Brachypodium Genomics

Özdemir, Bahar Soğutmaz; Hernández, Pilar; Filiz, Ertuğrul; Budak, Hikmet

doi:10.1155/2008/536104

Cited by 41 publications

(34 citation statements)

References 32 publications

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“…The close phylogenetic relationship between Brachypodium and wheat is also reflected in the strong similarity of their gene sequences (Ozdemir et al 2008). Indeed, there is a general coincidence in the order of Brachypodium genes and those of the other species of the tribe Triticeae, while the genome size is similar to that of rice.…”

Section: Introductionmentioning

confidence: 97%

“…distachyon has a rapid generation cycle under optimized conditions (8-12 weeks), does not grow very tall (20-30 cm) at high planting densities, requires few demanding growth resources, shows good environmental adaptation ) and the 2n = 10 forms do not require vernalization (Draper et al 2001;Ozdemir et al 2008;Vogel et al 2006). The species B. distachyon has been used to protect rural soils from erosion, especially in slope areas where water runoff, wind and other agents cause soil loss.…”

Section: Introductionmentioning

confidence: 99%

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Prolamin storage proteins and alloploidy in wild populations of the small grass Brachypodium distachyon (L.) P. Beauv.

et al. 2011

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This paper reports the glutenin diversity of a collection of 23 wild populations of the grass Brachypodium distachyon collected in the Mediterranean and southern areas of the Iberian Peninsula. The plant material studied included the three different cytotypes of this species: 2n = 10, 2n = 20 and 2n = 30. A specific method of extraction was used to isolate the glutenin subunits from the caryopsis. Separation by sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE) showed them to correspond to wheat low-molecular-weight glutenin subunits (LMW-GS). Twenty-two LMW-GS-like were identified that showed great diversity within and between populations. All the populations investigated were polymorphic for the endosperm proteins studied. The 2n = 30 forms had the largest number of subunits; these were also more diverse than those of the 2n = 10 or 2n = 20 forms. The 2n = 10 forms, the most common in the higher, interior areas of the Iberian Peninsula, showed the smallest subunit variation. In fact, negative correlations were found between subunit diversity and altitude and longitude. In contrast, a positive correlation was detected with the annual average temperature and the indices of thermicity and Mediterraneity. The similarity between the populations was estimated using the Sorensen-Dice coefficient, calculated on the basis of the presence/absence of the 22 LMW-GS proteins. The similarity indices were used to produce a dendrogram using the unweighted pair-group method with arithmetic means (UPGMA). This method produced three main groups corresponding to the three cytotypes. An analysis was made of the possible correlation between eco-geographic and climatic factors and the gene diversity and polymorphism shown in the populations. The diversity correlated positively with the number of chromosomes (2n), annual mean temperature, index of thermicity and index of Mediterraneity. In contrast, diversity correlated negatively with altitude, longitude and index of precipitation during the summer. The number of chromosomes correlated negatively with altitude, longitude and precipitation during summer and positively with all the other climatic indices. These results are coherent with the fact that diploid forms were more common in areas of the interior and at higher altitude, where the climate is more extreme.

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Section: Introductionmentioning

confidence: 97%

Section: Introductionmentioning

confidence: 99%

Prolamin storage proteins and alloploidy in wild populations of the small grass Brachypodium distachyon (L.) P. Beauv.

et al. 2011

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“…In addition to a complete genome sequence, additional genetic and molecular resources include an expressed sequence tag and bacterial artificial chromosome libraries, microarrays, collections of natural strains, and the development of mutant populations (http:// www.brachypodium.org/). Brachypodium has also been shown to be syntenic with other grass genomes making it applicable for comparative genomics [12][13][14].…”

Section: Introductionmentioning

confidence: 99%

Natural Variation of Flowering Time and Vernalization Responsiveness in Brachypodium distachyon

et al. 2010

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Dedicated bioenergy crops require certain characteristics to be economically viable and environmentally sustainable. Perennial grasses, which can provide large amounts of biomass over multiple years, are one option being investigated to grow on marginal agricultural land. Recently, a grass species (Brachypodium distachyon) has been developed as a model to better understand grass physiology and ecology. Here, we report on the flowering time variability of natural Brachypodium accessions in response to temperature and light cues. Changes in both environmental parameters greatly influence when a given accession will flower, and natural Brachypodium accessions broadly group into winter and spring annuals. Similar to what has been discovered in wheat and barley, we find that a portion of the phenotypic variation is associated with changes in expression of orthologs of VRN genes, and thus, VRN genes are a possible target for modifying flowering time in grass family bioenergy crops.

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“…Hence, the Brachypodium genome is expected to show greater gene colinearity to the genomes of major cool season cereal grain and forage grasses and will be more useful in gene discovery in large Triticeae genomes such as wheat and barley (Garvin et al 2008;Opanowicz et al 2008;Ozdemir et al 2008). In addition, the annual species in the genus Brachypodium possess a range of desirable biological features that make it well suited for functional genomics.…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2009

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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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Brachypodium Genomics

Cited by 41 publications

References 32 publications

Prolamin storage proteins and alloploidy in wild populations of the small grass Brachypodium distachyon (L.) P. Beauv.

Prolamin storage proteins and alloploidy in wild populations of the small grass Brachypodium distachyon (L.) P. Beauv.

Natural Variation of Flowering Time and Vernalization Responsiveness in Brachypodium distachyon

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

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