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Lang PLM, Erberich JM, Lopez L, Weiß CL, Amador G, Fung HF, Latorre SM, Lasky JR, Burbano HA, Expósito-Alonso M, Bergmann DC. Century-long timelines of herbarium genomes predict plant stomatal response to climate change. Nat Ecol Evol 2024; 8:1641-1653. [PMID: 39117952 PMCID: PMC11383800 DOI: 10.1038/s41559-024-02481-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 06/21/2024] [Indexed: 08/10/2024]
Abstract
Dissecting plant responses to the environment is key to understanding whether and how plants adapt to anthropogenic climate change. Stomata, plants' pores for gas exchange, are expected to decrease in density following increased CO2 concentrations, a trend already observed in multiple plant species. However, it is unclear whether such responses are based on genetic changes and evolutionary adaptation. Here we make use of extensive knowledge of 43 genes in the stomatal development pathway and newly generated genome information of 191 Arabidopsis thaliana historical herbarium specimens collected over 193 years to directly link genetic variation with climate change. While we find that the essential transcription factors SPCH, MUTE and FAMA, central to stomatal development, are under strong evolutionary constraints, several regulators of stomatal development show signs of local adaptation in contemporary samples from different geographic regions. We then develop a functional score based on known effects of gene knock-out on stomatal development that recovers a classic pattern of stomatal density decrease over the past centuries, suggesting a genetic component contributing to this change. This approach combining historical genomics with functional experimental knowledge could allow further investigations of how different, even in historical samples unmeasurable, cellular plant phenotypes may have already responded to climate change through adaptive evolution.
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Affiliation(s)
- Patricia L M Lang
- Department of Biology, Stanford University, Stanford, CA, USA.
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA.
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA.
| | - Joel M Erberich
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Lua Lopez
- Department of Biological Sciences, California State University San Bernardino, San Bernardino, CA, USA
- Department of Biology, Pennsylvania State University, University Park, PA, USA
| | - Clemens L Weiß
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Gabriel Amador
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Hannah F Fung
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Sergio M Latorre
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London, UK
- Research Group for Ancient Genomics and Evolution, Department of Molecular Biology, Max Planck Institute for Biology, Tübingen, Germany
| | - Jesse R Lasky
- Department of Biology, Pennsylvania State University, University Park, PA, USA
| | - Hernán A Burbano
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London, UK
- Research Group for Ancient Genomics and Evolution, Department of Molecular Biology, Max Planck Institute for Biology, Tübingen, Germany
| | - Moisés Expósito-Alonso
- Department of Biology, Stanford University, Stanford, CA, USA
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, USA
- Department of Global Ecology, Carnegie Institution for Science, Stanford, CA, USA
- Department of Integrative Biology, University of California, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
| | - Dominique C Bergmann
- Department of Biology, Stanford University, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
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2
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Kisvarga S, Hamar-Farkas D, Horotán K, Gyuricza C, Ražná K, Kučka M, Harenčár Ľ, Neményi A, Lantos C, Pauk J, Solti Á, Simon E, Bibi D, Mukherjee S, Török K, Tilly-Mándy A, Papp L, Orlóci L. Investigation of a Perspective Urban Tree Species, Ginkgo biloba L., by Scientific Analysis of Historical Old Specimens. PLANTS (BASEL, SWITZERLAND) 2024; 13:1470. [PMID: 38891279 PMCID: PMC11175039 DOI: 10.3390/plants13111470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 05/18/2024] [Accepted: 05/24/2024] [Indexed: 06/21/2024]
Abstract
In this study, we examined over 200-year-old Ginkgo biloba L. specimens under different environmental conditions. The overall aim was to explore which factors influence their vitality and general fitness in urban environments and thus their ability to tolerate stressful habitats. In order to determine this, we used a number of different methods, including histological examinations (stomatal density and size) and physiological measurements (peroxidase enzyme activity), as well as assessing the air pollution tolerance index (APTI). The investigation of the genetic relationships between individuals was performed using flow cytometry and miRNA marker methods. The genetic tests revealed that all individuals are diploid, whereas the lus-miR168 and lus-miR408 markers indicated a kinship relation between them. These results show that the effect of different habitat characteristics can be detected through morphological and physiological responses, thus indicating relatively higher stress values for all studied individuals. A significant correlation can be found between the level of adaptability and the relatedness of the examined individuals. These results suggest that Ginkgo biloba L. is well adapted to an environment with increased stress factors and therefore suitable for use in urban areas.
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Affiliation(s)
- Szilvia Kisvarga
- Ornamental Plant and Green System Management Research Group, Institute of Landscape Architecture, Urban Planning and Garden Art, Hungarian University of Agriculture and Life Sciences (MATE), 1223 Budapest, Hungary; (S.K.); (A.N.); (L.O.)
| | - Dóra Hamar-Farkas
- Ornamental Plant and Green System Management Research Group, Institute of Landscape Architecture, Urban Planning and Garden Art, Hungarian University of Agriculture and Life Sciences (MATE), 1223 Budapest, Hungary; (S.K.); (A.N.); (L.O.)
- Department of Floriculture and Dendrology, Institute of Landscape Architecture, Urban Planning and Garden Art, Hungarian University of Agriculture and Life Sciences (MATE), 1223 Budapest, Hungary;
| | - Katalin Horotán
- Institute of Biology, Eszterházy Károly Catholic University, 3300 Eger, Hungary;
| | - Csaba Gyuricza
- Institute of Agronomy, Hungarian University of Agriculture and Life Sciences (MATE), 1118 Gödöllő, Hungary
| | - Katarína Ražná
- Institute of Plant and Environmental Sciences, Faculty of Agrobiology and Food Resources, Slovak University of Agriculture in Nitra, 94976 Nitra, Slovakia; (K.R.); (M.K.); (Ľ.H.)
| | - Matúš Kučka
- Institute of Plant and Environmental Sciences, Faculty of Agrobiology and Food Resources, Slovak University of Agriculture in Nitra, 94976 Nitra, Slovakia; (K.R.); (M.K.); (Ľ.H.)
| | - Ľubomír Harenčár
- Institute of Plant and Environmental Sciences, Faculty of Agrobiology and Food Resources, Slovak University of Agriculture in Nitra, 94976 Nitra, Slovakia; (K.R.); (M.K.); (Ľ.H.)
| | - András Neményi
- Ornamental Plant and Green System Management Research Group, Institute of Landscape Architecture, Urban Planning and Garden Art, Hungarian University of Agriculture and Life Sciences (MATE), 1223 Budapest, Hungary; (S.K.); (A.N.); (L.O.)
| | - Csaba Lantos
- Cereal Research Non-Profit Company, 6726 Szeged, Hungary; (C.L.); (J.P.)
| | - János Pauk
- Cereal Research Non-Profit Company, 6726 Szeged, Hungary; (C.L.); (J.P.)
| | - Ádám Solti
- Department of Plant Physiology and Molecular Plant Biology, Eötvös Loránd University, 1117 Budapest, Hungary;
| | - Edina Simon
- Eötvös Loránd Research Network, University of Debrecen, 4032 Debrecen, Hungary;
- Anthropocene Ecology Research Group, Department of Ecology, University of Debrecen, 4032 Debrecen, Hungary; (D.B.); (S.M.)
| | - Dina Bibi
- Anthropocene Ecology Research Group, Department of Ecology, University of Debrecen, 4032 Debrecen, Hungary; (D.B.); (S.M.)
| | - Semonti Mukherjee
- Anthropocene Ecology Research Group, Department of Ecology, University of Debrecen, 4032 Debrecen, Hungary; (D.B.); (S.M.)
| | - Katalin Török
- Eotvos Lorand Res Network (ELKH), Institute of Plant Biology, Biological Research Centre, 6722 Szeged, Hungary;
| | - Andrea Tilly-Mándy
- Department of Floriculture and Dendrology, Institute of Landscape Architecture, Urban Planning and Garden Art, Hungarian University of Agriculture and Life Sciences (MATE), 1223 Budapest, Hungary;
| | - László Papp
- Füvészkert Botanical Garden, Eötvös Loránd University, 1053 Budapest, Hungary;
| | - László Orlóci
- Ornamental Plant and Green System Management Research Group, Institute of Landscape Architecture, Urban Planning and Garden Art, Hungarian University of Agriculture and Life Sciences (MATE), 1223 Budapest, Hungary; (S.K.); (A.N.); (L.O.)
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3
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Mishra LS, Cook SD, Kushwah S, Isaksson H, Straub IR, Abele M, Mishra S, Ludwig C, Libby E, Funk C. Overexpression of the plastidial pseudo-protease AtFtsHi3 enhances drought tolerance while sustaining plant growth. PHYSIOLOGIA PLANTARUM 2024; 176:e14370. [PMID: 38818570 DOI: 10.1111/ppl.14370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 04/18/2024] [Accepted: 04/25/2024] [Indexed: 06/01/2024]
Abstract
With climate change, droughts are expected to be more frequent and severe, severely impacting plant biomass and quality. Here, we show that overexpressing the Arabidopsis gene AtFtsHi3 (FtsHi3OE) enhances drought-tolerant phenotypes without compromising plant growth. AtFtsHi3 encodes a chloroplast envelope pseudo-protease; knock-down mutants (ftshi3-1) are found to be drought tolerant but exhibit stunted growth. Altered AtFtsHi3 expression therefore leads to drought tolerance, while only diminished expression of this gene leads to growth retardation. To understand the underlying mechanisms of the enhanced drought tolerance, we compared the proteomes of ftshi3-1 and pFtsHi3-FtsHi3OE (pFtsHi3-OE) to wild-type plants under well-watered and drought conditions. Drought-related processes like osmotic stress, water transport, and abscisic acid response were enriched in pFtsHi3-OE and ftshi3-1 mutants following their enhanced drought response compared to wild-type. The knock-down mutant ftshi3-1 showed an increased abundance of HSP90, HSP93, and TIC110 proteins, hinting at a potential downstream role of AtFtsHi3 in chloroplast pre-protein import. Mathematical modeling was performed to understand how variation in the transcript abundance of AtFtsHi3 can, on the one hand, lead to drought tolerance in both overexpression and knock-down lines, yet, on the other hand, affect plant growth so differently. The results led us to hypothesize that AtFtsHi3 may form complexes with at least two other protease subunits, either as homo- or heteromeric structures. Enriched amounts of AtFtsH7/9, AtFtsH11, AtFtsH12, and AtFtsHi4 in ftshi3-1 suggest a possible compensation mechanism for these proteases in the hexamer.
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Affiliation(s)
| | - Sam D Cook
- Department of Chemistry, Umeå University, Umeå, Sweden
| | | | - Hanna Isaksson
- Department of Mathematics and Mathematical Statistics, Integrated Science Lab (Icelab), Umeå University, Umeå, Sweden
- IceLab, Umeå University, Umeå, Sweden
| | - Isabella R Straub
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), School of Life Sciences Weihenstephan, Technical University of Munich (TUM), Freising, Germany
| | - Miriam Abele
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), School of Life Sciences Weihenstephan, Technical University of Munich (TUM), Freising, Germany
| | - Sanatkumar Mishra
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Christina Ludwig
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), School of Life Sciences Weihenstephan, Technical University of Munich (TUM), Freising, Germany
| | - Eric Libby
- Department of Mathematics and Mathematical Statistics, Integrated Science Lab (Icelab), Umeå University, Umeå, Sweden
- IceLab, Umeå University, Umeå, Sweden
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4
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Yoshiyama Y, Wakabayashi Y, Mercer KL, Kawabata S, Kobayashi T, Tabuchi T, Yamori W. Natural genetic variation in dynamic photosynthesis is correlated with stomatal anatomical traits in diverse tomato species across geographical habitats. JOURNAL OF EXPERIMENTAL BOTANY 2024:erae082. [PMID: 38606772 DOI: 10.1093/jxb/erae082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 02/23/2024] [Indexed: 04/13/2024]
Abstract
Plants grown under field conditions experience fluctuating light. Understanding the natural genetic variations for a similarly dynamic photosynthetic response among untapped germplasm resources, as well as the underlying mechanisms, may offer breeding strategies to improve production using molecular approaches. Here, we measured gas exchange under fluctuating light, along with stomatal density and size, in eight wild tomato species and two tomato cultivars. The photosynthetic induction response showed significant diversity, with some wild species having faster induction rates than the two cultivars. Species with faster photosynthetic induction rates had higher daily integrated photosynthesis, but lower average water use efficiency because of high stomatal conductance under natural fluctuating light. The variation in photosynthetic induction was closely associated with the speed of stomatal responses, highlighting its critical role in maximizing photosynthesis under fluctuating light conditions. Moreover, stomatal size was negatively correlated with stomatal density within a species, and plants with smaller stomata at a higher density had a quicker photosynthetic response than those with larger stomata at lower density. Our findings show that the response of stomatal conductance plays a pivotal role in photosynthetic induction, with smaller stomata at higher density proving advantageous for photosynthesis under fluctuating light in tomato species. The interspecific variation in the rate of stomatal responses could offer an untapped resource for optimizing dynamic photosynthetic responses under field conditions.
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Affiliation(s)
- Yugo Yoshiyama
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Nishitokyo, Tokyo, Japan
| | - Yu Wakabayashi
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Nishitokyo, Tokyo, Japan
| | - Kristin L Mercer
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Nishitokyo, Tokyo, Japan
- Ohio State University, Department of Horticulture and Crop Science, Columbus, OH, USA
| | - Saneyuki Kawabata
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Nishitokyo, Tokyo, Japan
| | - Takayuki Kobayashi
- Department of Advanced Food Sciences, College of Agriculture, Tamagawa University, Machida, Tokyo, Japan
| | - Toshihito Tabuchi
- Department of Advanced Food Sciences, College of Agriculture, Tamagawa University, Machida, Tokyo, Japan
| | - Wataru Yamori
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Nishitokyo, Tokyo, Japan
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5
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Tran VH, Nolting KM, Donovan LA, Temme AA. Cultivated sunflower ( Helianthus annuus L.) has lower tolerance of moderate drought stress than its con-specific wild relative, but the underlying traits remain elusive. PLANT DIRECT 2024; 8:e581. [PMID: 38585190 PMCID: PMC10995449 DOI: 10.1002/pld3.581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 02/29/2024] [Accepted: 03/03/2024] [Indexed: 04/09/2024]
Abstract
Cultivated crops are generally expected to have less abiotic stress tolerance than their wild relatives. However, this assumption is not well supported by empirical literature and may depend on the type of stress and how it is imposed, as well as the measure of tolerance being used. Here, we investigated whether wild and cultivated accessions of Helianthus annuus differed in stress tolerance assessed as proportional decline in biomass due to drought and whether wild and cultivated accessions differed in trait responses to drought and trait associations with tolerance. In a greenhouse study, H. annuus accessions in the two domestication classes (eight cultivated and eight wild accessions) received two treatments: a well-watered control and a moderate drought implemented as a dry down followed by maintenance at a predetermined soil moisture level with automated irrigation. Treatments were imposed at the seedling stage, and plants were harvested after 2 weeks of treatment. The proportional biomass decline in response to drought was 24% for cultivated H. annuus accessions but was not significant for the wild accessions. Thus, using the metric of proportional biomass decline, the cultivated accessions had less drought tolerance. Among accessions, there was no tradeoff between drought tolerance and vigor assessed as biomass in the control treatment. In a multivariate analysis, wild and cultivated accessions did not differ from each other or in response to drought for a subset of morphological, physiological, and allocational traits. Analyzed individually, traits varied in response to drought in wild and/or cultivated accessions, including declines in specific leaf area, leaf theoretical maximum stomatal conductance (gsmax), and stomatal pore length, but there was no treatment response for stomatal density, succulence, or the ability to osmotically adjust. Focusing on traits associations with tolerance, plasticity in gsmax was the most interesting because its association with tolerance differed by domestication class (although the effects were relatively weak) and thus might contribute to lower tolerance of cultivated sunflower. Our H. annuus results support the expectation that stress tolerance is lower in crops than wild relatives under some conditions. However, determining the key traits that underpin differences in moderate drought tolerance between wild and cultivated H. annuus remains elusive.
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Affiliation(s)
- Vivian H. Tran
- Department of Plant BiologyUniversity of GeorgiaAthensGeorgiaUSA
| | | | - Lisa A. Donovan
- Department of Plant BiologyUniversity of GeorgiaAthensGeorgiaUSA
| | - Andries A. Temme
- Department of Plant BiologyUniversity of GeorgiaAthensGeorgiaUSA
- Department of Plant BreedingWageningen University & ResearchWageningenNetherlands
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6
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Herrera JC, Savoi S, Dostal J, Elezovic K, Chatzisavva M, Forneck A, Savi T. The legacy of past droughts induces water-sparingly behaviour in Grüner Veltliner grapevines. PLANT BIOLOGY (STUTTGART, GERMANY) 2024. [PMID: 38315499 DOI: 10.1111/plb.13620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 01/08/2024] [Indexed: 02/07/2024]
Abstract
Drought is becoming more frequent and severe in numerous wine-growing regions. Nevertheless, limited research has examined the legacy of recurrent droughts, focusing on leaf physiology and anatomy over consecutive seasons. We investigated drought legacies (after 2 years of drought exposure) in potted grapevines, focusing on stomatal behaviour under well-watered conditions during the third year. Vines were subjected for two consecutive years to short- (SD) or long-term (LD) seasonal droughts, or well-watered conditions (WW). In the third year, all plants were grown without water limitation. Water potential and gas exchange were monitored throughout the three seasons, while leaf morpho-anatomical traits were measured at the end of the third year. During droughts (1st and 2nd year), stem water potential of SD and LD plants fell below -1.1 MPa, with a consequent 75% reduction in stomatal conductance (gs ) compared to WW. In the 3rd year, when all vines were daily irrigated to soil capacity (midday stem water potential ~ -0.3 MPa), 45% lower values of gs were observed in the ex-LD group compared to both ex-SD and ex-WW. Reduced midrib vessel diameter, lower leaf theoretical hydraulic conductivity, and smaller stomata were measured in ex-LD leaves compared to ex-SD and ex-WW, likely contributing to the reduced gas exchange. Our findings suggest that grapevines exposed to drought may adopt a more water-conserving strategy in subsequent seasons, irrespective of current soil water availability, with the degree of change influenced by the intensity and duration of past drought events.
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Affiliation(s)
- J C Herrera
- Department of Crop Sciences, Institute of Viticulture and Pomology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - S Savoi
- Department of Agricultural, Forest and Food Sciences, University of Turin, Grugliasco, Italy
| | - J Dostal
- Department of Crop Sciences, Institute of Viticulture and Pomology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - K Elezovic
- Department of Crop Sciences, Institute of Viticulture and Pomology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - M Chatzisavva
- Department of Crop Sciences, Institute of Viticulture and Pomology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - A Forneck
- Department of Crop Sciences, Institute of Viticulture and Pomology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - T Savi
- Department of Integrative Biology and Biodiversity Research, Institute of Botany, University of Natural Resources and Life Sciences, Vienna, Austria
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7
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Kishino H, Nakamichi R, Kitada S. Genetic adaptations in the population history of Arabidopsis thaliana. G3 (BETHESDA, MD.) 2023; 13:jkad218. [PMID: 37748020 PMCID: PMC10700115 DOI: 10.1093/g3journal/jkad218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 05/26/2023] [Accepted: 09/14/2023] [Indexed: 09/27/2023]
Abstract
A population encounters a variety of environmental stresses, so the full source of its resilience can only be captured by collecting all the signatures of adaptation to the selection of the local environment in its population history. Based on the multiomic data of Arabidopsis thaliana, we constructed a database of phenotypic adaptations (p-adaptations) and gene expression (e-adaptations) adaptations in the population. Through the enrichment analysis of the identified adaptations, we inferred a likely scenario of adaptation that is consistent with the biological evidence from experimental work. We analyzed the dynamics of the allele frequencies at the 23,880 QTLs of 174 traits and 8,618 eQTLs of 1,829 genes with respect to the total SNPs in the genomes and identified 650 p-adaptations and 3,925 e-adaptations [false discovery rate (FDR) = 0.05]. The population underwent large-scale p-adaptations and e-adaptations along 4 lineages. Extremely cold winters and short summers prolonged seed dormancy and expanded the root system architecture. Low temperatures prolonged the growing season, and low light intensity required the increased chloroplast activity. The subtropical and humid environment enhanced phytohormone signaling pathways in response to the biotic and abiotic stresses. Exposure to heavy metals selected alleles for lower heavy metal uptake from soil, lower growth rate, lower resistance to bacteria, and higher expression of photosynthetic genes were selected. The p-adaptations are directly interpretable, while the coadapted gene expressions reflect the physiological requirements for the adaptation. The integration of this information characterizes when and where the population has experienced environmental stress and how the population responded at the molecular level.
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Affiliation(s)
- Hirohisa Kishino
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
- Research and Development Initiative, Chuo University, 1-13-27 Kasuga, Bunkyo-ku, Tokyo 112-8551, Japan
| | - Reiichiro Nakamichi
- Fisheries Resources Institute, Japan Fisheries Research and Education Agency, 2-12-4 Fukuura, Kanazawa-ku, Yokohama, Kanagawa 236-8648, Japan
| | - Shuichi Kitada
- Graduate School of Marine Science and Technology, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato-ku, Tokyo 108-8477, Japan
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Zhang K, Xue M, Qin F, He Y, Zhou Y. Natural polymorphisms in ZmIRX15A affect water-use efficiency by modulating stomatal density in maize. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:2560-2573. [PMID: 37572352 PMCID: PMC10651153 DOI: 10.1111/pbi.14153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 05/11/2023] [Accepted: 07/31/2023] [Indexed: 08/14/2023]
Abstract
Stomatal density (SD) is closely related to crop drought resistance. Understanding the genetic basis for natural variation in SD may facilitate efforts to improve water-use efficiency. Here, we report a genome-wide association study for SD in maize seedlings, which identified 18 genetic variants that could be resolved to seven candidate genes. A 3-bp insertion variant (InDel1089) in the last exon of Zea mays (Zm) IRX15A (Irregular xylem 15A) had the most significant association with SD and modulated the translation of ZmIRX15A mRNA by affecting its secondary structure. Dysfunction of ZmIRX15A increased SD, leading to an increase in the transpiration rate and CO2 assimilation efficiency. ZmIRX15A encodes a xylan deposition enzyme and its disruption significantly decreased xylan abundance in secondary cell wall composition. Transcriptome analysis revealed a substantial alteration of the expression of genes involved in stomatal complex morphogenesis and drought response in the loss-of-function of ZmIRX15A mutant. Overall, our study provides important genetic insights into the natural variation of leaf SD in maize, and the identified loci or genes can serve as direct targets for enhancing drought resistance in molecular-assisted maize breeding.
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Affiliation(s)
- Kun Zhang
- State Key Laboratory of Plant Physiology and BiochemistryEngineering Research Center of Plant Growth RegulatorCollege of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| | - Ming Xue
- Jiangsu Key Laboratory of Crop Genetics and PhysiologyCo‐Innovation Center for Modern Production Technology of Grain CropsKey Laboratory of Plant Functional Genomics of the Ministry of EducationYangzhou UniversityYangzhouChina
| | - Feng Qin
- State Key Laboratory of Plant Physiology and BiochemistryCollege of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Yan He
- National Maize Improvement Center of ChinaCollege of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| | - Yuyi Zhou
- State Key Laboratory of Plant Physiology and BiochemistryEngineering Research Center of Plant Growth RegulatorCollege of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
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9
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Bhadra S, Leitch IJ, Onstein RE. From genome size to trait evolution during angiosperm radiation. Trends Genet 2023; 39:728-735. [PMID: 37582671 DOI: 10.1016/j.tig.2023.07.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 07/21/2023] [Accepted: 07/24/2023] [Indexed: 08/17/2023]
Abstract
Angiosperm diversity arises from trait flexibility and repeated evolutionary radiations, but the role of genomic characters in these radiations remains unclear. In this opinion article, we discuss how genome size can influence angiosperm diversification via its intricate link with cell size, tissue packing, and physiological processes which, in turn, influence the macroevolution of functional traits. We propose that integrating genome size, functional traits, and phylogenetic data across a wide range of lineages allows us to test whether genome size decrease consistently leads to increased trait flexibility, while genome size increase constrains trait evolution. Combining theories from molecular biology, functional ecology and macroevolution, we provide a framework to better understand the role of genome size in trait evolution, evolutionary radiations, and the global distribution of angiosperms.
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Affiliation(s)
- Sreetama Bhadra
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstraße 4, D-04103, Leipzig, Germany; Leipzig University, Ritterstraße 26, 04109 Leipzig, Germany.
| | - Ilia J Leitch
- Royal Botanic Gardens, Kew, Kew Green, Richmond TW9 3AE, UK
| | - Renske E Onstein
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstraße 4, D-04103, Leipzig, Germany; Leipzig University, Ritterstraße 26, 04109 Leipzig, Germany; Naturalis Biodiversity Center, Darwinweg 2, 2333 CR Leiden, The Netherlands
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10
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Ng M, McCormick A, Utz RM, Heberling JM. Herbarium specimens reveal century-long trait shifts in poison ivy due to anthropogenic CO 2 emissions. AMERICAN JOURNAL OF BOTANY 2023; 110:e16225. [PMID: 37551738 DOI: 10.1002/ajb2.16225] [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: 04/13/2023] [Revised: 07/17/2023] [Accepted: 07/19/2023] [Indexed: 08/09/2023]
Abstract
PREMISE Previous experimental studies have shown that poison ivy (Toxicodendron radicans; Anacardicaceae) responds to elevated CO2 with increased leaf production, water-use efficiency, and toxicity (allergenic urushiol). However, long-term field data suggest no increase in poison ivy abundance over time. Using herbarium specimens, we examined whether poison ivy and other species shifted leaf traits under natural conditions with increasing atmospheric CO2 (pCO2 ) over the past century. METHODS We measured stomatal density, leaf area, leaf N, leaf C:N, leaf carbon isotope discrimination (Δleaf ), and intrinsic water-use efficiency (iWUE) from 327 specimens collected from 1838 to 2020 across Pennsylvania. We compared poison ivy's responses to two evolutionarily related tree species, Toxicodendron vernix and Rhus typhina (Anacardiacae) and one ecological analog, Parthenocissus quinquefolia (Vitaceae), a common co-occurring liana. RESULTS Stomatal density significantly decreased (P < 0.05) in poison ivy and the ecologically similar liana P. quinquefolia over the past century, but did not change in the related trees T. vernix and R. typhina. None of these species showed significant trends in changes in leaf N or C:N. Surprisingly, in poison ivy, but not the other species, Δleaf increased with increased pCO2 , corresponding to significant declines in iWUE over time. CONCLUSIONS In contrast to the results of short-term experimental studies, iWUE decreased in poison ivy over the last century. Trait responses to pCO2 varied by species. Herbarium specimens suggest that realized long-term plant physiological responses to increased CO2 may not be reflected in short-term experimental growth studies, highlighting the value of collections.
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Affiliation(s)
- Molly Ng
- Section of Botany, Carnegie Museum of Natural History, Pittsburgh, PA 15213, USA
| | - Alyssa McCormick
- Falk School of Sustainability, Chatham University, Gibsonia, PA 15044, USA
| | - Ryan M Utz
- Falk School of Sustainability, Chatham University, Gibsonia, PA 15044, USA
| | - J Mason Heberling
- Section of Botany, Carnegie Museum of Natural History, Pittsburgh, PA 15213, USA
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11
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Arab MM, Askari H, Aliniaeifard S, Mokhtassi-Bidgoli A, Estaji A, Sadat-Hosseini M, Sohrabi SS, Mesgaran MB, Leslie CA, Brown PJ, Vahdati K. Natural variation in photosynthesis and water use efficiency of locally adapted Persian walnut populations under drought stress and recovery. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 201:107859. [PMID: 37406405 DOI: 10.1016/j.plaphy.2023.107859] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Revised: 06/17/2023] [Accepted: 06/21/2023] [Indexed: 07/07/2023]
Abstract
Persian walnut is a drought-sensitive species with considerable genetic variation in the photosynthesis and water use efficiency of its populations, which is largely unexplored. Here, we aimed to elucidate changes in the efficiency of photosynthesis and water content using a diverse panel of 60 walnut families which were submitted to a progressive drought for 24 days, followed by two weeks of re-watering. Severe water-withholding reduced leaf relative water content (RWC) by 20%, net photosynthetic rate (Pn) by 50%, stomatal conductance (gs) by 60%, intercellular CO2 concentration (Ci) by 30%, and transpiration rate (Tr) by 50%, but improved water use efficiency (WUE) by 25%. Severe water-withholding also inhibited photosystem II functionality as indicated by reduced quantum yield of intersystem electron transport (φEo) and transfer of electrons per reaction center (ET0/RC), also enhanced accumulation of QA (VJ) resulted in the reduction of the photosynthetic performance (PIABS) and maximal quantum yield of PSII (FV/FM); while elevated quantum yield of energy dissipation (φDo), energy fluxes for absorption (ABS/RC) and dissipated energy flux (DI0/RC) in walnut families. Cluster analysis classified families into three main groups (tolerant, moderately tolerant, and sensitive), with the tolerant group from dry climates exhibiting lesser alterations in assessed parameters than the other groups. Multivariate analysis of phenotypic data demonstrated that RWC and biophysical parameters related to the chlorophyll fluorescence such as FV/FM, φEo, φDo, PIABS, ABS/RC, ET0/RC, and DI0/RC represent fast, robust and non-destructive biomarkers for walnut performance under drought stress. Finally, phenotype-environment association analysis showed significant correlation of some photosynthetic traits with geoclimatic factors, suggesting a key role of climate and geography in the adaptation of walnut to its habitat conditions.
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Affiliation(s)
- Mohammad M Arab
- Department of Horticulture, College of Aburaihan, University of Tehran, Tehran, Iran.
| | - Hossein Askari
- Department of Plant Sciences and Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran.
| | - Sasan Aliniaeifard
- Photosynthesis Laboratory, Department of Horticulture, College of Aburaihan, University of Tehran, Tehran, Iran.
| | - Ali Mokhtassi-Bidgoli
- Department of Agronomy, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran.
| | - Ahmad Estaji
- Department of Horticultural Sciences, Faculty of Agriculture, University of Vali-E-Asr, Rafsanjan, Iran.
| | | | - Seyed Sajad Sohrabi
- Department of Plant Production and Genetic Engineering, Faculty of Agriculture, Lorestan University, Khorramabad, Iran.
| | - Mohsen B Mesgaran
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA.
| | - Charles A Leslie
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA.
| | - Patrick J Brown
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA.
| | - Kourosh Vahdati
- Department of Horticulture, College of Aburaihan, University of Tehran, Tehran, Iran.
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12
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Al-Salman Y, Cano FJ, Pan L, Koller F, Piñeiro J, Jordan D, Ghannoum O. Anatomical drivers of stomatal conductance in sorghum lines with different leaf widths grown under different temperatures. PLANT, CELL & ENVIRONMENT 2023; 46:2142-2158. [PMID: 37066624 DOI: 10.1111/pce.14592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 03/29/2023] [Accepted: 04/03/2023] [Indexed: 06/08/2023]
Abstract
Sustaining crop productivity and resilience in water-limited environments and under rising temperatures are matters of concern worldwide. We investigated the leaf anatomical traits that underpin our recently identified link between leaf width (LW) and intrinsic water use efficiency (iWUE), as traits of interest in plant breeding. Ten sorghum lines with varying LW were grown under three temperatures to expand the range of variation of both LW and gas exchange rates. Leaf gas exchange, surface morphology and cross-sectional anatomy were measured and analysed using structural equations modelling. Narrower leaves had lower stomatal conductance (gs ) and higher iWUE across growth temperatures. They also had smaller intercellular airspaces, stomatal size, percentage of open stomatal aperture relative to maximum, hydraulic pathway, mesophyll thickness, and leaf mass per area. Structural modelling revealed a developmental association among leaf anatomical traits that underpinned gs variation in sorghum. Growing temperature and LW both impacted leaf gas exchange rates, but only LW directly impacted leaf anatomy. Wider leaves may be more productive under well-watered conditions, but consume more water for growth and development, which is detrimental under water stress.
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Affiliation(s)
- Yazen Al-Salman
- ARC Centre of Excellence for Translational Photosynthesis, Canberra, ACT, Australia
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, Australia
| | - Francisco J Cano
- ARC Centre of Excellence for Translational Photosynthesis, Canberra, ACT, Australia
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, Australia
- Instituto de Ciencias Forestales (ICIFOR-INIA), CSIC, Madrid, Spain
| | - Ling Pan
- ARC Centre of Excellence for Translational Photosynthesis, Canberra, ACT, Australia
- Department of Grassland Science, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Fiona Koller
- ARC Centre of Excellence for Translational Photosynthesis, Canberra, ACT, Australia
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, Australia
| | - Juan Piñeiro
- Department of Biology, IVAGRO, Campus de Excelencia Internacional Agroalimentario, Capus del Rio San Pedro, University of Cádiz, Puerto Real, Spain
| | - David Jordan
- ARC Centre of Excellence for Translational Photosynthesis, Canberra, ACT, Australia
- Hermitage Research Facility, The University of Queensland, Warwick, Queensland, Australia
- Agri-Science Queensland, Department of Agriculture & Fisheries, Hermitage Research Facility, Warwick, Queensland, Australia
| | - Oula Ghannoum
- ARC Centre of Excellence for Translational Photosynthesis, Canberra, ACT, Australia
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, Australia
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13
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Nunes TDG, Berg LS, Slawinska MW, Zhang D, Redt L, Sibout R, Vogel JP, Laudencia-Chingcuanco D, Jesenofsky B, Lindner H, Raissig MT. Regulation of hair cell and stomatal size by a hair cell-specific peroxidase in the grass Brachypodium distachyon. Curr Biol 2023; 33:1844-1854.e6. [PMID: 37086717 DOI: 10.1016/j.cub.2023.03.089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 02/23/2023] [Accepted: 03/31/2023] [Indexed: 04/24/2023]
Abstract
The leaf epidermis is the outermost cell layer forming the interface between plants and the atmosphere that must both provide a robust barrier against (a)biotic stressors and facilitate carbon dioxide uptake and leaf transpiration.1 To achieve these opposing requirements, the plant epidermis developed a wide range of specialized cell types such as stomata and hair cells. Although factors forming these individual cell types are known,2,3,4,5 it is poorly understood how their number and size are coordinated. Here, we identified a role for BdPRX76/BdPOX, a class III peroxidase, in regulating hair cell and stomatal size in the model grass Brachypodium distachyon. In bdpox mutants, prickle hair cells were smaller and stomata were longer. Because stomatal density remained unchanged, the negative correlation between stomatal size and density was disrupted in bdpox and resulted in higher stomatal conductance and lower intrinsic water-use efficiency. BdPOX was exclusively expressed in hair cells, suggesting that BdPOX cell-autonomously promotes hair cell size and indirectly restricts stomatal length. Cell-wall autofluorescence and lignin stainings indicated a role for BdPOX in the lignification or crosslinking of related phenolic compounds at the hair cell base. Ectopic expression of BdPOX in the stomatal lineage increased phenolic autofluorescence in guard cell (GC) walls and restricted stomatal elongation in bdpox. Together, we highlight a developmental interplay between hair cells and stomata that optimizes epidermal functionality. We propose that cell-type-specific changes disrupt this interplay and lead to compensatory developmental defects in other epidermal cell types.
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Affiliation(s)
- Tiago D G Nunes
- Centre for Organismal Studies Heidelberg, Heidelberg University, 69120 Heidelberg, Germany
| | - Lea S Berg
- Institute of Plant Sciences, University of Bern, 3013 Bern, Switzerland
| | - Magdalena W Slawinska
- Centre for Organismal Studies Heidelberg, Heidelberg University, 69120 Heidelberg, Germany
| | - Dan Zhang
- Centre for Organismal Studies Heidelberg, Heidelberg University, 69120 Heidelberg, Germany
| | - Leonie Redt
- Centre for Organismal Studies Heidelberg, Heidelberg University, 69120 Heidelberg, Germany
| | - Richard Sibout
- UR1268 BIA (Biopolymères Interactions Assemblages), INRAE, Nantes 44300, France
| | - John P Vogel
- DOE Joint Genome Institute, Berkeley, CA 94720, USA; University of California, Berkeley, Berkeley, CA 94720, USA
| | | | - Barbara Jesenofsky
- Centre for Organismal Studies Heidelberg, Heidelberg University, 69120 Heidelberg, Germany
| | - Heike Lindner
- Centre for Organismal Studies Heidelberg, Heidelberg University, 69120 Heidelberg, Germany; Institute of Plant Sciences, University of Bern, 3013 Bern, Switzerland
| | - Michael T Raissig
- Centre for Organismal Studies Heidelberg, Heidelberg University, 69120 Heidelberg, Germany; Institute of Plant Sciences, University of Bern, 3013 Bern, Switzerland.
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14
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Estarague A, Violle C, Vile D, Hany A, Martino T, Moulin P, Vasseur F. Plant–herbivore interactions: Experimental demonstration of genetic variability in plant–plant signalling. Evol Appl 2023; 16:772-780. [PMID: 37124083 PMCID: PMC10130558 DOI: 10.1111/eva.13531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 01/12/2023] [Accepted: 01/15/2023] [Indexed: 03/31/2023] Open
Abstract
Plant-herbivore interactions mediated by plant-plant signalling have been documented in different species but its within-species variability has hardly been quantified. Here, we tested if herbivore foraging activity on plants was influenced by a prior contact with a damaged plant and if the effect of such plant-plant signalling was variable across 113 natural genotypes of Arabidopsis thaliana. We filmed the activity of the generalist herbivore Cornu aspersum during 1 h on two plants differing only in a prior contact with a damaged plant or not. We recorded each snails' first choice, and measured its first duration on a plant, the proportion of time spent on both plants and leaf consumption. Overall, plant-plant signalling modified the foraging activity of herbivores in A. thaliana. On average, snails spent more time and consumed more of plants that experienced a prior contact with a damaged plant. However, the effects of plant-plant signalling on snail behaviour was variable: depending on genotype identity, plant-plant signalling made undamaged plants more repellant or attractive to snails. Genome-wide associations revealed that genes related to stress coping ability and jasmonate pathway were associated to this variation. Together, our findings highlight the adaptive significance of plant-plant signalling for plant-herbivore interactions.
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Affiliation(s)
- Aurélien Estarague
- CEFE, Univ Montpellier, CNRS, EPHE, IRDMontpellierFrance
- LEPSE, Univ Montpellier, INRAE, Institut AgroMontpellierFrance
| | - Cyrille Violle
- CEFE, Univ Montpellier, CNRS, EPHE, IRDMontpellierFrance
| | - Denis Vile
- LEPSE, Univ Montpellier, INRAE, Institut AgroMontpellierFrance
| | - Anaïs Hany
- CEFE, Univ Montpellier, CNRS, EPHE, IRDMontpellierFrance
| | | | - Pierre Moulin
- CEFE, Univ Montpellier, CNRS, EPHE, IRDMontpellierFrance
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15
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Caine RS, Harrison EL, Sloan J, Flis PM, Fischer S, Khan MS, Nguyen PT, Nguyen LT, Gray JE, Croft H. The influences of stomatal size and density on rice abiotic stress resilience. THE NEW PHYTOLOGIST 2023; 237:2180-2195. [PMID: 36630602 PMCID: PMC10952745 DOI: 10.1111/nph.18704] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 12/05/2022] [Indexed: 06/17/2023]
Abstract
A warming climate coupled with reductions in water availability and rising salinity are increasingly affecting rice (Oryza sativa) yields. Elevated temperatures combined with vapour pressure deficit (VPD) rises are causing stomatal closure, further reducing plant productivity and cooling. It is unclear what stomatal size (SS) and stomatal density (SD) will best suit all these environmental extremes. To understand how stomatal differences contribute to rice abiotic stress resilience, we screened the stomatal characteristics of 72 traditionally bred varieties. We found significant variation in SS, SD and calculated anatomical maximal stomatal conductance (gsmax ) but did not identify any varieties with SD and gsmax as low as transgenic OsEPF1oe plants. Traditionally bred varieties with high SD and small SS (resulting in higher gsmax ) typically had lower biomasses, and these plants were more resilient to drought than low SD and large SS plants, which were physically larger. None of the varieties assessed were as resilient to drought or salinity as low SD OsEPF1oe transgenic plants. High SD and small SS rice displayed faster stomatal closure during increasing temperature and VPD, but photosynthesis and plant cooling were reduced. Compromises will be required when choosing rice SS and SD to tackle multiple future environmental stresses.
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Affiliation(s)
- Robert S. Caine
- Plants, Photosynthesis and Soil, School of BiosciencesUniversity of SheffieldS10 2TNSheffieldUK
- Institute for Sustainable Food, School of BiosciencesUniversity of SheffieldSheffieldS10 2TNUK
| | - Emily L. Harrison
- Plants, Photosynthesis and Soil, School of BiosciencesUniversity of SheffieldS10 2TNSheffieldUK
| | - Jen Sloan
- Plants, Photosynthesis and Soil, School of BiosciencesUniversity of SheffieldS10 2TNSheffieldUK
| | - Paulina M. Flis
- Future Food Beacon of Excellence and the School of BiosciencesUniversity of NottinghamNottinghamNG7 2RDUK
| | - Sina Fischer
- Future Food Beacon of Excellence and the School of BiosciencesUniversity of NottinghamNottinghamNG7 2RDUK
| | - Muhammad S. Khan
- Plants, Photosynthesis and Soil, School of BiosciencesUniversity of SheffieldS10 2TNSheffieldUK
| | - Phuoc Trong Nguyen
- High Agricultural Technology Research InstituteG9‐11, Street 31, Area 586, Phu Thu Ward, Cai Rang DistrictCan Tho CityVietnam
| | - Lang Thi Nguyen
- High Agricultural Technology Research InstituteG9‐11, Street 31, Area 586, Phu Thu Ward, Cai Rang DistrictCan Tho CityVietnam
| | - Julie E. Gray
- Plants, Photosynthesis and Soil, School of BiosciencesUniversity of SheffieldS10 2TNSheffieldUK
- Institute for Sustainable Food, School of BiosciencesUniversity of SheffieldSheffieldS10 2TNUK
| | - Holly Croft
- Plants, Photosynthesis and Soil, School of BiosciencesUniversity of SheffieldS10 2TNSheffieldUK
- Institute for Sustainable Food, School of BiosciencesUniversity of SheffieldSheffieldS10 2TNUK
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16
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Li L, Jin Z, Huang R, Zhou J, Song F, Yao L, Li P, Lu W, Xiao L, Quan M, Zhang D, Du Q. Leaf physiology variations are modulated by natural variations that underlie stomatal morphology in Populus. PLANT, CELL & ENVIRONMENT 2023; 46:150-170. [PMID: 36285358 DOI: 10.1111/pce.14471] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 05/26/2022] [Accepted: 05/28/2022] [Indexed: 06/16/2023]
Abstract
Stomata are essential for photosynthesis and abiotic stress tolerance. Here, we used multiomics approaches to dissect the genetic architecture and adaptive mechanisms that underlie stomatal morphology in Populus tomentosa juvenile natural population (303 accessions). We detected 46 candidate genes and 15 epistatic gene-pairs, associated with 5 stomatal morphologies and 18 leaf development and photosynthesis traits, through genome-wide association studies. Expression quantitative trait locus mapping revealed that stomata-associated gene loci were significantly associated with the expression of leaf-related genes; selective sweep analysis uncovered significant differentiation in the allele frequencies of genes that underlie stomatal variations. An allelic regulatory network operating under drought stress and adequate precipitation conditions, with three key regulators (DUF538, TRA2 and AbFH2) and eight interacting genes, was identified that might regulate leaf physiology via modulation of stomatal shape and density. Validation of candidate gene variations in drought-tolerant and F1 hybrid populations of P. tomentosa showed that the DUF538, TRA2 and AbFH2 loci cause functional stabilisation of spatiotemporal regulatory, whose favourable alleles can be faithfully transmitted to offspring. This study provides insights concerning leaf physiology and stress tolerance via the regulation of stomatal determination in perennial plants.
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Affiliation(s)
- Lianzheng Li
- National Engineering Research Center of Tree breeding and Ecological restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P.R. 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, P.R. China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P.R. China
| | - Zhuoying Jin
- National Engineering Research Center of Tree breeding and Ecological restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P.R. 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, P.R. China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P.R. China
| | - Rui Huang
- National Engineering Research Center of Tree breeding and Ecological restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P.R. 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, P.R. China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P.R. China
| | - Jiaxuan Zhou
- National Engineering Research Center of Tree breeding and Ecological restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P.R. 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, P.R. China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P.R. China
| | - Fangyuan Song
- National Engineering Research Center of Tree breeding and Ecological restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P.R. 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, P.R. China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P.R. China
| | - Liangchen Yao
- National Engineering Research Center of Tree breeding and Ecological restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P.R. 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, P.R. China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P.R. China
| | - Peng Li
- National Engineering Research Center of Tree breeding and Ecological restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P.R. 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, P.R. China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P.R. China
| | - Wenjie Lu
- National Engineering Research Center of Tree breeding and Ecological restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P.R. 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, P.R. China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P.R. China
| | - Liang Xiao
- National Engineering Research Center of Tree breeding and Ecological restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P.R. 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, P.R. China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P.R. China
| | - Mingyang Quan
- National Engineering Research Center of Tree breeding and Ecological restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P.R. 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, P.R. China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P.R. China
| | - Deqiang Zhang
- National Engineering Research Center of Tree breeding and Ecological restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P.R. 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, P.R. China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P.R. China
| | - Qingzhang Du
- National Engineering Research Center of Tree breeding and Ecological restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P.R. 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, P.R. China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P.R. China
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17
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Lertngim N, Ruangsiri M, Klinsawang S, Raksatikan P, Thunnom B, Siangliw M, Toojinda T, Siangliw JL. Photosynthetic Plasticity and Stomata Adjustment in Chromosome Segment Substitution Lines of Rice Cultivar KDML105 under Drought Stress. PLANTS (BASEL, SWITZERLAND) 2022; 12:94. [PMID: 36616222 PMCID: PMC9823560 DOI: 10.3390/plants12010094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 12/14/2022] [Accepted: 12/16/2022] [Indexed: 06/17/2023]
Abstract
The impact of increasing drought periods on crop yields as a result of global climate change is a major concern in modern agriculture. Thus, a greater understanding of crop physiological responses under drought stress can guide breeders to develop new cultivars with enhanced drought tolerance. In this study, selected chromosome segment substitution lines of KDML105 (KDML105-CSSL) were grown in the Plant Phenomics Center of Kasetsart University in Thailand under well-watered and drought-stressed conditions. Physiological traits were measured by observing gas exchange dynamics and using a high-throughput phenotyping platform. Furthermore, because of its impact on plant internal gas and water regulation, stomatal morphological trait variation was recorded. The results show that KDML105-CSS lines exhibited plasticity responses to enhance water-use efficiency which increased by 3.62%. Moreover, photosynthesis, stomatal conductance and transpiration decreased by approximately 40% and plant height was reduced by 17.69%. Stomatal density tended to decrease and was negatively correlated with stomatal size, and stomata on different sides of the leaves responded differently under drought stress. Under drought stress, top-performing KDML105-CSS lines with high net photosynthesis had shorter plant height and improved IWUE, as influenced by an increase in stomatal density on the upper leaf side and a decrease on the lower leaf side.
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Affiliation(s)
- Narawitch Lertngim
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Phahonyothin, Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand
| | - Mathurada Ruangsiri
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Phahonyothin, Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand
| | - Suparad Klinsawang
- Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Kamphaeng Saen, Nakhon Pathom 73140, Thailand
| | - Pimpa Raksatikan
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Phahonyothin, Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand
| | - Burin Thunnom
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Phahonyothin, Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand
| | - Meechai Siangliw
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Phahonyothin, Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand
| | - Theerayut Toojinda
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Phahonyothin, Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand
| | - Jonaliza Lanceras Siangliw
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Phahonyothin, Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand
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18
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Volk K, Braasch J, Ahlering M, Hamilton JA. Environmental contributions to the evolution of trait differences in Geum triflorum: Implications for restoration. AMERICAN JOURNAL OF BOTANY 2022; 109:1822-1837. [PMID: 36151780 DOI: 10.1002/ajb2.16061] [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: 02/14/2022] [Revised: 06/21/2022] [Accepted: 06/21/2022] [Indexed: 06/16/2023]
Abstract
PREMISE How the environment influences the distribution of trait variation across a species' range has important implications for seed transfer during restoration. Evolution across environments could influence fitness when individuals are transferred into new environments. Here, we evaluate the role the environment has had on the distribution of genetic variance for traits important to adaptation. METHODS In a common garden experiment, we quantified trait differentiation for populations of Geum triflorum sourced from three distinct ecoregions and evaluated the ability of climate to predict trait variation. Populations were sourced from the Manitoba and Great Lake alvar ecoregions that experience predictable extremes in seasonal water availability and the prairie ecoregion which exhibits unpredictable changes in water availability. RESULTS Plants sourced from alvar ecoregions exhibited smaller but more stomata and greater intrinsic water-use efficiency relative to prairie plant populations, supporting the evolution of ecotypic differences. Estimates of standing genetic variance and heritable genetic variation for quantitative traits suggest alvar populations have greater adaptive potential. However, low evolvability suggests all populations likely have limited capacity to evolve in response to environmental change. CONCLUSIONS These results highlight the importance of the environment in influencing the evolution and distribution of genetic differences across populations used as seed sources for restoration. Additionally, these data may inform recommendations for seed transfer across novel environments and our expectations of populations' adaptive potential.
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Affiliation(s)
- Kate Volk
- North Dakota State University, Department of Biological Sciences, Fargo, ND, 58102, USA
| | - Joseph Braasch
- North Dakota State University, Department of Biological Sciences, Fargo, ND, 58102, USA
- Rutgers University Camden, Department of Biological Sciences, Camden, NJ, 08102, USA
| | | | - Jill A Hamilton
- North Dakota State University, Department of Biological Sciences, Fargo, ND, 58102, USA
- Pennsylvania State University, Department of Ecosystem Science and Management, University Park, PA, 16802, USA
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19
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Earley AM, Temme AA, Cotter CR, Burke JM. Genomic regions associate with major axes of variation driven by gas exchange and leaf construction traits in cultivated sunflower (Helianthus annuus L.). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:1425-1438. [PMID: 35815412 PMCID: PMC9545426 DOI: 10.1111/tpj.15900] [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: 04/20/2022] [Revised: 07/01/2022] [Accepted: 07/06/2022] [Indexed: 06/15/2023]
Abstract
Stomata and leaf veins play an essential role in transpiration and the movement of water throughout leaves. These traits are thus thought to play a key role in the adaptation of plants to drought and a better understanding of the genetic basis of their variation and coordination could inform efforts to improve drought tolerance. Here, we explore patterns of variation and covariation in leaf anatomical traits and analyze their genetic architecture via genome-wide association (GWA) analyses in cultivated sunflower (Helianthus annuus L.). Traits related to stomatal density and morphology as well as lower-order veins were manually measured from digital images while the density of minor veins was estimated using a novel deep learning approach. Leaf, stomatal, and vein traits exhibited numerous significant correlations that generally followed expectations based on functional relationships. Correlated suites of traits could further be separated along three major principal component (PC) axes that were heavily influenced by variation in traits related to gas exchange, leaf hydraulics, and leaf construction. While there was limited evidence of colocalization when individual traits were subjected to GWA analyses, major multivariate PC axes that were most strongly influenced by several traits related to gas exchange or leaf construction did exhibit significant genomic associations. These results provide insight into the genetic basis of leaf trait covariation and showcase potential targets for future efforts aimed at modifying leaf anatomical traits in sunflower.
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Affiliation(s)
- Ashley M. Earley
- Department of Plant BiologyUniversity of GeorgiaAthensGeorgiaUSA
| | - Andries A. Temme
- Department of Plant BiologyUniversity of GeorgiaAthensGeorgiaUSA
- Division of Intensive Plant Food SystemsHumboldt‐Universität zu Berlin10117BerlinGermany
| | | | - John M. Burke
- Department of Plant BiologyUniversity of GeorgiaAthensGeorgiaUSA
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20
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Chen Y, Zhu W, Yan T, Chen D, Jiang L, Chen ZH, Wu D. Stomatal morphological variation contributes to global ecological adaptation and diversification of Brassica napus. PLANTA 2022; 256:64. [PMID: 36029339 DOI: 10.1007/s00425-022-03982-4] [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: 06/29/2022] [Accepted: 08/22/2022] [Indexed: 06/15/2023]
Abstract
Stomatal density and guard cell length of 274 global core germplasms of rapeseed reveal that the stomatal morphological variation contributes to global ecological adaptation and diversification of Brassica napus. Stomata are microscopic structures of plants for the regulation of CO2 assimilation and transpiration. Stomatal morphology has changed substantially in the adaptation to the external environment during land plant evolution. Brassica napus is a major crop to produce oil, livestock feed and biofuel in the world. However, there are few studies on the regulatory genes controlling stomatal development and their interaction with environmental factors as well as the genetic mechanism of adaptive variation in B. napus. Here, we characterized stomatal density (SD) and guard cell length (GL) of 274 global core germplasms at seedling stage. It was found that among the significant phenotypic variation, European germplasms are mostly winter rapeseed with high stomatal density and small guard cell length. However, the germplasms from Asia (especially China) are semi-winter rapeseed, which is characterized by low stomatal density and large guard cell length. Through selective sweep analysis and homology comparison, we identified several candidate genes related to stomatal density and guard cell length, including Epidermal Patterning Factor2 (EPF2; BnaA09g23140D), Epidermal Patterning Factor Like4 (EPFL4; BnaC01g22890D) and Suppressor of LLP1 (SOL1 BnaC01g22810D). Haplotype and phylogenetic analysis showed that natural variation in EPF2, EPFL4 and SOL1 is closely associated with the winter, spring, and semi-winter rapeseed ecotypes. In summary, this study demonstrated for the first time the relation between stomatal phenotypic variation and ecological adaptation in rapeseed, which is useful for future molecular breeding of rapeseed in the context of evolution and domestication of key stomatal traits and global climate change.
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Affiliation(s)
- Yeke Chen
- Department of Agronomy, Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou, 310058, China
| | - Weizhuo Zhu
- Department of Agronomy, Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou, 310058, China
| | - Tao Yan
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, China
| | - Danyi Chen
- Department of Agronomy, Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou, 310058, China
| | - Lixi Jiang
- Department of Agronomy, Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou, 310058, China
| | - Zhong-Hua Chen
- School of Science, Western Sydney University, Penrith, NSW, Australia.
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia.
| | - Dezhi Wu
- Department of Agronomy, Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou, 310058, China.
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, China.
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21
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Abstract
Water-use efficiency (WUE) is the ratio of biomass produced per unit of water consumed; thus, it can be altered by genetic factors that affect either side of the ratio. In the present study, we exploited natural variation for WUE to discover loci affecting either biomass accumulation or water use as factors affecting WUE. Genome-wide association studies (GWAS) using integrated WUE measured through carbon isotope discrimination (δ13C) of Arabidopsis thaliana accessions identified genomic regions associated with WUE. Reverse genetic analysis of 70 candidate genes selected based on the GWAS results and transcriptome data identified 25 genes affecting WUE as measured by gravimetric and δ13C analyses. Mutants of four genes had higher WUE than wild type, while mutants of the other 21 genes had lower WUE. The differences in WUE were caused by either altered biomass or water consumption (or both). Stomatal density (SD) was not a primary cause of altered WUE in these mutants. Leaf surface temperatures indicated that transpiration differed for mutants of 16 genes, but generally biomass accumulation had a greater effect on WUE. The genes we identified are involved in diverse cellular processes, including hormone and calcium signaling, meristematic activity, photosynthesis, flowering time, leaf/vasculature development, and cell wall composition; however, none of them had been previously linked to WUE. Thus, our study successfully identified effectors of WUE that can be used to understand the genetic basis of WUE and improve crop productivity.
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22
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Li S, Yu S, Zhang Y, Zhu D, Li F, Chen B, Mei F, Du L, Ding L, Chen L, Song J, Kang Z, Mao H. Genome-wide association study revealed TaHXK3-2A as a candidate gene controlling stomatal index in wheat seedlings. PLANT, CELL & ENVIRONMENT 2022; 45:2306-2323. [PMID: 35545896 DOI: 10.1111/pce.14342] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 12/01/2021] [Accepted: 12/01/2021] [Indexed: 06/15/2023]
Abstract
Stomata are important channels for the control of gas exchange between plants and the atmosphere. To examine the genetic architecture of wheat stomatal index, we performed a genome-wide association study (GWAS) using a panel of 539 wheat accessions and 450 678 polymorphic single nucleotide polymorphisms (SNPs) that were detected using wheat-specific 660K SNP array. A total of 130 SNPs were detected to be significantly associated with stomatal index in both leaf surfaces of wheat seedlings. These significant SNPs were distributed across 16 chromosomes and involved 2625 candidate genes which participate in stress response, metabolism and cell/organ development. Subsequent bulk segregant analysis (BSA), combined with GWAS identified one major haplotype on chromosome 2A, that is responsible for stomatal index on the abaxial leaf surface. Candidate gene association analysis revealed that genetic variation in the promoter region of the hexokinase gene TaHXK3-2A was significantly associated with the stomatal index. Moreover, transgenic analysis confirmed that TaHXK3-2A overexpression in wheat decreased the size of leaf pavement cells but increased stomatal density through the glucose metabolic pathway, resulting in drought sensitivity among TaHXK3-2A transgenic lines due to an increased transpiration rate. Taken together, these results provide valuable insights into the genetic control of the stomatal index in wheat seedlings.
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Affiliation(s)
- Shumin Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
| | - Shizhou Yu
- Molecular Genetics Key Laboratory of China Tobacco, Guizhou Academy of Tobacco Science, Guiyang, Guizhou, China
| | - Yifang Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
| | - Dehe Zhu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
| | - Fangfang Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
| | - Bin Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
| | - Fangming Mei
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
| | - Linying Du
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Science, Northwest A&F University, Yangling, Shaanxi, China
| | - Li Ding
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
| | - Lei Chen
- School of Life Sciences, Yantai University, Yantai, Shandong, China
| | - Jiancheng Song
- School of Life Sciences, Yantai University, Yantai, Shandong, China
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
| | - Hude Mao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
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23
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Pérez-Bueno ML, Illescas-Miranda J, Martín-Forero AF, de Marcos A, Barón M, Fenoll C, Mena M. An extremely low stomatal density mutant overcomes cooling limitations at supra-optimal temperature by adjusting stomatal size and leaf thickness. FRONTIERS IN PLANT SCIENCE 2022; 13:919299. [PMID: 35937324 PMCID: PMC9355609 DOI: 10.3389/fpls.2022.919299] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 06/27/2022] [Indexed: 05/25/2023]
Abstract
The impact of global warming on transpiration and photosynthesis would compromise plant fitness, impacting on crop yields and ecosystem functioning. In this frame, we explored the performance of a set of Arabidopsis mutants carrying partial or total loss-of-function alleles of stomatal development genes and displaying distinct stomatal abundances. Using microscopy and non-invasive imaging techniques on this genotype collection, we examined anatomical leaf and stomatal traits, plant growth and development, and physiological performance at optimal (22°C) and supra-optimal (30°C) temperatures. All genotypes showed thermomorphogenetic responses but no signs of heat stress. Data analysis singled out an extremely low stomatal abundance mutant, spch-5. At 22°C, spch-5 had lower transpiration and warmer leaves than the wild type. However, at 30°C, this mutant developed larger stomata and thinner leaves, paralleled by a notable cooling capacity, similar to that of the wild type. Despite their low stomatal density (SD), spch-5 plants grown at 30°C showed no photosynthesis or growth penalties. The behavior of spch-5 at supra-optimal temperature exemplifies how the effect of very low stomatal numbers can be counteracted by a combination of larger stomata and thinner leaves. Furthermore, it provides a novel strategy for coping with high growth temperatures.
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Affiliation(s)
- María Luisa Pérez-Bueno
- Facultad de Ciencias Ambientales y Bioquímica, Universidad de Castilla-La Mancha, Toledo, Spain
- Departamento de Bioquímica, Biología Celular y Molecular de Plantas, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain
- Departamento de Fisiología Vegetal, Universidad de Granada, Granada, Spain
| | | | - Amanda F. Martín-Forero
- Facultad de Ciencias Ambientales y Bioquímica, Universidad de Castilla-La Mancha, Toledo, Spain
| | - Alberto de Marcos
- Facultad de Ciencias Ambientales y Bioquímica, Universidad de Castilla-La Mancha, Toledo, Spain
| | - Matilde Barón
- Departamento de Bioquímica, Biología Celular y Molecular de Plantas, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain
| | - Carmen Fenoll
- Facultad de Ciencias Ambientales y Bioquímica, Universidad de Castilla-La Mancha, Toledo, Spain
| | - Montaña Mena
- Facultad de Ciencias Ambientales y Bioquímica, Universidad de Castilla-La Mancha, Toledo, Spain
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24
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McCoy JE, McHale LK, Kantar M, Jardón-Barbolla L, Mercer KL. Environment of origin and domestication affect morphological, physiological, and agronomic response to water deficit in chile pepper (Capsicum sp.). PLoS One 2022; 17:e0260684. [PMID: 35700182 PMCID: PMC9197065 DOI: 10.1371/journal.pone.0260684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 05/22/2022] [Indexed: 11/18/2022] Open
Abstract
Global climate change is having a significant effect on agriculture by causing greater precipitation variability and an increased risk of drought. To mitigate these effects, it is important to identify specific traits, adaptations, and germplasm that improve tolerance to soil water deficit. Local varieties, known as landraces, have undergone generations of farmer-mediated selection and can serve as sources of variation, specifically for tolerance to abiotic stress. Landraces can possess local adaptations, where accessions adapted to a particular environment will outperform others grown under the same conditions. We explore adaptations to water deficit in chile pepper landraces from across an environmental gradient in Mexico, a center of crop domestication and diversity, as well in improved varieties bred for the US. In the present study, we evaluated 25 US and Mexico accessions in a greenhouse experiment under well-watered and water deficit conditions and measured morphological, physiological, and agronomic traits. Accession and irrigation regime influenced plant biomass and height, while branching, CO2 assimilation, and fruit weight were all influenced by an interaction between accession and irrigation. A priori group contrasts revealed possible adaptations to water deficit for branching, CO2 assimilation, and plant height associated with geographic origin, domestication level, and pepper species. Additionally, within the Mexican landraces, the number of primary branches had a strong relationship with precipitation from the environment of origin. This work provides insight into chile pepper response to water deficit and adaptation to drought and identifies possibly tolerant germplasm.
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Affiliation(s)
- Jack E. McCoy
- Department of Horticulture and Crop Science, Ohio State University, Columbus, OH, United States of America
| | - Leah K. McHale
- Department of Horticulture and Crop Science, Ohio State University, Columbus, OH, United States of America
| | - Michael Kantar
- Department of Tropical Plant and Soil Sciences, University of Hawai’i, Manoa, Honolulu, HI, United States of America
| | - Lev Jardón-Barbolla
- Centro de Investigaciones Interdisciplinarias en Ciencias y Humanidades, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Kristin L. Mercer
- Department of Horticulture and Crop Science, Ohio State University, Columbus, OH, United States of America
- * E-mail:
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25
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Polania JA, Salazar-Chavarría V, Gonzalez-Lemes I, Acosta-Maspons A, Chater CCC, Covarrubias AA. Contrasting Phaseolus Crop Water Use Patterns and Stomatal Dynamics in Response to Terminal Drought. FRONTIERS IN PLANT SCIENCE 2022; 13:894657. [PMID: 35712594 PMCID: PMC9194640 DOI: 10.3389/fpls.2022.894657] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Accepted: 05/05/2022] [Indexed: 06/15/2023]
Abstract
Terminal drought stress affects more than half of the areas planted with common bean (Phaseolus vulgaris), the main food legume globally, generating severe yield losses. Phenotyping water deficit responses and water use are central strategies to develop improved terminal drought resilience. The exploration and exploitation of genetic diversity in breeding programs are gaining importance, with a particular interest in related species with great adaptation to biotic and abiotic factors. This is the case with tepary beans (Phaseolus acutifolius), a bean that evolved and was domesticated in arid conditions and is considered well adapted to drought and heat stress. Under greenhouse conditions, using one genotype of tepary beans (resistant to drought) and two of common beans (one resistant and one susceptible to terminal drought), we evaluated phenotypic differences in traits such as water use efficiency (WUE), transpiration efficiency, rate of photosynthesis, photosynthetic efficiency, stomatal density, stomatal index, stomatal size, and the threshold for transpiration decline under well-watered and terminal drought conditions. Our results indicate two different water use strategies in drought-resistant genotypes: one observed in common bean aimed at conserving soil water by closing stomata early, inhibiting stomatal development, and limiting growth; and the other observed in tepary bean, where prolonged stomatal opening and higher carbon fixation, combined with no changes in stomata distribution, lead to higher biomass accumulation. Strategies that contribute to drought adaptation combined with other traits, such as greater mobilization of photoassimilates to the formation of reproductive structures, confer bean drought resistance and are useful targets in breeding programs.
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Affiliation(s)
- Jose A. Polania
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Violeta Salazar-Chavarría
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Ingrid Gonzalez-Lemes
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Alexis Acosta-Maspons
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Caspar C. C. Chater
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, United Kingdom
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | - Alejandra A. Covarrubias
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
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26
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Cowling SB, Treeintong P, Ferguson J, Soltani H, Swarup R, Mayes S, Murchie EH. Out of Africa: characterizing the natural variation in dynamic photosynthetic traits in a diverse population of African rice (Oryza glaberrima). JOURNAL OF EXPERIMENTAL BOTANY 2022. [PMID: 34657157 DOI: 10.5281/zenodo.5555931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
African rice (Oryza glaberrima) has adapted to challenging environments and is a promising source of genetic variation. We analysed dynamics of photosynthesis and morphology in a reference set of 155 O. glaberrima accessions. Plants were grown in an agronomy glasshouse to late tillering stage. Photosynthesis induction from darkness and the decrease in low light was measured by gas exchange and chlorophyll fluorescence along with root and shoot biomass, stomatal density, and leaf area. Steady-state and kinetic responses were modelled. We describe extensive natural variation in O. glaberrima for steady-state, induction, and reduction responses of photosynthesis that has value for gene discovery and crop improvement. Principal component analyses indicated key clusters of plant biomass, kinetics of photosynthesis (CO2 assimilation, A), and photoprotection induction and reduction (measured by non-photochemical quenching, NPQ), consistent with diverse adaptation. Accessions also clustered according to countries with differing water availability, stomatal conductance (gs), A, and NPQ, indicating that dynamic photosynthesis has adaptive value in O. glaberrima. Kinetics of NPQ, A, and gs showed high correlation with biomass and leaf area. We conclude that dynamic photosynthetic traits and NPQ are important within O. glaberrima, and we highlight NPQ kinetics and NPQ under low light.
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Affiliation(s)
- Sophie B Cowling
- Division of Plant and Crop Science, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, UK
| | - Pracha Treeintong
- Division of Plant and Crop Science, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, UK
| | - John Ferguson
- Division of Plant and Crop Science, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, UK
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | - Hamidreza Soltani
- Advanced Data Analysis Centre, University of Nottingham, Sutton Bonington Campus, Loughborough, UK
| | - Ranjan Swarup
- Division of Plant and Crop Science, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, UK
| | - Sean Mayes
- Division of Plant and Crop Science, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, UK
| | - Erik H Murchie
- Division of Plant and Crop Science, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, UK
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27
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Cowling SB, Treeintong P, Ferguson J, Soltani H, Swarup R, Mayes S, Murchie EH. Out of Africa: characterizing the natural variation in dynamic photosynthetic traits in a diverse population of African rice (Oryza glaberrima). JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:3283-3298. [PMID: 34657157 PMCID: PMC9126740 DOI: 10.1093/jxb/erab459] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 10/15/2021] [Indexed: 05/15/2023]
Abstract
African rice (Oryza glaberrima) has adapted to challenging environments and is a promising source of genetic variation. We analysed dynamics of photosynthesis and morphology in a reference set of 155 O. glaberrima accessions. Plants were grown in an agronomy glasshouse to late tillering stage. Photosynthesis induction from darkness and the decrease in low light was measured by gas exchange and chlorophyll fluorescence along with root and shoot biomass, stomatal density, and leaf area. Steady-state and kinetic responses were modelled. We describe extensive natural variation in O. glaberrima for steady-state, induction, and reduction responses of photosynthesis that has value for gene discovery and crop improvement. Principal component analyses indicated key clusters of plant biomass, kinetics of photosynthesis (CO2 assimilation, A), and photoprotection induction and reduction (measured by non-photochemical quenching, NPQ), consistent with diverse adaptation. Accessions also clustered according to countries with differing water availability, stomatal conductance (gs), A, and NPQ, indicating that dynamic photosynthesis has adaptive value in O. glaberrima. Kinetics of NPQ, A, and gs showed high correlation with biomass and leaf area. We conclude that dynamic photosynthetic traits and NPQ are important within O. glaberrima, and we highlight NPQ kinetics and NPQ under low light.
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Affiliation(s)
- Sophie B Cowling
- Division of Plant and Crop Science, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, UK
| | - Pracha Treeintong
- Division of Plant and Crop Science, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, UK
| | - John Ferguson
- Division of Plant and Crop Science, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, UK
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | - Hamidreza Soltani
- Advanced Data Analysis Centre, University of Nottingham, Sutton Bonington Campus, Loughborough, UK
| | - Ranjan Swarup
- Division of Plant and Crop Science, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, UK
| | - Sean Mayes
- Division of Plant and Crop Science, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, UK
| | - Erik H Murchie
- Division of Plant and Crop Science, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, UK
- Correspondence:
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28
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Faralli M, Bontempo L, Bianchedi PL, Moser C, Bertamini M, Lawson T, Camin F, Stefanini M, Varotto C. Natural variation in stomatal dynamics drives divergence in heat stress tolerance and contributes to seasonal intrinsic water-use efficiency in Vitis vinifera (subsp. sativa and sylvestris). JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:3238-3250. [PMID: 34929033 DOI: 10.1093/jxb/erab552] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 12/20/2021] [Indexed: 05/20/2023]
Abstract
Stomata control CO2 uptake for photosynthesis and water loss through transpiration, thus playing a key role in leaf thermoregulation, water-use efficiency (iWUE), and plant productivity. In this work, we investigated the relationship between several leaf traits and hypothesized that stomatal behavior to fast (i.e. minutes) environmental changes co-determines, along with steady-state traits, the physiological response of grapevine to the surrounding fluctuating environment over the growing season. No relationship between iWUE, heat stress tolerance, and stomatal traits was observed in field-grown grapevine, suggesting that other physiological mechanisms are involved in determining leaf evaporative cooling capacity and the seasonal ratio of CO2 uptake (A) to stomatal conductance (gs). Indeed, cultivars that in the field had an unexpected combination of high iWUE but low sensitivity to thermal stress displayed a quick stomatal closure to light, but a sluggish closure to increased vapor pressure deficit (VPD) levels. This strategy, aiming both at conserving water under a high to low light transition and in prioritizing evaporative cooling under a low to high VPD transition, was mainly observed in the cultivars Regina and Syrah. Moreover, cultivars with different known responses to soil moisture deficit or high air VPD (isohydric versus anisohydric) had opposite behavior under fluctuating environments, with the isohydric cultivar showing slow stomatal closure to reduced light intensity but quick temporal responses to VPD manipulation. We propose that stomatal behavior to fast environmental fluctuations can play a critical role in leaf thermoregulation and water conservation under natural field conditions in grapevine.
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Affiliation(s)
- Michele Faralli
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, via Mach 1, 38098 San Michele all'Adige (TN), Italy
- Center Agriculture Food Environment (C3A), University of Trento, Via Mach 1, 38098 San Michele all'Adige (TN), Italy
| | - Luana Bontempo
- Department of Food Quality and Nutrition, Research and Innovation Centre, Fondazione Edmund Mach, via Mach 1, 38098 San Michele all'Adige (TN), Italy
| | - Pier Luigi Bianchedi
- Technology Transfer Centre, Fondazione Edmund Mach, via Mach 1, 38098 San Michele all'Adige (TN), Italy
| | - Claudio Moser
- Genomics and Biology of Fruit Crops Department, Research and Innovation Centre, Fondazione Edmund Mach, via Mach 1, 38098 San Michele all'Adige (TN), Italy
| | - Massimo Bertamini
- Center Agriculture Food Environment (C3A), University of Trento, Via Mach 1, 38098 San Michele all'Adige (TN), Italy
- Research and Innovation Centre, Fondazione Edmund Mach, via Mach 1, 38098 San Michele all'Adige (TN), Italy
| | - Tracy Lawson
- School of Life Sciences, University of Essex, Colchester, UK
| | - Federica Camin
- Department of Food Quality and Nutrition, Research and Innovation Centre, Fondazione Edmund Mach, via Mach 1, 38098 San Michele all'Adige (TN), Italy
- Center Agriculture Food Environment (C3A), University of Trento, Via Mach 1, 38098 San Michele all'Adige (TN), Italy
- International Atomic Energy Agency, Vienna International Centre, PO Box 100, A-1400 Vienna, Austria
| | - Marco Stefanini
- Genomics and Biology of Fruit Crops Department, Research and Innovation Centre, Fondazione Edmund Mach, via Mach 1, 38098 San Michele all'Adige (TN), Italy
| | - Claudio Varotto
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, via Mach 1, 38098 San Michele all'Adige (TN), Italy
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Eljebbawi A, Savelli B, Libourel C, Estevez JM, Dunand C. Class III Peroxidases in Response to Multiple Abiotic Stresses in Arabidopsis thaliana Pyrenean Populations. Int J Mol Sci 2022; 23:ijms23073960. [PMID: 35409333 PMCID: PMC8999671 DOI: 10.3390/ijms23073960] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 03/29/2022] [Accepted: 03/29/2022] [Indexed: 02/04/2023] Open
Abstract
Class III peroxidases constitute a plant-specific multigene family, where 73 genes have been identified in Arabidopsis thaliana. These genes are members of the reactive oxygen species (ROS) regulatory network in the whole plant, but more importantly, at the root level. In response to abiotic stresses such as cold, heat, and salinity, their expression is significantly modified. To learn more about their transcriptional regulation, an integrative phenotypic, genomic, and transcriptomic study was executed on the roots of A. thaliana Pyrenean populations. Initially, the root phenotyping highlighted 3 Pyrenean populations to be tolerant to cold (Eaux), heat (Herr), and salt (Grip) stresses. Then, the RNA-seq analyses on these three populations, in addition to Col-0, displayed variations in CIII Prxs expression under stressful treatments and between different genotypes. Consequently, several CIII Prxs were particularly upregulated in the tolerant populations, suggesting novel and specific roles of these genes in plant tolerance against abiotic stresses.
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Affiliation(s)
- Ali Eljebbawi
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, INP, 31326 Toulouse, France; (A.E.); (B.S.); (C.L.)
| | - Bruno Savelli
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, INP, 31326 Toulouse, France; (A.E.); (B.S.); (C.L.)
| | - Cyril Libourel
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, INP, 31326 Toulouse, France; (A.E.); (B.S.); (C.L.)
| | - José Manuel Estevez
- Fundación Instituto Leloir and IIBBA-CONICET, Av. Patricias Argentinas 435, Buenos Aires C1405BWE, Argentina;
- Centro de Biotecnología Vegetal, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago CP 8370146, Chile
- ANID—Millennium Science Initiative Program—Millennium Institute for Integrative Biology (iBio) Millennium Nucleus for the Development of Super Adaptable Plants (MN-SAP), Santiago CP 8370146, Chile
| | - Christophe Dunand
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, INP, 31326 Toulouse, France; (A.E.); (B.S.); (C.L.)
- Correspondence:
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30
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Monroe JG, Cai H, Des Marais DL. Diversity in nonlinear responses to soil moisture shapes evolutionary constraints in Brachypodium. G3 (BETHESDA, MD.) 2021; 11:jkab334. [PMID: 34570202 PMCID: PMC8664479 DOI: 10.1093/g3journal/jkab334] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 09/15/2021] [Indexed: 12/03/2022]
Abstract
Water availability is perhaps the greatest environmental determinant of plant yield and fitness. However, our understanding of plant-water relations is limited because-like many studies of organism-environment interaction-it is primarily informed by experiments considering performance at two discrete levels-wet and dry-rather than as a continuously varying environmental gradient. Here, we used experimental and statistical methods based on function-valued traits to explore genetic variation in responses to a continuous soil moisture gradient in physiological and morphological traits among 10 genotypes across two species of the model grass genus Brachypodium. We find that most traits exhibit significant genetic variation and nonlinear responses to soil moisture variability. We also observe differences in the shape of these nonlinear responses between traits and genotypes. Emergent phenomena arise from this variation including changes in trait correlations and evolutionary constraints as a function of soil moisture. Our results point to the importance of considering diversity in nonlinear organism-environment relationships to understand plastic and evolutionary responses to changing climates.
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Affiliation(s)
- J Grey Monroe
- Department of Plant Sciences, University of California at Davis, Davis, CA 95616, USA
| | - Haoran Cai
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - David L Des Marais
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- The Arnold Arboretum of Harvard University, Boston, MA 02130, USA
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31
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Eng WH, Ho WS, Ling KH. In vitro induction and identification of polyploid Neolamarckia cadamba plants by colchicine treatment. PeerJ 2021; 9:e12399. [PMID: 34760387 PMCID: PMC8556713 DOI: 10.7717/peerj.12399] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 10/06/2021] [Indexed: 11/20/2022] Open
Abstract
Polyploidization has played a crucial role in plant breeding and crop improvement. However, studies on the polyploidization of tropical tree species are still very scarce in this region. This paper described the in vitro induction and identification of polyploid plants of Neolamarckia cadamba by colchicine treatment. N. cadamba belongs to the Rubiaceae family is a natural tetraploid plant with 44 chromosomes (2n = 4x = 44). Nodal segments were treated with colchicine (0.1%, 0.3% and 0.5%) for 24 h and 48 h before transferring to shoot regeneration medium. Flow cytometry (FCM) and chromosome count were employed to determine the ploidy level and chromosome number of the regenerants, respectively. Of 180 colchicine-treated nodal segments, 39, 14 and 22 were tetraploids, mixoploids and octoploids, respectively. The highest percentage of polyploidization (20% octoploids; 6.7% mixoploids) was observed after treated with 0.3% colchicine for 48 h. The DNA content of tetraploid (4C) and octoploid (8C) was 2.59 ± 0.09 pg and 5.35 ± 0.24 pg, respectively. Mixoploid plants are made up of mixed tetraploid and octoploid cells. Chromosome count confirmed that tetraploid cell has 44 chromosomes and colchicine-induced octoploid cell has 88 chromosomes. Both octoploids and mixoploids grew slower than tetraploids under in vitro conditions. Morphological characterizations showed that mixoploid and octoploid leaves had thicker leaf blades, thicker midrib, bigger stomata size, lower stomata density, higher SPAD value and smaller pith layer than tetraploids. This indicates that polyploidization has changed and resulted in traits that are predicted to increase photosynthetic capacity of N. cadamba. These novel polyploid plants could be valuable resources for advanced N. cadamba breeding programs to produce improved clones for planted forest development.
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Affiliation(s)
- Wee Hiang Eng
- Faculty of Resource Science and Technology, Universiti Malaysia Sarawak, Kota Samarahan, Sarawak, Malaysia
| | - Wei Seng Ho
- Faculty of Resource Science and Technology, Universiti Malaysia Sarawak, Kota Samarahan, Sarawak, Malaysia
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32
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Ferguson JN, Fernandes SB, Monier B, Miller ND, Allen D, Dmitrieva A, Schmuker P, Lozano R, Valluru R, Buckler ES, Gore MA, Brown PJ, Spalding EP, Leakey ADB. Machine learning-enabled phenotyping for GWAS and TWAS of WUE traits in 869 field-grown sorghum accessions. PLANT PHYSIOLOGY 2021; 187:1481-1500. [PMID: 34618065 PMCID: PMC9040483 DOI: 10.1093/plphys/kiab346] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 06/29/2021] [Indexed: 05/04/2023]
Abstract
Sorghum (Sorghum bicolor) is a model C4 crop made experimentally tractable by extensive genomic and genetic resources. Biomass sorghum is studied as a feedstock for biofuel and forage. Mechanistic modeling suggests that reducing stomatal conductance (gs) could improve sorghum intrinsic water use efficiency (iWUE) and biomass production. Phenotyping to discover genotype-to-phenotype associations remains a bottleneck in understanding the mechanistic basis for natural variation in gs and iWUE. This study addressed multiple methodological limitations. Optical tomography and a machine learning tool were combined to measure stomatal density (SD). This was combined with rapid measurements of leaf photosynthetic gas exchange and specific leaf area (SLA). These traits were the subject of genome-wide association study and transcriptome-wide association study across 869 field-grown biomass sorghum accessions. The ratio of intracellular to ambient CO2 was genetically correlated with SD, SLA, gs, and biomass production. Plasticity in SD and SLA was interrelated with each other and with productivity across wet and dry growing seasons. Moderate-to-high heritability of traits studied across the large mapping population validated associations between DNA sequence variation or RNA transcript abundance and trait variation. A total of 394 unique genes underpinning variation in WUE-related traits are described with higher confidence because they were identified in multiple independent tests. This list was enriched in genes whose Arabidopsis (Arabidopsis thaliana) putative orthologs have functions related to stomatal or leaf development and leaf gas exchange, as well as genes with nonsynonymous/missense variants. These advances in methodology and knowledge will facilitate improving C4 crop WUE.
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Affiliation(s)
- John N Ferguson
- Institute for Genomic Biology, University of Illinois at
Urbana-Champaign, Urbana, Illinois 61901, USA
| | - Samuel B Fernandes
- Institute for Genomic Biology, University of Illinois at
Urbana-Champaign, Urbana, Illinois 61901, USA
| | - Brandon Monier
- Institute for Genomic Diversity, Cornell University, Ithaca, New
York 14853, USA
| | - Nathan D Miller
- Department of Botany, University of Wisconsin, Madison, Wisconsin
53706, USA
| | - Dylan Allen
- Institute for Genomic Biology, University of Illinois at
Urbana-Champaign, Urbana, Illinois 61901, USA
| | - Anna Dmitrieva
- Institute for Genomic Biology, University of Illinois at
Urbana-Champaign, Urbana, Illinois 61901, USA
| | - Peter Schmuker
- Institute for Genomic Biology, University of Illinois at
Urbana-Champaign, Urbana, Illinois 61901, USA
| | - Roberto Lozano
- Plant Breeding and Genetics Section, School of Integrative Plant Science,
Cornell University, Ithaca, New York 14853, USA
| | - Ravi Valluru
- Institute for Genomic Diversity, Cornell University, Ithaca, New
York 14853, USA
- Present address: Lincoln Institute for Agri-Food Technology,
University of Lincoln, Lincoln LN2 2LG, UK
| | - Edward S Buckler
- Institute for Genomic Diversity, Cornell University, Ithaca, New
York 14853, USA
- Plant Breeding and Genetics Section, School of Integrative Plant Science,
Cornell University, Ithaca, New York 14853, USA
| | - Michael A Gore
- Plant Breeding and Genetics Section, School of Integrative Plant Science,
Cornell University, Ithaca, New York 14853, USA
| | - Patrick J Brown
- Institute for Genomic Biology, University of Illinois at
Urbana-Champaign, Urbana, Illinois 61901, USA
- Present address: Section of Agricultural Plant Biology,
Department of Plant Sciences, University of California Davis, California 95616,
USA
| | - Edgar P Spalding
- Department of Botany, University of Wisconsin, Madison, Wisconsin
53706, USA
| | - Andrew D B Leakey
- Institute for Genomic Biology, University of Illinois at
Urbana-Champaign, Urbana, Illinois 61901, USA
- Department of Crop Sciences, University of Illinois at
Urbana-Champaign, Urbana, Illinois 61901, USA
- Department of Plant Biology, University of Illinois at
Urbana-Champaign, Urbana, Illinois 61901, USA
- Author for communication: ,
Present address: Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA,
UK
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33
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Xie J, Fernandes SB, Mayfield-Jones D, Erice G, Choi M, E Lipka A, Leakey ADB. Optical topometry and machine learning to rapidly phenotype stomatal patterning traits for maize QTL mapping. PLANT PHYSIOLOGY 2021; 187:1462-1480. [PMID: 34618057 PMCID: PMC8566313 DOI: 10.1093/plphys/kiab299] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 05/26/2021] [Indexed: 05/03/2023]
Abstract
Stomata are adjustable pores on leaf surfaces that regulate the tradeoff of CO2 uptake with water vapor loss, thus having critical roles in controlling photosynthetic carbon gain and plant water use. The lack of easy, rapid methods for phenotyping epidermal cell traits have limited discoveries about the genetic basis of stomatal patterning. A high-throughput epidermal cell phenotyping pipeline is presented here and used for quantitative trait loci (QTL) mapping in field-grown maize (Zea mays). The locations and sizes of stomatal complexes and pavement cells on images acquired by an optical topometer from mature leaves were automatically determined. Computer estimated stomatal complex density (SCD; R2 = 0.97) and stomatal complex area (SCA; R2 = 0.71) were strongly correlated with human measurements. Leaf gas exchange traits were genetically correlated with the dimensions and proportions of stomatal complexes (rg = 0.39-0.71) but did not correlate with SCD. Heritability of epidermal traits was moderate to high (h2 = 0.42-0.82) across two field seasons. Thirty-six QTL were consistently identified for a given trait in both years. Twenty-four clusters of overlapping QTL for multiple traits were identified, with univariate versus multivariate single marker analysis providing evidence consistent with pleiotropy in multiple cases. Putative orthologs of genes known to regulate stomatal patterning in Arabidopsis (Arabidopsis thaliana) were located within some, but not all, of these regions. This study demonstrates how discovery of the genetic basis for stomatal patterning can be accelerated in maize, a C4 model species where these processes are poorly understood.
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Affiliation(s)
- Jiayang Xie
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Samuel B Fernandes
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Center for Digital Agriculture, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Dustin Mayfield-Jones
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Center for Digital Agriculture, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Gorka Erice
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Min Choi
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Alexander E Lipka
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Center for Digital Agriculture, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Andrew D B Leakey
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Center for Digital Agriculture, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Author for communication: , cor2">Present address: Agrotecnologías Naturales S.L., 43762 Tarragona, Spain
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34
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Ferguson JN, Fernandes SB, Monier B, Miller ND, Allen D, Dmitrieva A, Schmuker P, Lozano R, Valluru R, Buckler ES, Gore MA, Brown PJ, Spalding EP, Leakey ADB. Machine learning-enabled phenotyping for GWAS and TWAS of WUE traits in 869 field-grown sorghum accessions. PLANT PHYSIOLOGY 2021; 187:1481-1500. [PMID: 34618065 DOI: 10.1093/plphys/kiab34] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 06/29/2021] [Indexed: 05/27/2023]
Abstract
Sorghum (Sorghum bicolor) is a model C4 crop made experimentally tractable by extensive genomic and genetic resources. Biomass sorghum is studied as a feedstock for biofuel and forage. Mechanistic modeling suggests that reducing stomatal conductance (gs) could improve sorghum intrinsic water use efficiency (iWUE) and biomass production. Phenotyping to discover genotype-to-phenotype associations remains a bottleneck in understanding the mechanistic basis for natural variation in gs and iWUE. This study addressed multiple methodological limitations. Optical tomography and a machine learning tool were combined to measure stomatal density (SD). This was combined with rapid measurements of leaf photosynthetic gas exchange and specific leaf area (SLA). These traits were the subject of genome-wide association study and transcriptome-wide association study across 869 field-grown biomass sorghum accessions. The ratio of intracellular to ambient CO2 was genetically correlated with SD, SLA, gs, and biomass production. Plasticity in SD and SLA was interrelated with each other and with productivity across wet and dry growing seasons. Moderate-to-high heritability of traits studied across the large mapping population validated associations between DNA sequence variation or RNA transcript abundance and trait variation. A total of 394 unique genes underpinning variation in WUE-related traits are described with higher confidence because they were identified in multiple independent tests. This list was enriched in genes whose Arabidopsis (Arabidopsis thaliana) putative orthologs have functions related to stomatal or leaf development and leaf gas exchange, as well as genes with nonsynonymous/missense variants. These advances in methodology and knowledge will facilitate improving C4 crop WUE.
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Affiliation(s)
- John N Ferguson
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61901, USA
| | - Samuel B Fernandes
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61901, USA
| | - Brandon Monier
- Institute for Genomic Diversity, Cornell University, Ithaca, New York 14853, USA
| | - Nathan D Miller
- Department of Botany, University of Wisconsin, Madison, Wisconsin 53706, USA
| | - Dylan Allen
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61901, USA
| | - Anna Dmitrieva
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61901, USA
| | - Peter Schmuker
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61901, USA
| | - Roberto Lozano
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853, USA
| | - Ravi Valluru
- Institute for Genomic Diversity, Cornell University, Ithaca, New York 14853, USA
| | - Edward S Buckler
- Institute for Genomic Diversity, Cornell University, Ithaca, New York 14853, USA
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853, USA
| | - Michael A Gore
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853, USA
| | - Patrick J Brown
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61901, USA
| | - Edgar P Spalding
- Department of Botany, University of Wisconsin, Madison, Wisconsin 53706, USA
| | - Andrew D B Leakey
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61901, USA
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61901, USA
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61901, USA
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35
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Depuydt T, Vandepoele K. Multi-omics network-based functional annotation of unknown Arabidopsis genes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 108:1193-1212. [PMID: 34562334 DOI: 10.1111/tpj.15507] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 09/20/2021] [Indexed: 06/13/2023]
Abstract
Unraveling gene function is pivotal to understanding the signaling cascades that control plant development and stress responses. As experimental profiling is costly and labor intensive, there is a clear need for high-confidence computational annotation. In contrast to detailed gene-specific functional information, transcriptomics data are widely available for both model and crop species. Here, we describe a novel automated function prediction method, which leverages complementary information from multiple expression datasets by analyzing study-specific gene co-expression networks. First, we benchmarked the prediction performance on recently characterized Arabidopsis thaliana genes, and showed that our method outperforms state-of-the-art expression-based approaches. Next, we predicted biological process annotations for known (n = 15 790) and unknown (n = 11 865) genes in A. thaliana and validated our predictions using experimental protein-DNA and protein-protein interaction data (covering >220 000 interactions in total), obtaining a set of high-confidence functional annotations. Our method assigned at least one validated annotation to 5054 (42.6%) unknown genes, and at least one novel validated function to 3408 (53.0%) genes with computational annotations only. These omics-supported functional annotations shed light on a variety of developmental processes and molecular responses, such as flower and root development, defense responses to fungi and bacteria, and phytohormone signaling, and help fill the information gap on biological process annotations in Arabidopsis. An in-depth analysis of two context-specific networks, modeling seed development and response to water deprivation, shows how previously uncharacterized genes function within the respective networks. Moreover, our automated function prediction approach can be applied in future studies to facilitate gene discovery for crop improvement.
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Affiliation(s)
- Thomas Depuydt
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, Vlaams Instituut voor Biotechnologie, Ghent, Belgium
| | - Klaas Vandepoele
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, Vlaams Instituut voor Biotechnologie, Ghent, Belgium
- Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium
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36
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Mateus NS, Florentino AL, Oliveira JB, Santos EF, Gaziola SA, Rossi ML, Linhares FS, Bendassolli JA, Azevedo RA, Lavres J. Leaf 13C and 15N composition shedding light on easing drought stress through partial K substitution by Na in eucalyptus species. Sci Rep 2021; 11:20158. [PMID: 34635753 PMCID: PMC8505639 DOI: 10.1038/s41598-021-99710-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 09/27/2021] [Indexed: 11/16/2022] Open
Abstract
This work aimed to investigate the partial K-replacement by Na supply to alleviate drought-induced stress in Eucalyptus species. Plant growth, leaf gas exchange parameters, water relations, oxidative stress (H2O2 and MDA content), chlorophyll concentration, carbon (C) and nitrogen (N) isotopic leaf composition (δ13C and δ15N) were analyzed. Drought tolerant E. urophylla and E. camaldulensis showed positive responses to the partial K substitution by Na, with similar dry mass yields, stomatal density and total stomatal pore area relative to the well K-supplied plants under both water conditions, suggesting that 50% of the K requirements is pressing for physiological functions that is poorly substituted by Na. Furthermore, E. urophylla and E. camaldulensis up-regulated leaf gas exchanges, leading to enhanced long-term water use efficiency (WUEL). Moreover, the partial K substitution by Na had no effects on plants H2O2, MDA, δ13C and δ15N, confirming that Na, to a certain extent, can effectively replace K in plants metabolism. Otherwise, the drought-sensitive E. saligna species was negatively affected by partial K replacement by Na, decreasing plants dry mass, even with up-regulated leaf gas exchange parameters. The exclusive Na-supplied plants showed K-deficient symptoms and lower growth, WUEL, and δ13C, besides higher Na accumulation, δ15N, H2O2 and MDA content.
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Affiliation(s)
- Nikolas Souza Mateus
- Center for Nuclear Energy in Agriculture, University of São Paulo, Avenida Centenario, 303. CP 96, Piracicaba, CEP, 13416-000, Brazil.
| | | | - Jessica Bezerra Oliveira
- Center for Nuclear Energy in Agriculture, University of São Paulo, Avenida Centenario, 303. CP 96, Piracicaba, CEP, 13416-000, Brazil
| | - Elcio Ferreira Santos
- Center for Nuclear Energy in Agriculture, University of São Paulo, Avenida Centenario, 303. CP 96, Piracicaba, CEP, 13416-000, Brazil
| | | | - Monica Lanzoni Rossi
- Center for Nuclear Energy in Agriculture, University of São Paulo, Avenida Centenario, 303. CP 96, Piracicaba, CEP, 13416-000, Brazil
| | - Francisco Scaglia Linhares
- Center for Nuclear Energy in Agriculture, University of São Paulo, Avenida Centenario, 303. CP 96, Piracicaba, CEP, 13416-000, Brazil
| | - José Albertino Bendassolli
- Center for Nuclear Energy in Agriculture, University of São Paulo, Avenida Centenario, 303. CP 96, Piracicaba, CEP, 13416-000, Brazil
| | - Ricardo Antunes Azevedo
- College of Agriculture Luiz de Queiroz, University of São Paulo, Piracicaba, 13418-900, Brazil
| | - José Lavres
- Center for Nuclear Energy in Agriculture, University of São Paulo, Avenida Centenario, 303. CP 96, Piracicaba, CEP, 13416-000, Brazil.
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Lee J, Murren CJ. Macroscopic variation in Arabidopsis mutants despite stomatal uniformity across soil nutrient environments. Genetica 2021; 149:253-266. [PMID: 34606015 DOI: 10.1007/s10709-021-00133-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 09/14/2021] [Indexed: 10/20/2022]
Abstract
Stomata are essential pores flanked by guard cells that control gas exchange in plants. We can utilize stomatal size and density measurements as a proxy for a plant's capacity for gas exchange. While stomatal responses to stressful environments are well studied; data are lacking in the responses across mutant genotypes of the same species in these trait and treatment interactions or genetic variation in phenotypic plasticity. We evaluated the effects of soil nutrient variation on macroscopic and stomatal traits of Arabidopsis thaliana T-DNA insertion mutants for which prior performance in a single benign growing condition were available. Nutrient-induced stress significantly impacted traits including plant biomass, height, fruit number, and leaf number which we denote as macroscopic traits. We found evidence that genotype by environment effects exist for macroscopic traits, yet total stomatal area variation, or "microscopic variation" across environments was modest. Divergence from the wildtype line varied by mutant background and these responses were variable among traits. These findings suggest that Arabidopsis employs a strategy of physiological compensation, sacrificing morphological traits to maintain stomatal production.
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Affiliation(s)
- Jamison Lee
- Department of Biology, College of Charleston, 66 George Street, Charleston, SC, 29424, USA
| | - Courtney J Murren
- Department of Biology, College of Charleston, 66 George Street, Charleston, SC, 29424, USA.
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38
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Das A, Prakash A, Dedon N, Doty A, Siddiqui M, Preston JC. Variation in climatic tolerance, but not stomatal traits, partially explains Pooideae grass species distributions. ANNALS OF BOTANY 2021; 128:83-95. [PMID: 33772589 PMCID: PMC8318108 DOI: 10.1093/aob/mcab046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Accepted: 03/24/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND AND AIMS Grasses in subfamily Pooideae live in some of the world's harshest terrestrial environments, from frigid boreal zones to the arid windswept steppe. It is hypothesized that the climate distribution of species within this group is driven by differences in climatic tolerance, and that tolerance can be partially explained by variation in stomatal traits. METHODS We determined the aridity index (AI) and minimum temperature of the coldest month (MTCM) for 22 diverse Pooideae accessions and one outgroup, and used comparative methods to assess predicted relationships for climate traits versus fitness traits, stomatal diffusive conductance to water (gw) and speed of stomatal closure following drought and/or cold. KEY RESULTS Results demonstrate that AI and MTCM predict variation in survival/regreening following drought/cold, and gw under drought/cold is positively correlated with δ 13C-measured water use efficiency (WUE). However, the relationship between climate traits and fitness under drought/cold was not explained by gw or speed of stomatal closure. CONCLUSIONS These findings suggest that Pooideae distributions are at least partly determined by tolerance to aridity and above-freezing cold, but that variation in tolerance is not uniformly explained by variation in stomatal traits.
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Affiliation(s)
- Aayudh Das
- The University of Vermont, Department of Plant Biology, Burlington, VT 05405, USA
| | - Anoob Prakash
- The University of Vermont, Department of Plant Biology, Burlington, VT 05405, USA
| | - Natalie Dedon
- The University of Vermont, Department of Plant Biology, Burlington, VT 05405, USA
| | - Alex Doty
- The University of Vermont, Department of Plant Biology, Burlington, VT 05405, USA
| | - Muniba Siddiqui
- The University of Vermont, Department of Plant Biology, Burlington, VT 05405, USA
| | - Jill C Preston
- The University of Vermont, Department of Plant Biology, Burlington, VT 05405, USA
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Bheemanahalli R, Wang C, Bashir E, Chiluwal A, Pokharel M, Perumal R, Moghimi N, Ostmeyer T, Caragea D, Jagadish SK. Classical phenotyping and deep learning concur on genetic control of stomatal density and area in sorghum. PLANT PHYSIOLOGY 2021; 186:1562-1579. [PMID: 33856488 PMCID: PMC8260133 DOI: 10.1093/plphys/kiab174] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 03/28/2021] [Indexed: 05/18/2023]
Abstract
Stomatal density (SD) and stomatal complex area (SCA) are important traits that regulate gas exchange and abiotic stress response in plants. Despite sorghum (Sorghum bicolor) adaptation to arid conditions, the genetic potential of stomata-related traits remains unexplored due to challenges in available phenotyping methods. Hence, identifying loci that control stomatal traits is fundamental to designing strategies to breed sorghum with optimized stomatal regulation. We implemented both classical and deep learning methods to characterize genetic diversity in 311 grain sorghum accessions for stomatal traits at two different field environments. Nearly 12,000 images collected from abaxial (Ab) and adaxial (Ad) leaf surfaces revealed substantial variation in stomatal traits. Our study demonstrated significant accuracy between manual and deep learning methods in predicting SD and SCA. In sorghum, SD was 32%-39% greater on the Ab versus the Ad surface, while SCA on the Ab surface was 2%-5% smaller than on the Ad surface. Genome-Wide Association Study identified 71 genetic loci (38 were environment-specific) with significant genotype to phenotype associations for stomatal traits. Putative causal genes underlying the phenotypic variation were identified. Accessions with similar SCA but carrying contrasting haplotypes for SD were tested for stomatal conductance and carbon assimilation under field conditions. Our findings provide a foundation for further studies on the genetic and molecular mechanisms controlling stomata patterning and regulation in sorghum. An integrated physiological, deep learning, and genomic approach allowed us to unravel the genetic control of natural variation in stomata traits in sorghum, which can be applied to other plants.
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Affiliation(s)
- Raju Bheemanahalli
- Department of Agronomy, Kansas State University, Manhattan, Kansas 66506, USA
| | - Chaoxin Wang
- Department of Computer Science, Kansas State University, Manhattan, Kansas 66506, USA
| | - Elfadil Bashir
- Agricultural Research Center, Kansas State University, Hays, Kansas 67601, USA
| | - Anuj Chiluwal
- Department of Agronomy, Kansas State University, Manhattan, Kansas 66506, USA
| | - Meghnath Pokharel
- Department of Agronomy, Kansas State University, Manhattan, Kansas 66506, USA
| | - Ramasamy Perumal
- Agricultural Research Center, Kansas State University, Hays, Kansas 67601, USA
| | - Naghmeh Moghimi
- Department of Agronomy, Kansas State University, Manhattan, Kansas 66506, USA
| | - Troy Ostmeyer
- Department of Agronomy, Kansas State University, Manhattan, Kansas 66506, USA
| | - Doina Caragea
- Department of Computer Science, Kansas State University, Manhattan, Kansas 66506, USA
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40
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Prakash PT, Banan D, Paul RE, Feldman MJ, Xie D, Freyfogle L, Baxter I, Leakey ADB. Correlation and co-localization of QTL for stomatal density, canopy temperature, and productivity with and without drought stress in Setaria. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:5024-5037. [PMID: 33893796 PMCID: PMC8219040 DOI: 10.1093/jxb/erab166] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 04/23/2021] [Indexed: 05/04/2023]
Abstract
Mechanistic modeling indicates that stomatal conductance could be reduced to improve water use efficiency (WUE) in C4 crops. Genetic variation in stomatal density and canopy temperature was evaluated in the model C4 genus, Setaria. Recombinant inbred lines (RILs) derived from a Setaria italica×Setaria viridis cross were grown with ample or limiting water supply under field conditions in Illinois. An optical profilometer was used to rapidly assess stomatal patterning, and canopy temperature was measured using infrared imaging. Stomatal density and canopy temperature were positively correlated but both were negatively correlated with total above-ground biomass. These trait relationships suggest a likely interaction between stomatal density and the other drivers of water use such as stomatal size and aperture. Multiple quantitative trait loci (QTL) were identified for stomatal density and canopy temperature, including co-located QTL on chromosomes 5 and 9. The direction of the additive effect of these QTL on chromosome 5 and 9 was in accordance with the positive phenotypic relationship between these two traits. This, along with prior experiments, suggests a common genetic architecture between stomatal patterning and WUE in controlled environments with canopy transpiration and productivity in the field, while highlighting the potential of Setaria as a model to understand the physiology and genetics of WUE in C4 species.
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Affiliation(s)
- Parthiban Thathapalli Prakash
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- International Rice Research Institute, Los Baños, Philippines
| | - Darshi Banan
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Rachel E Paul
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | | | - Dan Xie
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, USA
| | - Luke Freyfogle
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Ivan Baxter
- Donald Danforth Plant Science Center, St Louis, MO, USA
| | - Andrew D B Leakey
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
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Wieters B, Steige KA, He F, Koch EM, Ramos-Onsins SE, Gu H, Guo YL, Sunyaev S, de Meaux J. Polygenic adaptation of rosette growth in Arabidopsis thaliana. PLoS Genet 2021; 17:e1008748. [PMID: 33493157 PMCID: PMC7861555 DOI: 10.1371/journal.pgen.1008748] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 02/04/2021] [Accepted: 12/10/2020] [Indexed: 12/16/2022] Open
Abstract
The rate at which plants grow is a major functional trait in plant ecology. However, little is known about its evolution in natural populations. Here, we investigate evolutionary and environmental factors shaping variation in the growth rate of Arabidopsis thaliana. We used plant diameter as a proxy to monitor plant growth over time in environments that mimicked latitudinal differences in the intensity of natural light radiation, across a set of 278 genotypes sampled within four broad regions, including an outgroup set of genotypes from China. A field experiment conducted under natural conditions confirmed the ecological relevance of the observed variation. All genotypes markedly expanded their rosette diameter when the light supply was decreased, demonstrating that environmental plasticity is a predominant source of variation to adapt plant size to prevailing light conditions. Yet, we detected significant levels of genetic variation both in growth rate and growth plasticity. Genome-wide association studies revealed that only 2 single nucleotide polymorphisms associate with genetic variation for growth above Bonferroni confidence levels. However, marginally associated variants were significantly enriched among genes with an annotated role in growth and stress reactions. Polygenic scores computed from marginally associated variants confirmed the polygenic basis of growth variation. For both light regimes, phenotypic divergence between the most distantly related population (China) and the various regions in Europe is smaller than the variation observed within Europe, indicating that the evolution of growth rate is likely to be constrained by stabilizing selection. We observed that Spanish genotypes, however, reach a significantly larger size than Northern European genotypes. Tests of adaptive divergence and analysis of the individual burden of deleterious mutations reveal that adaptive processes have played a more important role in shaping regional differences in rosette growth than maladaptive evolution. The rate at which plants grow is a major functional trait in plant ecology. However, little is known about its genetic variation in natural populations. Here, we investigate genetic and environmental factors shaping variation in the growth rate of Arabidopsis thaliana and ask whether genetic variation in plant growth contributes to adaptation to local environmental conditions. We grew plants under two light regimes that mimic latitudinal differences in the intensity of natural light radiation, and measured plant diameter as it grew over time. When the light supply was decreased, plant diameter grew more slowly but reached a markedly larger final size, confirming that plants can adjust their growth to prevailing light conditions. Yet, we also detected significant levels of genetic variation both in growth rate and in how the growth dynamics is adjusted to the light conditions. We show that this variation is encoded by many loci of small effect that are hard to locate in the genome but overall significantly enriched among genes associated with growth and stress reactions. We further observe that Spanish genotypes tended to reach, on average, a significantly larger rosette size than Northern European genotypes. Tests of adaptive divergence indicate that these differences may reflect adaptation to local environmental conditions.
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Affiliation(s)
| | - Kim A. Steige
- Institute of Botany, University of Cologne, Cologne, Germany
| | - Fei He
- Institute of Botany, University of Cologne, Cologne, Germany
| | - Evan M. Koch
- Genetics Division, Brigham & Women's Hospital and Harvard Medical School, Boston MA, United States of America
- Department of Biomedical Informatics, Harvard Medical School, Boston MA, United States of America
| | | | - Hongya Gu
- State Key Laboratory for Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, China
| | - Ya-Long Guo
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Shamil Sunyaev
- Genetics Division, Brigham & Women's Hospital and Harvard Medical School, Boston MA, United States of America
- Department of Biomedical Informatics, Harvard Medical School, Boston MA, United States of America
| | - Juliette de Meaux
- Institute of Botany, University of Cologne, Cologne, Germany
- * E-mail:
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Metz J, Lampei C, Bäumler L, Bocherens H, Dittberner H, Henneberg L, de Meaux J, Tielbörger K. Rapid adaptive evolution to drought in a subset of plant traits in a large-scale climate change experiment. Ecol Lett 2020; 23:1643-1653. [PMID: 32851791 DOI: 10.1111/ele.13596] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 07/20/2020] [Indexed: 12/17/2022]
Abstract
Rapid evolution of traits and of plasticity may enable adaptation to climate change, yet solid experimental evidence under natural conditions is scarce. Here, we imposed rainfall manipulations (+30%, control, -30%) for 10 years on entire natural plant communities in two Eastern Mediterranean sites. Additional sites along a natural rainfall gradient and selection analyses in a greenhouse assessed whether potential responses were adaptive. In both sites, our annual target species Biscutella didyma consistently evolved earlier phenology and higher reproductive allocation under drought. Multiple arguments suggest that this response was adaptive: it aligned with theory, corresponding trait shifts along the natural rainfall gradient, and selection analyses under differential watering in the greenhouse. However, another seven candidate traits did not evolve, and there was little support for evolution of plasticity. Our results provide compelling evidence for rapid adaptive evolution under climate change. Yet, several non-evolving traits may indicate potential constraints to full adaptation.
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Affiliation(s)
- Johannes Metz
- Plant Ecology & Nature Conservation, Institute of Biology & Chemistry, University of Hildesheim, Hildesheim, Germany.,Plant Ecology Group, Institute of Evolution and Ecology, University of Tübingen, Tübingen, Germany
| | - Christian Lampei
- Biodiversity and Ecosystem Research, Institute of Landscape Ecology, University of Münster, Münster, Germany
| | - Laura Bäumler
- Plant Ecology Group, Institute of Evolution and Ecology, University of Tübingen, Tübingen, Germany
| | - Hervé Bocherens
- Senckenberg Centre for Human Evolution and Palaeoenvironment, and Department of Geosciences, Biogeology, University of Tübingen, Tübingen, Germany
| | - Hannes Dittberner
- Plant Molecular Ecology, Institute of Botany, University of Cologne, Cologne, Germany
| | - Lorenz Henneberg
- Plant Ecology Group, Institute of Evolution and Ecology, University of Tübingen, Tübingen, Germany
| | - Juliette de Meaux
- Plant Molecular Ecology, Institute of Botany, University of Cologne, Cologne, Germany
| | - Katja Tielbörger
- Plant Ecology Group, Institute of Evolution and Ecology, University of Tübingen, Tübingen, Germany
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43
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Lorts CM, Lasky JR. Competition × drought interactions change phenotypic plasticity and the direction of selection on Arabidopsis traits. THE NEW PHYTOLOGIST 2020; 227:1060-1072. [PMID: 32267968 DOI: 10.1111/nph.16593] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 03/28/2020] [Indexed: 06/11/2023]
Abstract
Populations often exhibit genetic diversity in traits involved in responses to abiotic stressors, but what maintains this diversity is unclear. Arabidopsis thaliana exhibits high within-population variation in drought response. One hypothesis is that competition, varying at small scales, promotes diversity in resource use strategies. However, little is known about natural variation in competition effects on Arabidopsis physiology. We imposed drought and competition treatments on diverse genotypes. We measured resource economics traits, physiology, and fitness to characterize plasticity and selection in response to treatments. Plastic responses to competition differed depending on moisture availability. We observed genotype-drought-competition interactions for relative fitness: competition had little effect on relative fitness under well-watered conditions, whereas competition caused rank changes in fitness under drought. Early flowering was always selected. Higher δ13 C was selected only in the harshest treatment (drought and competition). Competitive context significantly changed the direction of selection on aboveground biomass and inflorescence height in well-watered environments. Our results highlight how local biotic conditions modify abiotic selection, in some cases promoting diversity in abiotic stress response. The ability of populations to adapt to environmental change may thus depend on small-scale biotic heterogeneity.
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Affiliation(s)
- Claire M Lorts
- Department of Biology, Pennsylvania State University, University Park, PA, 16802, USA
| | - Jesse R Lasky
- Department of Biology, Pennsylvania State University, University Park, PA, 16802, USA
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44
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Li LF, Cushman SA, He YX, Li Y. Genome sequencing and population genomics modeling provide insights into the local adaptation of weeping forsythia. HORTICULTURE RESEARCH 2020; 7:130. [PMID: 32821413 PMCID: PMC7395120 DOI: 10.1038/s41438-020-00352-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 05/24/2020] [Accepted: 05/24/2020] [Indexed: 05/06/2023]
Abstract
Understanding the genetic basis underlying the local adaptation of nonmodel species is a fundamental goal in evolutionary biology. In this study, we explored the genetic mechanisms of the local adaptation of Forsythia suspensa using genome sequence and population genomics data obtained from specific-locus amplified fragment sequencing. We assembled a high-quality reference genome of weeping forsythia (Scaffold N50 = 7.3 Mb) using ultralong Nanopore reads. Then, genome-wide comparative analysis was performed for 15 natural populations of weeping forsythia across its current distribution range. Our results revealed that candidate genes associated with local adaptation are functionally correlated with solar radiation, temperature and water variables across heterogeneous environmental scenarios. In particular, solar radiation during the period of fruit development and seed drying after ripening, cold, and drought significantly contributed to the adaptive differentiation of F. suspensa. Natural selection exerted by environmental factors contributed substantially to the population genetic structure of F. suspensa. Our results supported the hypothesis that adaptive differentiation should be highly pronounced in the genes involved in signal crosstalk between different environmental variables. Our population genomics study of F. suspensa provides insights into the fundamental genetic mechanisms of the local adaptation of plant species to climatic gradients.
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Affiliation(s)
- Lin-Feng Li
- Innovation Platform of Molecular Biology, College of Forestry, Henan Agricultural University, Zhengzhou, China
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, 200438 China
| | - Samuel A. Cushman
- U.S. Forest Service, Rocky Mountain Research Station, 2500 S. Pine Knoll Dr., Flagstaff, Arizona USA
| | - Yan-Xia He
- School of Life Sciences, Henan University, Kaifeng, China
| | - Yong Li
- Innovation Platform of Molecular Biology, College of Forestry, Henan Agricultural University, Zhengzhou, China
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Magaña Ugarte R, Escudero A, Sánchez Mata D, Gavilán RG. Changes in Foliar Functional Traits of S. pyrenaicus subsp. carpetanus under the Ongoing Climate Change: A Retrospective Survey. PLANTS (BASEL, SWITZERLAND) 2020; 9:E395. [PMID: 32210120 PMCID: PMC7154879 DOI: 10.3390/plants9030395] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 03/16/2020] [Accepted: 03/18/2020] [Indexed: 05/27/2023]
Abstract
The sensitivity of stomatal behavior and patterning (i.e., distribution, density, size) to environmental stimuli, renders them crucial for defining the physiological performance of leaves. Thus, assessing long-term modifications in stomatal traits in conserved specimens arises as a valuable eco-physiological approach to predict how the rising trend of warmer, drier summers could affect plant fitness; particularly in mountain areas already experiencing climate aggravation and lacking the related monitoring schemes like Mediterranean high-mountains. Variations in foliar and stomatal traits were studied in conserved specimens of Senecio pyrenaicus subsp. carpetanus from Sierra de Guadarrama over the past 71 years. Our findings revealed decreasing trends in leaf width, stomatal size, and increasing tendency in stomatal density, all correlated with the recent 30-year climate exacerbation in these mountains. This evidenced a positive selection favoring traits that allow safeguarding plant performance under drier, hotter weather conditions. The significant relation between stomatal traits and climatic variables upholds the role of stomatal patterning in sensing environmental cues in this species, feasibly optimizing physiological responses involved in the growth-water loss trade-off. The transition to smaller, densely packed stomata observed in recent decades could indicate local-adaptive plasticity in this species, enhancing stomatal response, as coarser environmental conditions take place in Sierra de Guadarrama.
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Affiliation(s)
- Rosina Magaña Ugarte
- Unidad de Botánica, Departamento de Farmacología, Farmacognosia y Botánica, Facultad de Farmacia, Universidad Complutense de Madrid, 28040 Madrid, Spain; (D.S.M.); (R.G.G.)
| | - Adrián Escudero
- Departamento de Biología y Geología, Física y Química Inorgánica, Universidad Rey Juan Carlos, 28933 Móstoles, Madrid, Spain;
| | - Daniel Sánchez Mata
- Unidad de Botánica, Departamento de Farmacología, Farmacognosia y Botánica, Facultad de Farmacia, Universidad Complutense de Madrid, 28040 Madrid, Spain; (D.S.M.); (R.G.G.)
| | - Rosario G. Gavilán
- Unidad de Botánica, Departamento de Farmacología, Farmacognosia y Botánica, Facultad de Farmacia, Universidad Complutense de Madrid, 28040 Madrid, Spain; (D.S.M.); (R.G.G.)
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Togninalli M, Seren Ü, Freudenthal JA, Monroe JG, Meng D, Nordborg M, Weigel D, Borgwardt K, Korte A, Grimm DG. AraPheno and the AraGWAS Catalog 2020: a major database update including RNA-Seq and knockout mutation data for Arabidopsis thaliana. Nucleic Acids Res 2020; 48:D1063-D1068. [PMID: 31642487 PMCID: PMC7145550 DOI: 10.1093/nar/gkz925] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 09/26/2019] [Accepted: 10/08/2019] [Indexed: 12/23/2022] Open
Abstract
Genome-wide association studies (GWAS) are integral for studying genotype-phenotype relationships and gaining a deeper understanding of the genetic architecture underlying trait variation. A plethora of genetic associations between distinct loci and various traits have been successfully discovered and published for the model plant Arabidopsis thaliana. This success and the free availability of full genomes and phenotypic data for more than 1,000 different natural inbred lines led to the development of several data repositories. AraPheno (https://arapheno.1001genomes.org) serves as a central repository of population-scale phenotypes in A. thaliana, while the AraGWAS Catalog (https://aragwas.1001genomes.org) provides a publicly available, manually curated and standardized collection of marker-trait associations for all available phenotypes from AraPheno. In this major update, we introduce the next generation of both platforms, including new data, features and tools. We included novel results on associations between knockout-mutations and all AraPheno traits. Furthermore, AraPheno has been extended to display RNA-Seq data for hundreds of accessions, providing expression information for over 28 000 genes for these accessions. All data, including the imputed genotype matrix used for GWAS, are easily downloadable via the respective databases.
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Affiliation(s)
- Matteo Togninalli
- Machine Learning and Computational Biology Lab, Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
- Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Ümit Seren
- Gregor Mendel Institute of Molecular Plant Biology, Vienna, Austria
| | - Jan A Freudenthal
- Center for Computational and Theoretical Biology, University Würzburg, Würzburg, Germany
| | - J Grey Monroe
- Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Dazhe Meng
- Gregor Mendel Institute of Molecular Plant Biology, Vienna, Austria
- Google, Mountain View, USA
| | - Magnus Nordborg
- Gregor Mendel Institute of Molecular Plant Biology, Vienna, Austria
| | - Detlef Weigel
- Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Karsten Borgwardt
- Machine Learning and Computational Biology Lab, Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
- Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Arthur Korte
- Center for Computational and Theoretical Biology, University Würzburg, Würzburg, Germany
| | - Dominik G Grimm
- Technical University of Munich, TUM Campus Straubing for Biotechnology and Sustainability, Bioinformatics, Straubing, Germany
- Weihenstephan-Triesdorf University of Applied Sciences, Bioinformatics, Straubing, Germany
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Fustier MA, Martínez-Ainsworth NE, Aguirre-Liguori JA, Venon A, Corti H, Rousselet A, Dumas F, Dittberner H, Camarena MG, Grimanelli D, Ovaskainen O, Falque M, Moreau L, de Meaux J, Montes-Hernández S, Eguiarte LE, Vigouroux Y, Manicacci D, Tenaillon MI. Common gardens in teosintes reveal the establishment of a syndrome of adaptation to altitude. PLoS Genet 2019; 15:e1008512. [PMID: 31860672 PMCID: PMC6944379 DOI: 10.1371/journal.pgen.1008512] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Revised: 01/06/2020] [Accepted: 11/07/2019] [Indexed: 12/14/2022] Open
Abstract
In plants, local adaptation across species range is frequent. Yet, much has to be discovered on its environmental drivers, the underlying functional traits and their molecular determinants. Genome scans are popular to uncover outlier loci potentially involved in the genetic architecture of local adaptation, however links between outliers and phenotypic variation are rarely addressed. Here we focused on adaptation of teosinte populations along two elevation gradients in Mexico that display continuous environmental changes at a short geographical scale. We used two common gardens, and phenotyped 18 traits in 1664 plants from 11 populations of annual teosintes. In parallel, we genotyped these plants for 38 microsatellite markers as well as for 171 outlier single nucleotide polymorphisms (SNPs) that displayed excess of allele differentiation between pairs of lowland and highland populations and/or correlation with environmental variables. Our results revealed that phenotypic differentiation at 10 out of the 18 traits was driven by local selection. Trait covariation along the elevation gradient indicated that adaptation to altitude results from the assembly of multiple co-adapted traits into a complex syndrome: as elevation increases, plants flower earlier, produce less tillers, display lower stomata density and carry larger, longer and heavier grains. The proportion of outlier SNPs associating with phenotypic variation, however, largely depended on whether we considered a neutral structure with 5 genetic groups (73.7%) or 11 populations (13.5%), indicating that population stratification greatly affected our results. Finally, chromosomal inversions were enriched for both SNPs whose allele frequencies shifted along elevation as well as phenotypically-associated SNPs. Altogether, our results are consistent with the establishment of an altitudinal syndrome promoted by local selective forces in teosinte populations in spite of detectable gene flow. Because elevation mimics climate change through space, SNPs that we found underlying phenotypic variation at adaptive traits may be relevant for future maize breeding.
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Affiliation(s)
- Margaux-Alison Fustier
- Génétique Quantitative et Evolution – Le Moulon, Université Paris-Saclay, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, Centre National de la Recherche Scientifique, AgroParisTech, Gif-sur-Yvette, France
| | - Natalia E. Martínez-Ainsworth
- Génétique Quantitative et Evolution – Le Moulon, Université Paris-Saclay, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, Centre National de la Recherche Scientifique, AgroParisTech, Gif-sur-Yvette, France
| | - Jonás A. Aguirre-Liguori
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Anthony Venon
- Génétique Quantitative et Evolution – Le Moulon, Université Paris-Saclay, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, Centre National de la Recherche Scientifique, AgroParisTech, Gif-sur-Yvette, France
| | - Hélène Corti
- Génétique Quantitative et Evolution – Le Moulon, Université Paris-Saclay, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, Centre National de la Recherche Scientifique, AgroParisTech, Gif-sur-Yvette, France
| | - Agnès Rousselet
- Génétique Quantitative et Evolution – Le Moulon, Université Paris-Saclay, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, Centre National de la Recherche Scientifique, AgroParisTech, Gif-sur-Yvette, France
| | - Fabrice Dumas
- Génétique Quantitative et Evolution – Le Moulon, Université Paris-Saclay, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, Centre National de la Recherche Scientifique, AgroParisTech, Gif-sur-Yvette, France
| | - Hannes Dittberner
- Institute of Botany, University of Cologne Biocenter, Cologne, Germany
| | - María G. Camarena
- Campo Experimental Bajío, InstitutoNacional de Investigaciones Forestales, Agrícolas y Pecuarias, Celaya, Mexico
| | - Daniel Grimanelli
- UMR Diversité, Adaptation et Développement des plantes, Université de Montpellier, Institut de Recherche pour le développement, Montpellier, France
| | - Otso Ovaskainen
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland
- Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
| | - Matthieu Falque
- Génétique Quantitative et Evolution – Le Moulon, Université Paris-Saclay, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, Centre National de la Recherche Scientifique, AgroParisTech, Gif-sur-Yvette, France
| | - Laurence Moreau
- Génétique Quantitative et Evolution – Le Moulon, Université Paris-Saclay, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, Centre National de la Recherche Scientifique, AgroParisTech, Gif-sur-Yvette, France
| | - Juliette de Meaux
- Institute of Botany, University of Cologne Biocenter, Cologne, Germany
| | - Salvador Montes-Hernández
- Campo Experimental Bajío, InstitutoNacional de Investigaciones Forestales, Agrícolas y Pecuarias, Celaya, Mexico
| | - Luis E. Eguiarte
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Yves Vigouroux
- UMR Diversité, Adaptation et Développement des plantes, Université de Montpellier, Institut de Recherche pour le développement, Montpellier, France
| | - Domenica Manicacci
- Génétique Quantitative et Evolution – Le Moulon, Université Paris-Saclay, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, Centre National de la Recherche Scientifique, AgroParisTech, Gif-sur-Yvette, France
| | - Maud I. Tenaillon
- Génétique Quantitative et Evolution – Le Moulon, Université Paris-Saclay, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, Centre National de la Recherche Scientifique, AgroParisTech, Gif-sur-Yvette, France
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48
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Delgado D, Sánchez-Bermejo E, de Marcos A, Martín-Jimenez C, Fenoll C, Alonso-Blanco C, Mena M. A Genetic Dissection of Natural Variation for Stomatal Abundance Traits in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2019; 10:1392. [PMID: 31781138 PMCID: PMC6859887 DOI: 10.3389/fpls.2019.01392] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 10/09/2019] [Indexed: 05/20/2023]
Abstract
Stomatal abundance varies widely across natural populations of Arabidopsis thaliana, and presumably affects plant performance because it influences water and CO2 exchange with the atmosphere and thence photosynthesis and transpiration. In order to determine the genetic basis of this natural variation, we have analyzed a recombinant inbred line (RIL) population derived from the wild accession Ll-0 and the reference strain Landsberg erecta (Ler), which show low and high stomatal abundance, respectively. Quantitative trait locus (QTL) analyses of stomatal index, stomatal density, and pavement cell density measured in the adaxial cotyledon epidermis, identified five loci. Three of the genomic regions affect all traits and were named MID (Modulator of Cell Index and Density) 1 to 3. MID2 is a large-effect QTL overlapping with ERECTA (ER), the er-1 allele from Ler increasing all trait values. Additional analyses of natural and induced loss-of-function er mutations in different genetic backgrounds revealed that ER dysfunctions have differential and opposite effects on the stomatal index in adaxial and abaxial cotyledon epidermis and confirmed that ER is the gene underlying MID2. Ll-0 alleles at MID1 and MID3 displayed moderate and positive effects on the various traits. Furthermore, detailed developmental studies tracking primary and satellite stomatal lineages show that MID3-Ll-0 allele promotes the spacing divisions that initiate satellite lineages, while the ER allele limits them. Finally, expression analyses suggest that ER and MID3 modulate satellization through partly different regulatory pathways. Our characterization of MID3 indicates that genetic modulation of satellization contributes to the variation for stomatal abundance in natural populations, and subsequently that this trait might be involved in plant adaptation.
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Affiliation(s)
- Dolores Delgado
- Facultad de Ciencias Ambientales y Bioquímica, Universidad de Castilla-La Mancha, Toledo, Spain
| | - Eduardo Sánchez-Bermejo
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Alberto de Marcos
- Facultad de Ciencias Ambientales y Bioquímica, Universidad de Castilla-La Mancha, Toledo, Spain
| | - Cristina Martín-Jimenez
- Facultad de Ciencias Ambientales y Bioquímica, Universidad de Castilla-La Mancha, Toledo, Spain
| | - Carmen Fenoll
- Facultad de Ciencias Ambientales y Bioquímica, Universidad de Castilla-La Mancha, Toledo, Spain
| | - Carlos Alonso-Blanco
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Montaña Mena
- Facultad de Ciencias Ambientales y Bioquímica, Universidad de Castilla-La Mancha, Toledo, Spain
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49
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Ortega A, de Marcos A, Illescas-Miranda J, Mena M, Fenoll C. The Tomato Genome Encodes SPCH, MUTE, and FAMA Candidates That Can Replace the Endogenous Functions of Their Arabidopsis Orthologs. FRONTIERS IN PLANT SCIENCE 2019; 10:1300. [PMID: 31736989 PMCID: PMC6828996 DOI: 10.3389/fpls.2019.01300] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 09/18/2019] [Indexed: 05/22/2023]
Abstract
Stomatal abundance determines the maximum potential for gas exchange between the plant and the atmosphere. In Arabidopsis, it is set during organ development through complex genetic networks linking epidermal differentiation programs with environmental response circuits. Three related bHLH transcription factors, SPCH, MUTE, and FAMA, act as positive drivers of stomata differentiation. Mutant alleles of some of these genes sustain different stomatal numbers in the mature organs and have potential to modify plant performance under different environmental conditions. However, knowledge about stomatal genes in dicotyledoneous crops is scarce. In this work, we identified the Solanum lycopersicum putative orthologs of these three master regulators and assessed their functional orthology by their ability to complement Arabidopsis loss-of-function mutants, the epidermal phenotypes elicited by their conditional overexpression, and the expression patterns of their promoter regions in Arabidopsis. Our results indicate that the tomato proteins are functionally equivalent to their Arabidopsis counterparts and that the tomato putative promoter regions display temporal and spatial expression domains similar to those reported for the Arabidopsis genes. In vivo tracking of tomato stomatal lineages in developing cotyledons revealed cell division and differentiation histories similar to those of Arabidopsis. Interestingly, the S. lycopersicum genome harbors a FAMA-like gene, expressed in leaves but functionally distinct from the true FAMA orthologue. Thus, the basic program for stomatal development in S. lycopersicum uses key conserved genetic determinants. This opens the possibility of modifying stomatal abundance in tomato through previously tested Arabidopsis alleles conferring altered stomata abundance phenotypes that correlate with physiological traits related to water status, leaf cooling, or photosynthesis.
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Affiliation(s)
| | | | | | - Montaña Mena
- Facultad de Ciencias Ambientales y Bioquímica, Universidad de Castilla-la Mancha, Toledo, Spain
| | - Carmen Fenoll
- Facultad de Ciencias Ambientales y Bioquímica, Universidad de Castilla-la Mancha, Toledo, Spain
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50
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Monroe JG, Gill B, Turner KG, McKay JK. Drought regimens predict life history strategies in Heliophila. THE NEW PHYTOLOGIST 2019; 223:2054-2062. [PMID: 31087648 DOI: 10.1111/nph.15919] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 05/01/2019] [Indexed: 06/09/2023]
Abstract
Explaining variation in life history strategies is an enduring goal of evolutionary biology and ecology. Early theory predicted that for plants, annual and perennial life histories reflect adaptations to environments that experience alternative drought regimens. Nevertheless, empirical support for this hypothesis from comparative analyses remains lacking. Here, we test classic life history theory in Heliophila L. (Brassicaceae), a diverse genus of flowering plants native to Africa, controlling for phylogeny and integrating 34 yr of satellite-based drought detection with 2192 herbaria occurrence records. We find that the common ancestor of these species was likely to be an annual, and that perenniality and annuality have repeatedly evolved, an estimated seven and five times, respectively. By comparing historical drought regimens, we show that annuals rather than perennial species occur in environments where droughts are significantly more frequent. We also find evidence that annual plants adapt to predictable drought regimens by escaping drought-prone seasons as seeds. These results yield compelling support for longstanding theoretical predictions by revealing the importance of drought frequency and predictability to explain plant life history. More broadly, this work highlights scalable approaches, integrating herbaria records and remote sensing to address outstanding questions in evolutionary ecology.
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Affiliation(s)
- J Grey Monroe
- Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO, 80521, USA
- College of Agriculture, Colorado State University, Fort Collins, CO, 80521, USA
| | - Brian Gill
- Institute for Environment and Society, Brown University, Providence, RI, 02912, USA
| | - Kathryn G Turner
- Biology Department, Pennsylvania State University, State College, PA, 16802, USA
| | - John K McKay
- College of Agriculture, Colorado State University, Fort Collins, CO, 80521, USA
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