Performing Department
(N/A)
Non Technical Summary
This research focuses on understanding and combating the threat posed by weeds that significantly hampers crop production. This work uses a weedy grass,Poa annua,as a model of study due to its global dominance, wide range of phenotypes, and genomic instability. Weeds likePoa annuacan drastically reduce agricultural yields, impacting food supply and economic stability. Given the growing global population and changing climate, it is crucial to develop effective strategies to manage these weeds. This project is not only relevant to farmers but also to the broader community, as it aims to enhance food security, promote environmental sustainability, and support economic resilience.To tackle this issue, our research will delve into the genetic makeup ofPoa annua. By studying its genome, we aim to understand how it adapts to different environmental conditions. Our approach involves sequencing the DNA and RNA of variousPoa annuasamples from diverse ecological regions spanning hot-dry Mediteranean climates and cool-wet alpine climates. This will help us identify genetic variations that allow the weed to thrive in diverse climates. Additionally, we will develop a computational tool to analyze genetic differences between these samples, which can be used for studying other similar organisms as well.The ultimate goal of our research is to uncover the genetic factors that makePoa annuaa successful and adaptable weed. By understanding these factors, we can devise new, science-based strategies to manage and control this weed more effectively. This will not only help farmers increase crop yields but also reduce the environmental impact of weed management practices. The insights gained from this study will be shared with the scientific community to inform future agricultural practices, ensuring a more sustainable and resilient food production system.
Animal Health Component
10%
Research Effort Categories
Basic
50%
Applied
10%
Developmental
40%
Goals / Objectives
Major Goals:The primary goal of this project is to uncover the genomic basis for environmental adaptation, polyploid evolution, and genome biology. Additionally, this research aims to develop computational software that will be accessible to a broad audience of researchers for exploring genetic divergence between closely related eukaryotic genomes. This work will provide significant insights into weed biology, contributing to the development of science-based strategies for agricultural resilience and sustainability.Objectives:Elucidate the Environmental Impact on Genome Architecture:Conduct genomic and transcriptomic sequencing of ecologically and phenotypically diverse accessions of weedyPoa annuato understand the influence of environmental factors on genome architecture, gene expression, and whole-plant morphology.Develop and Implement a Novel Computational Tool:Create a computational tool that leverages syntenic long terminal repeat (LTR) retrotransposons to resolve the evolutionary history of recently diverged genomes, such as the allotetraploid genomes of weedyPoa annua. This tool will be designed for widespread use by researchers studying genetic divergence in eukaryotic genomes.Perform Segregational Analysis:Conduct segregational analysis in the offspring of chromosomally unstablePoa annuato investigate the inheritance patterns and stability of genomic features in weedy and plastic species.
Project Methods
Methods for Aim 1Sample Collection and Classification:Seed Collection:Seeds ofPoa annuawill be collected from two distinct climates: boreal (subarctic) and Mediterranean. The Köppen climate classification system will be used to identify and classify accessions.Boreal Climates:Defined as Dfc, Dfd, Dwc, Dwd, Dsc, Dsd, or E.Mediterranean Climates:Defined as Csa, Csb, and Csc.Phenotypic Classification:Dwarf-Type Plants:Plants with an average tiller length ≤ 4 cm and average leaf length ≤ 5 cm.Wild-Type Plants:Plants with an average tiller length ≥ 23 cm and average leaf length ≥ 12 cm.Sequencing and Genome Assembly:Long-Read Sequencing:Oxford Nanopore PromethION 2 will be used, providing 80-120 Gb of ultra-long reads per flow cell, yielding 23-34× coverage per haplotype at $900 per sample.Supplementary Sequencing:Each genome will be supplemented with 100 Gb of Q30 short-read sequencing and Hi-C chromatin capture.Genome Assembly:Genomes will be assembled using HiFiasm, with gene and TE annotations via MAKER and EDTA, respectively.Data Analysis:Structural Analysis:Whole-genome alignment and syntenic analysis will elucidate structural differences among accessions.Homoeologous Exchanges:Analysis using pipelines such as Benson et al. 2023 and Hufford et al. 2021.RNA Sequencing:Nanopore direct RNA sequencing to capture full-length transcripts, mapped to reference genomes to study expression patterns and DNA methylation status using Remora.Methods for Aim 2Experimental Design:Selection of Accessions:SixteenP. annuaaccessions (8 dwarf-boreal and 8 wild-Mediterranean) will be selected for long-read DNA and RNA sequencing.SynLTR Analysis:Flanking Sequence Extraction:Use synLTR to extract 500 bp up- and downstream of intact LTR elements.Homologous Comparisons:Comparing publicly available parental genomes to their homologous pairs inP. annuato pinpoint hybridization events.Genetic Distance Measurement:Adjust comparisons to analyze genetic distances between dwarf-boreal and wild-Mediterranean populations.Data Analysis and Expected Results:Benchmarking SynLTR:Optimization and benchmarking of synLTR for accurate timescale estimation of evolutionary perturbations.Comparative Genomics:Public release of tools for broad utility in genomic divergence studies across eukaryotic genomes.Methods for Aim 3Experimental Design:Sample Population:100 offspring from an S1P. annuaheterozygous for large-scale chromosomal modifications.Growth Conditions:Offspring will be grown in a field site and phenotyped for various traits (e.g., germination time, anthesis time, rosette diameter, tiller number, culm length, shoot RGB color, seed number, seedling viability).Genotyping:Moderate-coverage Illumina sequencing (9× coverage per haplotype).Data Analysis:Segregation Analysis:Use of one-way ANOVA, linear regression, and Tukey HSD to study phenotypic associations with chromosomal modifications.QTL Mapping:Utilization of tools like tensorQTL to study genetic associations with plant phenotypes.Genomic Insights:Investigation into the impact of genome size on selective pressures and environmental resilience in polyploid crops and weeds.