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To survive potentially lethal winter conditions, perennial species arrest their growth, form specialized structures to protect their meristems (buds), enter a dormant state and induce cold hardiness. For many decades, photoperiod and low temperatures have been recognized as the seasonal cues of this transition (Battey, 2000). Nonetheless, we know little about the mechanisms of response to these seasonal cues. Understanding the regulation of dormancy induction is critical for our ability to adapt superior genotypes of economically important species to new locations. More urgently, we lack the ability to confidently predict how perennials will respond to climate change-associated alterations in seasonal temperature regimes. Inappropriate timing of growth cessation could alter growing-season duration, increase susceptibility to freezing injury and potentially affect the subsequent dormancy status of overwintering buds (Tanino et al., 2010). Several novel molecular players have been added to our understanding of perennial seasonal response in the last few years (Horvath, 2009). However, for use in predicting population responses to climate change we need to know which of these regulators drive the phenotypic diversity within a species. The paper by Rohde et al., in this issue of New Phytologist (pp. 106–121), represents an excellent example of the integration of previous work on known molecular regulators of phenology and global transcriptome profiling with the genetic and phenotypic diversity found in natural and created populations of Populus spp. This work highlights the exciting state of perennial biology research, where powerful modern genomic and molecular methodologies are being integrated with classic quantitative trait locus (QTL) mapping approaches to understand life-history traits not present in annual models.
‘… an excellent tool to clarify a previously opaque series of distinct developmental stages.’
Setting the stages
Previous literature on autumnal phenology has used the appearance of bud set as a visual marker of the vegetative growth response of perennials to dormancy-inducing conditions. The use of bud set as a marker is understandable because it is easily scored in the field on large numbers of individuals. However, visual bud set represents the end point of what can be an extended process of plant response to seasonal cues. Before bud set, addition of new leaf modules slows and is accompanied by a dramatic reduction in the length of the internodes. A new developmental programme is initiated as some of the primordial leaves or stipules are converted to bud scales, which eventually grow to encapsulate the meristem and the remaining leaf initials (Lubbock, 1899). Ultimately, the remaining leaf initials and the meristem slow their cell division and the meristem enters a dormant state (Olsen, 2003; Horvath et al., 2005).
Rohde et al. have introduced a growth cessation and bud set scoring system reminiscent of floral and fruit developmental stages in agricultural species. Their rational system has allowed them to quantitatively assess stages of the process from active growth to bud set. With obvious modification for species-specific morphologies, this approach can be adopted by others in the field as an excellent tool to clarify a previously opaque series of distinct developmental stages. A particularly novel finding of this work is that the duration of growth cessation or bud development is phenotypically variable and independent of the traditionally scored date of onset or completion of these two developmental events.
QTL mapping in the post-genomic era
Identifying regulatory genes in perennial systems has been hindered by the lack of naturally occurring mutants and the significant investments required to generate novel germplasm. The work of Rohde et al. illustrates the opportunities made available to researchers in perennial biology by post-genomic resources. Quantitative trait locus mapping of bud set phenology has been performed previously in Populus and in other tree species, but QTL intervals could only be compared with the mapped location of a very limited number of genes with any hypothetical involvement in bud set. The recent availability of the sequenced Populus trichocarpa genome now allows the specific DNA sequence falling within mapped QTL loci to be identified (Tuskan et al., 2006). This ability permits the discovery of previously unknown regulators of bud dormancy, bypassing the inefficient process of selecting potential candidate genes from weakly analogous processes in annual models.
What is also exciting about conducting QTL mapping in a genome-sequenced species is the opportunity to integrate the large data sets of global transcriptome profiling into the experiments. Differential expression experiments with microarray and high-throughput sequencing methods tend to generate large numbers of significantly differentially expressed genes, and assigning a priority to the analysis of these genes is a challenge. Rohde et al. integrated previous microarray experiments of gene expression throughout the seasonal transition to dormant buds and successfully localized a subset of these genes into the robust QTLs defined in their study. The potential for these genes to be involved in growth cessation and establishment has now been verified by two independent means, strengthening their consideration as important regulators.
The more the merrier: multiple genome sequenced models for winter dormancy are now available
Long-term investment in Populus spp. has developed them as workhorses of the tree biology world for use in reverse genetic and global transcriptome profiling experiments. These species are more challenging as a tool for forward genetics because of a long generation time and a dioecious character (Taylor, 2002). Rohde et al. highlight the power of integrating all three approaches. Excitingly, with the recent release of genome sequences of grape (Vitis vinifera), peach (Prunus persica) and apple (Malusdomestica), three more woody perennial systems are now available for integrated genetic and genomic approaches (Velasco et al., 2007) (http://www.rosaceae.org). Peach and apple are well-established models for the genetic and physiological analysis of perennial life-history traits. Chilling requirements for bud break and bloom date are economically significant traits in these species and there are active breeding programmes around the world for these traits. Peach is particularly amenable for forward genetic studies because it has a small genome (approximately half the size of the P. trichocarpa genome) with little duplication history, is self-fertile, has a generation time as short as 2–4 yr and significant genomic resources are available (Shulaev et al., 2008). Recent work has demonstrated the utility of peach to map and sequence candidate genes for important winter-dormancy traits (Bielenberg et al., 2008; Fan et al., 2010). Apple, in turn, possesses a very robust transformation capability for reverse genetics (Shulaev et al., 2008).
Research on several species will be needed to truly understand ecosystem-level phenological responses to climate change because induction of growth cessation, bud set and bud flush is regulated differently in different species. For example, in Malus and Pyrus spp. growth cessation and bud set appear to be regulated by low temperatures alone without the involvement of photoperiod (Heide & Prestrud, 2005). While trees dominate the discussion of perenniality, many herbaceous species also develop buds and enter winter dormancy, often from underground structures (Horvath et al., 2002). It is clear that parallel work on multiple plant systems will be important to incorporate the biological diversity of perennial species. The community of perennial biology researchers will need to continue to be adept at applying data and concepts gained from one system to another.