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Genome wide association mapping for resistance to multiple fungal pathogens in a panel issued from a broad composite cross-population of tetraploid wheat Triticum turgidum

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Abstract

Few resistance genes providing defence against the major fungal diseases septoria tritici blotch (STB), septoria nodorum blotch, leaf rust (LR), and an emerging wheat blast disease have been identified in durum wheat. We identified sixteen fungal disease-associated QTL through genome-wide association mapping of 180 inbred lines sampled from a durum wheat Composite Cross-population. Two STB resistance-associated QTL mapped to chromosome 3A, one of which colocalizes with Stb6, a known resistance gene previously identified in bread wheat. This partial resistance could be conferred by a new allele of Stb6 or another paralogous gene. The second locus is associated with a reduction in pycnidia density, a recently identified and poorly understood form of resistance. A resistance QTL strongly associated with LR, and colocalizing with Lr61, was observed in a 3.24 Mbp region on chromosome 6B. QTL mapping of LR resistance following treatment by chitin used in the context of inducer treatment was also investigated. Using a combination of resistance alleles at these loci could confer durable resistance to multiple fungal diseases and aid durum wheat breeders in their fight against these fungal pathogens.

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Acknowledgements

Highbred, CASDAR-BURRITOS, FSOV-WEAB and in particular Richard Oliver (Curtin University, Australia) for providing purified Tox1.

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Author notes

  1. Elsa Ballini and Muriel Tavaud have contributed equally to this publication.

  2. Jacques David and Jean-Benoit Morel have contributed equally to the design.

Authors and Affiliations

  1. BGPI, CIRAD, INRAE, Institut Agro, Univ Montpellier, Montpellier, France

    Elsa Ballini, Aurélie Ducasse & Jean-Benoit Morel

  2. AGAP, CIRAD, INRAE, Institut Agro, Univ Montpellier, Montpellier, France

    Muriel Tavaud, Dimitri Sanchez, Pierre Roumet & Jacques David

  3. GDEC, INRAE, Genetics Diversity and Ecophysiology of Cereals, Université Clermont Auvergne, 63000, Clermont-Ferrand, France

    Etienne Paux, Jonathan Kitt & Gilles Charmet

  4. Arvalis, Station Expérimentale, Boigneville, France

    Delphine Audigeos

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ESM_1

Manhattan plots from association mapping in the EPO durum wheat panel of 180 lines for SNB and WB traits. The map is based on Zavitan v2.0. A1 Septoria nodorum blotch SNB isolate inoculation chromosome A, B1 chromosome B. A2 Septoria nodorum blotch Tox1 infiltration chromosome A, B2 chromosome B. A3 Wheat blast BR43 isolate inoculation chromosome A, B3 chromosome B. A4 Wheat blast BR32 isolate inoculation chromosome A, B4 chromosome B (TIFF 453 kb)

ESM_2

Manhattan plots from association mapping in the EPO durum wheat panel of 180 lines for STB and LR traits. The map is based on Zavitan v2.0. A1 Septoria tritici blotch STB isolate inoculation, % of surface with necrose, chromosome A, B1 chromosome B. A2 Septoria tritici blotch STB isolate inoculation, % of surface with pycnidia chromosome A, B2 chromosome B. A3 Leaf rust isolate inoculation, mock treated 6 h before inoculation, chromosome A, B3 chromosome B. A4 Leaf rust isolate inoculation, chitin treated 6 h before inoculation, chromosome A, B4 chromosome B (TIFF 363 kb)

ESM_3

Annotation of candidate genes for SNB_Tox7A and SNB_Nec4B. Annotation and genome location are based on Zavitan v2.0 (XLSX 18 kb)

ESM_4

Histogram of STB symptoms in EPO lines. The % of diseased leaf area was recorded for necrosis symptoms (dark grey) and % of surface with pycnidia for pycnidia production (light grey) (TIFF 54 kb)

ESM_5

A Number of EPO lines carrying each allele at the STB_Pyc3A and STB_Nec3A loci. B Number of EPO lines and Elite lines resistant for pycnidia density, depending on their genotype at STB_Pyc3A. The number of resistant lines and the total number of lines carrying the corresponding allele are represented. The frequency of the resistant phenotype is in parenthesis. C Resistance of selected EPO lines and Elite lines based on percentage of necrotic leaf area and depending of their genotype at STB_Nec3A and at Stb6. The number of resistant lines and the total number of lines carrying the corresponding allele are represented. The frequency of the resistant phenotype is shown in parenthesis (JPEG 95 kb)

ESM_6

A Sequence of the kinase at Stb6 locus. The three alleles identified in this study (Stb6-7, Stb6-1, and Stb6-12) were aligned with seven previously published alleles (Saintenac et al. 2018). B Amino acid changes due to the different nucleotide polymorphism are indicated (TIFF 1274 kb)

ESM_7

Sequence alignment of AvrStb6 allele in both isolates P1a and M1a. Two other isolates carrying AvrStb6 allele (1E4, 323) and 1A5 (VirStb6) were sequenced and aligned on three of the published sequences (Hap2, Hap3 and Hap11) found in Brunner and McDonald 2018 (TIFF 53 kb)

ESM_8

A Distribution of leaf rust severity evaluated as the percentage of leaf surface covered with pustules after prophylactic induction with chitin treatment (dark grey) or following mock treatment (light grey). B Boxplot of leaf rust severity for completely resistant and partially resistant lines. Complete resistance was considered when no pustules were observed on the leaf surface (JPEG 31 kb)

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Ballini, E., Tavaud, M., Ducasse, A. et al. Genome wide association mapping for resistance to multiple fungal pathogens in a panel issued from a broad composite cross-population of tetraploid wheat Triticum turgidum. Euphytica 216, 92 (2020). https://doi.org/10.1007/s10681-020-02631-9

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