Activity 1: Harnessing the diversity of wheat

Proposed genome sequecning strategy

Tier 1: High-quality reference assembly

Producing high-quality de novo genome sequences for six novel genomes of Ae. markgrafii (C), Ae. comosa (M), Ae. speltoides (S), Ae. umbellulata (U), Ae. Uniaristata (N), and Ae. Mutica (T).

Genome size estimates by flow cytometry

Species Genome 1C1 (Gbp) 1C2 (Gbp)
Ae. markgrafii C 4.84 4.3±0.013
Ae. comosa M 5.53 5.3±0.014
Ae. speltoides S 5.81 5.5±0.005
Ae. umbellulata U 5.38 5.1±0.014
Ae. uniaristata N
Ae. mutica T

1 Eilam, T., et al., Genome size and genome evolution in diploid Triticeae species. Genome, 2007. 50: 1029-37.
Eilam, T., et al., Nuclear DNA amount and genome downsizing in natural and synthetic allopolyploids of the genera Aegilops and Triticum. Genome, 2008. 51: 616-27.
2 Our estimates

Tier 2: Reference guided assembly

Generating mid-coverage assemblies of at least 50 accessions using 30× read-depth of Oxford Nanopore, 10× read-depth of 10X Genomics and 10× read-depth of Illumina short reads technologies (Table 1.2) to enable the identification of single nucleotide variation (SNV), PAV and CNV, and a large proportion of structural variants

Mid-coverage assemblies of at least 50 accessions

Accesion Species Genome Activity Tissue Seed
Carberry T. aestivum ABD 2.2 √ √
Stettler T. aestivum ABD 2.2 √ √
27 SHWs1 T. aestivum ABD 1.1/1.2/2.2 √ √
Canthatch T. aestivum ABD 3.1 √ √
RL5710 T. aestivum AB 3.1 √ √
Stewart 63 T. durum AB 3.1 √ √
DT6962 T. durum AB 3.2 √ √
D04X.00.003 T. durum AB 3.2 √ √
13 accessions T. turgidum ssp AB 1.1 √ √
13 accessions Aegilops sp Tetra/Hexa 1.1 √(9/13) √(9/13)
22 NAM parents T. aestivum ABD 2.2 √ √

1 Includes NAM SHW parents
2 Replacement for Transcend: Assembly available based on ONT trial

Tier 3: Imputed assembly
  • perform low-coverage sequencing (~1×) of more than 350 accessions using standard Illumina short read sequencing with the aim to define haplotypes and increase the potential to identify rare alleles.
  • 350 accessions of diploid, tetraploid and hexaploid from 23 Aegilops species and 4 Triticum species including many subspecies

    • Genetic diversity of 350 accessions

  • Selection will be based on genetic diversity, deepening the Aegilops representation and covering the subspecies of T. aestivum and T. turgidum
  • Selection of tetraploid species

    • Wild emmer wheat (T. dicoccoides)

    Domesticated emmer wheat (T. dicoccum)

    Durum wheat landraces (T. durum)

    186 accessions representing Fertile Crescent region where grow WEW natural populations

    139 accessions from 29 countries

    140 accessions from 39 countries