Dataset Information

Brachypodium distachyon as a model system for studies of copper transport in cereal crops.

ABSTRACT: Copper (Cu) is an essential micronutrient that performs a remarkable array of functions in plants including photosynthesis, cell wall remodeling, flowering, and seed set. Of the world's major cereal crops, wheat, barley, and oat are the most sensitive to Cu deficiency. Cu deficient soils include alkaline soils, which occupy approximately 30% of the world's arable lands, and organic soils that occupy an estimated 19% of arable land in Europe. We used Brachypodium distachyon (brachypodium) as a proxy for wheat and other grain cereals to initiate analyses of the molecular mechanisms underlying their increased susceptibility to Cu deficiency. In this report, we focus on members of the CTR/COPT family of Cu transporters because their homologs in A. thaliana are transcriptionally upregulated in Cu-limited conditions and are involved either in Cu uptake from soils into epidermal cells in the root, or long-distance transport and distribution of Cu in photosynthetic tissues. We found that of five COPT proteins in brachypodium, BdCOPT3, and BdCOPT4 localize to the plasma membrane and are transcriptionally upregulated in roots and leaves by Cu deficiency. We also found that BdCOPT3, BdCOPT4, and BdCOPT5 confer low affinity Cu transport, in contrast to their counterparts in A. thaliana that confer high affinity Cu transport. These data suggest that increased sensitivity to Cu deficiency in some grass species may arise from lower efficiency and, possibly, other properties of components of Cu uptake and tissue partitioning systems and reinforce the importance of using brachypodium as a model for the comprehensive analyses of Cu homeostasis in cereal crops.

SUBMITTER: Jung HI

PROVIDER: S-EPMC4039008 | biostudies-other | 2014

REPOSITORIES: biostudies-other

ACCESS DATA

Publications

Brachypodium distachyon as a model system for studies of copper transport in cereal crops.

Jung Ha-Il HI Gayomba Sheena R SR Yan Jiapei J Vatamaniuk Olena K OK

Frontiers in plant science 20140530

Copper (Cu) is an essential micronutrient that performs a remarkable array of functions in plants including photosynthesis, cell wall remodeling, flowering, and seed set. Of the world's major cereal crops, wheat, barley, and oat are the most sensitive to Cu deficiency. Cu deficient soils include alkaline soils, which occupy approximately 30% of the world's arable lands, and organic soils that occupy an estimated 19% of arable land in Europe. We used Brachypodium distachyon (brachypodium) as a pr ...[more]

PMID: 24910638

Similar Datasets

Project description:Comparative genomics have facilitated the mining of biological information from a genome sequence, through the detection of similarities and differences with genomes of closely or more distantly related species. By using such comparative approaches, knowledge can be transferred from the model to non-model organisms and insights can be gained in the structural and evolutionary patterns of specific genes. In the absence of sequenced genomes for allergenic grasses, this study was aimed at understanding the structure, organisation and expression profiles of grass pollen allergens using the genomic data from Brachypodium distachyon as it is phylogenetically related to the allergenic grasses. Combining genomic data with the anther RNA-Seq dataset revealed 24 pollen allergen genes belonging to eight allergen groups mapping on the five chromosomes in B. distachyon. High levels of anther-specific expression profiles were observed for the 24 identified putative allergen-encoding genes in Brachypodium. The genomic evidence suggests that gene encoding the group 5 allergen, the most potent trigger of hay fever and allergic asthma originated as a pollen specific orphan gene in a common grass ancestor of Brachypodium and Triticiae clades. Gene structure analysis showed that the putative allergen-encoding genes in Brachypodium either lack or contain reduced number of introns. Promoter analysis of the identified Brachypodium genes revealed the presence of specific cis-regulatory sequences likely responsible for high anther/pollen-specific expression. With the identification of putative allergen-encoding genes in Brachypodium, this study has also described some important plant gene families (e.g. expansin superfamily, EF-Hand family, profilins etc) for the first time in the model plant Brachypodium. Altogether, the present study provides new insights into structural characterization and evolution of pollen allergens and will further serve as a base for their functional characterization in related grass species.

Project description:Background and aimsBrachypodium distachyon is being widely investigated across the world as a model plant for temperate cereals. This annual plant has three cytotypes (2n = 10, 20, 30) that are still regarded as part of a single species. Here, a multidisciplinary study has been conducted on a representative sampling of the three cytotypes to investigate their evolutionary relationships and origins, and to elucidate if they represent separate species.MethodsStatistical analyses of 15 selected phenotypic traits were conducted in individuals from 36 lines or populations. Cytogenetic analyses were performed through flow cytometry, fluorescence in situ hybridization (FISH) with genomic (GISH) and multiple DNA sequences as probes, and comparative chromosome painting (CCP). Phylogenetic analyses were based on two plastid (ndhF, trnLF) and five nuclear (ITS, ETS, CAL, DGAT, GI) genes from different Brachypodium lineages, whose divergence times and evolutionary rates were estimated.Key resultsThe phenotypic analyses detected significant differences between the three cytotypes and demonstrated stability of characters in natural populations. Genome size estimations, GISH, FISH and CCP confirmed that the 2n = 10 and 2n = 20 cytotypes represent two different diploid taxa, whereas the 2n = 30 cytotype represents the allotetraploid derived from them. Phylogenetic analysis demonstrated that the 2n = 20 and 2n = 10 cytotypes emerged from two independent lineages that were, respectively, the maternal and paternal genome donors of the 2n = 30 cytotype. The 2n = 20 lineage was older and mutated significantly faster than the 2n = 10 lineage and all the core perennial Brachypodium species.ConclusionsThe substantial phenotypic, cytogenetic and molecular differences detected among the three B. distachyon sensu lato cytotypes are indicative of major speciation processes within this complex that allow their taxonomic separation into three distinct species. We have kept the name B. distachyon for the 2n = 10 cytotype and have described two novel species as B. stacei and B. hybridum for, respectively, the 2n = 20 and 2n = 30 cytotypes.

Dataset Information

Brachypodium distachyon as a model system for studies of copper transport in cereal crops.

Publications

Brachypodium distachyon as a model system for studies of copper transport in cereal crops.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets