Erin Doody

Transposons drive genetic diversity and evolution by altering the genomic landscape over time. Here, we describe D ELAYED AB AXIAL TRICHOMES ( DAB ), a Helitron/RC transposable element in Arabidopsis thaliana that has a role in vegetative phase change and gametogenesis. A genome-wide association study (GWAS) for the timing of abaxial trichome development (an adult leaf trait) in A. thaliana revealed a conserved haplotype of polymorphisms within DAB that delays abaxial trichome production. CRISPR-Cas9-induced deletions of DAB are gametophytic pollen-lethal, indicating that this locus is also required for pollen production. DAB produces 24-nucleotide siRNAs with sequence complementarity to genes involved in embryogenesis, gametogenesis, and seed development. DAB also impacts the expression of ARGONAUTE genes, genes involved in RNA-directed DNA methylation (RdDM), as well as genes in several key genetic pathways. This global effect on gene expression suggests that DAB may have functions beyond those identified in this study.

Summary: The flowers of angiosperms are extraordinarily diverse. While most floral variation is visible to the naked eye, this diversity goes beyond the macroscale: Floral organs comprise an underappreciated range of cell types that generate a multitude of patterns across their surfaces and give rise to novel structures. Because diverse cell patterns provide adaptations to biotic and abiotic factors, they also contribute to angiosperm evolution and speciation. Yet, how such diversity originates remains to be understood. In this review, we focus on petals, which together form the corolla, to examine the mechanisms patterning floral surfaces at the cellular level. We summarize current research aiming to understand how cell fate specification and controlled cell growth (proliferation and expansion) are achieved with high spatial resolution during petal development. We also examine the adaptive potential for such patterns and how they contribute to plant fitness and diversification. Finally, we discuss promising directions for future research on the evolution of petal patterning at the microscale and identify outstanding questions that technological advances now make it possible to address.

Traffic lines are transgenic stocks of Arabidopsis thaliana that contain a pair of linked seed-specific eGFP and DsRed markers. These stocks were originally developed for the purpose of studying recombination, but can also be used to follow the inheritance of unmarked chromosomes placed in trans to the marked chromosome. They are particularly useful for this latter purpose if the distance between markers is short, making double recombination within this interval relatively rare. We generated 163 traffic lines that cover the Arabidopsis genome in overlapping intervals of approximately 1.2 Mb (6.9 cM). These stocks make it possible to predict the genotype of a plant based on its seed fluorescence (or lack thereof) and facilitate many experiments in genetic analysis that are difficult, tedious, or expensive to perform using current techniques. Here, we show how these lines enable a phenotypic analysis of alleles with weak or variable phenotypes, genetic mapping of novel mutations, introducing transgenes into a lethal or sterile genetic background, and separating closely linked mutations.

The juvenile-to-adult transition in plants is known as vegetative phase change and is marked by changes in the expression of leaf traits in response to a decrease in the level of miR156 and miR157. To determine whether this is the only mechanism of vegetative phase change, we measured the appearance of phase-specific leaf traits in 70 natural accessions of Arabidopsis thaliana. We found that leaf shape was poorly correlated with abaxial trichome production (two adult traits), that variation in these traits was not necessarily correlated with the level of miR156, and that there was little to no correlation between the appearance of adult-specific vegetative traits and flowering time. We identified eight quantitative trait loci controlling phase-specific vegetative traits from a cross between the Columbia (Col-0) and Shakdara (Sha) accessions. Only one of these quantitative trait loci includes genes known to regulate vegetative phase change (MIR156A and TOE1), which were expressed at levels consistent with the precocious phenotype of Sha. Our results suggest that vegetative phase change is regulated both by the miR156/SPL module and by genes specific to different vegetative traits, and that natural variation in vegetative phase change can arise from either source.

Shoot development in plants is divided into two phases, a vegetative phase and a reproductive phase. Vegetative growth also has two distinct juvenile and adult phases, the transition between which is termed vegetative phase change . To understand how this developmental transition is regulated in natural populations of plants, we grew a group of 70 accessions of Arabidopsis thaliana and measured the appearance of traits associated with vegetative and reproductive phase change. We found that these transitions were uncorrelated, implying they are regulated by different mechanisms. Furthermore, an analysis of accessions from Central Asia revealed that precocious changes in leaf shape poorly correlated with the timing of abaxial trichome production (an adult trait) and with variation in the level of miR156 (a key regulator of vegetative phase change). This suggests the timing of vegetative phase change is regulated by more than one mechanism. To identify the genes responsible for the precocious vegetative phenotype of these accessions, we used a set of recombinant inbred lines derived from a cross between the standard lab strain, Col-0, and one of these accessions, Shakdara. We identified eight quantitative trait loci involved in the vegetative phase change, some of which regulated different components of leaf development. All of these loci were distinct from those that regulate flowering time. These data provide the foundation for future studies to identify the loci and the regulatory networks responsible for natural variation in the timing of vegetative phase change in A. thaliana .

Summary: Plants transition through juvenile and adult phases of vegetative development in a process known as vegetative phase change (VPC). In poplars (genus Populus) the differences between these stages are subtle, making it difficult to determine when this transition occurs. Previous studies of VPC in poplars have relied on plants propagated in vitro, leaving the natural progression of this process unknown. We examined developmental morphology of seed‐grown and in vitro derived Populus tremula × alba (clone 717‐1B4), and compared the phenotype of these to transgenics with manipulated miR156 expression, the master regulator of VPC. In seed‐grown plants, most traits changed from node‐to‐node during the first 3 months of development but remained constant after node 25. Many traits remained unchanged in clones over‐expressing miR156, or were enhanced when miR156 was lowered, demonstrating their natural progression is regulated by the miR156/SPL pathway. The characteristic leaf fluttering of Populus is one of these miR156‐regulated traits. Vegetative development in plants grown from culture mirrored that of seed‐grown plants, allowing direct comparison between plants often used in research and those found in nature. These results provide a foundation for further research on the role of VPC in the ecology and evolution of this economically important genus.