Differential gene expression during seed germination in barley (Hordeum vulgare L.)

A barley cDNA macroarray comprising 1,440 unique genes was used to analyze the spatial and temporal patterns of gene expression in embryo, scutellum and endosperm tissue during different stages of germination. Among the set of expressed genes, 69 displayed the highest mRNA level in endosperm tissue, 58 were up-regulated in both embryo and scutellum, 11 were specifically expressed in the embryo and 16 in scutellum tissue. Based on Blast X analyses, 70% of the differentially expressed genes could be assigned a putative function. One set of genes, expressed in both embryo and scutellum tissue, included functions in cell division, protein translation, nucleotide metabolism, carbohydrate metabolism and some transporters. The other set of genes expressed in endosperm encodes several metabolic pathways including carbohydrate and amino acid metabolism as well as protease inhibitors and storage proteins. As shown for a storage protein and a trypsin inhibitor, the endosperm of the germinating barley grain contains a considerable amount of residual mRNA which was produced during seed development and which is degraded during early stages of germination. Based on similar expression patterns in the endosperm tissue, we identified 29 genes which may undergo the same degradation process. Electronic Publication     

Functional association between malting quality trait components and cDNA array based expression patterns in barley (Hordeum vulgare L.)

We developed an approach for relating differences in gene expression to the phenotypic variation of a trait of interest. This allows the identification of candidate genes for traits that display quantitative variation. To validate the principle, gene expression was monitored on a cDNA array with 1400 ESTs to identify genes involved in the variation of the complex trait malting quality in barley. RNA profiles were monitored during grain germination in a set of 10 barley genotypes that had been characterized for 6 quality-associated trait components. The selection of the candidate genes was achieved via a correlation of dissimilarity matrices that were based on (i) trait variation and (ii) gene expression data. As expected, a comparison based on the complete set of differentially-expressed genes did not reveal any correlation between the matrices, because not all genes that show differential expression between the 10 cultivars are responsible for the observed differences in malting quality. However, by iteratively taking out one gene (with replacement) and re-computing the correlation, those genes that are positively contributing to the correlation could be identified. Using this procedure between 17 and 30 candidate genes were identified for each of the six malting parameters analysed. In addition to genes of unknown function, the list of candidates contains well-known malting-related genes. Five out of eight mapped candidate genes display linkage to known QTLs for malting quality traits. The described functional association strategy may provide an efficient link between functional genomics and plant breeding.     

Detection of genetic determinants that define the difference in photoperiod sensitivity of Triticum aestivum L. near-isogenic lines

Identification of genetic determinants that define different degrees of line sensitivity to the photoperiod was acomplished using near-isogenic lines of the soft hexaploid wheat Triticum aestivum L. using SSR markers and markers specific to the Vrn and Ppd genes. It was established that the Ppd-s line contains a dominant Ppd-D1a allele located on chromosome 2D. This allele is characterized by a large deletion in the gene promoter region. For two other lines (Ppd-m and Ppd-w), introgression of the Ppd-B1 gene on chromosome 2B was detected from the parental Sonora variety, which is insensitive to the day length; however, the previously described Ppd-B1a.1 allele was not found. Another polymorphism that can cause weak photoperiodic sensitivity, an increased copy number of the Ppd-B1 gene, was detected for these lines.