Integrating genomics to understand dioecy and herbicide selectivity in weeds

Abstract

Recent advances in genomics have made the characterization of plant genomes, including those of weedy species, increasingly feasible. High-quality reference genomes are now becoming available for several weeds, thanks to efforts led by the International Weed Genomics Consortium. These assemblies rely on long-read sequencing, optical mapping, and chromatin conformation (Hi-C) technologies to generate highly contiguous genomes that capture the structural complexity of weedy species. This dissertation includes two research chapters showing how genomics can enhance weed science by resolving repetitive regions and enabling quicker gene identification through reference genome annotation, all while placing gene locations within a clear genomic context. Chapter one introduces foundational concepts in de novo genome assembly, the biology of sex determination in dioecious plants, and the mechanisms of herbicide action and resistance. These topics provide the background for the following research chapters. Chapter two focuses on Cirsium arvense, a dioecious and highly invasive weed species, highlighting the importance of reference genomes for studying sex chromosomes. A WZ sex determination system is proposed, with Chromosome 6 identified as the probable sex chromosome pair. This chapter provides a detailed analysis of the sex chromosomes, including synteny analysis, identification of potential sex-linked regions, and the distribution of transposable elements (TEs). These analyses indicate that the sex-determining region does not show substantial TE enrichment but exhibits about a 10 kb loss of synteny between sex chromosomes. Additionally, sex-biased and sex-limited gene expression were examined. Notably, only 6.5% of expressed genes displayed differential expression between sexes, with male-limited expression more widespread across the genome, while female-limited expression was primarily confined to the sex chromosome. Finally, chapter three illustrates how annotated genomes could facilitate downstream functional studies. A yeast two-hybrid library was developed to investigate the interaction between auxinic herbicide receptors (TIR1/AFB) and the Aux/IAA16 coreceptor, including both resistant and susceptible alleles affecting dicamba resistance in Bassia scoparia. Dicamba, 2,4-D, dichlorprop, and fluroxypyr were tested at concentrations of 500 and 1000 µM. Among them, only dichlorprop interacted with the resistant allele when in combination with TIR1. These in vitro results were contrasted with dose-response experiments on whole plants employing the same herbicides. However, the interaction patterns seen in vitro did not align with the responses observed in the dose responses, indicating that other factors influence herbicide action. Together, these chapters highlight how reference genomes and functional genomics tools can enhance our understanding of weed biology, genome evolution, and herbicide physiology, by providing insights that inform the development of more effective and sustainable weed management strategies.