TEOSINTE Project: Comparative Genomics of Maize's Wild Relatives (Teosinte)

Description

Project Start: 01.10.2021

Project Status: Active

Responsible Investigator: Joseph Atemia

Supervisor: Asis Hallab

Project Partners: Alicia Mastretta-Yanes (Instituto de Ecologia, UNAM, Mexico), Ana Wegier (Jardín Botánico, Instituto de Biologia, UNAM, México)

Crop wild relatives represent important sources of genetic variation that could be of great aid to breeding programs, especially regarding adaptation to extreme environmental conditions [ISBN:978-1-78064-197-3]. Maize close wild relatives are teosintes, which have a wide ecogeographic distribution in Mexico spanning extreme ranges of precipitation and temperatures [doi:10.1371/journal.pone.0192676]. The identification of the genetic variants associated with adaptation to such conditions is a necessary step in order to better monitor, conserve and use such diversity in applied projects. As part of preliminary research, the Mexican partners performed an extensive teosinte sampling, including ca. 4000 individuals of 276 populations of all the 7 teosinte species and subspecies distributed in Mexico. These samples were phenotyped in a greenhouse common garden, and genotyping by sequencing (GBS) was applied yielding ca. 60,000 SNPs. Ecogeographical analyses were also performed [doi:10.1371/journal.pone.0192676]. This dataset encompasses probably the most complete teosinte sampling done so far providing genomic data at a population level. However, teosinte genomes have proved to be incredibly diverse and complex, and during the course of domestication the differences among maize and its parental teosintes (​Zea mays ssp. ​ parviglumis and ssp. ​ mexicana) not only included re-shuffling allele-frequencies,but also structural and expression changes [doi:10.1038/ng.2309]. Therefore, fully exploring the variation associated to teosinte adaptation to diverse environments requires new approaches. Here, we aim to identify the genetic variants associated with teosinte adaptation to different environmental conditions, in the context of the genomic changes associated with domestication.

Funding

This project is funded by the German Ministry for Science and Education (BMBF 031B0921).

Data and Code Availability

• Genotyping-by-sequencing (GBS) data was provided by Mexican patterns. The data is publiclly available under the following publised papers:

  • Ecogeography of Teosinte
  • Genomic Diversity and Population Structure of Teosinte (Zea spp.) and Its Conservation Implications

• All code is contained in this git repository. Because the material (data) is contained in large files these cannot be included. Please write to the authors with affiliation to the Forschungszentrum Jülich (FZJ) to obtain the data files. For FZJ researches All data and code is stored on the compute cluster of the Forschungszentrum Jülich, Institute of Bio- and Geosciences (IBG), Bioinformatics (IBG-4). There all code regarding the population genetics analysis is stored in this directory: /mnt/data/joseph/TEOSINTE

Directory Structure

1. Project Overview

   • Overall Description of the project.

2. assay

3. runs

   • GAPIT GWAS results outputs

4. sudies

   • Initial 'raw' data
   • Processed data eventually used in the GWAS analysis using GAPIT – Genome Association and Prediction Integrated Tool.

5. workflows

   • Contains the following subdirectories that habours scipts and respective results files:

     • admixture_plots
     • climate_factor_intersections
     • genetic_diversity
     • gwas_gapit_pipeline
     • gwas_ps_robustness
     • phenotype_distribution_plots
     • phylogeny_based_GBS
     • preprocessing_data
     • snp_gene_neighborhood_pipeline

   • The file GWAS_Research_Methodology.md documents the steps and order of the whole analysis.