmQTL showed little overlap with QTL for the metabolite levels themselves. Moreover, the intervals they mapped to harbored few metabolism-associated genes, suggesting that the canalization of metabolism is largely controlled by regulatory genes.
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Affiliation(s)
- Saleh Alseekh
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Hao Tong
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Federico Scossa
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
- Consiglio per la Ricerca in Agricoltura e l'analisi dell'Economia Agraria, 00134 Rome, Italy
| | - Yariv Brotman
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
- Department of Life Sciences, Ben Gurion University of the Negev, 653 Beersheva, Israel
| | - Florian Vigroux
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Takayuki Tohge
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Itai Ofner
- Faculty of Agriculture, The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture at the Hebrew University of Jerusalem, Rehovot 76100, Israel
| | - Dani Zamir
- Faculty of Agriculture, The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture at the Hebrew University of Jerusalem, Rehovot 76100, Israel
| | - Zoran Nikoloski
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
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Mao T, Li J, Wen Z, Wu T, Wu C, Sun S, Jiang B, Hou W, Li W, Song Q, Wang D, Han T. Association mapping of loci controlling genetic and environmental interaction of soybean flowering time under various photo-thermal conditions. BMC Genomics 2017; 18:415. [PMID: 28549456 PMCID: PMC5446728 DOI: 10.1186/s12864-017-3778-3] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 05/10/2017] [Indexed: 12/05/2022] Open
Abstract
BACKGROUND Soybean (Glycine max (L.) Merr.) is a short day plant. Its flowering and maturity time are controlled by genetic and environmental factors, as well the interaction between the two factors. Previous studies have shown that both genetic and environmental factors, mainly photoperiod and temperature, control flowering time of soybean. Additionally, these studies have reported gene × gene and gene × environment interactions on flowering time. However, the effects of quantitative trait loci (QTL) in response to photoperiod and temperature have not been well evaluated. The objectives of the current study were to identify the effects of loci associated with flowering time under different photo-thermal conditions and to understand the effects of interaction between loci and environment on soybean flowering. METHODS Different photoperiod and temperature combinations were obtained by adjusting sowing dates (spring sowing and summer sowing) or day-length (12 h, 16 h). Association mapping was performed on 91 soybean cultivars from different maturity groups (MG000-VIII) using 172 SSR markers and 5107 SNPs from the Illumina SoySNP6K iSelectBeadChip. The effects of the interaction between QTL and environments on flowering time were also analysed using the QTXNetwork. RESULTS Large-effect loci were detected on Gm 11, Gm 16 and Gm 20 as in previous reports. Most loci associated with flowering time are sensitive to photo-thermal conditions. Number of loci associated with flowering time was more under the long day (LD) than under the short day (SD) condition. The variation of flowering time among the soybean cultivars mostly resulted from the epistasis × environment and additive × environment interactions. Among the three candidate loci, i.e. Gm04_4497001 (near GmCOL3a), Gm16_30766209 (near GmFT2a and GmFT2b) and Gm19_47514601 (E3 or GmPhyA3), the Gm04_4497001 may be the key locus interacting with other loci for controlling soybean flowering time. CONCLUSION The effects of loci associated with the flowering time of soybean were dependent upon the photo-thermal conditions. This study facilitates the understanding of the genetic mechanism of soybean flowering and molecular breeding for the improvement of soybean adaptability to specific and/or broad regions.
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Affiliation(s)
- Tingting Mao
- College of Agriculture, Northeast Agricultural University, Harbin, 150030 Heilongjiang China
- MOA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Science, the Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, 100081 China
| | - Jinyu Li
- MOA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Science, the Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, 100081 China
| | - Zixiang Wen
- Department of Plant, Soil and Microbial Sciences, Michigan State University, 1066 Bogue St., Rm. A384-E, East Lansing, MI 48824-1325 USA
| | - Tingting Wu
- MOA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Science, the Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, 100081 China
| | - Cunxiang Wu
- MOA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Science, the Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, 100081 China
| | - Shi Sun
- MOA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Science, the Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, 100081 China
| | - Bingjun Jiang
- MOA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Science, the Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, 100081 China
| | - Wensheng Hou
- MOA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Science, the Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, 100081 China
| | - Wenbin Li
- College of Agriculture, Northeast Agricultural University, Harbin, 150030 Heilongjiang China
| | - Qijian Song
- Soybean Genomics and Improvement Laboratory, US Department of Agriculture, Agricultural Research Service (USDA-ARS), 10300 Baltimore Ave, Beltsville, MD 20705 USA
| | - Dechun Wang
- Department of Plant, Soil and Microbial Sciences, Michigan State University, 1066 Bogue St., Rm. A384-E, East Lansing, MI 48824-1325 USA
| | - Tianfu Han
- College of Agriculture, Northeast Agricultural University, Harbin, 150030 Heilongjiang China
- MOA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Science, the Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, 100081 China
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Yadav A, Radhakrishnan A, Panda A, Singh A, Sinha H, Bhanot G. The Modular Adaptive Ribosome. PLoS One 2016; 11:e0166021. [PMID: 27812193 PMCID: PMC5094737 DOI: 10.1371/journal.pone.0166021] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 10/23/2016] [Indexed: 11/18/2022] Open
Abstract
The ribosome is an ancient machine, performing the same function across organisms. Although functionally unitary, recent experiments suggest specialized roles for some ribosomal proteins. Our central thesis is that ribosomal proteins function in a modular fashion to decode genetic information in a context dependent manner. We show through large data analyses that although many ribosomal proteins are essential with consistent effect on growth in different conditions in yeast and similar expression across cell and tissue types in mice and humans, some ribosomal proteins are used in an environment specific manner. The latter set of variable ribosomal proteins further function in a coordinated manner forming modules, which are adapted to different environmental cues in different organisms. We show that these environment specific modules of ribosomal proteins in yeast have differential genetic interactions with other pathways and their 5’UTRs show differential signatures of selection in yeast strains, presumably to facilitate adaptation. Similarly, we show that in higher metazoans such as mice and humans, different modules of ribosomal proteins are expressed in different cell types and tissues. A clear example is nervous tissue that uses a ribosomal protein module distinct from the rest of the tissues in both mice and humans. Our results suggest a novel stratification of ribosomal proteins that could have played a role in adaptation, presumably to optimize translation for adaptation to diverse ecological niches and tissue microenvironments.
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Affiliation(s)
- Anupama Yadav
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, 400005, India
| | - Aparna Radhakrishnan
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, 400005, India
| | - Anshuman Panda
- Department of Physics, Rutgers University, Piscataway, New Jersey 08854, United States of America
| | - Amartya Singh
- Department of Physics, Rutgers University, Piscataway, New Jersey 08854, United States of America
| | - Himanshu Sinha
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, 400005, India
- Department of Biotechnology, Indian Institute of Technology Madras, Chennai 600036, India
- Initiative for Biological Systems Engineering, Indian Institute of Technology Madras, Chennai 600036, India
- * E-mail: (HS); (GB)
| | - Gyan Bhanot
- Department of Physics, Rutgers University, Piscataway, New Jersey 08854, United States of America
- Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, New Jersey 08854, United States of America
- The Cancer Institute of New Jersey, New Brunswick, New Jersey 08903, United States of America
- * E-mail: (HS); (GB)
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Espinosa-Soto C. Selection for distinct gene expression properties favours the evolution of mutational robustness in gene regulatory networks. J Evol Biol 2016; 29:2321-2333. [DOI: 10.1111/jeb.12959] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2016] [Accepted: 07/26/2016] [Indexed: 11/27/2022]
Affiliation(s)
- C. Espinosa-Soto
- Instituto de Física; Universidad Autónoma de San Luis Potosí; San Luis Potosí Mexico
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Méndez-Vigo B, Savic M, Ausín I, Ramiro M, Martín B, Picó FX, Alonso-Blanco C. Environmental and genetic interactions reveal FLOWERING LOCUS C as a modulator of the natural variation for the plasticity of flowering in Arabidopsis. PLANT, CELL & ENVIRONMENT 2016; 39:282-94. [PMID: 26173848 DOI: 10.1111/pce.12608] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Revised: 06/30/2015] [Accepted: 07/02/2015] [Indexed: 05/12/2023]
Abstract
The timing of flowering initiation depends strongly on the environment, a property termed as the plasticity of flowering. Such plasticity determines the adaptive potential of plants because it provides phenotypic buffer against environmental changes, and its natural variation contributes to evolutionary adaptation. We addressed the genetic mechanisms of the natural variation for this plasticity in Arabidopsis thaliana by analysing a population of recombinant inbred lines derived from Don-0 and Ler accessions collected from distinct climates. Quantitative trait locus (QTL) mapping in four environmental conditions differing in photoperiod, vernalization treatment and ambient temperature detected the folllowing: (i) FLOWERING LOCUS C (FLC) as a large effect QTL affecting flowering time differentially in all environments; (ii) numerous QTL displaying smaller effects specifically in some conditions; and (iii) significant genetic interactions between FLC and other loci. Hence, the variation for the plasticity of flowering is determined by a combination of environmentally sensitive and specific QTL, and epistasis. Analysis of FLC from Don identified a new and more active allele likely caused by a cis-regulatory deletion covering the non-coding RNA COLDAIR. Further characterization of four FLC natural alleles showed different environmental and genetic interactions. Thus, FLC appears as a major modulator of the natural variation for the plasticity of flowering to multiple environmental factors.
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Affiliation(s)
- Belén Méndez-Vigo
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, 28049, Spain
| | - Marija Savic
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, 28049, Spain
| | - Israel Ausín
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, 28049, Spain
| | - Mercedes Ramiro
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, 28049, Spain
| | - Beatriz Martín
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, 28049, Spain
| | - F Xavier Picó
- Departamento de Ecología Integrativa, Estación Biológica de Doñana (EBD), Sevilla, 41092, Spain
| | - Carlos Alonso-Blanco
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, 28049, Spain
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