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Gupta S, Groen SC, Zaidem ML, Sajise AGC, Calic I, Natividad MA, McNally KL, Vergara GV, Satija R, Franks SJ, Singh RK, Joly-Lopez Z, Purugganan MD. Systems genomics of salinity stress response in rice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.31.596807. [PMID: 38895411 PMCID: PMC11185513 DOI: 10.1101/2024.05.31.596807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Populations can adapt to stressful environments through changes in gene expression. However, the role of gene regulation in mediating stress response and adaptation remains largely unexplored. Here, we use an integrative field dataset obtained from 780 plants of Oryza sativa ssp. indica (rice) grown in a field experiment under normal or moderate salt stress conditions to examine selection and evolution of gene expression variation under salinity stress conditions. We find that salinity stress induces increased selective pressure on gene expression. Further, we show that trans-eQTLs rather than cis-eQTLs are primarily associated with rice's gene expression under salinity stress, potentially via a few master-regulators. Importantly, and contrary to the expectations, we find that cis-trans reinforcement is more common than cis-trans compensation which may be reflective of rice diversification subsequent to domestication. We further identify genetic fixation as the likely mechanism underlying this compensation/reinforcement. Additionally, we show that cis- and trans-eQTLs are under different selection regimes, giving us insights into the evolutionary dynamics of gene expression variation. By examining genomic, transcriptomic, and phenotypic variation across a rice population, we gain insights into the molecular and genetic landscape underlying adaptive salinity stress responses, which is relevant for other crops and other stresses.
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Affiliation(s)
- Sonal Gupta
- Center for Genomics and Systems Biology, New York University, New York, NY USA
| | - Simon C Groen
- Center for Genomics and Systems Biology, New York University, New York, NY USA
- Department of Nematology and Department of Botany & Plant Sciences, University of California, Riverside, CA USA
- Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, CA USA
| | - Maricris L. Zaidem
- Center for Genomics and Systems Biology, New York University, New York, NY USA
- Department of Biology, University of Oxford, Oxford, England
| | | | - Irina Calic
- Department of Biological Sciences, Fordham University, Bronx, NY USA
- Inari Agriculture Nv, Gent, Belgium
| | | | | | - Georgina V. Vergara
- International Rice Research Institute, Los Baños, Philippines
- Institute of Crop Science, University of the Philippines, Los Baños, Philippines
| | - Rahul Satija
- Center for Genomics and Systems Biology, New York University, New York, NY USA
- New York Genome Center, New York, NY USA
| | - Steven J. Franks
- Department of Biological Sciences, Fordham University, Bronx, NY USA
| | - Rakesh K. Singh
- International Rice Research Institute, Los Baños, Philippines
- International Center for Biosaline Agriculture, Dubai, UAE (current affiliation)
| | - Zoé Joly-Lopez
- Center for Genomics and Systems Biology, New York University, New York, NY USA
- Département de Chimie, Université du Quebéc à Montréal, Montreal, Quebec, Canada
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Million CR, Wijeratne S, Karhoff S, Cassone BJ, McHale LK, Dorrance AE. Molecular mechanisms underpinning quantitative resistance to Phytophthora sojae in Glycine max using a systems genomics approach. FRONTIERS IN PLANT SCIENCE 2023; 14:1277585. [PMID: 38023885 PMCID: PMC10662313 DOI: 10.3389/fpls.2023.1277585] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 10/16/2023] [Indexed: 12/01/2023]
Abstract
Expression of quantitative disease resistance in many host-pathogen systems is controlled by genes at multiple loci, each contributing a small effect to the overall response. We used a systems genomics approach to study the molecular underpinnings of quantitative disease resistance in the soybean-Phytophthora sojae pathosystem, incorporating expression quantitative trait loci (eQTL) mapping and gene co-expression network analysis to identify the genes putatively regulating transcriptional changes in response to inoculation. These findings were compared to previously mapped phenotypic (phQTL) to identify the molecular mechanisms contributing to the expression of this resistance. A subset of 93 recombinant inbred lines (RILs) from a Conrad × Sloan population were inoculated with P. sojae isolate 1.S.1.1 using the tray-test method; RNA was extracted, sequenced, and the normalized read counts were genetically mapped from tissue collected at the inoculation site 24 h after inoculation from both mock and inoculated samples. In total, more than 100,000 eQTLs were mapped. There was a switch from predominantly cis-eQTLs in the mock treatment to an almost entirely nonoverlapping set of predominantly trans-eQTLs in the inoculated treatment, where greater than 100-fold more eQTLs were mapped relative to mock, indicating vast transcriptional reprogramming due to P. sojae infection occurred. The eQTLs were organized into 36 hotspots, with the four largest hotspots from the inoculated treatment corresponding to more than 70% of the eQTLs, each enriched for genes within plant-pathogen interaction pathways. Genetic regulation of trans-eQTLs in response to the pathogen was predicted to occur through transcription factors and signaling molecules involved in plant-pathogen interactions, plant hormone signal transduction, and MAPK pathways. Network analysis identified three co-expression modules that were correlated with susceptibility to P. sojae and associated with three eQTL hotspots. Among the eQTLs co-localized with phQTLs, two cis-eQTLs with putative functions in the regulation of root architecture or jasmonic acid, as well as the putative master regulators of an eQTL hotspot nearby a phQTL, represent candidates potentially underpinning the molecular control of these phQTLs for resistance.
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Affiliation(s)
- Cassidy R. Million
- Department of Plant Pathology, The Ohio State University, Wooster, OH, United States
- Center for Soybean Research and Center for Applied Plant Sciences, The Ohio State University, Columbus, OH, United States
| | - Saranga Wijeratne
- Molecular and Cellular Imaging Center, The Ohio State University, Wooster, OH, United States
| | - Stephanie Karhoff
- Center for Soybean Research and Center for Applied Plant Sciences, The Ohio State University, Columbus, OH, United States
- Translational Plant Sciences Graduate Program, The Ohio State University, Columbus, OH, United States
| | - Bryan J. Cassone
- Center for Soybean Research and Center for Applied Plant Sciences, The Ohio State University, Columbus, OH, United States
- Department of Biology, Brandon University, Brandon, Manitoba, MB, Canada
| | - Leah K. McHale
- Center for Soybean Research and Center for Applied Plant Sciences, The Ohio State University, Columbus, OH, United States
- Department of Horticulture and Crop Science, The Ohio State University, Columbus, OH, United States
| | - Anne E. Dorrance
- Department of Plant Pathology, The Ohio State University, Wooster, OH, United States
- Center for Soybean Research and Center for Applied Plant Sciences, The Ohio State University, Columbus, OH, United States
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Santos C, Martins DC, González-Bernal MJ, Rubiales D, Vaz Patto MC. Integrating Phenotypic and Gene Expression Linkage Mapping to Dissect Rust Resistance in Chickling Pea. FRONTIERS IN PLANT SCIENCE 2022; 13:837613. [PMID: 35463408 PMCID: PMC9021875 DOI: 10.3389/fpls.2022.837613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 02/23/2022] [Indexed: 06/14/2023]
Abstract
Rusts are among the most important foliar biotrophic fungal diseases in legumes. Lathyrus cicera crop can be severely damaged by Uromyces pisi, to which partial resistance has been identified. Nevertheless, the underlying genetic basis and molecular mechanisms of this resistance are poorly understood in L. cicera. To prioritise the causative variants controlling partial resistance to rust in L. cicera, a recombinant inbred line (RIL) population, segregating for response to this pathogen, was used to combine the detection of related phenotypic- and expression-quantitative trait loci (pQTLs and eQTLs, respectively). RILs' U. pisi disease severity (DS) was recorded in three independent screenings at seedling (growth chamber) and in one season of exploratory screening at adult plant stage (semi-controlled field conditions). A continuous DS range was observed in both conditions and used for pQTL mapping. Different pQTLs were identified under the growth chamber and semi-controlled field conditions, indicating a distinct genetic basis depending on the plant developmental stage and/or the environment. Additionally, the expression of nine genes related to U. pisi resistance in L. cicera was quantified for each RIL individual and used for eQTL mapping. One cis-eQTL and one trans-eQTL were identified controlling the expression variation of one gene related to rust resistance - a member of glycosyl hydrolase family 17. Integrating phenotyping, gene expression and linkage mapping allowed prioritising four candidate genes relevant for disease-resistance precision breeding involved in adaptation to biotic stress, cellular, and organelle homeostasis, and proteins directly involved in plant defence.
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Affiliation(s)
- Carmen Santos
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Davide Coelho Martins
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | | | - Diego Rubiales
- Institute for Sustainable Agriculture, Consejo Superior de Investigaciones Científicas, Córdoba, Spain
| | - Maria Carlota Vaz Patto
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
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Quan M, Liu X, Du Q, Xiao L, Lu W, Fang Y, Li P, Ji L, Zhang D. Genome-wide association studies reveal the coordinated regulatory networks underlying photosynthesis and wood formation in Populus. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:5372-5389. [PMID: 33733665 DOI: 10.1093/jxb/erab122] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Accepted: 03/16/2021] [Indexed: 06/12/2023]
Abstract
Photosynthesis and wood formation underlie the ability of trees to provide renewable resources and perform ecological functions; however, the genetic basis and regulatory pathways coordinating these two linked processes remain unclear. Here, we used a systems genetics strategy, integrating genome-wide association studies, transcriptomic analyses, and transgenic experiments, to investigate the genetic architecture of photosynthesis and wood properties among 435 unrelated individuals of Populus tomentosa, and unravel the coordinated regulatory networks resulting in two trait categories. We detected 222 significant single-nucleotide polymorphisms, annotated to 177 candidate genes, for 10 traits of photosynthesis and wood properties. Epistasis uncovered 74 epistatic interactions for phenotypes. Strikingly, we deciphered the coordinated regulation patterns of pleiotropic genes underlying phenotypic variations for two trait categories. Furthermore, expression quantitative trait nucleotide mapping and coexpression analysis were integrated to unravel the potential transcriptional regulatory networks of candidate genes coordinating photosynthesis and wood properties. Finally, heterologous expression of two pleiotropic genes, PtoMYB62 and PtoMYB80, in Arabidopsis thaliana demonstrated that they control regulatory networks balancing photosynthesis and stem secondary cell wall components, respectively. Our study provides insights into the regulatory mechanisms coordinating photosynthesis and wood formation in poplar, and should facilitate genetic breeding in trees via molecular design.
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Affiliation(s)
- Mingyang Quan
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, P. R. China
- National Engineering Laboratory for Tree Breeding, 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
| | - Xin Liu
- National Engineering Laboratory for Tree Breeding, 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
| | - Qingzhang Du
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, P. R. China
- National Engineering Laboratory for Tree Breeding, 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
| | - Liang Xiao
- National Engineering Laboratory for Tree Breeding, 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
| | - Wenjie Lu
- National Engineering Laboratory for Tree Breeding, 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
| | - Yuanyuan Fang
- National Engineering Laboratory for Tree Breeding, 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
| | - Peng Li
- National Engineering Laboratory for Tree Breeding, 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
| | - Li Ji
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, P. R. China
- National Engineering Laboratory for Tree Breeding, 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
| | - Deqiang Zhang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, P. R. China
- National Engineering Laboratory for Tree Breeding, 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
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McGowan MT, Zhang Z, Ficklin SP. Chromosomal characteristics of salt stress heritable gene expression in the rice genome. BMC Genom Data 2021; 22:17. [PMID: 34044788 PMCID: PMC8162008 DOI: 10.1186/s12863-021-00970-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 05/06/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Gene expression is potentially an important heritable quantitative trait that mediates between genetic variation and higher-level complex phenotypes through time and condition-dependent regulatory interactions. Therefore, we sought to explore both the genomic and condition-specific characteristics of gene expression heritability within the context of chromosomal structure. RESULTS Heritability was estimated for biological gene expression using a diverse, 84-line, Oryza sativa (rice) population under optimal and salt-stressed conditions. Overall, 5936 genes were found to have heritable expression regardless of condition and 1377 genes were found to have heritable expression only during salt stress. These genes with salt-specific heritable expression are enriched for functional terms associated with response to stimulus and transcription factor activity. Additionally, we discovered that highly and lowly expressed genes, and genes with heritable expression are distributed differently along the chromosomes in patterns that follow previously identified high-throughput chromosomal conformation capture (Hi-C) A/B chromatin compartments. Furthermore, multiple genomic hot-spots enriched for genes with salt-specific heritability were identified on chromosomes 1, 4, 6, and 8. These hotspots were found to contain genes functionally enriched for transcriptional regulation and overlaps with a previously identified major QTL for salt-tolerance in rice. CONCLUSIONS Investigating the heritability of traits, and in-particular gene expression traits, is important towards developing a basic understanding of how regulatory networks behave across a population. This work provides insights into spatial patterns of heritable gene expression at the chromosomal level.
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Affiliation(s)
- Matthew T McGowan
- Molecular Plant Sciences Program, Washington State University, French Ad 324G, Pullman, WA, 99164, USA.
| | - Zhiwu Zhang
- Molecular Plant Sciences Program, Washington State University, French Ad 324G, Pullman, WA, 99164, USA.,Department of Crops and Soils, Washington State University, 105 Johnson Hall, Pullman, WA, 99164, USA
| | - Stephen P Ficklin
- Molecular Plant Sciences Program, Washington State University, French Ad 324G, Pullman, WA, 99164, USA.,Department of Horticulture, Washington State University, 149 Johnson Hall, Pullman, WA, 99164, USA
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Abstract
Distinguishing which traits have evolved under natural selection, as opposed to neutral evolution, is a major goal of evolutionary biology. Several tests have been proposed to accomplish this, but these either rely on false assumptions or suffer from low power. Here, I introduce an approach to detecting selection that makes minimal assumptions and only requires phenotypic data from ∼10 individuals. The test compares the phenotypic difference between two populations to what would be expected by chance under neutral evolution, which can be estimated from the phenotypic distribution of an F2 cross between those populations. Simulations show that the test is robust to variation in the number of loci affecting the trait, the distribution of locus effect sizes, heritability, dominance, and epistasis. Comparing its performance to the QTL sign test-an existing test of selection that requires both genotype and phenotype data-the new test achieves comparable power with 50- to 100-fold fewer individuals (and no genotype data). Applying the test to empirical data spanning over a century shows strong directional selection in many crops, as well as on naturally selected traits such as head shape in Hawaiian Drosophila and skin color in humans. Applied to gene expression data, the test reveals that the strength of stabilizing selection acting on mRNA levels in a species is strongly associated with that species' effective population size. In sum, this test is applicable to phenotypic data from almost any genetic cross, allowing selection to be detected more easily and powerfully than previously possible.
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Affiliation(s)
- Hunter B Fraser
- Department of Biology, Stanford University, Stanford, CA 94305
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Pongrac P, Fischer S, Thompson JA, Wright G, White PJ. Early Responses of Brassica oleracea Roots to Zinc Supply Under Sufficient and Sub-Optimal Phosphorus Supply. FRONTIERS IN PLANT SCIENCE 2020; 10:1645. [PMID: 31998335 PMCID: PMC6962232 DOI: 10.3389/fpls.2019.01645] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 11/21/2019] [Indexed: 05/24/2023]
Abstract
Shoot zinc (Zn) concentration in Brassica oleracea is affected by soil Zn and phosphorus (P) supply. Most problematic is the negative impact of P fertilizers on Zn concentrations in crops, which makes balancing yield and mineral quality challenging. To evaluate early molecular mechanisms involved in the accumulation of large shoot Zn concentrations regardless of the P supply, two B. oleracea accessions differing in root architecture and root exudates were grown hydroponically for two weeks with different combinations of P and Zn supply. Ionome profiling and deep RNA sequencing of roots revealed interactions of P and Zn in planta, without apparent phenotypic effects. In addition, increasing P supply did not reduce tissue Zn concentration. Substantial changes in gene expression in response to different P and/or Zn supplies in roots of both accessions ensured nutritionally sufficient P and Zn uptake. Numerous genes were differentially expressed after changing Zn or P supply and most of them were unique to only one accession, highlighting their different strategies in achieving nutrient sufficiency. Thus, different gene networks responded to the changing P and Zn supply in the two accessions. Additionally, enrichment analysis of gene ontology classes revealed that genes involved in lipid metabolism, response to starvation, and anion transport mechanisms were most responsive to differences in P and Zn supply in both accessions. The results agreed with previously studies demonstrating alterations in P and Zn transport and phospholipid metabolism in response to reduced P and Zn supply. It is anticipated that improved knowledge of genes responsive to P or Zn supply will help illuminate the roles in uptake and accumulation of P and Zn and might identify candidate genes for breeding high-yield-high-Zn brassicas.
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Affiliation(s)
- Paula Pongrac
- Ecological Science Group, The James Hutton Institute, Dundee, United Kingdom
- Low and Medium Energy Physics, Jožef Stefan Institute, Ljubljana, Slovenia
| | - Sina Fischer
- Future Food Beacon of Excellence and School of Biosciences, University of Nottingham, Loughborough, United Kingdom
| | | | - Gladys Wright
- Ecological Science Group, The James Hutton Institute, Dundee, United Kingdom
| | - Philip J. White
- Ecological Science Group, The James Hutton Institute, Dundee, United Kingdom
- Distinguished Scientist Fellowship Program, King Saud University, Riyadh, Saudi Arabia
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El-Soda M, Neris Moreira C, Goredema-Matongera N, Jamar D, Koornneef M, Aarts MGM. QTL and candidate genes associated with leaf anion concentrations in response to phosphate supply in Arabidopsis thaliana. BMC PLANT BIOLOGY 2019; 19:410. [PMID: 31533608 PMCID: PMC6751748 DOI: 10.1186/s12870-019-1996-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 08/29/2019] [Indexed: 05/25/2023]
Abstract
BACKGROUND Phosphorus is often present naturally in the soil as inorganic phosphate, Pi, which bio-availability is limited in many ecosystems due to low soil solubility and mobility. Plants respond to low Pi with a Pi Starvation Response, involving Pi sensing and long-distance signalling. There is extensive cross-talk between Pi homeostasis mechanisms and the homeostasis mechanism for other anions in response to Pi availability. RESULTS Recombinant Inbred Line (RIL) and Genome Wide Association (GWA) mapping populations, derived from or composed of natural accessions of Arabidopsis thaliana, were grown under sufficient and deficient Pi supply. Significant treatment effects were found for all traits and significant genotype x treatment interactions for the leaf Pi and sulphate concentrations. Using the RIL/QTL population, we identified 24 QTLs for leaf concentrations of Pi and other anions, including a major QTL for leaf sulphate concentration (SUL2) mapped to the bottom of chromosome (Chr) 1. GWA mapping found 188 SNPs to be associated with the measured traits, corresponding to 152 genes. One of these SNPs, associated with leaf Pi concentration, mapped to PP2A-1, a gene encoding an isoform of the catalytic subunit of a protein phosphatase 2A. Of two additional SNPs, associated with phosphate use efficiency (PUE), one mapped to AT5G49780, encoding a leucine-rich repeat protein kinase involved in signal transduction, and the other to SIZ1, a gene encoding a SUMO E3 ligase, and a known regulator of P starvation-dependent responses. One SNP associated with leaf sulphate concentration was found in SULTR2;1, encoding a sulphate transporter, known to enhance sulphate translocation from root to shoot under P deficiency. Finally, one SNP was mapped to FMO GS-OX4, a gene encoding glucosinolate S-oxygenase involved in glucosinolate biosynthesis, which located within the confidence interval of the SUL2 locus. CONCLUSION We identified several candidate genes with known functions related to anion homeostasis in response to Pi availability. Further molecular studies are needed to confirm and validate these candidate genes and understand their roles in examined traits. Such knowledge will contribute to future breeding for improved crop PUE .
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Affiliation(s)
- Mohamed El-Soda
- Department of Genetics, Faculty of Agriculture, Cairo University, Giza, 12613 Egypt
| | - Charles Neris Moreira
- Laboratory of Genetics, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Nakai Goredema-Matongera
- Department of Research and Specialist Services, Maize Breeding Programme, Crop Breeding Institute, P. O. Box CY550 Causeway, Harare, Zimbabwe
| | - Diaan Jamar
- Laboratory of Plant Physiology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Maarten Koornneef
- Laboratory of Genetics, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Mark G. M. Aarts
- Laboratory of Genetics, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
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Integrating transcriptomic network reconstruction and eQTL analyses reveals mechanistic connections between genomic architecture and Brassica rapa development. PLoS Genet 2019; 15:e1008367. [PMID: 31513571 PMCID: PMC6759183 DOI: 10.1371/journal.pgen.1008367] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 09/24/2019] [Accepted: 08/13/2019] [Indexed: 12/01/2022] Open
Abstract
Plant developmental dynamics can be heritable, genetically correlated with fitness and yield, and undergo selection. Therefore, characterizing the mechanistic connections between the genetic architecture governing plant development and the resulting ontogenetic dynamics of plants in field settings is critically important for agricultural production and evolutionary ecology. We use hierarchical Bayesian Function-Valued Trait (FVT) models to estimate Brassica rapa growth curves throughout ontogeny, across two treatments, and in two growing seasons. We find genetic variation for plasticity of growth rates and final sizes, but not the inflection point (transition from accelerating to decelerating growth) of growth curves. There are trade-offs between growth rate and duration, indicating that selection for maximum yields at early harvest dates may come at the expense of late harvest yields and vice versa. We generate eigengene modules and determine which are co-expressed with FVT traits using a Weighted Gene Co-expression Analysis. Independently, we seed a Mutual Rank co-expression network model with FVT traits to identify specific genes and gene networks related to FVT. GO-analyses of eigengene modules indicate roles for actin/cytoskeletal genes, herbivore resistance/wounding responses, and cell division, while MR networks demonstrate a close association between metabolic regulation and plant growth. We determine that combining FVT Quantitative Trait Loci (QTL) and MR genes/WGCNA eigengene expression profiles better characterizes phenotypic variation than any single data type (i.e. QTL, gene, or eigengene alone). Our network analysis allows us to employ a targeted eQTL analysis, which we use to identify regulatory hotspots for FVT. We examine cis vs. trans eQTL that mechanistically link FVT QTL with structural trait variation. Colocalization of FVT, gene, and eigengene eQTL provide strong evidence for candidate genes influencing plant height. The study is the first to explore eQTL for FVT, and specifically do so in agroecologically relevant field settings. We estimate the developmental dynamics of plant growth using mathematical functions to fit continuous functions to discrete plant height data collected throughout growth, and we use the parameters defining these mathematical functions as data. We identify genomic regions controlling plant growth and filter a novel transcriptomic data set using network reconstruction models to identify the genes and eigengenes associated with plant height. We combine these genomic and transcriptomic data to predict variation in plant height, and we use quantitative genetics to mechanistically connect plant genetics, transcriptomics, and development. Our approach demonstrates two powerful methods for the type of data reduction (FVT modeling and gene expression network reconstruction for targeted eQTL analyses) and data integration that will be necessary for driving forward the field of genetics in the post-genomic era. To the best of our knowledge, we are the first to apply these techniques to continuous models of plant development, and the first to do so in agroecologically relevant field settings.
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Pang J, Fu J, Zong N, Wang J, Song D, Zhang X, He C, Fang T, Zhang H, Fan Y, Wang G, Zhao J. Kernel size-related genes revealed by an integrated eQTL analysis during early maize kernel development. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 98:19-32. [PMID: 30548709 PMCID: PMC6850110 DOI: 10.1111/tpj.14193] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 10/05/2018] [Accepted: 11/16/2018] [Indexed: 05/21/2023]
Abstract
In maize, kernel traits strongly impact overall grain yields, and it is known that sophisticated spatiotemporal programs of gene expression coordinate kernel development, so advancing our knowledge of kernel development can help efforts to improve grain yields. Here, using phenotype, genotype and transcriptomics data of maize kernels at 5 and 15 days after pollination (DAP) for a large association mapping panel, we employed multiple quantitative genetics approaches-genome-wide association studies (GWAS) as well as expression quantitative trait loci (eQTL) and quantitative trait transcript (QTT) analyses-to gain insights about molecular genetic basis of kernel development in maize. This resulted in the identification of 137 putative kernel length-related genes at 5 DAP, of which 43 are located in previously reported QTL regions. Strikingly, we identified an eQTL that overlaps the locus encoding a maize homolog of the recently described m6 A methylation reader protein ECT2 from Arabidopsis; this putative epi eQTL is associated with 53 genes and may represent a master epi-transcriptomic regulator of kernel development. Notably, among the genes associated with this epi eQTL, 10 are for the main storage proteins in the maize endosperm (zeins) and two are known regulators of zein expression or endosperm development (Opaque2 and ZmICE1). Collectively, beyond cataloging and characterizing genomic attributes of a large number of eQTL associated with kernel development in maize, our study highlights how an eQTL approach can bolster the impact of both GWAS and QTT studies and can drive insights about the basic biology of plants.
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Affiliation(s)
- Junling Pang
- Biotechnology Research InstituteChinese Academy of Agricultural SciencesBeijing100081China
| | - Junjie Fu
- Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijing100081China
| | - Na Zong
- Biotechnology Research InstituteChinese Academy of Agricultural SciencesBeijing100081China
| | - Jing Wang
- Biotechnology Research InstituteChinese Academy of Agricultural SciencesBeijing100081China
| | - Dandan Song
- Biotechnology Research InstituteChinese Academy of Agricultural SciencesBeijing100081China
| | - Xia Zhang
- Biotechnology Research InstituteChinese Academy of Agricultural SciencesBeijing100081China
| | - Cheng He
- Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijing100081China
| | - Ting Fang
- Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijing100081China
| | - Hongwei Zhang
- Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijing100081China
| | - Yunliu Fan
- Biotechnology Research InstituteChinese Academy of Agricultural SciencesBeijing100081China
| | - Guoying Wang
- Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijing100081China
| | - Jun Zhao
- Biotechnology Research InstituteChinese Academy of Agricultural SciencesBeijing100081China
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11
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Naureen Z, Sham A, Al Ashram H, Gilani SA, Al Gheilani S, Mabood F, Hussain J, Al Harrasi A, AbuQamar SF. Effect of phosphate nutrition on growth, physiology and phosphate transporter expression of cucumber seedlings. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2018; 127:211-222. [PMID: 29614440 DOI: 10.1016/j.plaphy.2018.03.028] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Revised: 03/22/2018] [Accepted: 03/23/2018] [Indexed: 06/08/2023]
Abstract
Although abundantly present in soils, inorganic phosphate (Pi) acquisition by plants is highly dependent on the transmembrane phosphate transporter (PT) gene family. Cucumber (Cucumis sativus) requires a large amount of phosphorus (P). The purpose of this study was to isolate the CsPT2-1 from cucumber roots, and to determine the influence of Pi nutrition on cucumber growth, metabolism and transcript levels of CsPT2-1 in tissues. Full length CsPT2-1 was cloned and phylogenetically identified. In two greenhouse experiments, P-deficient seedlings provided with low or high P concentrations were sampled at 10 and 21 days post treatment, respectively. Addition of P dramatically reduced growth of roots but not shoots. Supplying plants with high P resulted in increased total protein in leaves. Acid phosphatase activity increased significantly in leaves at any rate higher than 4 mM P. Increasing P concentration had a notable decrease in glucose concentrations in leaves of plants supplied with >0.5 mM P. In roots, glucose and starch concentrations increased with increasing P supply. Steady-state transcript levels of CsPT2-1 were high in P-deprived roots, but declined when plants were provided >10 mM P. To our knowledge, this is the first report focusing on a PT and its expression levels in cucumber.
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Affiliation(s)
- Zakira Naureen
- Department of Biological Sciences and Chemistry, University of Nizwa, Nizwa, Oman
| | - Arjun Sham
- Department of Biology, United Arab Emirates University, P.O. Box 15551, Al-Ain, United Arab Emirates
| | - Hibatullah Al Ashram
- Department of Biology, United Arab Emirates University, P.O. Box 15551, Al-Ain, United Arab Emirates
| | - Syed A Gilani
- Department of Biological Sciences and Chemistry, University of Nizwa, Nizwa, Oman
| | - Salma Al Gheilani
- Department of Biological Sciences and Chemistry, University of Nizwa, Nizwa, Oman
| | - Fazal Mabood
- Department of Biological Sciences and Chemistry, University of Nizwa, Nizwa, Oman
| | - Javid Hussain
- Department of Biological Sciences and Chemistry, University of Nizwa, Nizwa, Oman
| | - Ahmed Al Harrasi
- UoN Chair of Oman's Medicinal Plants and Marine Natural Products, University of Nizwa, Oman
| | - Synan F AbuQamar
- Department of Biology, United Arab Emirates University, P.O. Box 15551, Al-Ain, United Arab Emirates.
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12
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Samad‐Zamini M, Schweiger W, Nussbaumer T, Mayer KF, Buerstmayr H. Time-course expression QTL-atlas of the global transcriptional response of wheat to Fusarium graminearum. PLANT BIOTECHNOLOGY JOURNAL 2017; 15:1453-1464. [PMID: 28332274 PMCID: PMC5633761 DOI: 10.1111/pbi.12729] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2016] [Revised: 01/11/2017] [Accepted: 03/16/2017] [Indexed: 05/09/2023]
Abstract
Fusarium head blight is a devastating disease of small grain cereals such as bread wheat (Triticum aestivum). The pathogen switches from a biotrophic to a nectrotrophic lifestyle in course of disease development forcing its host to adapt its defence strategies. Using a genetical genomics approach, we illustrate genome-wide reconfigurations of genetic control over transcript abundances between two decisive time points after inoculation with the causative pathogen Fusarium graminearum. Whole transcriptome measurements have been recorded for 163 lines of a wheat doubled haploid population segregating for several resistance genes yielding 15 552 at 30 h and 15 888 eQTL at 50 h after inoculation. The genetic map saturated with transcript abundance-derived markers identified of a novel QTL on chromosome 6A, besides the previously reported QTL Fhb1 and Qfhs.ifa-5A. We find a highly different distribution of eQTL between time points with about 40% of eQTL being unique for the respective assessed time points. But also for more than 20% of genes governed by eQTL at either time point, genetic control changes in time. These changes are reflected in the dynamic compositions of three major regulatory hotspots on chromosomes 2B, 4A and 5A. In particular, control of defence-related biological mechanisms concentrated in the hotspot at 4A shift to hotspot 2B as the disease progresses. Hotspots do not colocalize with phenotypic QTL, and within their intervals no higher than expected number of eQTL was detected. Thus, resistance conferred by either QTL is mediated by few or single genes.
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Affiliation(s)
- Mina Samad‐Zamini
- Institute for Biotechnology in Plant Production (IFA‐Tulln)BOKU ‐ University of Natural Resources and Life SciencesTullnAustria
| | - Wolfgang Schweiger
- Institute for Biotechnology in Plant Production (IFA‐Tulln)BOKU ‐ University of Natural Resources and Life SciencesTullnAustria
- Present address:
BIOMIN Research CenterTulln3430Austria
| | - Thomas Nussbaumer
- Plant Genome and Systems BiologyHelmholtz Zentrum MünchenNeuherbergGermany
- Present address:
Division of Computational System BiologyDepartment of Microbiology and Ecosystem ScienceUniversity of ViennaVienna1090Austria
| | - Klaus F.X. Mayer
- Plant Genome and Systems BiologyHelmholtz Zentrum MünchenNeuherbergGermany
| | - Hermann Buerstmayr
- Institute for Biotechnology in Plant Production (IFA‐Tulln)BOKU ‐ University of Natural Resources and Life SciencesTullnAustria
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13
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Using RNA-Seq for Genomic Scaffold Placement, Correcting Assemblies, and Genetic Map Creation in a Common Brassica rapa Mapping Population. G3-GENES GENOMES GENETICS 2017; 7:2259-2270. [PMID: 28546385 PMCID: PMC5499133 DOI: 10.1534/g3.117.043000] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Brassica rapa is a model species for agronomic, ecological, evolutionary, and translational studies. Here, we describe high-density SNP discovery and genetic map construction for a B. rapa recombinant inbred line (RIL) population derived from field collected RNA sequencing (RNA-Seq) data. This high-density genotype data enables the detection and correction of putative genome misassemblies and accurate assignment of scaffold sequences to their likely genomic locations. These assembly improvements represent 7.1-8.0% of the annotated B. rapa genome. We demonstrate how using this new resource leads to a significant improvement for QTL analysis over the current low-density genetic map. Improvements are achieved by the increased mapping resolution and by having known genomic coordinates to anchor the markers for candidate gene discovery. These new molecular resources and improvements in the genome annotation will benefit the Brassicaceae genomics community and may help guide other communities in fine-tuning genome annotations.
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14
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Chai HH, Ho WK, Graham N, May S, Massawe F, Mayes S. A Cross-Species Gene Expression Marker-Based Genetic Map and QTL Analysis in Bambara Groundnut. Genes (Basel) 2017; 8:genes8020084. [PMID: 28241413 PMCID: PMC5333073 DOI: 10.3390/genes8020084] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Revised: 01/09/2017] [Accepted: 01/11/2017] [Indexed: 12/04/2022] Open
Abstract
Bambara groundnut (Vigna subterranea (L.) Verdc.) is an underutilised legume crop, which has long been recognised as a protein-rich and drought-tolerant crop, used extensively in Sub-Saharan Africa. The aim of the study was to identify quantitative trait loci (QTL) involved in agronomic and drought-related traits using an expression marker-based genetic map based on major crop resources developed in soybean. The gene expression markers (GEMs) were generated at the (unmasked) probe-pair level after cross-hybridisation of bambara groundnut leaf RNA to the Affymetrix Soybean Genome GeneChip. A total of 753 markers grouped at an LOD (Logarithm of odds) of three, with 527 markers mapped into linkage groups. From this initial map, a spaced expression marker-based genetic map consisting of 13 linkage groups containing 218 GEMs, spanning 982.7 cM (centimorgan) of the bambara groundnut genome, was developed. Of the QTL detected, 46% were detected in both control and drought treatment populations, suggesting that they are the result of intrinsic trait differences between the parental lines used to construct the cross, with 31% detected in only one of the conditions. The present GEM map in bambara groundnut provides one technically feasible route for the translation of information and resources from major and model plant species to underutilised and resource-poor crops.
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Affiliation(s)
- Hui Hui Chai
- Biotechnology Research Centre, School of Biosciences, University of Nottingham Malaysia Campus, Jalan Broga, Semenyih 43500, Selangor Darul Ehsan, Malaysia.
| | - Wai Kuan Ho
- Biotechnology Research Centre, School of Biosciences, University of Nottingham Malaysia Campus, Jalan Broga, Semenyih 43500, Selangor Darul Ehsan, Malaysia.
- Crops For the Future, Jalan Broga, Semenyih 43500, Selangor Darul Ehsan, Malaysia.
| | - Neil Graham
- Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Leics, Loughborough LE12 5RD, UK.
| | - Sean May
- Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Leics, Loughborough LE12 5RD, UK.
| | - Festo Massawe
- Biotechnology Research Centre, School of Biosciences, University of Nottingham Malaysia Campus, Jalan Broga, Semenyih 43500, Selangor Darul Ehsan, Malaysia.
- Crops For the Future, Jalan Broga, Semenyih 43500, Selangor Darul Ehsan, Malaysia.
| | - Sean Mayes
- Biotechnology Research Centre, School of Biosciences, University of Nottingham Malaysia Campus, Jalan Broga, Semenyih 43500, Selangor Darul Ehsan, Malaysia.
- Crops For the Future, Jalan Broga, Semenyih 43500, Selangor Darul Ehsan, Malaysia.
- Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Leics, Loughborough LE12 5RD, UK.
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15
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Zhang Y, Thomas CL, Xiang J, Long Y, Wang X, Zou J, Luo Z, Ding G, Cai H, Graham NS, Hammond JP, King GJ, White PJ, Xu F, Broadley MR, Shi L, Meng J. QTL meta-analysis of root traits in Brassica napus under contrasting phosphorus supply in two growth systems. Sci Rep 2016; 6:33113. [PMID: 27624881 PMCID: PMC5021999 DOI: 10.1038/srep33113] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 08/22/2016] [Indexed: 12/23/2022] Open
Abstract
A high-density SNP-based genetic linkage map was constructed and integrated with a previous map in the Tapidor x Ningyou7 (TNDH) Brassica napus population, giving a new map with a total of 2041 molecular markers and an average marker density which increased from 0.39 to 0.97 (0.82 SNP bin) per cM. Root and shoot traits were screened under low and 'normal' phosphate (Pi) supply using a 'pouch and wick' system, and had been screened previously in an agar based system. The P-efficient parent Ningyou7 had a shorter primary root length (PRL), greater lateral root density (LRD) and a greater shoot biomass than the P-inefficient parent Tapidor under both treatments and growth systems. Quantitative trait loci (QTL) analysis identified a total of 131 QTL, and QTL meta-analysis found four integrated QTL across the growth systems. Integration reduced the confidence interval by ~41%. QTL for root and shoot biomass were co-located on chromosome A3 and for lateral root emergence were co-located on chromosomes A4/C4 and C8/C9. There was a major QTL for LRD on chromosome C9 explaining ~18% of the phenotypic variation. QTL underlying an increased LRD may be a useful breeding target for P uptake efficiency in Brassica.
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Affiliation(s)
- Ying Zhang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China
| | - Catherine L. Thomas
- Plant and Crop Sciences Division, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, United Kingdom
| | - Jinxia Xiang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China
| | - Yan Long
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiaohua Wang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China
| | - Jun Zou
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China
| | - Ziliang Luo
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China
| | - Guangda Ding
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China
| | - Hongmei Cai
- Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China
| | - Neil S. Graham
- Plant and Crop Sciences Division, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, United Kingdom
| | - John P. Hammond
- School of Agriculture, Policy and Development, University of Reading, Reading RG6 6AR, United Kingdom
- Southern Cross Plant Science, Southern Cross University, Lismore NSW 2480, Australia
| | - Graham J. King
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China
- Plant and Crop Sciences Division, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, United Kingdom
- Southern Cross Plant Science, Southern Cross University, Lismore NSW 2480, Australia
| | - Philip J. White
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom
- King Saud University, Riyadh 11451, Kingdom of Saudi Arabia
| | - Fangsen Xu
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China
| | - Martin R. Broadley
- Plant and Crop Sciences Division, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, United Kingdom
| | - Lei Shi
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China
| | - Jinling Meng
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China
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16
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Ranjan A, Budke JM, Rowland SD, Chitwood DH, Kumar R, Carriedo L, Ichihashi Y, Zumstein K, Maloof JN, Sinha NR. eQTL Regulating Transcript Levels Associated with Diverse Biological Processes in Tomato. PLANT PHYSIOLOGY 2016; 172:328-40. [PMID: 27418589 PMCID: PMC5074602 DOI: 10.1104/pp.16.00289] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 07/11/2016] [Indexed: 05/18/2023]
Abstract
Variation in gene expression, in addition to sequence polymorphisms, is known to influence developmental, physiological, and metabolic traits in plants. Genetic mapping populations have facilitated identification of expression quantitative trait loci (eQTL), the genetic determinants of variation in gene expression patterns. We used an introgression population developed from the wild desert-adapted Solanum pennellii and domesticated tomato (Solanum lycopersicum) to identify the genetic basis of transcript level variation. We established the effect of each introgression on the transcriptome and identified approximately 7,200 eQTL regulating the steady-state transcript levels of 5,300 genes. Barnes-Hut t-distributed stochastic neighbor embedding clustering identified 42 modules revealing novel associations between transcript level patterns and biological processes. The results showed a complex genetic architecture of global transcript abundance pattern in tomato. Several genetic hot spots regulating a large number of transcript level patterns relating to diverse biological processes such as plant defense and photosynthesis were identified. Important eQTL regulating transcript level patterns were related to leaf number and complexity as well as hypocotyl length. Genes associated with leaf development showed an inverse correlation with photosynthetic gene expression, but eQTL regulating genes associated with leaf development and photosynthesis were dispersed across the genome. This comprehensive eQTL analysis details the influence of these loci on plant phenotypes and will be a valuable community resource for investigations on the genetic effects of eQTL on phenotypic traits in tomato.
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Affiliation(s)
- Aashish Ranjan
- Department of Plant Biology, University of California, Davis, California 95616
| | - Jessica M Budke
- Department of Plant Biology, University of California, Davis, California 95616
| | - Steven D Rowland
- Department of Plant Biology, University of California, Davis, California 95616
| | - Daniel H Chitwood
- Department of Plant Biology, University of California, Davis, California 95616
| | - Ravi Kumar
- Department of Plant Biology, University of California, Davis, California 95616
| | - Leonela Carriedo
- Department of Plant Biology, University of California, Davis, California 95616
| | - Yasunori Ichihashi
- Department of Plant Biology, University of California, Davis, California 95616
| | - Kristina Zumstein
- Department of Plant Biology, University of California, Davis, California 95616
| | - Julin N Maloof
- Department of Plant Biology, University of California, Davis, California 95616
| | - Neelima R Sinha
- Department of Plant Biology, University of California, Davis, California 95616
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17
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Xu Y. Envirotyping for deciphering environmental impacts on crop plants. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2016; 129:653-673. [PMID: 26932121 PMCID: PMC4799247 DOI: 10.1007/s00122-016-2691-5] [Citation(s) in RCA: 106] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Accepted: 02/08/2016] [Indexed: 05/17/2023]
Abstract
Global climate change imposes increasing impacts on our environments and crop production. To decipher environmental impacts on crop plants, the concept "envirotyping" is proposed, as a third "typing" technology, complementing with genotyping and phenotyping. Environmental factors can be collected through multiple environmental trials, geographic and soil information systems, measurement of soil and canopy properties, and evaluation of companion organisms. Envirotyping contributes to crop modeling and phenotype prediction through its functional components, including genotype-by-environment interaction (GEI), genes responsive to environmental signals, biotic and abiotic stresses, and integrative phenotyping. Envirotyping, driven by information and support systems, has a wide range of applications, including environmental characterization, GEI analysis, phenotype prediction, near-iso-environment construction, agronomic genomics, precision agriculture and breeding, and development of a four-dimensional profile of crop science involving genotype (G), phenotype (P), envirotype (E) and time (T) (developmental stage). In the future, envirotyping needs to zoom into specific experimental plots and individual plants, along with the development of high-throughput and precision envirotyping platforms, to integrate genotypic, phenotypic and envirotypic information for establishing a high-efficient precision breeding and sustainable crop production system based on deciphered environmental impacts.
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Affiliation(s)
- Yunbi Xu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, 100081, Beijing, China.
- International Maize and Wheat Improvement Center (CIMMYT), El Batan, Texcoco, CP 56130, Mexico.
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18
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Basnet RK, Del Carpio DP, Xiao D, Bucher J, Jin M, Boyle K, Fobert P, Visser RGF, Maliepaard C, Bonnema G. A Systems Genetics Approach Identifies Gene Regulatory Networks Associated with Fatty Acid Composition in Brassica rapa Seed. PLANT PHYSIOLOGY 2016; 170:568-85. [PMID: 26518343 PMCID: PMC4704567 DOI: 10.1104/pp.15.00853] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 10/27/2015] [Indexed: 05/19/2023]
Abstract
Fatty acids in seeds affect seed germination and seedling vigor, and fatty acid composition determines the quality of seed oil. In this study, quantitative trait locus (QTL) mapping of fatty acid and transcript abundance was integrated with gene network analysis to unravel the genetic regulation of seed fatty acid composition in a Brassica rapa doubled haploid population from a cross between a yellow sarson oil type and a black-seeded pak choi. The distribution of major QTLs for fatty acids showed a relationship with the fatty acid types: linkage group A03 for monounsaturated fatty acids, A04 for saturated fatty acids, and A05 for polyunsaturated fatty acids. Using a genetical genomics approach, expression quantitative trait locus (eQTL) hotspots were found at major fatty acid QTLs on linkage groups A03, A04, A05, and A09. An eQTL-guided gene coexpression network of lipid metabolism-related genes showed major hubs at the genes BrPLA2-ALPHA, BrWD-40, a number of seed storage protein genes, and the transcription factor BrMD-2, suggesting essential roles for these genes in lipid metabolism. Three subnetworks were extracted for the economically important and most abundant fatty acids erucic, oleic, linoleic, and linolenic acids. Network analysis, combined with comparison of the genome positions of cis- or trans-eQTLs with fatty acid QTLs, allowed the identification of candidate genes for genetic regulation of these fatty acids. The generated insights in the genetic architecture of fatty acid composition and the underlying complex gene regulatory networks in B. rapa seeds are discussed.
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Affiliation(s)
- Ram Kumar Basnet
- Wageningen UR Plant Breeding, Wageningen University and Research, 6708PB Wageningen, The Netherlands (R.K.B., D.P.D.C., D.X., J.B., R.G.F.V., C.M., G.B.);Centre for BioSystems Genomics, 6708PB Wageningen, The Netherlands (R.K.B., R.G.F.V., C.M.);Department of Agricultural Biotechnology, National Academy of Agricultural Science, Rural Development Administration, Suwon 441-707, Korea (M.J.); andNational Research Council of Canada, Saskatoon, Saskatchewan, Canada SK S7N 0W9 (K.B., P.F.)
| | - Dunia Pino Del Carpio
- Wageningen UR Plant Breeding, Wageningen University and Research, 6708PB Wageningen, The Netherlands (R.K.B., D.P.D.C., D.X., J.B., R.G.F.V., C.M., G.B.);Centre for BioSystems Genomics, 6708PB Wageningen, The Netherlands (R.K.B., R.G.F.V., C.M.);Department of Agricultural Biotechnology, National Academy of Agricultural Science, Rural Development Administration, Suwon 441-707, Korea (M.J.); andNational Research Council of Canada, Saskatoon, Saskatchewan, Canada SK S7N 0W9 (K.B., P.F.)
| | - Dong Xiao
- Wageningen UR Plant Breeding, Wageningen University and Research, 6708PB Wageningen, The Netherlands (R.K.B., D.P.D.C., D.X., J.B., R.G.F.V., C.M., G.B.);Centre for BioSystems Genomics, 6708PB Wageningen, The Netherlands (R.K.B., R.G.F.V., C.M.);Department of Agricultural Biotechnology, National Academy of Agricultural Science, Rural Development Administration, Suwon 441-707, Korea (M.J.); andNational Research Council of Canada, Saskatoon, Saskatchewan, Canada SK S7N 0W9 (K.B., P.F.)
| | - Johan Bucher
- Wageningen UR Plant Breeding, Wageningen University and Research, 6708PB Wageningen, The Netherlands (R.K.B., D.P.D.C., D.X., J.B., R.G.F.V., C.M., G.B.);Centre for BioSystems Genomics, 6708PB Wageningen, The Netherlands (R.K.B., R.G.F.V., C.M.);Department of Agricultural Biotechnology, National Academy of Agricultural Science, Rural Development Administration, Suwon 441-707, Korea (M.J.); andNational Research Council of Canada, Saskatoon, Saskatchewan, Canada SK S7N 0W9 (K.B., P.F.)
| | - Mina Jin
- Wageningen UR Plant Breeding, Wageningen University and Research, 6708PB Wageningen, The Netherlands (R.K.B., D.P.D.C., D.X., J.B., R.G.F.V., C.M., G.B.);Centre for BioSystems Genomics, 6708PB Wageningen, The Netherlands (R.K.B., R.G.F.V., C.M.);Department of Agricultural Biotechnology, National Academy of Agricultural Science, Rural Development Administration, Suwon 441-707, Korea (M.J.); andNational Research Council of Canada, Saskatoon, Saskatchewan, Canada SK S7N 0W9 (K.B., P.F.)
| | - Kerry Boyle
- Wageningen UR Plant Breeding, Wageningen University and Research, 6708PB Wageningen, The Netherlands (R.K.B., D.P.D.C., D.X., J.B., R.G.F.V., C.M., G.B.);Centre for BioSystems Genomics, 6708PB Wageningen, The Netherlands (R.K.B., R.G.F.V., C.M.);Department of Agricultural Biotechnology, National Academy of Agricultural Science, Rural Development Administration, Suwon 441-707, Korea (M.J.); andNational Research Council of Canada, Saskatoon, Saskatchewan, Canada SK S7N 0W9 (K.B., P.F.)
| | - Pierre Fobert
- Wageningen UR Plant Breeding, Wageningen University and Research, 6708PB Wageningen, The Netherlands (R.K.B., D.P.D.C., D.X., J.B., R.G.F.V., C.M., G.B.);Centre for BioSystems Genomics, 6708PB Wageningen, The Netherlands (R.K.B., R.G.F.V., C.M.);Department of Agricultural Biotechnology, National Academy of Agricultural Science, Rural Development Administration, Suwon 441-707, Korea (M.J.); andNational Research Council of Canada, Saskatoon, Saskatchewan, Canada SK S7N 0W9 (K.B., P.F.)
| | - Richard G F Visser
- Wageningen UR Plant Breeding, Wageningen University and Research, 6708PB Wageningen, The Netherlands (R.K.B., D.P.D.C., D.X., J.B., R.G.F.V., C.M., G.B.);Centre for BioSystems Genomics, 6708PB Wageningen, The Netherlands (R.K.B., R.G.F.V., C.M.);Department of Agricultural Biotechnology, National Academy of Agricultural Science, Rural Development Administration, Suwon 441-707, Korea (M.J.); andNational Research Council of Canada, Saskatoon, Saskatchewan, Canada SK S7N 0W9 (K.B., P.F.)
| | - Chris Maliepaard
- Wageningen UR Plant Breeding, Wageningen University and Research, 6708PB Wageningen, The Netherlands (R.K.B., D.P.D.C., D.X., J.B., R.G.F.V., C.M., G.B.);Centre for BioSystems Genomics, 6708PB Wageningen, The Netherlands (R.K.B., R.G.F.V., C.M.);Department of Agricultural Biotechnology, National Academy of Agricultural Science, Rural Development Administration, Suwon 441-707, Korea (M.J.); andNational Research Council of Canada, Saskatoon, Saskatchewan, Canada SK S7N 0W9 (K.B., P.F.)
| | - Guusje Bonnema
- Wageningen UR Plant Breeding, Wageningen University and Research, 6708PB Wageningen, The Netherlands (R.K.B., D.P.D.C., D.X., J.B., R.G.F.V., C.M., G.B.);Centre for BioSystems Genomics, 6708PB Wageningen, The Netherlands (R.K.B., R.G.F.V., C.M.);Department of Agricultural Biotechnology, National Academy of Agricultural Science, Rural Development Administration, Suwon 441-707, Korea (M.J.); andNational Research Council of Canada, Saskatoon, Saskatchewan, Canada SK S7N 0W9 (K.B., P.F.)
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19
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King GJ. Crop epigenetics and the molecular hardware of genotype × environment interactions. FRONTIERS IN PLANT SCIENCE 2015; 6:968. [PMID: 26594221 PMCID: PMC4635209 DOI: 10.3389/fpls.2015.00968] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Accepted: 10/22/2015] [Indexed: 05/04/2023]
Abstract
Crop plants encounter thermal environments which fluctuate on a diurnal and seasonal basis. Future climate resilient cultivars will need to respond to thermal profiles reflecting more variable conditions, and harness plasticity that involves regulation of epigenetic processes and complex genomic regulatory networks. Compartmentalization within plant cells insulates the genomic central processing unit within the interphase nucleus. This review addresses the properties of the chromatin hardware in which the genome is embedded, focusing on the biophysical and thermodynamic properties of DNA, histones and nucleosomes. It explores the consequences of thermal and ionic variation on the biophysical behavior of epigenetic marks such as DNA cytosine methylation (5mC), and histone variants such as H2A.Z, and how these contribute to maintenance of chromatin integrity in the nucleus, while enabling specific subsets of genes to be regulated. Information is drawn from theoretical molecular in vitro studies as well as model and crop plants and incorporates recent insights into the role epigenetic processes play in mediating between environmental signals and genomic regulation. A preliminary speculative framework is outlined, based on the evidence of what appears to be a cohesive set of interactions at molecular, biophysical and electrostatic level between the various components contributing to chromatin conformation and dynamics. It proposes that within plant nuclei, general and localized ionic homeostasis plays an important role in maintaining chromatin conformation, whilst maintaining complex genomic regulation that involves specific patterns of epigenetic marks. More generally, reversible changes in DNA methylation appear to be consistent with the ability of nuclear chromatin to manage variation in external ionic and temperature environment. Whilst tentative, this framework provides scope to develop experimental approaches to understand in greater detail the internal environment of plant nuclei. It is hoped that this will generate a deeper understanding of the molecular mechanisms underlying genotype × environment interactions that may be beneficial for long-term improvement of crop performance in less predictable climates.
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Affiliation(s)
- Graham J. King
- Southern Cross Plant Science, Southern Cross University, Lismore, NSW, Australia
- National Key Laboratory for Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Crops for the Future, Biotechnology and Breeding Systems, Semenyih, Malaysia
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20
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Hübner S, Korol AB, Schmid KJ. RNA-Seq analysis identifies genes associated with differential reproductive success under drought-stress in accessions of wild barley Hordeum spontaneum. BMC PLANT BIOLOGY 2015; 15:134. [PMID: 26055625 PMCID: PMC4459662 DOI: 10.1186/s12870-015-0528-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2014] [Accepted: 05/20/2015] [Indexed: 05/20/2023]
Abstract
BACKGROUND The evolutionary basis of reproductive success in different environments is of major interest in the study of plant adaptation. Since the reproductive stage is particularly sensitive to drought, genes affecting reproductive success during this stage are key players in the evolution of adaptive mechanisms. We used an ecological genomics approach to investigate the reproductive response of drought-tolerant and sensitive wild barley accessions originating from different habitats in the Levant. RESULTS We sequenced mRNA extracted from spikelets at the flowering stage in drought-treated and control plants. The barley genome was used for a reference-guided assembly and differential expression analysis. Our approach enabled to detect biological processes affecting grain production under drought stress. We detected novel candidate genes and differentially expressed alleles associated with drought tolerance. Drought associated genes were shown to be more conserved than non-associated genes, and drought-tolerance genes were found to evolve more rapidly than other drought associated genes. CONCLUSIONS We show that reproductive success under drought stress is not a habitat-specific trait but a shared physiological adaptation that appeared to evolve recently in the evolutionary history of wild barley. Exploring the genomic basis of reproductive success under stress in crop wild progenitors is expected to have considerable ecological and economical applications.
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Affiliation(s)
- Sariel Hübner
- Department of Evolutionary and Environmental Biology, University of Haifa, Mt. Carmel 31905, Haifa, Israel.
- Current address: Department of Botany, University of British Columbia, Vancouver, Canada.
| | - Abraham B Korol
- Department of Evolutionary and Environmental Biology, University of Haifa, Mt. Carmel 31905, Haifa, Israel.
| | - Karl J Schmid
- Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, D-70593, Stuttgart, Germany.
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21
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Fan F, Cui B, Zhang T, Qiao G, Ding G, Wen X. The temporal transcriptomic response of Pinus massoniana seedlings to phosphorus deficiency. PLoS One 2014; 9:e105068. [PMID: 25165828 PMCID: PMC4148236 DOI: 10.1371/journal.pone.0105068] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Accepted: 07/20/2014] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Phosphorus (P) is an essential macronutrient for plant growth and development. Several genes involved in phosphorus deficiency stress have been identified in various plant species. However, a whole genome understanding of the molecular mechanisms involved in plant adaptations to low P remains elusive, and there is particularly little information on the genetic basis of these acclimations in coniferous trees. Masson pine (Pinus massoniana) is grown mainly in the tropical and subtropical regions in China, many of which are severely lacking in inorganic phosphate (Pi). In previous work, we described an elite P. massoniana genotype demonstrating a high tolerance to Pi-deficiency. METHODOLOGY/PRINCIPAL FINDINGS To further investigate the mechanism of tolerance to low P, RNA-seq was performed to give an idea of extent of expression from the two mixed libraries, and microarray whose probes were designed based on the unigenes obtained from RNA-seq was used to elucidate the global gene expression profiles for the long-term phosphorus starvation. A total of 70,896 unigenes with lengths ranging from 201 to 20,490 bp were assembled from 112,108,862 high quality reads derived from RNA-Seq libraries. We identified 1,396 and 943 transcripts that were differentially regulated (P<0.05) under P1 (0.01 mM P) and P2 (0.06 mM P) Pi-deficiency conditions, respectively. Numerous transcripts were consistently differentially regulated under Pi deficiency stress, many of which were also up- or down-regulated in other species under the corresponding conditions, and are therefore ideal candidates for monitoring the P status of plants. The results also demonstrated the impact of different Pi starvation levels on global gene expression in Masson pine. CONCLUSIONS/SIGNIFICANCE To our knowledge, this work provides the first insight into the molecular mechanisms involved in acclimation to long-term Pi starvation and different Pi availability levels in coniferous trees.
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Affiliation(s)
- Fuhua Fan
- Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous region (Guizhou University), Ministry of Education, Institute of Agro-bioengineering, Guizhou University, Guiyang, Guizhou Province, People’s Republic of China
- School of Forestry Science, Guizhou University, Guiyang, Guizhou Province, People’s Republic of China
- The School of Nuclear Technology and Chemical and Biological, Hubei University of Science and Technology, Xianning, Hubei Province, People’s Republic of China
| | - Bowen Cui
- Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous region (Guizhou University), Ministry of Education, Institute of Agro-bioengineering, Guizhou University, Guiyang, Guizhou Province, People’s Republic of China
| | - Ting Zhang
- Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous region (Guizhou University), Ministry of Education, Institute of Agro-bioengineering, Guizhou University, Guiyang, Guizhou Province, People’s Republic of China
| | - Guang Qiao
- Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous region (Guizhou University), Ministry of Education, Institute of Agro-bioengineering, Guizhou University, Guiyang, Guizhou Province, People’s Republic of China
| | - Guijie Ding
- School of Forestry Science, Guizhou University, Guiyang, Guizhou Province, People’s Republic of China
| | - Xiaopeng Wen
- Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous region (Guizhou University), Ministry of Education, Institute of Agro-bioengineering, Guizhou University, Guiyang, Guizhou Province, People’s Republic of China
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22
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Zhou L, Bawa R, Holliday JA. Exome resequencing reveals signatures of demographic and adaptive processes across the genome and range of black cottonwood (Populus trichocarpa). Mol Ecol 2014; 23:2486-99. [PMID: 24750333 DOI: 10.1111/mec.12752] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2013] [Revised: 04/09/2014] [Accepted: 04/11/2014] [Indexed: 12/11/2022]
Abstract
Extant variation in temperate and boreal plant species has been influenced by both demographic histories associated with Pleistocene glacial cycles and adaptation to local climate. We used sequence capture to investigate the role of these neutral and adaptive processes in shaping diversity in black cottonwood (Populus trichocarpa). Nucleotide diversity and Tajima's D were lowest at replacement sites and highest at intergenic sites, while LD showed the opposite pattern. With samples grouped into three populations arrayed latitudinally, effective population size was highest in the north, followed by south and centre, and LD was highest in the south followed by the north and centre, suggesting a possible northern glacial refuge. FST outlier analysis revealed that promoter, 5'-UTR and intronic sites were enriched for outliers compared with coding regions, while no outliers were found among intergenic sites. Codon usage bias was evident, and genes with synonymous outliers had 30% higher average expression compared with genes containing replacement outliers. These results suggest divergent selection related to regulation of gene expression is important to local adaptation in P. trichocarpa. Finally, within-population selective sweeps were much more pronounced in the central population than in putative northern and southern refugia, which may reflect the different demographic histories of the populations and concomitant effects on signatures of genetic hitchhiking from standing variation.
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Affiliation(s)
- L Zhou
- Department of Forest Resources and Environmental Conservation, Virginia Polytechnic Institute and State University, 304 Cheatham Hall, Blacksburg, VA, 24061, USA
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23
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Graham NS, Hammond JP, Lysenko A, Mayes S, O Lochlainn S, Blasco B, Bowen HC, Rawlings CJ, Rios JJ, Welham S, Carion PWC, Dupuy LX, King GJ, White PJ, Broadley MR. Genetical and comparative genomics of Brassica under altered Ca supply identifies Arabidopsis Ca-transporter orthologs. THE PLANT CELL 2014; 26:2818-30. [PMID: 25082855 PMCID: PMC4145116 DOI: 10.1105/tpc.114.128603] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Revised: 06/09/2014] [Accepted: 07/14/2014] [Indexed: 05/18/2023]
Abstract
Although Ca transport in plants is highly complex, the overexpression of vacuolar Ca(2+) transporters in crops is a promising new technology to improve dietary Ca supplies through biofortification. Here, we sought to identify novel targets for increasing plant Ca accumulation using genetical and comparative genomics. Expression quantitative trait locus (eQTL) mapping to 1895 cis- and 8015 trans-loci were identified in shoots of an inbred mapping population of Brassica rapa (IMB211 × R500); 23 cis- and 948 trans-eQTLs responded specifically to altered Ca supply. eQTLs were screened for functional significance using a large database of shoot Ca concentration phenotypes of Arabidopsis thaliana. From 31 Arabidopsis gene identifiers tagged to robust shoot Ca concentration phenotypes, 21 mapped to 27 B. rapa eQTLs, including orthologs of the Ca(2+) transporters At-CAX1 and At-ACA8. Two of three independent missense mutants of BraA.cax1a, isolated previously by targeting induced local lesions in genomes, have allele-specific shoot Ca concentration phenotypes compared with their segregating wild types. BraA.CAX1a is a promising target for altering the Ca composition of Brassica, consistent with prior knowledge from Arabidopsis. We conclude that multiple-environment eQTL analysis of complex crop genomes combined with comparative genomics is a powerful technique for novel gene identification/prioritization.
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Affiliation(s)
- Neil S Graham
- Plant and Crop Sciences Division, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, United Kingdom
| | - John P Hammond
- School of Agriculture, Policy, and Development, University of Reading, Earley Gate, Whiteknights, Reading RG6 6AR, United Kingdom
| | - Artem Lysenko
- Computational and Systems Biology Department, Rothamsted Research, West Common, Harpenden AL5 2JQ, United Kingdom
| | - Sean Mayes
- Crops for the Future Research Centre, Jalan Broga, 43500 Semenyih, Selangor Darul Ehsan, Malaysia
| | - Seosamh O Lochlainn
- Plant and Crop Sciences Division, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, United Kingdom
| | - Bego Blasco
- Plant and Crop Sciences Division, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, United Kingdom
| | - Helen C Bowen
- Warwick HRI, University of Warwick, Wellesbourne CV35 9EF, United Kingdom
| | - Chris J Rawlings
- Computational and Systems Biology Department, Rothamsted Research, West Common, Harpenden AL5 2JQ, United Kingdom
| | - Juan J Rios
- Plant and Crop Sciences Division, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, United Kingdom
| | - Susan Welham
- Computational and Systems Biology Department, Rothamsted Research, West Common, Harpenden AL5 2JQ, United Kingdom
| | - Pierre W C Carion
- Computational and Systems Biology Department, Rothamsted Research, West Common, Harpenden AL5 2JQ, United Kingdom
| | - Lionel X Dupuy
- James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom
| | - Graham J King
- Southern Cross Plant Science, Southern Cross University, Lismore, New South Wales 2480, Australia
| | - Philip J White
- James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom College of Science, King Saud University, Riyadh 11451, Kingdom of Saudi Arabia
| | - Martin R Broadley
- Plant and Crop Sciences Division, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, United Kingdom
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24
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Bloomfield JA, Rose TJ, King GJ. Sustainable harvest: managing plasticity for resilient crops. PLANT BIOTECHNOLOGY JOURNAL 2014; 12:517-33. [PMID: 24891039 PMCID: PMC4207195 DOI: 10.1111/pbi.12198] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Accepted: 04/14/2014] [Indexed: 05/18/2023]
Abstract
Maintaining crop production to feed a growing world population is a major challenge for this period of rapid global climate change. No consistent conceptual or experimental framework for crop plants integrates information at the levels of genome regulation, metabolism, physiology and response to growing environment. An important role for plasticity in plants is assisting in homeostasis in response to variable environmental conditions. Here, we outline how plant plasticity is facilitated by epigenetic processes that modulate chromatin through dynamic changes in DNA methylation, histone variants, small RNAs and transposable elements. We present examples of plant plasticity in the context of epigenetic regulation of developmental phases and transitions and map these onto the key stages of crop establishment, growth, floral initiation, pollination, seed set and maturation of harvestable product. In particular, we consider how feedback loops of environmental signals and plant nutrition affect plant ontogeny. Recent advances in understanding epigenetic processes enable us to take a fresh look at the crosstalk between regulatory systems that confer plasticity in the context of crop development. We propose that these insights into genotype × environment (G × E) interaction should underpin development of new crop management strategies, both in terms of information-led agronomy and in recognizing the role of epigenetic variation in crop breeding.
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Affiliation(s)
- Justin A Bloomfield
- Southern Cross Plant Science, Southern Cross UniversityLismore, NSW, Australia
| | - Terry J Rose
- Southern Cross Plant Science, Southern Cross UniversityLismore, NSW, Australia
| | - Graham J King
- Southern Cross Plant Science, Southern Cross UniversityLismore, NSW, Australia
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25
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Wray GA. Genomics and the Evolution of Phenotypic Traits. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2013. [DOI: 10.1146/annurev-ecolsys-110512-135828] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Evolutionary genetics has entered an unprecedented era of discovery, catalyzed in large part by the development of technologies that provide information about genome sequence and function. An important benefit is the ability to move beyond a handful of model organisms in lab settings to identify the genetic basis for evolutionarily interesting traits in many organisms in natural settings. Other benefits are the abilities to identify causal mutations and validate their phenotypic consequences more readily and in many more species. Genomic technologies have reinvigorated interest in some of the most fundamental and persistent questions in evolutionary genetics, revealed previously unsuspected evolutionary phenomena, and opened the door to a wide range of new questions.
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Affiliation(s)
- Gregory A. Wray
- Department of Biology and Institute for Genome Sciences & Policy, Duke University, Durham, North Carolina 27701
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26
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Des Marais DL, Hernandez KM, Juenger TE. Genotype-by-Environment Interaction and Plasticity: Exploring Genomic Responses of Plants to the Abiotic Environment. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2013. [DOI: 10.1146/annurev-ecolsys-110512-135806] [Citation(s) in RCA: 256] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- David L. Des Marais
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas 78712;
| | - Kyle M. Hernandez
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas 78712;
| | - Thomas E. Juenger
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas 78712;
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712
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27
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Shi L, Shi T, Broadley MR, White PJ, Long Y, Meng J, Xu F, Hammond JP. High-throughput root phenotyping screens identify genetic loci associated with root architectural traits in Brassica napus under contrasting phosphate availabilities. ANNALS OF BOTANY 2013; 112:381-9. [PMID: 23172414 PMCID: PMC3698377 DOI: 10.1093/aob/mcs245] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2012] [Accepted: 09/25/2012] [Indexed: 05/18/2023]
Abstract
BACKGROUND AND AIMS Phosphate (Pi) deficiency in soils is a major limiting factor for crop growth worldwide. Plant growth under low Pi conditions correlates with root architectural traits and it may therefore be possible to select these traits for crop improvement. The aim of this study was to characterize root architectural traits, and to test quantitative trait loci (QTL) associated with these traits, under low Pi (LP) and high Pi (HP) availability in Brassica napus. METHODS Root architectural traits were characterized in seedlings of a double haploid (DH) mapping population (n = 190) of B. napus ['Tapidor' × 'Ningyou 7' (TNDH)] using high-throughput phenotyping methods. Primary root length (PRL), lateral root length (LRL), lateral root number (LRN), lateral root density (LRD) and biomass traits were measured 12 d post-germination in agar at LP and HP. KEY RESULTS In general, root and biomass traits were highly correlated under LP and HP conditions. 'Ningyou 7' had greater LRL, LRN and LRD than 'Tapidor', at both LP and HP availability, but smaller PRL. A cluster of highly significant QTL for LRN, LRD and biomass traits at LP availability were identified on chromosome A03; QTL for PRL were identified on chromosomes A07 and C06. CONCLUSIONS High-throughput phenotyping of Brassica can be used to identify root architectural traits which correlate with shoot biomass. It is feasible that these traits could be used in crop improvement strategies. The identification of QTL linked to root traits under LP and HP conditions provides further insights on the genetic basis of plant tolerance to P deficiency, and these QTL warrant further dissection.
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Affiliation(s)
- Lei Shi
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Taoxiong Shi
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Martin R. Broadley
- Plant and Crop Sciences Division, School of Biosciences, Sutton Bonington Campus, University of Nottingham, Loughborough LE12 5RD, UK
| | | | - Yan Long
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Jinling Meng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Fangsen Xu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - John P. Hammond
- School of Plant Biology and Institute of Agriculture, University of Western Australia, Crawley, WA 6009, Australia
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28
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Juenger TE. Natural variation and genetic constraints on drought tolerance. CURRENT OPINION IN PLANT BIOLOGY 2013; 16:274-81. [PMID: 23462639 DOI: 10.1016/j.pbi.2013.02.001] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2013] [Revised: 01/30/2013] [Accepted: 02/01/2013] [Indexed: 05/20/2023]
Abstract
Drought is a central abiotic stress for both natural plant populations and agricultural crops. Substantial natural genetic variation in drought resistance traits has been identified in plant populations, crop species, and laboratory model systems. In particular, studies in Arabidopsis thaliana have discovered variation in a number of key physiological traits involved in plant-water relations that may underlie evolved drought stress responses among accessions. Despite this abundant variation, we still know little about the complex genetic architecture of drought tolerance or its role in constraining evolution. Unfortunately, few natural allelic variants have been cloned for drought related traits--progress cloning QTL, the use of RNA-sequencing methods for evaluating gene expression responses to soil drying, and improved methodology for exploring complex multivariate data all hold promise for moving the field forward. In particular, a better understanding of the molecular nature of pleiotropic gene action and the genetics of phenotypic plasticity will give insight into local adaptation in plants and provide new avenues for improving crops.
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Affiliation(s)
- Thomas E Juenger
- Section of Integrative Biology and Institute of Cellular and Molecular Biology, University of Texas at Austin, 2401 Speedway Boulevard, Austin, TX 78712, USA.
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29
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Shi T, Li R, Zhao Z, Ding G, Long Y, Meng J, Xu F, Shi L. QTL for yield traits and their association with functional genes in response to phosphorus deficiency in Brassica napus. PLoS One 2013; 8:e54559. [PMID: 23382913 PMCID: PMC3557265 DOI: 10.1371/journal.pone.0054559] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2012] [Accepted: 12/14/2012] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Oilseed rape (Brassica napus L.) is one of the most important oil crops. A primary limitation to the cultivation of this crop is the lack of available phosphorus (P) in soils. To elucidate the genetic control of P deficiency tolerance in Brassica napus, quantitative trait locus (QTL) for seed yield and yield related-traits in response to P deficiency were identified using a double haploid mapping population (TN DH) derived from a cross between a P-efficient cultivar, Ningyou 7 and a P-inefficient cultivar, Tapidor. RESULTS Three field trials were conducted to determine seed yield (SY), plant height (PH), number of primary branches (BN), height to the first primary branch (FBH), relative first primary branch height (RBH), pod number per plant (PN), seed number per pod (SN) and seed weight of 1,000 seeds (SW) in 188 lines of TN DH population exposed to low P (LP) and optimal P (OP) conditions. P deficiency decreased PH, BN, SN, PN and SY, and increased FBH and RBH with no effect on SW. Three reproducible LP-specific QTL regions were identified on chromosomes A2, A3 and A5 that controlled SN, PN and SW respectively. In addition, six reproducible constitutive regions were also mapped with two each for SY-LP on A2, and FBH-LP on C6 and one each for PH-LP and SW-LP on A3. About 30 markers derived from 19 orthologous genes involved in Arabidopsis P homeostasis were mapped on 24 QTL regions by comparative mapping between Arabidopsis and Brassica napus. Among these genes, GPT1, MGD2 and SIZ1 were associated with two major loci regulating SY-LP and other yield-related traits on A2 between 77.1 and 95.0 cM. CONCLUSION The stable QTLs detected under LP conditions and their candidate genes may provide useful information for marker-assisted selection in breeding high-yield B. napus varieties with improved P efficiency.
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Affiliation(s)
- Taoxiong Shi
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Ruiyuan Li
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Zunkang Zhao
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Guangda Ding
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Yan Long
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Jinling Meng
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Fangsen Xu
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Lei Shi
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
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Veneklaas EJ, Lambers H, Bragg J, Finnegan PM, Lovelock CE, Plaxton WC, Price CA, Scheible WR, Shane MW, White PJ, Raven JA. Opportunities for improving phosphorus-use efficiency in crop plants. THE NEW PHYTOLOGIST 2012; 195:306-320. [PMID: 22691045 DOI: 10.1111/j.1469-8137.2012.04190.x] [Citation(s) in RCA: 345] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Limitation of grain crop productivity by phosphorus (P) is widespread and will probably increase in the future. Enhanced P efficiency can be achieved by improved uptake of phosphate from soil (P-acquisition efficiency) and by improved productivity per unit P taken up (P-use efficiency). This review focuses on improved P-use efficiency, which can be achieved by plants that have overall lower P concentrations, and by optimal distribution and redistribution of P in the plant allowing maximum growth and biomass allocation to harvestable plant parts. Significant decreases in plant P pools may be possible, for example, through reductions of superfluous ribosomal RNA and replacement of phospholipids by sulfolipids and galactolipids. Improvements in P distribution within the plant may be possible by increased remobilization from tissues that no longer need it (e.g. senescing leaves) and reduced partitioning of P to developing grains. Such changes would prolong and enhance the productive use of P in photosynthesis and have nutritional and environmental benefits. Research considering physiological, metabolic, molecular biological, genetic and phylogenetic aspects of P-use efficiency is urgently needed to allow significant progress to be made in our understanding of this complex trait.
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Affiliation(s)
- Erik J Veneklaas
- School of Plant Biology, The University of Western Australia, Crawley, WA 6009, Australia
- Institute of Agriculture, The University of Western Australia, Crawley, WA 6009Australia
| | - Hans Lambers
- School of Plant Biology, The University of Western Australia, Crawley, WA 6009, Australia
- Institute of Agriculture, The University of Western Australia, Crawley, WA 6009Australia
| | - Jason Bragg
- CSIRO Plant Industry, GPO Box 1600, Canberra, ACT 2601, Australia
| | - Patrick M Finnegan
- School of Plant Biology, The University of Western Australia, Crawley, WA 6009, Australia
- Institute of Agriculture, The University of Western Australia, Crawley, WA 6009Australia
| | - Catherine E Lovelock
- School of Biological Sciences, The University of Queensland, St Lucia, QLD 4072, Australia
| | - William C Plaxton
- Department of Biology and Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada K7L 3N6
| | - Charles A Price
- School of Plant Biology, The University of Western Australia, Crawley, WA 6009, Australia
| | | | - Michael W Shane
- School of Plant Biology, The University of Western Australia, Crawley, WA 6009, Australia
| | - Philip J White
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - John A Raven
- School of Plant Biology, The University of Western Australia, Crawley, WA 6009, Australia
- Division of Plant Sciences, University of Dundee at the James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
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Love CG, Andongabo AE, Wang J, Carion PWC, Rawlings CJ, King GJ. InterStoreDB: a generic integration resource for genetic and genomic data. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2012; 54:345-55. [PMID: 22494395 DOI: 10.1111/j.1744-7909.2012.01120.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Associating phenotypic traits and quantitative trait loci (QTL) to causative regions of the underlying genome is a key goal in agricultural research. InterStoreDB is a suite of integrated databases designed to assist in this process. The individual databases are species independent and generic in design, providing access to curated datasets relating to plant populations, phenotypic traits, genetic maps, marker loci and QTL, with links to functional gene annotation and genomic sequence data. Each component database provides access to associated metadata, including data provenance and parameters used in analyses, thus providing users with information to evaluate the relative worth of any associations identified. The databases include CropStoreDB, for management of population, genetic map, QTL and trait measurement data, SeqStoreDB for sequence-related data and AlignStoreDB, which stores sequence alignment information, and allows navigation between genetic and genomic datasets. Genetic maps are visualized and compared using the CMAP tool, and functional annotation from sequenced genomes is provided via an EnsEMBL-based genome browser. This framework facilitates navigation of the multiple biological domains involved in genetics and genomics research in a transparent manner within a single portal. We demonstrate the value of InterStoreDB as a tool for Brassica research. InterStoreDB is available from: http://www.interstoredb.org.
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Affiliation(s)
- Christopher G Love
- Ludwig Institute for Cancer Research, Centre for Medical Research, Royal Melbourne Hospital, Royal Parade, Parkville, Victoria 3050, Australia.
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Fita A, Bowen HC, Hayden RM, Nuez F, Picó B, Hammond JP. Diversity in expression of phosphorus (P) responsive genes in Cucumis melo L. PLoS One 2012; 7:e35387. [PMID: 22536378 PMCID: PMC3334927 DOI: 10.1371/journal.pone.0035387] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2011] [Accepted: 03/15/2012] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Phosphorus (P) is a major limiting nutrient for plant growth in many soils. Studies in model species have identified genes involved in plant adaptations to low soil P availability. However, little information is available on the genetic bases of these adaptations in vegetable crops. In this respect, sequence data for melon now makes it possible to identify melon orthologues of candidate P responsive genes, and the expression of these genes can be used to explain the diversity in the root system adaptation to low P availability, recently observed in this species. METHODOLOGY AND FINDINGS Transcriptional responses to P starvation were studied in nine diverse melon accessions by comparing the expression of eight candidate genes (Cm-PAP10.1, Cm-PAP10.2, Cm-RNS1, Cm-PPCK1, Cm-transferase, Cm-SQD1, Cm-DGD1 and Cm-SPX2) under P replete and P starved conditions. Differences among melon accessions were observed in response to P starvation, including differences in plant morphology, P uptake, P use efficiency (PUE) and gene expression. All studied genes were up regulated under P starvation conditions. Differences in the expression of genes involved in P mobilization and remobilization (Cm-PAP10.1, Cm-PAP10.2 and Cm-RNS1) under P starvation conditions explained part of the differences in P uptake and PUE among melon accessions. The levels of expression of the other studied genes were diverse among melon accessions, but contributed less to the phenotypical response of the accessions. CONCLUSIONS This is the first time that these genes have been described in the context of P starvation responses in melon. There exists significant diversity in gene expression levels and P use efficiency among melon accessions as well as significant correlations between gene expression levels and phenotypical measurements.
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Affiliation(s)
- Ana Fita
- Centro de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Valencia, Spain.
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Cubillos FA, Coustham V, Loudet O. Lessons from eQTL mapping studies: non-coding regions and their role behind natural phenotypic variation in plants. CURRENT OPINION IN PLANT BIOLOGY 2012; 15:192-8. [PMID: 22265229 DOI: 10.1016/j.pbi.2012.01.005] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2011] [Revised: 12/17/2011] [Accepted: 01/03/2012] [Indexed: 05/24/2023]
Abstract
Even if considerable progress has been achieved towards the understanding of natural variation in plant systems, the contribution of transcript abundance variation to phenotypic diversity remains unappreciated. Over the last decade, efforts to characterise the genome-wide expression variation in natural accessions, structured populations and hybrids have improved our knowledge of the contribution of non-coding polymorphisms to gene expression regulation. Moreover, new studies are helping to unravel the role of expression polymorphisms and their orchestrated performance. Recent advances involving classical linkage analysis, GWAS and improved eQTL mapping strategies will provide a greater resolution to determine the genetic variants shaping the broad diversity in plant systems.
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Affiliation(s)
- Francisco A Cubillos
- Institut Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech, F-78000 Versailles, France
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Nussaume L, Kanno S, Javot H, Marin E, Pochon N, Ayadi A, Nakanishi TM, Thibaud MC. Phosphate Import in Plants: Focus on the PHT1 Transporters. FRONTIERS IN PLANT SCIENCE 2011; 2:83. [PMID: 22645553 PMCID: PMC3355772 DOI: 10.3389/fpls.2011.00083] [Citation(s) in RCA: 281] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2011] [Accepted: 11/03/2011] [Indexed: 05/17/2023]
Abstract
The main source of phosphorus for plants is inorganic phosphate (Pi), which is characterized by its poor availability and low mobility. Uptake of this element from the soil relies heavily upon the PHT1 transporters, a specific family of plant plasma membrane proteins that were identified by homology with the yeast PHO84 Pi transporter. Since the discovery of PHT1 transporters in 1996, various studies have revealed that their function is controlled by a highly complex network of regulation. This review will summarize the current state of research on plant PHT1 multigenic families, including physiological, biochemical, molecular, cellular, and genetics studies.
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Affiliation(s)
- Laurent Nussaume
- IBEB-SBVME Laboratoire de Biologie du Développement des Plantes, UMR6191 CNRS-Commissariat à l’Energie Atomique et aux Energies Alternatives Cadarache, Université Aix-Marseille, F-13108 Saint-Paul-lez-DuranceFrance
| | - Satomi Kanno
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-kuTokyo, Japan 113-8657
| | - Hélène Javot
- IBEB-SBVME Laboratoire de Biologie du Développement des Plantes, UMR6191 CNRS-Commissariat à l’Energie Atomique et aux Energies Alternatives Cadarache, Université Aix-Marseille, F-13108 Saint-Paul-lez-DuranceFrance
| | - Elena Marin
- IBEB-SBVME Laboratoire de Biologie du Développement des Plantes, UMR6191 CNRS-Commissariat à l’Energie Atomique et aux Energies Alternatives Cadarache, Université Aix-Marseille, F-13108 Saint-Paul-lez-DuranceFrance
| | - Nathalie Pochon
- IBEB-SBVME Laboratoire de Biologie du Développement des Plantes, UMR6191 CNRS-Commissariat à l’Energie Atomique et aux Energies Alternatives Cadarache, Université Aix-Marseille, F-13108 Saint-Paul-lez-DuranceFrance
| | - Amal Ayadi
- IBEB-SBVME Laboratoire de Biologie du Développement des Plantes, UMR6191 CNRS-Commissariat à l’Energie Atomique et aux Energies Alternatives Cadarache, Université Aix-Marseille, F-13108 Saint-Paul-lez-DuranceFrance
| | - Tomoko M. Nakanishi
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-kuTokyo, Japan 113-8657
| | - Marie-Christine Thibaud
- IBEB-SBVME Laboratoire de Biologie du Développement des Plantes, UMR6191 CNRS-Commissariat à l’Energie Atomique et aux Energies Alternatives Cadarache, Université Aix-Marseille, F-13108 Saint-Paul-lez-DuranceFrance
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Hammond JP, Broadley MR, Bowen HC, Spracklen WP, Hayden RM, White PJ. Gene expression changes in phosphorus deficient potato (Solanum tuberosum L.) leaves and the potential for diagnostic gene expression markers. PLoS One 2011; 6:e24606. [PMID: 21935429 PMCID: PMC3173461 DOI: 10.1371/journal.pone.0024606] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2011] [Accepted: 08/14/2011] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND There are compelling economic and environmental reasons to reduce our reliance on inorganic phosphate (Pi) fertilisers. Better management of Pi fertiliser applications is one option to improve the efficiency of Pi fertiliser use, whilst maintaining crop yields. Application rates of Pi fertilisers are traditionally determined from analyses of soil or plant tissues. Alternatively, diagnostic genes with altered expression under Pi limiting conditions that suggest a physiological requirement for Pi fertilisation, could be used to manage Pifertiliser applications, and might be more precise than indirect measurements of soil or tissue samples. RESULTS We grew potato (Solanum tuberosum L.) plants hydroponically, under glasshouse conditions, to control their nutrient status accurately. Samples of total leaf RNA taken periodically after Pi was removed from the nutrient solution were labelled and hybridised to potato oligonucleotide arrays. A total of 1,659 genes were significantly differentially expressed following Pi withdrawal. These included genes that encode proteins involved in lipid, protein, and carbohydrate metabolism, characteristic of Pi deficient leaves and included potential novel roles for genes encoding patatin like proteins in potatoes. The array data were analysed using a support vector machine algorithm to identify groups of genes that could predict the Pi status of the crop. These groups of diagnostic genes were tested using field grown potatoes that had either been fertilised or unfertilised. A group of 200 genes could correctly predict the Pi status of field grown potatoes. CONCLUSIONS This paper provides a proof-of-concept demonstration for using microarrays and class prediction tools to predict the Pi status of a field grown potato crop. There is potential to develop this technology for other biotic and abiotic stresses in field grown crops. Ultimately, a better understanding of crop stresses may improve our management of the crop, improving the sustainability of agriculture.
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Affiliation(s)
- John P Hammond
- Division of Plant and Crop Sciences, University of Nottingham, Loughborough, United Kingdom.
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Delker C, Quint M. Expression level polymorphisms: heritable traits shaping natural variation. TRENDS IN PLANT SCIENCE 2011; 16:481-488. [PMID: 21700486 DOI: 10.1016/j.tplants.2011.05.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2011] [Revised: 05/12/2011] [Accepted: 05/18/2011] [Indexed: 05/31/2023]
Abstract
Natural accessions of many species harbor a wealth of genetic variation visible in a large array of phenotypes. Although expression level polymorphisms (ELPs) in several genes have been shown to contribute to variation in diverse traits, their general impact on adaptive variation has likely been underestimated. At present, ELPs have predominantly been correlated to quantitative trait loci (eQTLs) that occupy central hubs in signaling networks, which pleiotropically affect numerous traits. To increase the sensitivity of detecting minor effect eQTLs or those that act in a trait-specific manner, we emphasize the need for more systematic approaches. This requires, but is not limited to, refining experimental designs such as reduction of tissue complexity and combinatorial methods including a priori defined networks.
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Affiliation(s)
- Carolin Delker
- Leibniz Institute of Plant Biochemistry, Independent Junior Research Group, Department of Molecular Signal Processing, Weinberg 3, 06120 Halle (Saale), Germany
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