Abundant transcripts of malting barley identified by serial analysis of gene expression (SAGE)

Abstract

SummarySerial analysis of gene expression (SAGE) was applied to the major cereal crop barley ( Hordeum vulgare ) to characterize the transcriptional profile of grain during the malting process. Seven SAGE libraries were generated from seed at different time points during malting, in addition to one library from dry mature seed. A total of 155 206 LongSAGE tags, representing 41 909 unique sequences, was generated. This study reports an in-depth analysis of the most abundant transcripts from each of eight specific time points in a malting barley time course. The 100 most abundant tags from each library were analysed to identify the putative functional role of highly abundant transcripts. The largest functional groups included transcripts coding for stress response and cell defence, ribosomal proteins and storage proteins. The most abundant tag represented B22EL8, a barley metallothionein, which showed significant up-regulation across the malting time course. Considerable changes in the abundance profiles of some of the highly abundant tags occurred at 24 h post-steeping, indicating that it may be an important time point for gene expression changes associated with barley seed germination.

Differentially expressed genes during malting and correlation with malting quality phenotypes in barley (Hordeum vulgare L.)

“…Up-regulation of genes involved in metabolism of carbohydrates, nucleotides, amino acids, and proteins during steeping indicates that a reactivation of metabolism was occurring. Twentyfour hours following steeping (day 1), extensive reprogramming of gene expression occurred, similar to what others have previously reported (Watson and Henry 2005;White et al 2006). Every functional category included in the analysis increased in the number of induced genes during the malting stages.…”

“…Genes involved in stress and defense response made up a major portion of diVerentially expressed transcripts in all four malting stages studied. Previous studies of germinating barley seeds have reported similar Wndings (Potokina et al 2002;Watson and Henry 2005;White et al 2006). This is not surprising since malting is not performed under aseptic conditions and barley seeds contain an inherent microbial Xora consisting of fungi, bacteria, and yeasts (Flannigan 2003).…”

“…DiVerentially expressed genes during germination in barley were also studied using cDNA arrays (Potokina et al 2002;Watson and Henry 2005). Using serial analysis of gene expression (SAGE) to conduct transcript proWling during malting in barley, the most abundant transcripts identiWed by (White et al 2006) overlapped with most genes identiWed in cDNA array-based studies (Potokina et al 2002;Watson and Henry 2005).…”

Structural and functional characterization of a winter malting barley

“…None of the 56 differentially expressed genes corresponded to proteins associated with mobilization of the major seed starch and storage protein reserves or cell wall carbohydrates during malting Potokina et al 2004;White et al 2006).…”

“…Large-scale gene expression technologies such as cDNA-and oligonucleotide-based arrays, and serial analysis of gene expression (SAGE) have proved to be useful to conduct transcript profiling during germination and malting (Lapitan et al 2009;Potokina et al 2002Potokina et al , 2004Watson and Henry 2005;White et al 2006), and to identify candidate genes for malting quality (Lapitan et al 2009;Potokina et al 2004Potokina et al , 2006.…”