Aquilegia as a new model species
We are part of a large collaborative group that is working to develop a wide range of genomic and genetic tools in the lower eudicot genus Aquilegia. This group is led by Scott Hodges of the Univ. of CA, Santa Barbara and also includes Magnus Norborg of USC , Jeff Tomkins of Clemson Univ. and Justin Borevitz of the Univ. of Chicago.
Why Aquilegia?
Five major features of Aquilegia make it an extraordinary opportunity for development as a model system for the study of adaptations to the environment: 1) species vary widely with respect to both the biotic and abiotic environments, 2) species are largely interfertile allowing the genetic dissection of traits, 3) speciation has occurred extremely rapidly resulting in low sequence variation among species, 4) species are diploid (n = 7) with a small genome (1C = 320-400 Mbp), and 5) genomic resources have already been developed including a genetic map, QTL identification for a number of traits, the isolation and characterization of floral developmental genes, two fingerprinted BAC libraries and an EST database.
The genus Aquilegia (Ranunculaceae) has been the subject of ecological, evolutionary and genetic studies for over 50 years (Hodges and Fulton, 2004). The genus consists of approximately 70 perennial taxa distributed in temperate North America, Europe and Asia and is noted for the nectar spurs that occur on each of the five petals of its flowers. These spurs are tubular outgrowths of the petals with a nectary at their base. Animals probe these tubes to obtain nectar and in doing so pollinate the plants. Although all species exhibit this general floral bauplan, the genus is remarkable for wide variation in floral morphology and color associated with different pollinators (Fig. 1). Floral features among species can range, for example, in nectar spur length (from < 1cm to > 12 cm), petal blade length (from 0 cm to > 3 cm), flower orientation (from pendant to upright), and flower color, (including blue, purple, red, yellow, green, and white species). Columbines also occur in diverse habitats, including shaded forests, alpine zones, desert springs, and serpentine outcrops (Munz, 1946). Some species have dramatic latitudinal and altitudinal ranges such as A. formosa (southern California to Alaska; sea level to 10,000 ft) and A. canadensis (Texas and Georgia to Canada). Thus, striking ranges of habitat occur both within and between species.
We plan to take several different experimental approaches to understanding the genetic basis of adaptations to the environment. First, we will develop genomic tools that will allow us to conduct fine-scale mapping of QTL, identify specific expression patterns for complex phenotypes and, ultimately, conduct comparative genomic studies. Second, as a pioneering example, we will identify the genetic basis for a major QTL for a pollinator preference trait, flower orientation, using fine mapping, gene expression profiling, linkage disequilibrium, and if successful, transgenic approaches. Third, we will investigate variation, at the sequence and expression levels, for a large number of candidate genes in the vegetative to floral transition pathway. The timing of this reproductive transition responds to the exquisite integration of environmental and endogenous cues and is closely tied to fitness. And fourth, we will map QTL for adaptations to divergent habitats and identify candidate genes using a very high density genetic map in recombinant inbred lines. These studies will provide a rich demonstration of the power that genomic techniques can bring to natural systems and set the stage for future studies, by a bourgeoning Aquilegia community, aimed at understanding how species adapt to the biotic and abiotic environment.
Objective 1: Construct recombinant inbred lines for A. formosa X A. and genotype them
with saturating molecular markers.
Objective 2: Construct integrated physical and genetic maps for A. formosa X A.
pubescens
Objective 4: Construct high-density oligo nucleotide arrays for both expression &
genotyping studies
Objective 5: Develop methods for transformation in Aquilegia.
Objective 6: Conduct fine-scale mapping and cloning of QTL for flower orientation using
array-based mapping,, association mapping, and expression studies.
Objective 7: Characterize the flowering time response in A. formosa.
Objective 8: Characterize the expression patterns, function, and evolution of candidate
flowering time genes in Aquilegia.
Objective 9: Identify novel vernalization-responsive genes using microarray expression
analyses.
Objective 10: Conduct high resolution QTL mapping for habitat associations and
determine the transcriptional response of these QTL in different habitats.
The first five objectives concern the creation of genomic tools for the dissection and analysis of traits associated with the biotic and abiotic environment. The second five objectives demonstrate the use of these tools for an analysis of the genetic basis of variation in floral morphology and development, as well as habitat associations. The Kramer lab is particularly focused on objectives 5 and 7-9.
Specifically, we have demonstrated the effective use of a reverse genetic technique, virus-induced gene silencing (VIGS), to study gene function in Aquilegia. Using Agrobacterium mediated transfer of tobacco rattle virus (TRV) based vectors, we have induced silencing of the PHYTOENE DESATURASE (AqPDS) and ANTHOCYANIDIN SYNTHASE (AqANS) genes in Aquilegia vulgaris (Gould and Kramer 2007). Our results show that TRV-VIGS in Aquilegia is suitable for high-throughput experiments and can be reproduced with high survival and silencing rates. In the future, data derived from VIGS analyses will be combined with large-scale sequencing and microarray experiments already underway in order to address both recent and ancient evolutionary questions.
Gould, B. and E. M. Kramer. (2007) Virus-induced gene silencing as a tool for functional
Hodges, S.A., and Fulton, M. (2004). Verne Grant and evolutionary studies of Aquilegia. New Phytol 161, 113-120.
Munz, P.A. (1946). Aquilegia: The cultivated and wild columbines. Gentes Herbarium 7, 1-150.
See also: Hodges and Kramer, 2007, Curr Biol 17, R992-994 Hodges and Kramer CurrBiol 2007.pdf
PDS silenced
ANS silenced
