1
|
Multiple Loci Control Variation in Plasticity to Foliar Shade Throughout Development in Arabidopsis thaliana. G3-GENES GENOMES GENETICS 2020; 10:4103-4114. [PMID: 32988993 PMCID: PMC7642929 DOI: 10.1534/g3.120.401259] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The shade avoidance response is a set of developmental changes exhibited by plants to avoid shading by competitors, and is an important model of adaptive plant plasticity. While the mechanisms of sensing shading by other plants are well-known and appear conserved across plants, less is known about the developmental mechanisms that result in the diverse array of morphological and phenological responses to shading. This is particularly true for traits that appear later in plant development. Here we use a nested association mapping (NAM) population of Arabidopsis thaliana to decipher the genetic architecture of the shade avoidance response in late-vegetative and reproductive plants. We focused on four traits: bolting time, rosette size, inflorescence growth rate, and inflorescence size, found plasticity in each trait in response to shade, and detected 17 total QTL; at least one of which is a novel locus not previously identified for shade responses in Arabidopsis. Using path analysis, we dissected each colocalizing QTL into direct effects on each trait and indirect effects transmitted through direct effects on earlier developmental traits. Doing this separately for each of the seven NAM populations in each environment, we discovered considerable heterogeneity among the QTL effects across populations, suggesting allelic series at multiple QTL or interactions between QTL and the genetic background or the environment. Our results provide insight into the development and variation in shade avoidance responses in Arabidopsis, and emphasize the value of directly modeling the relationships among traits when studying the genetics of complex developmental syndromes.
Collapse
|
2
|
Juyo Rojas DK, Soto Sedano JC, Ballvora A, Léon J, Mosquera Vásquez T. Novel organ-specific genetic factors for quantitative resistance to late blight in potato. PLoS One 2019; 14:e0213818. [PMID: 31310605 PMCID: PMC6634379 DOI: 10.1371/journal.pone.0213818] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 06/23/2019] [Indexed: 01/25/2023] Open
Abstract
Potato, Solanum tuberosum, is one of the major consumed food in the world, being the basis of the diet of millions of people. The main limiting and destructive disease of potato is late blight, caused by Phytophtora infestans. Here, we present a multi-environmental analysis of the response to P. infestans using an association panel of 150 accessions of S. tuberosum Group Phureja, evaluated in two localities in Colombia. Disease resistance data were merged with a genotyping matrix of 83,862 SNPs obtained by 2b-restriction site–associated DNA and Genotyping by sequencing approaches into a Genome-wide association study. We are reporting 16 organ-specific QTL conferring resistance to late blight. These QTL explain between 13.7% and 50.9% of the phenotypic variance. Six and ten QTL were detected for resistance response in leaves and stem, respectively. In silico analysis revealed 15 candidate genes for resistance to late blight. Four of them have no functional genome annotation, while eleven candidate genes code for diverse proteins, including a leucine-rich repeat kinase.
Collapse
Affiliation(s)
| | | | - Agim Ballvora
- University of Bonn, Institute of Crop Science and Resource Conservation Plant Breeding, Katzenburgweg, Bonn, Germany
| | - Jens Léon
- University of Bonn, Institute of Crop Science and Resource Conservation Plant Breeding, Katzenburgweg, Bonn, Germany
| | - Teresa Mosquera Vásquez
- Universidad Nacional de Colombia, sede Bogotá, Facultad de Ciencias Agrarias, Bogotá, Colombia
- * E-mail:
| |
Collapse
|
3
|
Zhang J, Zuo X, Lv P, Zhao S, Zhao X. Plant Functional Trait Response to Habitat Change and Grazing in a Semiarid Grassland: Unravelling Species Turnover and Intraspecific Variation Effects. POLISH JOURNAL OF ECOLOGY 2019. [DOI: 10.3161/15052249pje2019.67.1.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Jing Zhang
- Naiman Desertification Research Station, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Science, Lanzhou, 730000
| | - Xiaoan Zuo
- Naiman Desertification Research Station, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Science, Lanzhou, 730000
| | - Peng Lv
- Naiman Desertification Research Station, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Science, Lanzhou, 730000
| | - Shenglong Zhao
- Urat Desert-grassland Research Station, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Science, Lanzhou, 730000
| | - Xueyong Zhao
- Naiman Desertification Research Station, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Science, Lanzhou, 730000
| |
Collapse
|
4
|
Juyo Rojas DK, Soto Sedano JC, Ballvora A, Léon J, Mosquera Vásquez T. Novel organ-specific genetic factors for quantitative resistance to late blight in potato. PLoS One 2019. [PMID: 31310605 DOI: 10.1101/567289] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2023] Open
Abstract
Potato, Solanum tuberosum, is one of the major consumed food in the world, being the basis of the diet of millions of people. The main limiting and destructive disease of potato is late blight, caused by Phytophtora infestans. Here, we present a multi-environmental analysis of the response to P. infestans using an association panel of 150 accessions of S. tuberosum Group Phureja, evaluated in two localities in Colombia. Disease resistance data were merged with a genotyping matrix of 83,862 SNPs obtained by 2b-restriction site-associated DNA and Genotyping by sequencing approaches into a Genome-wide association study. We are reporting 16 organ-specific QTL conferring resistance to late blight. These QTL explain between 13.7% and 50.9% of the phenotypic variance. Six and ten QTL were detected for resistance response in leaves and stem, respectively. In silico analysis revealed 15 candidate genes for resistance to late blight. Four of them have no functional genome annotation, while eleven candidate genes code for diverse proteins, including a leucine-rich repeat kinase.
Collapse
Affiliation(s)
| | | | - Agim Ballvora
- University of Bonn, Institute of Crop Science and Resource Conservation Plant Breeding, Katzenburgweg, Bonn, Germany
| | - Jens Léon
- University of Bonn, Institute of Crop Science and Resource Conservation Plant Breeding, Katzenburgweg, Bonn, Germany
| | - Teresa Mosquera Vásquez
- Universidad Nacional de Colombia, sede Bogotá, Facultad de Ciencias Agrarias, Bogotá, Colombia
| |
Collapse
|
5
|
Baker RL, Leong WF, Welch S, Weinig C. Mapping and Predicting Non-Linear Brassica rapa Growth Phenotypes Based on Bayesian and Frequentist Complex Trait Estimation. G3 (BETHESDA, MD.) 2018; 8:1247-1258. [PMID: 29467188 PMCID: PMC5873914 DOI: 10.1534/g3.117.300350] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 02/08/2018] [Indexed: 12/23/2022]
Abstract
Predicting phenotypes based on genotypes and understanding the effects of complex multi-locus traits on plant performance requires a description of the underlying developmental processes, growth trajectories, and their genomic architecture. Using data from Brassica rapa genotypes grown in multiple density settings and seasons, we applied a hierarchical Bayesian Function-Valued Trait (FVT) approach to fit logistic growth curves to leaf phenotypic data (length and width) and characterize leaf development. We found evidence of genetic variation in phenotypic plasticity of rate and duration of leaf growth to growing season. In contrast, the magnitude of the plastic response for maximum leaf size was relatively small, suggesting that growth dynamics vs. final leaf sizes have distinct patterns of environmental sensitivity. Consistent with patterns of phenotypic plasticity, several QTL-by-year interactions were significant for parameters describing leaf growth rates and durations but not leaf size. In comparison to frequentist approaches for estimating leaf FVT, Bayesian trait estimation resulted in more mapped QTL that tended to have greater average LOD scores and to explain a greater proportion of trait variance. We then constructed QTL-based predictive models for leaf growth rate and final size using data from one treatment (uncrowded plants in one growing season). Models successfully predicted non-linear developmental phenotypes for genotypes not used in model construction and, due to a lack of QTL-by-treatment interactions, predicted phenotypes across sites differing in plant density.
Collapse
Affiliation(s)
- R L Baker
- Department of Biology, Miami University, Oxford, OH 45056,
| | - W F Leong
- Department of Agronomy, Kansas State University, Manhattan, KS 66506
| | - S Welch
- Department of Agronomy, Kansas State University, Manhattan, KS 66506
| | - C Weinig
- Department of Molecular Biology and
- Department of Botany, University of Wyoming, Laramie, WY 82071
| |
Collapse
|
6
|
Edwards CE, Ewers BE, Weinig C. Genotypic variation in biomass allocation in response to field drought has a greater affect on yield than gas exchange or phenology. BMC PLANT BIOLOGY 2016; 16:185. [PMID: 27558796 PMCID: PMC4997677 DOI: 10.1186/s12870-016-0876-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 08/16/2016] [Indexed: 05/05/2023]
Abstract
BACKGROUND Plant performance in agricultural and natural settings varies with moisture availability, and understanding the range of potential drought responses and the underlying genetic architecture is important for understanding how plants will respond to both natural and artificial selection in various water regimes. Here, we raised genotypes of Brassica rapa under well-watered and drought treatments in the field. Our primary goal was to understand the genetic architecture and yield effects of different drought-escape and dehydration-avoidance strategies. RESULTS Drought treatments reduced soil moisture by 62 % of field capacity. Drought decreased biomass accumulation and fruit production by as much as 48 %, whereas instantaneous water-use efficiency and root:shoot ratio increased. Genotypes differed in the mean value of all traits and in the sensitivity of biomass accumulation, root:shoot ratio, and fruit production to drought. Bivariate correlations involving gas-exchange and phenology were largely constant across environments, whereas those involving root:shoot varied across treatments. Although root:shoot was typically unrelated to gas-exchange or yield under well-watered conditions, genotypes with low to moderate increases in root:shoot allocation in response to drought survived the growing season, maintained maximum photosynthesis levels, and produced more fruit than genotypes with the greatest root allocation under drought. QTL for gas-exchange and yield components (total biomass or fruit production) had common effects across environments while those for root:shoot were often environment-specific. CONCLUSIONS Increases in root allocation beyond those needed to survive and maintain favorable water relations came at the cost of fruit production. The environment-specific effects of root:shoot ratio on yield and the differential expression of QTL for this trait across water regimes have important implications for efforts to improve crops for drought resistance.
Collapse
Affiliation(s)
- Christine E Edwards
- Department of Botany, University of Wyoming, Laramie, WY, 82071, USA.
- Current Address: Center for Conservation and Sustainable Development, Missouri Botanical Garden, PO Box 299, St. Louis, MO, 63166, USA.
| | - Brent E Ewers
- Department of Botany, University of Wyoming, Laramie, WY, 82071, USA
- Program in Ecology, University of Wyoming, Laramie, WY, 82071, USA
| | - Cynthia Weinig
- Department of Botany, University of Wyoming, Laramie, WY, 82071, USA
- Program in Ecology, University of Wyoming, Laramie, WY, 82071, USA
- Department of Molecular Biology, University of Wyoming, Laramie, WY, 82071, USA
| |
Collapse
|
7
|
Zuo X, Zhou X, Lv P, Zhao X, Zhang J, Wang S, Yue X. Testing Associations of Plant Functional Diversity with Carbon and Nitrogen Storage along a Restoration Gradient of Sandy Grassland. FRONTIERS IN PLANT SCIENCE 2016; 7:189. [PMID: 26925089 PMCID: PMC4759253 DOI: 10.3389/fpls.2016.00189] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Accepted: 02/04/2016] [Indexed: 05/08/2023]
Abstract
The trait-based approach shows that ecosystem function is strongly affected by plant functional diversity as reflected by the traits of the most abundant species (community-weighted mean, CWM) and functional dispersion (FDis). Effects of CWM and FDis individually support the biomass ratio hypothesis and the niche complementarity hypothesis. However, there is little empirical evidence on the relative roles of CWM traits and FDis in explaining the carbon (C) and nitrogen (N) storage in grassland ecosystems. We measured plant functional traits in the 34 most abundant species across 24 sites along a restoration gradient of sandy grassland (mobile dune, semi-fixed dune, fixed dune, and grassland) in Horqin Sand Land, northern China. Thereafter, we calculated the CWM traits, the functional divergence of each single trait (FDvar) and the trait dispersion of multiple traits (FDis). We also measured the C and N storage in plant, litter, root, and soil. Using a stepwise multiple regression analysis, we further assessed which of the functional diversity components best explained C and N storage in the sandy grassland restoration. We found consistent links between C or N storage and leaf traits related to plant resource use strategy. However, the CWM of plant height was retained as an important predictor of C and N storage in plant, litter, soil, and total ecosystem in the final multiple models. CWMs of specific leaf area and plant height best predicted soil C and N storage and total ecosystem N storage. FDis was one of good predictors of litter C and N storage as well as total ecosystem C storage. These results suggest that ecosystem C and N pools in the sandy grassland restoration are primarily associated with the traits of the most abundant species in communities, thereby supporting the biomass ratio hypothesis. The positive associations of FDis with C storage in litter and total ecosystem provide evidence to support the niche complementarity hypothesis. Both functional traits of dominant species and traits' dispersion in plant communities could contribute to explaining total ecosystem C storage. Thus, single- and multi-trait indices of functional composition play a crucial role in predicting C storage in sandy grasslands.
Collapse
Affiliation(s)
- Xiaoan Zuo
- Naiman Desertification Research Station, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of SciencesLanzhou, China
- Laboratory of Stress Ecophysiology and Biotechnology, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of SciencesLanzhou, China
- *Correspondence: Xiaoan Zuo, ;
| | - Xin Zhou
- Naiman Desertification Research Station, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of SciencesLanzhou, China
| | - Peng Lv
- Naiman Desertification Research Station, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of SciencesLanzhou, China
| | - Xueyong Zhao
- Naiman Desertification Research Station, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of SciencesLanzhou, China
| | - Jing Zhang
- Naiman Desertification Research Station, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of SciencesLanzhou, China
| | - Shaokun Wang
- Naiman Desertification Research Station, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of SciencesLanzhou, China
- Laboratory of Stress Ecophysiology and Biotechnology, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of SciencesLanzhou, China
| | - Xiyuan Yue
- Naiman Desertification Research Station, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of SciencesLanzhou, China
| |
Collapse
|
8
|
Dambreville A, Lauri PÉ, Normand F, Guédon Y. Analysing growth and development of plants jointly using developmental growth stages. ANNALS OF BOTANY 2015; 115:93-105. [PMID: 25452250 PMCID: PMC4284117 DOI: 10.1093/aob/mcu227] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Revised: 08/18/2014] [Accepted: 09/26/2014] [Indexed: 05/25/2023]
Abstract
BACKGROUND AND AIMS Plant growth, the increase of organ dimensions over time, and development, the change in plant structure, are often studied as two separate processes. However, there is structural and functional evidence that these two processes are strongly related. The aim of this study was to investigate the co-ordination between growth and development using mango trees, which have well-defined developmental stages. METHODS Developmental stages, determined in an expert way, and organ sizes, determined from objective measurements, were collected during the vegetative growth and flowering phases of two cultivars of mango, Mangifera indica. For a given cultivar and growth unit type (either vegetative or flowering), a multistage model based on absolute growth rate sequences deduced from the measurements was first built, and then growth stages deduced from the model were compared with developmental stages. KEY RESULTS Strong matches were obtained between growth stages and developmental stages, leading to a consistent definition of integrative developmental growth stages. The growth stages highlighted growth asynchronisms between two topologically connected organs, namely the vegetative axis and its leaves. CONCLUSIONS Integrative developmental growth stages emphasize that developmental stages are closely related to organ growth rates. The results are discussed in terms of the possible physiological processes underlying these stages, including plant hydraulics, biomechanics and carbohydrate partitioning.
Collapse
Affiliation(s)
- Anaëlle Dambreville
- CIRAD, UPR HortSys, 97455 Saint-Pierre Cedex, Réunion Island, France, INRA, UMR AGAP, 34098 Montpellier, France and CIRAD, UMR AGAP and Inria, Virtual Plants, 34095 Montpellier, France CIRAD, UPR HortSys, 97455 Saint-Pierre Cedex, Réunion Island, France, INRA, UMR AGAP, 34098 Montpellier, France and CIRAD, UMR AGAP and Inria, Virtual Plants, 34095 Montpellier, France
| | - Pierre-Éric Lauri
- CIRAD, UPR HortSys, 97455 Saint-Pierre Cedex, Réunion Island, France, INRA, UMR AGAP, 34098 Montpellier, France and CIRAD, UMR AGAP and Inria, Virtual Plants, 34095 Montpellier, France
| | - Frédéric Normand
- CIRAD, UPR HortSys, 97455 Saint-Pierre Cedex, Réunion Island, France, INRA, UMR AGAP, 34098 Montpellier, France and CIRAD, UMR AGAP and Inria, Virtual Plants, 34095 Montpellier, France
| | - Yann Guédon
- CIRAD, UPR HortSys, 97455 Saint-Pierre Cedex, Réunion Island, France, INRA, UMR AGAP, 34098 Montpellier, France and CIRAD, UMR AGAP and Inria, Virtual Plants, 34095 Montpellier, France
| |
Collapse
|
9
|
Borzak CL, Potts BM, Davies NW, O'Reilly-Wapstra JM. Population divergence in the ontogenetic trajectories of foliar terpenes of a Eucalyptus species. ANNALS OF BOTANY 2015; 115:159-170. [PMID: 25434028 PMCID: PMC4284115 DOI: 10.1093/aob/mcu222] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Revised: 08/27/2014] [Accepted: 09/26/2014] [Indexed: 06/02/2023]
Abstract
BACKGROUND AND AIMS The development of plant secondary metabolites during early life stages can have significant ecological and evolutionary implications for plant-herbivore interactions. Foliar terpenes influence a broad range of ecological interactions, including plant defence, and their expression may be influenced by ontogenetic and genetic factors. This study investigates the role of these factors in the expression of foliar terpene compounds in Eucalyptus globulus seedlings. METHODS Seedlings were sourced from ten families each from three genetically distinct populations, representing relatively high and low chemical resistance to mammalian herbivory. Cotyledon-stage seedlings and consecutive leaf pairs of true leaves were harvested separately across an 8-month period, and analysed for eight monoterpene compounds and six sesquiterpene compounds. KEY RESULTS Foliar terpenes showed a series of dynamic changes with ontogenetic trajectories differing between populations and families, as well as between and within the two major terpene classes. Sesquiterpenes changed rapidly through ontogeny and expressed opposing trajectories between compounds, but showed consistency in pattern between populations. Conversely, changed expression in monoterpene trajectories was population- and compound-specific. CONCLUSIONS The results suggest that adaptive opportunities exist for changing levels of terpene content through ontogeny, and evolution may exploit the ontogenetic patterns of change in these compounds to create a diverse ontogenetic chemical mosaic with which to defend the plant. It is hypothesized that the observed genetically based patterns in terpene ontogenetic trajectories reflect multiple changes in the regulation of genes throughout different terpene biosynthetic pathways.
Collapse
Affiliation(s)
- Christina L Borzak
- School of Biological Sciences and National Centre for Future Forest Industries, University of Tasmania, Private Bag 55, Hobart, Tasmania, 7001, Australia and Central Science Laboratory, University of Tasmania, Private Bag 74, Hobart, Tasmania, 7001, Australia
| | - Brad M Potts
- School of Biological Sciences and National Centre for Future Forest Industries, University of Tasmania, Private Bag 55, Hobart, Tasmania, 7001, Australia and Central Science Laboratory, University of Tasmania, Private Bag 74, Hobart, Tasmania, 7001, Australia
| | - Noel W Davies
- School of Biological Sciences and National Centre for Future Forest Industries, University of Tasmania, Private Bag 55, Hobart, Tasmania, 7001, Australia and Central Science Laboratory, University of Tasmania, Private Bag 74, Hobart, Tasmania, 7001, Australia
| | - Julianne M O'Reilly-Wapstra
- School of Biological Sciences and National Centre for Future Forest Industries, University of Tasmania, Private Bag 55, Hobart, Tasmania, 7001, Australia and Central Science Laboratory, University of Tasmania, Private Bag 74, Hobart, Tasmania, 7001, Australia
| |
Collapse
|