NSF Postdoctoral Fellowship in Biology: Overcoming Barriers to Wild Species Improvement through Genetic Analysis of an Evolutionary Novelty in the Solanum

Satterlee, James W, Cold Spring Harbor NY

Investigators

Abstract

This action funds an NSF Plant Genome Postdoctoral Research Fellowship in Biology for FY 2023. The fellowship supports a research and training plan in a host laboratory for the Fellow who also presents a plan to broaden participation in biology. The title of the research and training plan for this fellowship to James Satterlee is ‘Overcoming barriers to wild species improvement through genetic analysis of an evolutionary novelty in the Solanum’. The host institution for the fellowship is the Cold Spring Harbor Laboratory and the sponsoring scientist is Dr. Zachary Lippman. How do genetic differences result in the evolutionarily novel traits observed across the tree of life, such as flowers in flowering plants or limbs in vertebrate animals? This research will address this question using the plant genus Solanum as a model system. Solanum contains familiar major crop species such as tomato, potato, and eggplant. Unlike tomato and potato however, the lineage that gave rise to eggplant evolved sharp prickles on their surface to deter herbivores. During the domestication of eggplant and other closely related regionally important crops, breeders selected cultivars lacking prickles. Using this trait variation as a starting point, this work will first identify the genes that control the development of prickles and then seek to address which types of genetic changes occurred to allow these genes to take on their new function(s). Practically, an understanding of the genetic control of prickle development will allow the rapid engineering of desirable prickle-less lines in agriculturally useful Solanum species. This project will include a public outreach component involving short-form scientific videos for social media dissemination as well as a yearly course open to the public on genome editing and crop improvement. The underlying genetic changes that give rise to phenotypic novelty remain poorly understood. Evolution of new gene function can be driven by changes in the cis-regulatory DNA sequence surrounding the gene coding sequence. Such sequence changes may allow a gene to take on a new expression pattern, conferring function in a new place or time while avoiding potential pleiotropic effects of coding sequence mutations. In this way, it is hypothesized that ancestral gene functions may be redeployed in a new context to produce morphological novelty with a conserved molecular toolkit. This research will test this hypothesis through an investigation of the genetic basis for the evolution of prickles, a relatively recent (~16 My old) morphological innovation, in the agriculturally important genus Solanum. New high-quality genome assemblies will be leveraged to map and identify genes involved in prickle development in multiple species. Next, this work will aim to understand how these genes were recruited into the prickle developmental pathway using a combination of single-cell transcriptomics, open chromatin profiling, and comparative genomic analysis to link prickle-associated gene expression patterns to their underlying regulatory basis. Genome editing will be used to verify the functions of candidate genes and their cis-regulatory sequences. Finally, heterologous expression of candidate drivers of prickle development will determine their sufficiency and relevance to the evolutionary emergence of novelty. Together, this work will advance understanding of the emergence of innovative traits in evolution and may suggest routes for the synthetic engineering of novel morphologies. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.