46
views
0
recommends
+1 Recommend
0 collections
    0
    shares
      • Record: found
      • Abstract: found
      • Article: found
      Is Open Access

      Crop epigenetics and the molecular hardware of genotype × environment interactions

      review-article

      Read this article at

      Bookmark
          There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

          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.

          Related collections

          Most cited references190

          • Record: found
          • Abstract: found
          • Article: not found

          Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning.

          Cytosine DNA methylation is important in regulating gene expression and in silencing transposons and other repetitive sequences. Recent genomic studies in Arabidopsis thaliana have revealed that many endogenous genes are methylated either within their promoters or within their transcribed regions, and that gene methylation is highly correlated with transcription levels. However, plants have different types of methylation controlled by different genetic pathways, and detailed information on the methylation status of each cytosine in any given genome is lacking. To this end, we generated a map at single-base-pair resolution of methylated cytosines for Arabidopsis, by combining bisulphite treatment of genomic DNA with ultra-high-throughput sequencing using the Illumina 1G Genome Analyser and Solexa sequencing technology. This approach, termed BS-Seq, unlike previous microarray-based methods, allows one to sensitively measure cytosine methylation on a genome-wide scale within specific sequence contexts. Here we describe methylation on previously inaccessible components of the genome and analyse the DNA methylation sequence composition and distribution. We also describe the effect of various DNA methylation mutants on genome-wide methylation patterns, and demonstrate that our newly developed library construction and computational methods can be applied to large genomes such as that of mouse.
            Bookmark
            • Record: found
            • Abstract: not found
            • Article: not found

            Na+ tolerance and Na+ transport in higher plants.

            M. Tester (2003)
            Tolerance to high soil [Na(+)] involves processes in many different parts of the plant, and is manifested in a wide range of specializations at disparate levels of organization, such as gross morphology, membrane transport, biochemistry and gene transcription. Multiple adaptations to high [Na(+)] operate concurrently within a particular plant, and mechanisms of tolerance show large taxonomic variation. These mechanisms can occur in all cells within the plant, or can occur in specific cell types, reflecting adaptations at two major levels of organization: those that confer tolerance to individual cells, and those that contribute to tolerance not of cells per se, but of the whole plant. Salt-tolerant cells can contribute to salt tolerance of plants; but we suggest that equally important in a wide range of conditions are processes involving the management of Na(+) movements within the plant. These require specific cell types in specific locations within the plant catalysing transport in a coordinated manner. For further understanding of whole plant tolerance, we require more knowledge of cell-specific transport processes and the consequences of manipulation of transporters and signalling elements in specific cell types.
              Bookmark
              • Record: found
              • Abstract: found
              • Article: found
              Is Open Access

              Climate variation explains a third of global crop yield variability

              Many studies have examined the role of mean climate change in agriculture, but an understanding of the influence of inter-annual climate variations on crop yields in different regions remains elusive. We use detailed crop statistics time series for ~13,500 political units to examine how recent climate variability led to variations in maize, rice, wheat and soybean crop yields worldwide. While some areas show no significant influence of climate variability, in substantial areas of the global breadbaskets, >60% of the yield variability can be explained by climate variability. Globally, climate variability accounts for roughly a third (~32–39%) of the observed yield variability. Our study uniquely illustrates spatial patterns in the relationship between climate variability and crop yield variability, highlighting where variations in temperature, precipitation or their interaction explain yield variability. We discuss key drivers for the observed variations to target further research and policy interventions geared towards buffering future crop production from climate variability.
                Bookmark

                Author and article information

                Contributors
                Journal
                Front Plant Sci
                Front Plant Sci
                Front. Plant Sci.
                Frontiers in Plant Science
                Frontiers Media S.A.
                1664-462X
                06 November 2015
                2015
                : 6
                : 968
                Affiliations
                [1] 1Southern Cross Plant Science, Southern Cross University , Lismore, NSW, Australia
                [2] 2National Key Laboratory for Crop Genetic Improvement, Huazhong Agricultural University , Wuhan, China
                [3] 3Crops for the Future, Biotechnology and Breeding Systems , Semenyih, Malaysia
                Author notes

                Edited by: Raúl Alvarez-Venegas, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mexico

                Reviewed by: Célia Baroux, Zurich-Basel Plant Science Center, Switzerland; Chris Helliwell, Commonwealth Scientific and Industrial Research Organisation, Australia

                *Correspondence: Graham J. King, graham.king@ 123456scu.edu.au

                This article was submitted to Plant Biotechnology, a section of the journal Frontiers in Plant Science.

                Article
                10.3389/fpls.2015.00968
                4635209
                69598c7d-6cc8-40f3-b5cf-58c416202499
                Copyright © 2015 King.

                This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

                History
                : 18 May 2015
                : 22 October 2015
                Page count
                Figures: 2, Tables: 0, Equations: 0, References: 241, Pages: 19, Words: 17686
                Funding
                Funded by: Southern Cross University 10.13039/501100001770
                Categories
                Plant Science
                Review

                Plant science & Botany
                crop epigenetics,chromatin dynamics,thermal homeostasis,ionic homeostasis,dna methylation,phenotypic plasticity,g × e interactions

                Comments

                Comment on this article