The α-gliadin genes from Brachypodium distachyon L. provide evidence for a significant gap in the current genome assembly

Chen, G. X.; Lv, Dongwen; Li, W. D.; Subburaj, Saminathan; Yu, Zitong; Wang, Y. J.; Li, X. H.; Wang, K.; Ye, X. G.; Ma, Wujun; Yan, Yueming

doi:10.1007/s10142-013-0353-0

Cited by 5 publications

(16 citation statements)

References 39 publications

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“…The isolated gliadin genes are highly conserved both in nucleotide sequences and deduced amino acids. Compared to wheat gliadin genes, common structures of alpha-gliadins, including signal peptide, repetitive domain, polyglutamine domain and unique domains, were also conserved in these deduced proteins (Chen et al 2014b). Consistent with the finding that few gliadin proteins were deposited in Brachypodium endosperm, most of the isolated gliadin genes were pseudogenes and only four of them have full length ORF (Chen et al 2014b).…”

Section: Annotation Of Brachypodium Storage Protein Genessupporting

confidence: 67%

“…Compared to wheat gliadin genes, common structures of alpha-gliadins, including signal peptide, repetitive domain, polyglutamine domain and unique domains, were also conserved in these deduced proteins (Chen et al 2014b). Consistent with the finding that few gliadin proteins were deposited in Brachypodium endosperm, most of the isolated gliadin genes were pseudogenes and only four of them have full length ORF (Chen et al 2014b). The same strategy was used to identify a total of 18 LMW-GS genes from Brachypodium, 2 from diploid accession Bd21 (Table 1) and 16 from five polyploidy accessions (Wang et al 2012).…”

Section: Annotation Of Brachypodium Storage Protein Genessupporting

confidence: 67%

“…Recently, Chen et al (2014b) reported that no gliadin protein was expressed in Brachypodium seeds based on A-PAGE, SDS-PAGE, RP-HPLC and western blotting analysis of the alcohol-soluble protein extract. Similarly, only traces of proteins could be recovered with alcohol solutions and very few bands were detectable on the SDS-PAGE gel (Larre et al 2010;Wang et al 2012).…”

Section: Gliadinsmentioning

confidence: 99%

“…Southern blot analyses using the probes of wheat prolamin genes suggested more than 10 copies of gliadin genes and 4-5 copies of LMW-GS are present in Brachypodium (Chen et al 2014b;Wang et al 2012). To further characterize the Brachypodium prolamin genes, allele specific primer pairs used for amplifying wheat prolamin genes were employed in PCR reactions using Brachypodium genomic DNAs as template (Chen et al 2014b;Subburaj et al 2014;Wang et al 2012). A total of 30 gliadin genes were cloned from 9 Brachypodium accessions, and 8 genes were obtained from Bd21 (Table 1) (Chen et al 2014b).…”

Section: Annotation Of Brachypodium Storage Protein Genesmentioning

confidence: 99%

“…To further characterize the Brachypodium prolamin genes, allele specific primer pairs used for amplifying wheat prolamin genes were employed in PCR reactions using Brachypodium genomic DNAs as template (Chen et al 2014b;Subburaj et al 2014;Wang et al 2012). A total of 30 gliadin genes were cloned from 9 Brachypodium accessions, and 8 genes were obtained from Bd21 (Table 1) (Chen et al 2014b). The isolated gliadin genes are highly conserved both in nucleotide sequences and deduced amino acids.…”

Section: Annotation Of Brachypodium Storage Protein Genesmentioning

confidence: 99%

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Brachypodium Seed: A Potential Model for Studying Grain Development of Cereal Crops

Thilmony

2015

Genetics and Genomics of Brachypodium

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Seeds of small grains are important resources for human and animal food. The understanding of seed biology is essential for crop improvement by increasing grain yields and nutritional value. In the last decade, Brachypodium distachyon has been developed as a model plant for temperate cereal grasses. Recently, several studies have been published that compare Brachypodium seed anatomy and grain development to those of wheat and barley. While seeds of these three species share many properties, distinct features were identified in Brachypodium, including relatively smaller endosperms with thick cell walls and irregularities in cell sizes in the aleurone layer. Brachypodium seeds have lower starch and higher (1,3;1,4)-β-glucan content, and lower prolamin and higher globulin protein contents, compared to its domesticated relatives. The sequences and expression of genes involved in starch biosynthesis are conserved between Brachypodium and domesticated cereals, but the expression of certain genes in Brachypodium seeds is earlier and at much lower levels, providing a possible explanation for their relatively low starch content. Proteomics analyses indicated that the predominant globulins in the storage proteins were the 11S type and that they are encoded by a multi-gene family. Less than 12 % of the storage proteins were of the prolamin class. Annotation of the Brachypodium genome revealed it contains much fewer prolamin genes than the genomes of wheat and maize, suggesting that the high levels of seed globulins in the former are at the expense of prolamins. The demonstration that expression of a wheat High-MolecularWeight glutenin gene promoter was endosperm-specific in Brachypodium transgenic plants opens the way for analyses of other gene promoters from cereal crop species that are difficult to transform. The ease of obtaining transgenic Brachypodium plants and the relatively large size of its seeds compared to its small stature make it an ideal system for research of seed properties including dormancy, germination and maturation.

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Section: Annotation Of Brachypodium Storage Protein Genessupporting

confidence: 67%

Section: Annotation Of Brachypodium Storage Protein Genessupporting

confidence: 67%

Section: Gliadinsmentioning

confidence: 99%

Section: Annotation Of Brachypodium Storage Protein Genesmentioning

confidence: 99%

Section: Annotation Of Brachypodium Storage Protein Genesmentioning

confidence: 99%

See 3 more Smart Citations

Brachypodium Seed: A Potential Model for Studying Grain Development of Cereal Crops

Thilmony

2015

Genetics and Genomics of Brachypodium

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Molecular characterization and evolutionary origins of farinin genes in Brachypodium distachyon L.

Subburaj

Luo

et al. 2015

J Appl Genetics

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Farinins are one of the oldest members of the gluten family in wheat and Aegilops species, and they influence dough properties. Here, we performed the first detailed molecular genetic study on farinin genes in Brachypodium distachyon L., the model species for Triticum aestivum. A total of 51 b-type farinin genes were cloned and characterized, including 27 functional and 24 non-functional pseudogenes from 14 different B. distachyon accessions. All genes were highly similar to those previously reported from wheat and Aegilops species. The identification of deduced amino acid sequences showed that b-type farinins across Triticeae genomes could be classified as b1-, b2-, b3-, and b4-type farinins; however, B. distachyon had only b3- and b4-type farinins. Real-time quantitative reverse transcription polymerase chain reaction (qRT-PCR) revealed that farinin genes are transcribed into mRNA in B. distachyon at much lower levels than in Triticeae, despite the presence of cis-acting elements in promoter regions. Phylogenetic analysis suggested that Brachypodium farinins may have closer relationships with common wheat and further confirmed four different types of b-type farinins in Triticeae and Brachypodium genomes, corresponding to b1, b2, b3 (group 1), and b4 (group 2). A putative evolutionary origin model of farinin genes in Brachypodium, Triticum, and the related species suggests that all b-type farinins diverged from their common ancestor ~3.2 million years ago (MYA). The b3 and b4 types could be considered older in the farinin family. The results explain the loss of b1- and b2-type farinin alleles in Brachypodium.

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Dynamic development of starch granules and the regulation of starch biosynthesis in Brachypodium distachyon: comparison with common wheat and Aegilops peregrina

et al. 2014

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BackgroundThorough understanding of seed starch biosynthesis and accumulation mechanisms is of great importance for agriculture and crop improvement strategies. We conducted the first comprehensive study of the dynamic development of starch granules and the regulation of starch biosynthesis in Brachypodium distachyon and compared the findings with those reported for common wheat (Chinese Spring, CS) and Aegilops peregrina.ResultsOnly B-granules were identified in Brachypodium Bd21, and the shape variation and development of starch granules were similar in the B-granules of CS and Bd21. Phylogenetic analysis showed that most of the Bd21 starch synthesis-related genes were more similar to those in wheat than in rice. Early expression of key genes in Bd21 starch biosynthesis mediate starch synthesis in the pericarp; intermediate-stage expression increases the number and size of starch granules. In contrast, these enzymes in CS and Ae. peregrina were mostly expressed at intermediate stages, driving production of new B-granules and increasing the granule size, respectively. Immunogold labeling showed that granule-bound starch synthase (GBSSI; related to amylose synthesis) was mainly present in starch granules: at lower levels in the B-granules of Bd21 than in CS. Furthermore, GBSSI was phosphorylated at threonine 183 and tyrosine 185 in the starch synthase catalytic domain in CS and Ae. peregrina, but neither site was phosphorylated in Bd21, suggesting GBSSI phosphorylation could improve amylose biosynthesis.ConclusionsBd21 contains only B-granules, and the expression of key genes in the three studied genera is consistent with the dynamic development of starch granules. GBSSI is present in greater amounts in the B-granules of CS than in Bd21; two phosphorylation sites (Thr183 and Tyr185) were found in Triticum and Aegilops; these sites were not phosphorylated in Bd21. GBSSI phosphorylation may reflect its importance in amylose synthesis.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-014-0198-2) contains supplementary material, which is available to authorized users.

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The α-gliadin genes from Brachypodium distachyon L. provide evidence for a significant gap in the current genome assembly

Cited by 5 publications

References 39 publications

Brachypodium Seed: A Potential Model for Studying Grain Development of Cereal Crops

Brachypodium Seed: A Potential Model for Studying Grain Development of Cereal Crops

Molecular characterization and evolutionary origins of farinin genes in Brachypodium distachyon L.

Dynamic development of starch granules and the regulation of starch biosynthesis in Brachypodium distachyon: comparison with common wheat and Aegilops peregrina

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