Submitted to: Functional and Integrative Genomics
Publication Type: Peer reviewed journal
Publication Acceptance Date: 1/23/2006
Publication Date: 3/18/2006
Citation: Druka, A., Muehlbauer, G., Druka, I., Caldo, R., Baumann, U., Rostoks, N., Schreiber, A., Wise, R.P., Close, T., Kleinhofs, A. 2006. An atlas of gene expression from seed to seed through barley development. Functional and Integrative Genomics. 6(3):202-211. Interpretive Summary: The Triticeae species wheat and barley synthesize the majority of the world's calorie rich dietary carbohydrate, amassing more than 720 metric tons in annual production. Despite their importance to humankind, genomic investigations have been hampered by their large genome sizes (17,000 and 5,300 Mbp for wheat and barley, respectively) with the allo-hexaploid genome of bread wheat prompting many to consider barley a model for the Triticeae. Barley is a true diploid inbreeder with seven pairs of metacentric chromosomes, a large collection of classically described mutant stocks, and an expanding collection of genomics resources. We report here a detailed examination of transcript abundance from seed to seed in a grass crop, which we propose will act as a reference for future studies in barley and other grasses including wheat, maize, and rice. The research is of high impact because basic processes in cereal crop development influence grain yield and quality. Knowledge of the basic mechanisms of cereal development will provide breeders with better tools, resulting in less damage to crops, therefore increasing sustainability and profitability.
Technical Abstract: We assessed the global regulation of gene expression from seed to seed during barley (Hordeum vulgare L.) development by quantifying transcript abundance in key tissues and developmental stages of two diverse genotypes using the Barley1 GeneChip. Differential abundance was observed both between tissues and between genotypes. Transcript population-based classification differentiated tissues and genotypes according to physiological and functional similarities. Patterns of transcript abundance were both descriptive and predictive and demonstrate how the transcriptome is re-programmed during development to fulfill the demands of specific biological functions. We demonstrate the hypothesis building potential of the dataset, and through free public access, propose it acts as both a reference and a catalyst for future hypothesis driven research in the grasses.