Genome-wide association study for septoria tritici blotch resistance reveals the occurrence and distribution of Stb6 in a historic Swiss landrace collection

Dutta, Anik; Croll, Daniel; McDonald, Bruce A.; Krattinger, Simon G.

doi:10.1007/s10681-021-02843-7

Cited by 4 publications

(5 citation statements)

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“…in European wheat cultivars for at least 100 years (Dutta et al, 2021;Stephens et al, 2021). Second, there was little nucleotide diversity in AvrCR4 in C. beticola.…”

Section: Discussionmentioning

confidence: 97%

“…First, the same wild‐type AvrCR4 sequence is found at a high frequency on both resistant and susceptible sugar beets growing on different continents (Figure 4a). In contrast, in Z. tritici the AvrStb6 gene is present in every isolate analysed to date and there is no predominant wild type, perhaps reflecting the use of Stb6 in European wheat cultivars for at least 100 years (Dutta et al., 2021; Stephens et al., 2021). Second, there was little nucleotide diversity in AvrCR4 in C. beticola .…”

Section: Discussionmentioning

confidence: 99%

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GWAS reveals a rapidly evolving candidate avirulence effector in the Cercospora leaf spot pathogen

Chen,

Keunecke,

Bemm

et al. 2023

Molecular Plant Pathology

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The major resistance gene BvCR4 recently bred into sugar beet hybrids provides a high level of resistance to Cercospora leaf spot caused by the fungal pathogen Cercospora beticola. The occurrence of pathogen strains that overcome BvCR4 was studied using field trials in Switzerland conducted under natural disease pressure. Virulence of a subset of these strains was evaluated in a field trial conducted under elevated artificial disease pressure. We created a new C. beticola reference genome and mapped whole genome sequences of 256 isolates collected in Switzerland and Germany. These were combined with virulence phenotypes to conduct three separate genome‐wide association studies (GWAS) to identify candidate avirulence genes. We identified a locus associated with avirulence containing a putative avirulence effector gene named AvrCR4. All virulent isolates either lacked AvrCR4 or had nonsynonymous mutations within the gene. AvrCR4 was present in all 74 isolates from non‐BvCR4 hybrids, whereas 33 of 89 isolates from BvCR4 hybrids carried a deletion. We also mapped genomic data from 190 publicly available US isolates to our new reference genome. The AvrCR4 deletion was found in only one of 95 unique isolates from non‐BvCR4 hybrids in the United States. AvrCR4 presents a unique example of an avirulence effector in which virulent alleles have only recently emerged. Most likely these were selected out of standing genetic variation after deployment of BvCR4. Identification of AvrCR4 will enable real‐time screening of C. beticola populations for the emergence and spread of virulent isolates.

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“…in European wheat cultivars for at least 100 years (Dutta et al, 2021;Stephens et al, 2021). Second, there was little nucleotide diversity in AvrCR4 in C. beticola.…”

Section: Discussionmentioning

confidence: 97%

Section: Discussionmentioning

confidence: 99%

GWAS reveals a rapidly evolving candidate avirulence effector in the Cercospora leaf spot pathogen

Chen,

Keunecke,

Bemm

et al. 2023

Molecular Plant Pathology

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“…Firstly, the same wild-type AvrCR4 sequence is found at a high frequency on both resistant and susceptible sugar beets growing on different continents (Figure 4a). In contrast, in Z. tritici the AvrStb6 gene is present in every isolate analyzed to date and there is no predominant wild-type, despite the use of Stb6 in European wheat cultivars for at least 100 (Dutta et al, 2021; Stephens et al, 2021). Secondly, there was little nucleotide diversity in AvrCR4 in C. beticola .…”

Section: Discussionmentioning

confidence: 98%

“…As a reference comparison, we consider diversity for the AvrStb6 gene found in the wheat pathogen Z. tritici. The Stb6 R-gene has been deployed in European wheat cultivars for at least 100 years (Dutta et al, 2021). The AvrStb6 gene found in every Z. tritici isolate analyzed to date (no deletions have been detected) encodes a protein containing 81 or 82 amino acids.…”

Section: Discussionmentioning

confidence: 99%

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Genome-wide association studies reveal a rapidly evolving candidate avirulence effector in the Cercospora leaf spot pathogenCercospora beticola

Chen

Keunecke

Bemm

et al. 2023

Preprint

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The major resistance gene BvCR4 recently bred into sugar beets provides a high level of resistance to Cercospora leaf spot caused by the fungal pathogen Cercospora beticola. The occurrence of pathogen strains virulent to BvCR4 was studied using field trials in Switzerland and Germany. Virulence of a subset of these strains was tested in a field trial conducted under elevated artificial disease pressure. We created a new C. beticola reference genome and mapped whole genome sequences of 256 field-collected isolates and combined this with the virulence phenotypes to conduct three separate GWAS to identify candidate avirulence genes. GWAS analyses identified a locus associated with avirulence containing a single candidate avirulence effector gene named AvrCR4. All virulent isolates either lacked AvrCR4 or had non-synonymous mutations within the gene. AvrCR4 was present in all 74 unique isolates obtained from non-BvCR4 hybrids, whereas 33 of 89 unique isolates obtained from BvCR4 hybrids carried this deletion. We also mapped genomic data from 190 publicly available isolates from the U.S to our new reference genome. The AvrCR4 deletion was found in only one of 95 unique isolates from non-BvCR4 hybrids in the U.S. AvrCR4 presents a unique example of an avirulence effector in which virulent alleles have only recently emerged. Most likely these were selected out of the standing genetic variation after deployment of a new major resistance gene. Identification of AvrCR4 will enable real-time screening of C. beticola populations for the emergence and spread of virulent isolates as well as long-term studies of effector evolution.

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Meta-analysis reveals consensus genomic regions associated with multiple disease resistance in wheat (Triticum aestivum L.)

et al. 2022

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In wheat, meta-QTLs (MQTLs), and candidate genes (CGs) were identi ed for multiple disease resistance (MDR). For this purpose, information was collected from 58 studies for mapping QTLs for resistance to one or more of the ve diseases. As many as 493 QTLs were available from these studies, which were distributed in ve diseases as follows: septoria tritici blotch (STB) 126 QTLs; septoria nodorum blotch (SNB), 103; fusarium head blight (FHB), 184; karnal bunt (KB), 66, and loose smut (LS), 14. Of these 493 QTLs, only 291 QTLs could be projected onto a consensus genetic map, giving 63 MQTLs. The CI of the MQTLs ranged from 0.04 to 15.31 cM with an average of 3.09 cM per MQTL. This is a ~ 4.39 fold reduction from the CI of initial QTLs, which ranged from 0 to 197.6 cM, with a mean of 13.57 cM. Of 63 MQTLs, 60 were anchored to the reference physical map of wheat (the physical interval of these MQTLs ranged from 0.30 to 726.01 Mb with an average of 74.09 Mb). Thirty-eight (38) of these MQTLs were veri ed using marker-trait associations (MTAs) derived from genome-wide association studies. As many as 874 CGs were also identi ed which were further investigated for differential expression using data from ve transcriptome studies, resulting in 194 differentially expressed genes (DEGs). Among the DEGs, 85 genes had functions previously reported to be associated with disease resistance. These results should prove useful for ne mapping of MDR genes and marker-assisted breeding.

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Genome-wide association study for septoria tritici blotch resistance reveals the occurrence and distribution of Stb6 in a historic Swiss landrace collection

Abstract: Genome-wide association study for septoria tritici blotch resistance reveals the occurrence and distribution of Stb6 in a historic Swiss landrace collection. Euphytica, 217(6).

Cited by 4 publications

References 63 publications

GWAS reveals a rapidly evolving candidate avirulence effector in the Cercospora leaf spot pathogen

GWAS reveals a rapidly evolving candidate avirulence effector in the Cercospora leaf spot pathogen

Genome-wide association studies reveal a rapidly evolving candidate avirulence effector in the Cercospora leaf spot pathogenCercospora beticola

Meta-analysis reveals consensus genomic regions associated with multiple disease resistance in wheat (Triticum aestivum L.)

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