Dormancy is a state of shifted physiological activities with cessation of growth. It occurs in seeds and vegetative propagules and enables plants to survive in adverse growing conditions. Traditional studies on dormancy-related problems have mostly focused on hormone changes along with environmental factors that have achieved great insight on these processes at the physiological level. The molecular nature and cellular basis of signals that carry out the processes of dormancy or dormancy breaking are largely unknown. Recent advances in plant genetics and genomics have provided assorted ways to investigate questions concerning dormancy. Various approaches such as developing genetic maps with DNA-based markers, e.g., amplified fragment length polymorphism (AFLP) and restriction fragment length polymorphism (RFLP), analyzing mutant lines, conducting quantitative trait loci (QTL) analysis, two-dimensional polyacrylamide gel electrophoresis, differential display, microarray, have been performed to resolve different issues related to dormancy. The phenotypic variation in dormant seeds or buds is continuous instead of discrete, and thus QTL analysis is desirable to identify the association between genetically determined phenotypes and specific genetic markers (RFLPs). Some aspects of QTL will be introduced. DNA microarray is a recently developed technology that is used to detect and quantitate large numbers of differences in gene expression simultaneously. We have used the DNA microarray technology to study underground bud dormancy and growth in leafy spurge (Euphorbia esula L.). The principle and versatility of DNA microarray will be introduced, and the strategy for applying this technology will be discussed.

Target regions for posttranscriptional silencing of transgenes often reside in the 3′ region of the coding sequence, although there are exceptions. To resolve if the target region is determined by the gene undergoing silencing rather than by the structure of the transgene loci or the plant genetic background, we have performed detailed analyses of target regions in three spontaneously β-glucuronidase (GUS) silencing tobacco lines of different origin. From quantitative cosuppression experiments, we show that the main target region in all three tobacco lines is found within the 3′ half of the GUS coding region but upstream of the last 200 nt. The quantities of small (21–25 nt) RNAs homologous to 5′ or 3′ regions of the GUS coding sequence were found to correlate approximately with the target strength of the corresponding regions. These results suggest that transgene locus structure and plant genetic background are not major determinants of silencing target regions. We also show that virus-induced gene silencing (VIGS) of GUS in Nicotiana benthamiana is induced equally effectively with Potato virus X carrying either the 5′ or 3′ third of the GUS coding region. This indicates that both regions can act as efficient inducers as well as targets of posttranscriptional silencing, although the 3′ region is the predominant target region in the spontaneously silencing transgenic plant lines examined. Finally, we investigated spreading of the target region in the N. benthamiana plants undergoing VIGS. Surprisingly, only evidence for spreading of the target region in the 5′-3′ direction was obtained. This finding may help explain why the majority of target regions examined to date lie within the 3′ region of transgenes.