Performing Department
(N/A)
Non Technical Summary
Plant and animal production, protection, and health
Animal Health Component
10%
Research Effort Categories
Basic
90%
Applied
10%
Developmental
(N/A)
Goals / Objectives
Research ObjectivesObjective 1: Determine the origins and historical hybridization patterns of weedy radish invasionObjective 2: Determine how climate influences crop-wild radish hybridizationObjective 3: Determine the genomic basis of hybrid radish success and climate adaptationTraining Goals- Develop expertise in population genomic analyses- Grow as a mentor and educator- Expand my professional network- Receive feedback on applications for my next position
Project Methods
Data collection methods:Herbarium specimen sampling will focus on 19th- and 20th-century specimens from heavily collected areas: the Northeast, paired coastal and inland sites from Southern and Northern CA, the Pacific Northwest, and the Southeast. I will also sample all 19th-century US specimens (n=15) and a set of European reference wild radish individuals to augment publicly available European sequences.I will collect climate data based on herbarium specimen year and GPS coordinates. Climate data will come from ClimateNA and NOAA. Data will include average precipitation and temperature for the year, total number of Growing Degree Days (GDD) over the radish growing season, wettest and driest month precipitation averages, and coldest and hottest month temperature averages. I will create a climate Principal Component Analysis (PCA) to summarize climate variables and base all grouping of samples by climate on cluster analysis of the PCA values.I will follow established protocols to successfully extract and sequence DNA from old herbarium specimens for genomic analysis. I will use magnetic bead extraction and spin column kits and sequence the full genome of each individual at low coverage (3x) with PE 150bp short-read sequencing. I will use established practices to clean sequence data and map it to the existing reference genome, and will combine my data and existing resources with analytical methods designed specifically for the analysis of low-coverage samples.Herbarium specimens record climate adaptation-associated traits. Some traits, such as the size and density of stomata, change the plant's ability to tolerate climatic conditions, while others shift the timing of growth (phenology) to avoid challenging climatic conditions. I will mentor undergraduates in using recent advances in imaging and machine learning to quickly collect data on phenology and stomata from herbarium specimens.Objective 1 methods: I will compare samples from the earliest time period in each invaded US region (NE, NW, CA, and SE) to contemporary samples from other US regions and samples from originating European regions. I will use principal component analysis (PCA) to cluster individuals based on genetic similarity, enabling us to determine the likely origins of US weedy radish and which US populations likely came from the same introductioneg. PCA will also identify the appropriate genetic groupings for downstream analyses. To identify hybrid specimens, I will use NGSadmix to estimate the proportion of each species's ancestry in an individual's genome. I will overlay hybrid ancestry proportions on the PCA to understand which hybrids group together, indicating genetic similarity. I will then use phylogenetic methods implemented with TreeMix to determine how the genetic groups are related. The geographic distribution of hybrids through time will further clarify patterns of spread. For example, if all hybrid herbarium specimens sampled across a region form a single genetic group, but hybrids first appear in the south and only later in the north, hybrids likely spread north from initial hybridization in the south. For each hybrid origin, I will determine when and how frequently hybridization resulted in gene flow. When hybrids reproduce, their parental genomes recombine, creating a genomic mosaic ancestry blocks derived from each parental species. In each subsequent generation of descendants, these genomic ancestry blocks get smaller due to additional rounds of recombination. If repeated hybridization leads to ongoing crop-wild gene flow, new large blocks of crop ancestry will appear through time in addition to smaller blocks from gene flow in earlier generations. Therefore, we can decipher the history of gene flow by investigating the distribution of crop ancestry block sizes in weedy radish genomes through time. I will estimate ancestry block sizes with ancestryHMM.Objective 2 methods: I will first use pre-hybridization crop and wild radish occurrence data to describe their climate niches and evaluate whether the climate variables distinguishing parental species' niches correlate with the amount of crop vs wild ancestry in hybrid genomes. Beyond climate, other environmental factors may also influence ancestry proportion, such as land use history and management practices like herbicide use. I will include these variables in the model from sources such as county land use surveys and Department of Pesticide Regulation reports to understand the relative importance of climate compared with other factors determining hybrid ancestry.Objective 3 methods: To understand the roles of gene flow and climate adaptation in the success of weedy radish, I will identify positively selected loci in each population (using the genetic groupings determined in objective 1). To do so, I will use a haplotype scan approach implemented in selscan to identify genomic regions (loci) that have undergone strong positive selection, indicating a role in invasive success. I will first compare these loci to regions of the genome showing unusual patterns of gene flow from Objective 1. I can then determine whether positively selected genetic variants (alleles) originated in the wild radish or were introduced through gene flow from the crop. Positively selected crop alleles in climate adaptation-associated loci will indicate genomic regions where crop gene flow has contributed to wild radish climate adaptation. More generally, I will quantify the proportion of positively selected alleles coming from crop gene flow to clarify how hybridization contributed to weedy radish invasion success overall. To identify loci involved in climate adaptation, I will conduct genetic admixture mapping with wild hybrids. Wild hybrids provide a huge advantage for admixture mapping in this system; radishes are annuals, so the ~100-year history of hybridization in California represents ~100 generations of hybridization. This large number of generations of hybridization should provide high resolution to identify causal loci. I will use two complementary mapping approaches: mapping loci associated with specific climate variables, and mapping loci controlling traits related to climate adaptation. Specifically, I will map phenology and stomatal traits. I will then compare these climate-associated loci to my list of postiviely selected loci to estimate the contribution of climate adaptation to the success of invasive weedy radish. To further investigate the role of all identified loci in the invasive success of wild radish, I will compare them to existing genome annotations to identify potential underlying genes.