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Boursiac Y, Protto V, Rishmawi L, Maurel C. Experimental and conceptual approaches to root water transport. PLANT AND SOIL 2022; 478:349-370. [PMID: 36277078 PMCID: PMC9579117 DOI: 10.1007/s11104-022-05427-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 04/03/2022] [Indexed: 05/05/2023]
Abstract
BACKGROUND Root water transport, which critically contributes to the plant water status and thereby plant productivity, has been the object of extensive experimental and theoretical studies. However, root systems represent an intricate assembly of cells in complex architectures, including many tissues at distinct developmental stages. Our comprehension of where and how molecular actors integrate their function in order to provide the root with its hydraulic properties is therefore still limited. SCOPE Based on current literature and prospective discussions, this review addresses how root water transport can be experimentally measured, what is known about the underlying molecular actors, and how elementary water transport processes are scaled up in numerical/mathematical models. CONCLUSIONS The theoretical framework and experimental procedures on root water transport that are in use today have been established a few decades ago. However, recent years have seen the appearance of new techniques and models with enhanced resolution, down to a portion of root or to the tissue level. These advances pave the way for a better comprehension of the dynamics of water uptake by roots in the soil.
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Affiliation(s)
- Yann Boursiac
- IPSiM, Univ Montpellier, CNRS, INRAE, Institut Agro, 34060 Montpellier, France
| | - Virginia Protto
- IPSiM, Univ Montpellier, CNRS, INRAE, Institut Agro, 34060 Montpellier, France
| | - Louai Rishmawi
- IPSiM, Univ Montpellier, CNRS, INRAE, Institut Agro, 34060 Montpellier, France
| | - Christophe Maurel
- IPSiM, Univ Montpellier, CNRS, INRAE, Institut Agro, 34060 Montpellier, France
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Sato Y, Takeda K, Nagano AJ. Neighbor QTL: an interval mapping method for quantitative trait loci underlying plant neighborhood effects. G3 (BETHESDA, MD.) 2021; 11:jkab017. [PMID: 33709120 PMCID: PMC8022948 DOI: 10.1093/g3journal/jkab017] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 01/11/2021] [Indexed: 12/13/2022]
Abstract
Phenotypes of sessile organisms, such as plants, rely not only on their own genotypes but also on those of neighboring individuals. Previously, we incorporated such neighbor effects into a single-marker regression using the Ising model of ferromagnetism. However, little is known regarding how neighbor effects should be incorporated in quantitative trait locus (QTL) mapping. In this study, we propose a new method for interval QTL mapping of neighbor effects, designated "neighbor QTL," the algorithm of which includes: (1) obtaining conditional self-genotype probabilities with recombination fraction between flanking markers; (2) calculating conditional neighbor genotypic identity using the self-genotype probabilities; and (3) estimating additive and dominance deviations for neighbor effects. Our simulation using F2 and backcross lines showed that the power to detect neighbor effects increased as the effective range decreased. The neighbor QTL was applied to insect herbivory on Col × Kas recombinant inbred lines of Arabidopsis thaliana. Consistent with previous results, the pilot experiment detected a self-QTL effect on the herbivory at the GLABRA1 locus. Regarding neighbor QTL effects on herbivory, we observed a weak QTL on the top of chromosome 4, at which a weak self-bolting QTL was also identified. The neighbor QTL method is available as an R package (https://cran.r-project.org/package=rNeighborQTL), providing a novel tool to investigate neighbor effects in QTL studies.
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Affiliation(s)
- Yasuhiro Sato
- Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency, Kawaguchi 332-0012, Japan
- Research Institute for Food and Agriculture, Ryukoku University, Shiga 520-2194, Japan
| | - Kazuya Takeda
- Center for Ecological Research, Kyoto University, Shiga 520-2113, Japan
| | - Atsushi J Nagano
- Faculty of Agriculture, Ryukoku University, Shiga 520-2194, Japan
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Zhou X, St Pierre CL, Gonzales NM, Zou J, Cheng R, Chitre AS, Sokoloff G, Palmer AA. Genome-Wide Association Study in Two Cohorts from a Multi-generational Mouse Advanced Intercross Line Highlights the Difficulty of Replication Due to Study-Specific Heterogeneity. G3 (BETHESDA, MD.) 2020; 10:951-965. [PMID: 31974095 PMCID: PMC7056977 DOI: 10.1534/g3.119.400763] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 10/17/2019] [Indexed: 12/12/2022]
Abstract
There has been extensive discussion of the "Replication Crisis" in many fields, including genome-wide association studies (GWAS). We explored replication in a mouse model using an advanced intercross line (AIL), which is a multigenerational intercross between two inbred strains. We re-genotyped a previously published cohort of LG/J x SM/J AIL mice (F34; n = 428) using a denser marker set and genotyped a new cohort of AIL mice (F39-43; n = 600) for the first time. We identified 36 novel genome-wide significant loci in the F34 and 25 novel loci in the F39-43 cohort. The subset of traits that were measured in both cohorts (locomotor activity, body weight, and coat color) showed high genetic correlations, although the SNP heritabilities were slightly lower in the F39-43 cohort. For this subset of traits, we attempted to replicate loci identified in either F34 or F39-43 in the other cohort. Coat color was robustly replicated; locomotor activity and body weight were only partially replicated, which was inconsistent with our power simulations. We used a random effects model to show that the partial replications could not be explained by Winner's Curse but could be explained by study-specific heterogeneity. Despite this heterogeneity, we performed a mega-analysis by combining F34 and F39-43 cohorts (n = 1,028), which identified four novel loci associated with locomotor activity and body weight. These results illustrate that even with the high degree of genetic and environmental control possible in our experimental system, replication was hindered by study-specific heterogeneity, which has broad implications for ongoing concerns about reproducibility.
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Affiliation(s)
- Xinzhu Zhou
- Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, CA, 92092
| | - Celine L St Pierre
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, 63110
| | | | - Jennifer Zou
- Department of Computer Science, University of California, Los Angeles, CA, 90095
| | | | | | - Greta Sokoloff
- Department of Psychological & Brain Sciences, University of Iowa, Iowa City, IO, 52242
| | - Abraham A Palmer
- Department of Psychiatry,
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, 92037 and
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van Rooijen R, Schulze S, Petzsch P, Westhoff P. Targeted misexpression of NAC052, acting in H3K4 demethylation, alters leaf morphological and anatomical traits in Arabidopsis thaliana. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:1434-1448. [PMID: 31740936 PMCID: PMC7031063 DOI: 10.1093/jxb/erz509] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 11/18/2019] [Indexed: 05/31/2023]
Abstract
In an effort to identify genetic regulators for the cell ontogeny around the veins in Arabidopsis thaliana leaves, an activation-tagged mutant line with altered leaf morphology and altered bundle sheath anatomy was characterized. This mutant had a small rosette area with wrinkled leaves and chlorotic leaf edges, as well as enhanced chloroplast numbers in the (pre-)bundle sheath tissue. It had a bundle-specific promoter from the gene GLYCINE DECARBOXYLASE SUBUNIT-T from the C4 species Flaveria trinervia (GLDTFt promoter) inserted in the coding region of the transcriptional repressor NAC052, functioning in H3K4 demethylation, in front of an alternative start codon in-frame with the natural start codon. Reconstruction of the mutation event of our activation-tagged line by creating a line expressing an N-terminally truncated sequence of NAC052 under control of the GLDTFt promoter confirmed the involvement of NAC052 in leaf development. Our study not only reveals leaf anatomic and transcriptomic effects of an N-terminally truncated NAC052 under control of the GLDTFt promoter, but also identifies NAC052 as a novel genetic regulator of leaf development.
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Affiliation(s)
- Roxanne van Rooijen
- Institute of Plant Molecular and Developmental Biology, Heinrich-Heine-University, Duesseldorf, Germany
- Cluster of Excellence on Plant Sciences ‘From Complex Traits towards Synthetic Modules’, Duesseldorf, Germany
| | - Stefanie Schulze
- Institute of Plant Molecular and Developmental Biology, Heinrich-Heine-University, Duesseldorf, Germany
| | - Patrick Petzsch
- Biologisch-Medizinisches Forschungszentrum (BMFZ), Genomics & Transcriptomics Labor (GTL), Heinrich-Heine-University, Duesseldorf, Germany
| | - Peter Westhoff
- Institute of Plant Molecular and Developmental Biology, Heinrich-Heine-University, Duesseldorf, Germany
- Cluster of Excellence on Plant Sciences ‘From Complex Traits towards Synthetic Modules’, Duesseldorf, Germany
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Marchadier E, Hanemian M, Tisné S, Bach L, Bazakos C, Gilbault E, Haddadi P, Virlouvet L, Loudet O. The complex genetic architecture of shoot growth natural variation in Arabidopsis thaliana. PLoS Genet 2019; 15:e1007954. [PMID: 31009456 PMCID: PMC6476473 DOI: 10.1371/journal.pgen.1007954] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 01/11/2019] [Indexed: 12/16/2022] Open
Abstract
One of the main outcomes of quantitative genetics approaches to natural variation is to reveal the genetic architecture underlying the phenotypic space. Complex genetic architectures are described as including numerous loci (or alleles) with small-effect and/or low-frequency in the populations, interactions with the genetic background, environment or age. Linkage or association mapping strategies will be more or less sensitive to this complexity, so that we still have an unclear picture of its extent. By combining high-throughput phenotyping under two environmental conditions with classical QTL mapping approaches in multiple Arabidopsis thaliana segregating populations as well as advanced near isogenic lines construction and survey, we have attempted to improve our understanding of quantitative phenotypic variation. Integrative traits such as those related to vegetative growth used in this work (highlighting either cumulative growth, growth rate or morphology) all showed complex and dynamic genetic architecture with respect to the segregating population and condition. The more resolutive our mapping approach, the more complexity we uncover, with several instances of QTLs visible in near isogenic lines but not detected with the initial QTL mapping, indicating that our phenotyping accuracy was less limiting than the mapping resolution with respect to the underlying genetic architecture. In an ultimate approach to resolve this complexity, we intensified our phenotyping effort to target specifically a 3Mb-region known to segregate for a major quantitative trait gene, using a series of selected lines recombined every 100kb. We discovered that at least 3 other independent QTLs had remained hidden in this region, some with trait- or condition-specific effects, or opposite allelic effects. If we were to extrapolate the figures obtained on this specific region in this particular cross to the genome- and species-scale, we would predict hundreds of causative loci of detectable phenotypic effect controlling these growth-related phenotypes.
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Affiliation(s)
- Elodie Marchadier
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78000, Versailles, France
| | - Mathieu Hanemian
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78000, Versailles, France
| | - Sébastien Tisné
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78000, Versailles, France
| | - Liên Bach
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78000, Versailles, France
| | - Christos Bazakos
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78000, Versailles, France
| | - Elodie Gilbault
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78000, Versailles, France
| | - Parham Haddadi
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78000, Versailles, France
| | - Laetitia Virlouvet
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78000, Versailles, France
| | - Olivier Loudet
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78000, Versailles, France
- * E-mail:
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Feldman AB, Leung H, Baraoidan M, Elmido-Mabilangan A, Canicosa I, Quick WP, Sheehy J, Murchie EH. Increasing Leaf Vein Density via Mutagenesis in Rice Results in an Enhanced Rate of Photosynthesis, Smaller Cell Sizes and Can Reduce Interveinal Mesophyll Cell Number. FRONTIERS IN PLANT SCIENCE 2017; 8:1883. [PMID: 29163607 PMCID: PMC5672787 DOI: 10.3389/fpls.2017.01883] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 10/17/2017] [Indexed: 05/07/2023]
Abstract
Improvements to leaf photosynthetic rates of crops can be achieved by targeted manipulation of individual component processes, such as the activity and properties of RuBisCO or photoprotection. This study shows that simple forward genetic screens of mutant populations can also be used to rapidly generate photosynthesis variants that are useful for breeding. Increasing leaf vein density (concentration of vascular tissue per unit leaf area) has important implications for plant hydraulic properties and assimilate transport. It was an important step to improving photosynthetic rates in the evolution of both C3 and C4 species and is a foundation or prerequisite trait for C4 engineering in crops like rice (Oryza sativa). A previous high throughput screen identified five mutant rice lines (cv. IR64) with increased vein densities and associated narrower leaf widths (Feldman et al., 2014). Here, these high vein density rice variants were analyzed for properties related to photosynthesis. Two lines were identified as having significantly reduced mesophyll to bundle sheath cell number ratios. All five lines had 20% higher light saturated photosynthetic capacity per unit leaf area, higher maximum carboxylation rates, dark respiration rates and electron transport capacities. This was associated with no significant differences in leaf thickness, stomatal conductance or CO2 compensation point between mutants and the wild-type. The enhanced photosynthetic rate in these lines may be a result of increased RuBisCO and electron transport component amount and/or activity and/or enhanced transport of photoassimilates. We conclude that high vein density (associated with altered mesophyll cell length and number) is a trait that may confer increased photosynthetic efficiency without increased transpiration.
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Affiliation(s)
| | - Hei Leung
- Plant Breeding, Genetics and Biotechnology, The International Rice Research Institute, Los Baños, Philippines
| | - Marietta Baraoidan
- Plant Breeding, Genetics and Biotechnology, The International Rice Research Institute, Los Baños, Philippines
| | | | - Irma Canicosa
- The C4 Rice Center, The International Rice Research Institute, Los Baños, Philippines
| | - William P. Quick
- The C4 Rice Center, The International Rice Research Institute, Los Baños, Philippines
- Department of Animal Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | - John Sheehy
- The C4 Rice Center, The International Rice Research Institute, Los Baños, Philippines
| | - Erik H. Murchie
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington, United Kingdom
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