Structural characterization of Brachypodium genome and its syntenic relationship with rice and wheat

Genomics and Gene Discovery Research Unit, USDA-ARS, Western Regional Research Center, 800 Buchanan Street, Albany, CA 94710, USA.
Plant Molecular Biology (Impact Factor: 4.07). 05/2009; 70(1). DOI: 10.1007/s11103-009-9456-3
Source: PubMed

ABSTRACT Brachypodium distachyon (Brachypodium) has been recently recognized as an emerging model system for both comparative and functional genomics in grass species. In this study, 55,221 repeat masked Brachypodium BAC end sequences (BES) were used for comparative analysis against the 12 rice pseudomolecules. The analysis revealed that ~26.4% of BES have significant matches with the rice genome and 82.4% of the matches were homologous to known genes. Further analysis of paired-end BES and ~1.0 Mb sequences from nine selected BACs proved to be useful in revealing conserved regions and regions that have undergone considerable genomic changes. Differential gene amplification, insertions/deletions and inversions appeared to be the common evolutionary events that caused variations of microcolinearity at different orthologous genomic regions. It was found that ~17% of genes in the two genomes are not colinear in the orthologous regions. Analysis of BAC sequences also revealed higher gene density (~9 kb/gene) and lower repeat DNA content (~13.1%) in Brachypodium when compared to the orthologous rice regions, consistent with the smaller size of the Brachypodium genome. The 119 annotated Brachypodium genes were BLASTN compared against the wheat EST database and deletion bin mapped wheat ESTs. About 77% of the genes retrieved significant matches in the EST database, while 9.2% matched to the bin mapped ESTs. In some cases, genes in single Brachypodium BACs matched to multiple ESTs that were mapped to the same deletion bins, suggesting that the Brachypodium genome will be useful for ordering wheat ESTs within the deletion bins and developing specific markers at targeted regions in the wheat genome.

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Available from: Frank M You, Aug 16, 2015
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    • "Moreover, Brachypodium has a small sequenced genome (272 Mbp), and spring and winter diploid accessions have been classified according to the capacity to flower with or without cold exposure (Vogel et al., 2010). There is strong chromosomal synteny between Brachypodium and other temperate cereals, and about 77 % of the genes retrieve significant matches in Triticeae EST databases (Huo et al., 2009). This body of evidence has led researchers to propose Brachypodium as an appropriate model to study the response of temperate cereals to their environment. "
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    ABSTRACT: Background and AimsCold is a major constraint for cereal cultivation under temperate climates. Winter-hardy plants interpret seasonal changes and can acquire the ability to resist sub-zero temperatures. This cold acclimation process is associated with physiological, biochemical and molecular alterations in cereals. Brachypodium distachyon is considered a powerful model system to study the response of temperate cereals to adverse environmental conditions. To date, little is known about the cold acclimation and freezing tolerance capacities of Brachypodium. The main objective of this study was to evaluate the cold hardiness of seven diploid Brachypodium accessions.Methods An integrated approach, involving monitoring of phenological indicators along with expression profiling of the major vernalization regulator VRN1 orthologue, was followed. In parallel, soluble sugars and proline contents were determined along with expression profiles of two COR genes in plants exposed to low temperatures. Finally, whole-plant freezing tests were performed to evaluate the freezing tolerance capacity of Brachypodium.Key ResultsCold treatment accelerated the transition from the vegetative to the reproductive phase in all diploid Brachypodium accessions tested. In addition, low temperature exposure triggered the gradual accumulation of BradiVRN1 transcripts in all accessions tested. These accessions exhibited a clear cold acclimation response by progressively accumulating proline, sugars and COR gene transcripts. However, whole-plant freezing tests revealed that these seven diploid accessions only have a limited capacity to develop freezing tolerance when compared with winter varieties of temperate cereals such as wheat and barley. Furthermore, little difference in terms of survival was observed among the accessions tested despite their previous classification as either spring or winter genotypes.Conclusions This study is the first to characterize the freezing tolerance capacities of B. distachyon and provides strong evidence that some diploid accessions such as Bd21 have a facultative growth habit.
    Annals of Botany 12/2013; 113(4). DOI:10.1093/aob/mct283 · 3.30 Impact Factor
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    • "The collinearity between Brachypodium and wheat was shown to be better than between rice and wheat (Huo et al. 2009). Highly overlapped gene sets between Brachypodium Table 3 Absolute quantification of the mRNA expression level of HMW-Glu1Dy genes from Bd21 and Chinese Spring. "
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    ABSTRACT: Brachypodium distachyon, a small wild grass within the Pooideae family, is a new model organism for exploring the functional genomics of cereal crops. It was shown to have close relationships to wheat, barley and rice. Here, we describe the molecular characterisation and evolutionary relationships of high molecular weight glutenin subunits (HMW-GS) genes from B. distachyon. Sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE), high performance capillary electrophoresis (HPCE) and liquid chromatography-tandem mass spectrometry (LC-MS/MS) analyses demonstrated that there was no HMW-GS expression in the Brachypodium grains due to the silencing of their encoding genes. Through allele-specific polymerase chain reaction (AS-PCR) amplification and cloning, a total of 13 HMW-GS encoding genes from diploid, tetraploid and hexaploid Brachypodium species were obtained, and all of them had typical structural features of y-type HMW-GS genes from common wheat and related species, particularly more similar to the 1Dy12 gene. However, the presence of an in-frame premature stop codon (TAG) at position 1521 in the coding region resulted in the conversion of all the genes to pseudogenes. Further, quantitative real-time PCR (qRT-PCR) analysis revealed that HMW-GS genes in B. distachyon displayed a similar trend, but with a low transcriptional expression profile during grain development due to the occurrence of the stop codon. Phylogenetic analysis showed that the highly conserved Glu-1-2 loci were presented in B. distachyon, which displayed close phylogenetic evolutionary relationships with Triticum and related species.
    Journal of applied genetics 12/2013; DOI:10.1007/s13353-013-0187-4 · 1.90 Impact Factor
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    • "Almost all of the stomatal development research has been undertaken on the model plant Arabidopsis, but to have greater relevance to agricultural crops, more research needs to be undertaken on other species to determine whether the mechanisms identified in Arabidopsis are conserved across species. B. distachyon would be an ideal model for cereals because of the close synteny between the genomes (Huo et al. 2009) and similar root and shoot development (Watt et al. 2009). Greater understanding of how the environment interacts with stomatal development is also needed as plasticity in TE may be a useful trait in different crops and different growing regions. "
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    ABSTRACT: Abstract Water use efficiency (or transpiration efficiency) describes the intrinsic trade-off between carbon fixation and water loss that occurs in dryland plants because water evaporates from the interstitial tissues of leaves whenever stomata open for CO2 acquisition. The transpiration efficiency of crop plants is generally low as they typically lose several 100-fold more water than the equivalent units of carbon fixed by photosynthesis. With the increasing demand for sustainable water use and increasing agricultural productivity, the need to improve transpiration efficiency (TE) of crops has received much attention, although this trait may not be beneficial in all water-limited environments. This chapter shows that TE is predominantly driven by hydraulic properties and genes that modulate TE are mostly involved in gas exchange. Genetic variation exists in crop plants for most of the respective traits, but more research is needed to determine their relative influence on TE under well-watered as well as water-limited conditions. Moreover, research is needed to demonstrate that improvements in TE will improve yields in different environments.
    Genomics & Breeding for Climate-Resilient Crops, Vol. 2, Vol. 2 edited by Kole C, 01/2013: chapter Chapter 6: pages 225-268; Springer- Verlag Berlin Heidelberg.
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