T3/Wheat Genotype Trial description

GDW 90K

- Global Durum Wheat Panel

Publication: The Global Durum WheatPanel (GDP): An International Platform to Identify and Exchange Beneficial Alleles
Methods: Tetraploids
Filter: MAF-unfiltered

NYS durum GBS

Protocol: GBS (Poland et al., 2012)
Methods: Durum wheat genome highlights past domestication
Debre Zeit - CIMMYT durum
Genotyping was done in USDA-ARS Eastern Regional Small Grains Genotyping Laboratory in Raleigh, NC

Exome Capture Watkins

- Watkins Core 2017

Raw data: Grassroots Data Repository
Protocol: Gardiner_et_al_2017_Watkins_exome_capture_SNP
Publication: Establishing the A. E. Watkins landrace cultivar collection
Publication: High-density genotyping of the A.E Watkins Collection

Promotor capture KSU 2020

- WheatCAP Regulatory

Protocol: Integrating genomic resources to present full gene and putative promoter capture probe sets for bread wheat

TGC-GTC 90K

- Tetraploid Wheat Global Collection

Publication: Durum wheat genome highlights past domestication signatures
Methods: Tetraploids

Exome capture KSU 2014

- 2014_HapMap_WEC

Publication: A haplotype map of allohexaploid wheat reveals distinct patterns of selection on homoeologous genomes

GBS restriction KSU 2014

- 2014_HapMap_GBS (62 diverse wheat lines)

Publication: A haplotype map of allohexaploid wheat reveals distinct patterns of selection on homoeologous genomes

Exome capture HapMap 2019

329 USA WheatCAP germplasm
Publication: Development of the Wheat Practical Haplotype Graph database
Publication: A haplotype map of allohexaploid wheat reveals distinct patterns of selection on homoeologous genomes
The final dataset after filtering for MAF>5 accessions, includes ~7 million SNPs and short indels detected using GATK

Exome capture Diversity 2019

1000 Exomes
Passport: 1000 exome germplasm
Publication: Exome sequencing highlights the role of wild-relative introgression in shaping the adaptive landscape of the wheat genome
Filter: minimum allele count = 2, MAF > 0.002 and missing genotype calls <25%

Exome capture 2017

- 2017_WheatCAP

Illumina 90K

Publication: high-density 90 000 single nucleotide polymorphism array

Illumina 9K

Publication: 9K iSelect BeadChip Assay

Accessions	Seedlots
Accessions		Breeding Program	Seedlot Name	Contents	Seedlot Location	Count	Weight(g)

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Funded By

T3 is part of the Wheat CAP project, supported by Agriculture and Food Research Initiative Competitive Grant no. 2011-68002-30029 from the USDA National Institute of Food and Agriculture.