Wild emmer wheat (Triticum turgidum subsp. dicoccoides) whole-genome sequencing data and analysis output files

Adhikari, Laxman 1 ; Olivera, Pablo2 ; Yu, Guotai1 ; Raupp, John3 ; Sela, Hanan4 ; Distelfeld, Assaf4 ; Wulff, Brande1 ; Steffenson, Brian2 ; Poland, Jesse 1

Published Mar 31, 2026 on Dryad. https://doi.org/10.5061/dryad.zcrjdfnmb

Abstract

Triticum turgidum L. subsp. dicoccoides, known as wild emmer wheat (WEW), is a tetraploid (2n = 4X = 28) relative and a progenitor of cultivated wheat. We conducted population genetics and evolutionary studies, along with dissecting the genetic basis of resistance to three rust diseases in WEW. Leveraging whole-genome sequencing (WGS) data (14 TB) from 291 accessions at approximately 9.5x coverage, we identified 3.4 million high-quality SNP markers and utilized them for phylogenetic clustering, principal component analysis, and population structure assessment. Additionally, we performed diversity and pairwise FST analysis among the subgroups identified by the population structure. For genome-wide association studies (GWAS), we investigated seedling-stage resistance in WEW against five races each of stem, leaf, and stripe/yellow rusts.

Authors: Laxman Adhikari, Pablo D. Olivera, John Raupp, Hanan Sela, Assaf Distelfeld, Marco Maccaferri, Matteo Bozzoli, Elisabetta Mazzucotelli, Andrea Brandolini, Roberto Tuberosa, Hakan Özkan, Brande B. H. Wulff, Brian J. Steffenson and Jesse Poland

Description: This README file explains the dataset.

Data Availability: The raw sequence reads (pair-end fastq files) generated using whole-genome sequencing (WGS) of the 291 wild emmer wheat (WEW) accessions (Triticum turgidum L. subsp. dicoccoides) were deposited at the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) with BioProject accession number PRJNA1007489. The fastq files were trimmed, aligned, and analyzed to identify single nucleotide polymorphisms (SNPs). The population genomics analysis was conducted using a 5% subset (3.4 million SNPs) of filtered quality SNPs (68 million).

Dataset: We provided R scripts (.Rmd files) for the population genomics analysis of wild emmer wheat, involving phylogenetic clustering, PCA, population structure, gene bank curation, and genome-wide association study (GWAS) used in the study. All required files are provided either as attachments along with the manuscript or as Dryad supplementary files. The sequence fastq files have been deposited at NCBI SRA. There are 291 pair-end fastq files that can be searched with the BioProject accession (PRJNA1007489). The fastq files were provided with the original names required to run the SNP calling pipeline. In this study, we called SNPs using bcftools. We also provided phenotype data along with the supplementary documents of the manuscript that can be used to run GWAS.

The fastq files can be searched at NCBI SRA:

https://www.ncbi.nlm.nih.gov/bioproject/1007489

Files	Description
data-curated.genoFile.dicoccoides.3.4.SNPs.for.pub.txt.zip	SNP matrix of the entire population used in the analysis
judaicum_Segregating.SNPs.txt.zip	SNP matrix including the segregating loci of the judaicum race of the WEW
Northern_Population_Segregating.SNPs.txt.zip	SNP matrix including the segregating loci of the Northern Population of the WEW
Southern_Levant_Segregating.SNPs.txt.zip	SNP matrix including the segregating loci of the Southern Levant (SL) population of the WEW
Line.info.dicoccoides.txt	Information about the geographical origin of the WEW accessions
lineinfo.dark.branches.rust.no.tip.xlsx	Disease severity score used to plot the phylogenetic tree vs. geography vs. disease severity
judaicum.LD.estimation.txt	Pairwise LD (r2) estimated for the judaicum race
Northen_Population.LD.estimation.txt	Pairwise LD (r2) estimated for the Northern Population
Southern.Levant_Population.LD.estimation.txt	Pairwise LD (r2) estimated for the Southern Levant (SL) Population
dicoccoides.WGS.panel.phylogenetic.tree.PCA.Pop.Str.Rmd	R script for genetic clustering, PCA analysis, and population structure
phylogeny.vs.geography.vs.diseasease.severity.TTKSK.as.example.Rmd	R script for genetic clustering vs. disease severity and geography
LD.Decay.plot_Rscript.WEW.Rmd	R script to generate LD decay plot
colorful.manhattan.and.SNP.density.Rmd	R script for Manhattan plot and SNP

Wild emmer wheat (Triticum turgidum subsp. dicoccoides) whole-genome sequencing data and analysis output files

Data files

Abstract

README: Dissecting the population structure, diversity and genetic architecture of rust resistance in wild emmer wheat (Triticum turgidum subsp. dicoccoides)

Methods