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Background: Dormancy of buds is a critical developmental process that allows perennial plants to survive extreme seasonal variations in climate. Dormancy transitions in underground crown buds of the model herbaceous perennial weed leafy spurge were investigated using a 23 K element cDNA microarray. These data represent the first large-scale transcriptome analysis of dormancy in underground buds of an herbaceous perennial species. Crown buds collected monthly from August through December, over a five year period, were used to monitor the changes in the transcriptome during dormancy transitions.

DORMANCY ASSOCIATED MADS-BOX (DAM) genes are related to AGAMOUS-LIKE 24 and SHORT VEGETATIVE PHASE genes of arabidopsis and are differentially regulated coordinately with endodormancy induction and release in buds of several perennial plant species. DAM genes were first shown to directly impact endodormancy in peach where a deletion of a series of DAM resulted in loss of endodormancy induction. We have cloned and characterized several MADS box genes from the model perennial weed leafy spurge. Leafy spurge DAM genes are preferentially expressed in shoot tips and buds in response to cold temperatures and day length in a manner that is relative to the level of endodormancy induced by various environmental conditions. Over-expression of one DAM gene in arabidopsis delays flowering. Additionally, we show that at least one DAM gene is differentially regulated by chromatin remodeling. Comparisons of the DAM gene promoters between poplar and leafy spurge have identified several conserved sequences that may be important for their expression patterns in response to dormancy-inducing stimuli.

We have previously shown that changes in gene expression occur in Arabidopsis thaliana. L. (Heyn) during cold acclimation (SJ Gilmour, RK Hajela, MF Thomashow [1988] Plant Physiol 87: 745-750). Here we report the isolation of cDNA clones of four cold-regulated (cor) genes from Arabidopsis and examine their expression in response to low temperature, abscisic acid (ABA), water stress, and heat shock. The results of Northem analysis indicated that the transcript levels for the four cor genes, represented by clones pHH7.2, pHH28, pHH29, and pHH67, increased markedly between I and 4 hours of cold treatment, reached a maximum at about 8 to 12 hours, and remained at elevated levels for as long as the plants were kept in the cold (up to 2 weeks). Retuming cold acclimated plants to control temperature resulted in the levels of the cor transcripts falling rapidly to those found in nonacclimated plants; this occurred within 4 hours for the transcrpts represented by pHH7.2 and pHH28, and 8 hours for those represented by pHH29 and pHH67. Nuclear run-on transcription assays indicated that the temperature-regulated expression of the cor genes represented by pHH7.2, pHH28, and pHH29 was controlled primarily at the posttranscriptional level while the cor gene represented by pHH67 was regulated largely at the transcriptional level. Northern analysis also indicated that the levels of cor gene transcripts increased in response to both ABA application and water stress, but not to heat shock. The possible significance of cor genes being regulated by both low temperature and water stress is discussed.

Seed dormancy has been associated with red grain color in cereal crops for a century. The association was linked to qSD7-1/qPC7, a cluster of quantitative trait loci for seed dormancy/pericarp color in weedy red rice. This research delimited qSD7-1/qPC7 to the Os07g11020 or Rc locus encoding a basic helix-loop-helix family transcription factor by intragenic recombinants and provided unambiguous evidence that the association arises from pleiotropy. The pleiotropic gene expressed in early developing seeds promoted expression of key genes for biosynthesis of abscisic acid (ABA), resulting in an increase in accumulation of the dormancy-inducing hormone; activated a conserved network of eight genes for flavonoid biosynthesis to produce the pigments in the lower epidermal cells of the pericarp tissue; and enhanced seed weight. Thus, the pleiotropic locus most likely controls the dormancy and pigment traits by regulating ABA and flavonoid biosynthetic pathways, respectively. The dormancy effect could be eliminated by a heat treatment, but could not be completely overcome by gibberellic acid or physical removal of the seed maternal tissues. The dormancy-enhancing alleles differentiated into two groups basically associated with tropical and temperate ecotypes of weedy rice. Of the pleiotropic effects, seed dormancy could contribute most to the weed adaptation. Pleiotropy prevents the use of the dormancy gene to improve resistance of white pericarp cultivars against pre-harvest sprouting through conventional breeding approaches. SEEDS acquire primary dormancy during development to enhance adaptation of wild species to diverse environments by distributing germination over time and space. Domestication tends to reduce dormancy by selection for rapid, uniform germination (Harlan et al. 1973). Differentiation in seed dormancy between cereal crops and wild relatives has been associated with seed morphologies (Nilsson-Ehle 1914;Johnson 1935) and quantitative trait loci (QTL). Cloning of validated dormancy loci provides in-depth insights into regulatory mechanisms underlying natural variation in this adaptive or domestication-related trait (Bentsink et al. 2006;Sugimoto et al. 2010).Weedy rice refers to Oryza spp., which competes with cultivated rice (Oryza sativa L. and O. glaberrima Steud.) from tropical to temperate areas (Oka 1988;Delouche et al. 2007). The most persistent type of weedy rice is red rice, which is characterized by a red pericarp color. Red rice has strong seed dormancy (Cohn and Hughes 1981;Noldin et al. 2006). Genetic analysis has associated pericarp color with seed dormancy in red rice (Gu et al. 2005a).This association was first reported for wheat (Triticum aestivum L.), where red grain genotypes were more dormant than the white ones, and this morphology has been used to select cultivars for resistance to pre-harvest sprouting (NilssonEhle 1914;Flintham 2000). However, it remains unknown if the association in rice, wheat, and other crops arises from a tight linkage between genes for these two trai...