Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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MiRNA regulation in the early development of barley seed

ABSTRACT: small RNA and degradome sequencing was carried out on samples isolated from developing barley grains. The datasets were analysed to identify putative miRNAs and their target mRNAs Samples were whole grain tissue (pericarp, embryo and endosperm) from developing barley grains. Three samples were used that pooled 1 to 5, 6-10 and 11-15 days post anthesis grains. For each sample a small RNA library and a degradome library (using the PARE method) was constructed and sequenced using the Illumina platform

ORGANISM(S): Hordeum vulgare

SUBMITTER: Jennifer Taylor

PROVIDER: E-GEOD-38755 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Transcriptomic analyses are particularly powerful in research when they are based on detailed underlying knowledge of developmental processes, morphological/anatomical features and biochemical/metabolic processes. Our work is based on our detailed knowledge of grain development and provides an invaluable resource for both Brachypodium grain development specifically and for comparative analyses to other species, including cereal crops. Grain development includes several transition points in addition to being preceded and succeeded by the fundamental developmental switches of fertilization and germination. Such complex process requires a larger sets of genes expressed in a highly-controlled manner. We have selected eight stages of developmental in Brachypodium distachyon encompassing these transitions and conducted comprehensive transcriptomic analyses to generate a valuable resource of the developmental transitions and the distinctive biological processes that are activated and/or repressed during grain development and germination. Comparison of the data generated in this project to other grasses, including the important crop species, and beyond will also shed light on the conservation and/or diversification in gene expression and function in an evolutionary context. Brachypodium distachyon grains (Bd-21 accession) were germinated on moist filter paper after stratification at 4°C for 48h. Five-day old seedlings were transferred to 9cm square pots with a 2:2:1 multipurpose compost: vermiculite: sand mix and grown under controlled environment conditions with a 18h photoperiod at 20°-22°C and light intensity of 180-200 umol/m/s. Tissue samples were collected from eight distinct developmental stages; pre-anthesis ovaries, young grains (1-3 DAA), middle length grains (3-8 DAA), full length grains (8-15 DAA), mature grains (15-20 DAA), mature grains without embryo, germinating grains and seedlings at 3-4 days after germination (Fig.1). Tissues were frozen in liquid nitrogen immediately after collection and were kept at -80°C until further analyses. Total RNA was isolated from frozen tissue samples using the Spectrum Plant Total RNA Kit (Sigma-Aldrich) following the manufacturer’s instructions. Three biological replicates were used for each stage of development. The RNA samples were treated with DNase I (New England Biolabs) in order to eliminate DNA contamination and their concentration was determined using a NanoDrop spectrophotometer (Thermo Fisher Scientific).

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MiRNA regulation in the early development of barley seed

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