The Genetic Basis Of Natural Variation In The Timing Of Vegetative Phase Change In Arabidopsis Thaliana

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Doctor of Philosophy (PhD)
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Arabidopsis thaliana
natural variation
vegetative phase change
Agricultural Science
Developmental Biology
Plant Sciences
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Doody, Erin E

Plants undergo developmental changes that impact their form and function as they grow. Post-embryonic vegetative growth is characterized by two distinct developmental transitions: vegetative and reproductive phase changes. While natural variation in the reproductive transition is well studied, the transition between juvenile and adult vegetative growth — vegetative phase change — is often overlooked. Vegetative phase change is regulated by the microRNA, miR156, and its targets, SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) genes, and this pathway is conserved across land plants. However, the amount of natural variation in this transition, and the mechanisms regulating vegetative phase change in natural populations of Arabidopsis thaliana was unknown when I began my thesis. To better understand this problem, I assessed the phenotypic and genetic diversity in 100 natural accessions of A. thaliana. I found a wide range in the timing of vegetative phase change, that this transition is not correlated with reproductive phase change, and that miR156 and SPL gene expression were not associated with the observed phenotypic variation. These results imply that vegetative phase change is independent of other developmental transitions and that unknown genetic loci are involved in its regulation. I used two approaches to determine the genetic loci regulating natural variation in vegetative phase change: quantitative trait loci (QTL) mapping in the Shahdara accession and a genome-wide association study (GWAS) in a group of diverse accessions. QTL mapping in Shahdara revealed at least eight loci involved in the regulation of vegetative phase change, indicating regulation of vegetative phase change is complex and quantitative. GWAS for the timing of vegetative phase change uncovered several QTLs regulating vegetative phase change. The most significant polymorphisms were within a region that encodes a 24-nucelotide small RNA locus (smRNA), which delays abaxial trichome production. Together, this thesis provides the groundwork for future studies of the complex basis of natural variation in the timing of vegetative phase change in A. thaliana and has revealed novel genetic loci involved in the regulation of this transition. Additionally, my work has highlighted the importance of using natural variation to provide insights into the regulation of quantitative developmental pathways.

Scott Poethig
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