Phenotypic and low coverage whole genome sequencing SNP data for the wheat diversity panel of 328 accessions

Phenotypic Data

Diversity Panel:

The panel includes 328 accessions encompassing 33 different species of cultivated wheats, synthetic hybrid wheat (SHWs), progenitor species and wild relatives (see the table below).

The information of all accessions in the panel is included in the file:328_accessions_wheat_diversity_panels_info.xlsx.

Summary of accessions in the genetic panel

Genome Species Category Ploidy Growth habit No. of accessions
Sb Ae. bicornis Wild relative Diploid Winter 7
UM Ae. biuncialis Wild relative Tetraploid Winter 8
UM Ae. columnaris Wild relative Tetraploid Winter 7
M Ae. comosa Wild relative Diploid Winter 8
DM/DDM Ae. crassa ssp. crassa Wild relative Teraploid/Hexaploid Winter 2
DDM Ae. vavilovii Wild relative Hexaploid Winter 11
DC Ae. cylindrica Wild relative Tetraploid Winter 7
MU Ae. geniculata Wild relative Tetraploid Winter 8
DMU Ae. juvenalis Wild relative Hexaploid Winter 2
SU> Ae. kotschyi Wild relative Tetraploid 8
Sl Ae. longissima Wild relative Diploid Winter 8
C Ae. markgrafii Wild relative Diploid Winter 8
T Ae. mutica Wild relative Diploid 8
UM Ae. neglectassp. neglecta Wild relative Teraploid Winter 7
UMN Ae. neglectassp. recta Wild relative Hexaploid Winter 11
SU Ae. peregrina Wild relative Tetraploid Winter 6
Ss Ae. searsii Wild relative Diploid Winter 10
Ssh Ae. sharonensis Wild relative Diploid Winter 3
S Ae. speltoides Progenitor or closely related species Diploid Winter 12
D Ae. tauschii Progenitor or closely related species Diploid Winter 12
UC/CU Ae. triuncialis Wild relative Tetraploid Winter 8
U Ae. umbellulata Wild relative Diploid Winter 8
N Ae. uniaristata (Zhuk.) Wild relative Hexaploid 5
DN Ae. ventricosa Wild relative Tetraploid Winter 8
V Haynaldia villosa Wild relative Diploid Winter 1
ABD T. aestivum (synt) Synthetic Hexaploid Wheat Hexaploid Winter-Winter 67
Am T. monococcum Progenitor or closely related species Diploid Winter 11
AtG T. timopheevii Wild relative Tetraploid Winter 8
AB T. turgidum Domesticated or cultivated wheat Tetraploid Spring 47
SAm T. turgidum (amphiploid) Wild relative Tetraploid Spring 1
A T. urartu Progenitor or closely related species Diploid Winter 5
GAAm T. zhukovskyi Wild relative Hexaploid Winter 4
Jb or Eb Th. bessarabicum Wild relative Hexaploid 1
19J+9JSt+14St Th. bessarabicum Wild relative Hexaploid 1

Phenotypic data:

  • Only a small set of accessions in this panel have phenotypic data.
  • Phenotypic data for Spring diversity panel: seven years at five locations. Each tab represents a disease -- Fusarium head blight (FHB), powdery mildew (PM), leaf rust (LR), stem rust (SR), or agronomic traits. Phenotypic data for winter diversity panel: seven years at five locations. Each tab represents a disease (FHB and LR from field but PM is indoor)
  • Leaf rust race specific tests done with six races on the winter and spring diversity panel.
  • FHB type II tests were done indoor. There are two sheets: one for winter panel and one for the spring panel. Lines have various number of replications

    • Field evaluation:

    Phenotyping of disease resistance and other agronomic traits was performed in separate field trials for the spring and winter panels. Trials for the spring and winter panels were carried out in several locations.

    For each panel, year and location, a completely randomized design with two replicates was used, except for several trials.

    LR race-specific response:

    Consecutive inoculations with six P. triticina isolates were performed for 360 accessions of the panels. All tests were performed under controlled greenhouse conditions at the Morden RDC, AAFC (Morden, Canada). Briefly, test lines and the Thatcher and Emerson check lines were sown into fiber trays at a rate of approximately 5 seeds per clump and 3 cm between clumps, which were inoculated with individual P. triticina isolates at the two-leaf stage as described by McCallum and Seto-Goh (2006). The isolates tested were 12-3 MBDS, 128-1 MBRJ, 74-2 MGBJ, 11-180-1 TDBG, 06-1-1 TDBG, and 77-2 TJBJ, which represent the prevalent leaf rust race groups across Canada (McCallum et al., 2016). Virulence and avirulence formulas for these isolates are given. Infection type (IT) was rated 12 days post-inoculation using a 0–4 scale (Stakman et al., 1962), where “;” = hypersensitive flecks, “0” = no uredinia or macroscopic sign of infection, “1” = small uredinia with necrosis, “2” = small to medium uredinia with chlorosis, “3” = medium uredinia without chlorosis or necrosis, “4” = large uredinia without chlorosis or necrosis. IT “;” and “0” to “2” were considered resistant, while “3” and “4” were considered susceptible (Long and Kolmer, 1989). The “+” or “−” IT qualifiers indicate larger or smaller than average uredinia, respectively. The “ = ” IT qualifier represents the lower size limit of the uredinia for the IT (Long and Kolmer, 1989). Plants with randomly distributed uredinia of variable sizes, or mesothetic response, were considered resistant and were rated with an “X” IT (Roelfs and Martens, 1988).

    Phenotypic data files

    Panel Traits Year Location Data file download link
    Spring + winter LR, FHB, PM, Agronimic traits (awn, height, days to heading, days to maturity, lodging, yield, TKW) 2016, 2017, 2018, 2019, 2020, 2021, 2022 PEI, LTB, OTT, SKT, MDN 328_accessions_2016_2017_2018_2019_2020_2021_2022_DivPanelS+W_LR_FHB_AGR_PM_Summary.xlsx
    Spring + winter LR infection type (IT) score and converted linear scale (1-9) 2019, 2021 MDN, indoor 328_accessions_LR_IT_scores_Stakman_and_linear_scale.xlsx

    LR: leaf rust; FHB: Fusarium head blight; PM: powdery mildew; TWK: thousand kernel weight; TSW: thousand seed weight.
    MDN: Morden, Manitoba; OTT: Ottawa, Ontario; SKT: Saskatoon, Saskatchewan, PEI: Prince Edward Island; LTB: Lethbridge, Alberta.

    Genomic Data

    The low coverage whole genome sequencing based SNP data will be available soon.