(External) Inter-species and Intra-population variation in Amaranthus species using whole genome sequencing

Advisor: Leonardo Galindo Gonzalez, Canadian Food Inspection Agency

Proposed UoG co-advisors: Sarah Adamowicz, Integrative Biology and Mehrdad Hajibabaei, Integrative Biology

The Molecular Identification Research Lab (MIRL) at the Canadian Food Inspection Agency in Ottawa uses molecular biology, omics and bioinformatics for identification of plants of regulatory concern including invasive and weedy species. 

Several plants of the genus Amaranthus (e.g., A. palmeri and A. tuberculatus) have negative impacts on the agricultural setting and have shown to decrease yields in important staple crops including soybean and corn. Additionally, these species have developed multiple herbicide resistance which makes management of these weeds very difficult. Climate change has resulted in an expansion of the latitudinal range of these species which is concerning for Canadian farming and trade. Phenotypic plasticity and hybridization make identification of these weedy species difficult when looking at plants in early stages of development or when looking at seeds that appear in trade commodities.

We used Illumina sequencing to assemble high copy regions including the chloroplast genomes and the nuclear ribosomal DNA of 29 samples spanning 15 Amaranthus species (including seven A. palmeri accessions from different geographical locations), to find polymorphisms that could be used as DNA barcodes to distinguish species. While some barcodes have already been found in these regions, most of the nuclear genome variation remains largely unexplored.

On this project we will use the available Illumina reads to perform whole-genome reference-based variant analysis to identify novel polymorphisms between the species of regulatory concern and their closest relatives. Command line tools are available (eg., Samtools/mpileup, FreeBayes, GATK) for this type of analyses, but variations and/or combination of these tools may be tested. We may also explore reference-free SNP discovery tools. A second stage of the project would comprise comparing different populations of A. palmeri, which is one of the most harmful species of the genus. The newly found polymorphisms can be used to develop species and population-specific sequence DNA barcodes that can be used for DNA fingerprinting, and study evolutionary relationships of the genus. Additionally, the polymorphic regions can be used to develop rapid diagnostic assays (e.g., PCR-based, CRISPR-Cas-based) to distinguish species when phenotypic characterization is not possible. Finally, the implementation and/or testing of bioinformatics pipelines for polymorphic discovery from whole genome sequencing reads, would provide a tool that can be easily transferred to other plant genera/species of concern.

The student project will be based on testing the variant discovery tools on different Amaranthus spp. (4-months). If work advances at a good pace by the end of June a second part of the project could be developed in 4 additional months depending on instructor approval. On this second part of the project, the student would explore populations within species and start writing a manuscript for publication.

This will be a remote position.

Knowledge and Skills:

• Unix/linux command line experience is essential.
• Programming (e.g.., python) would be an asset.
• Knowledge in genomics, including genome assembly and/or variant analysis is necessary.
• Knowledge in plant biology would be an asset.