Abstract
Frogeye leaf spot, caused by the fungus Cercospora sojina, is a threat to soybeans in the southeastern and midwestern United States that can be controlled by crop genetic resistance. Limited genetic resistance to the disease has been reported, and only three sources of resistance have been used in modern soybean breeding. To discover novel sources and identify the genomic locations of resistance that could be used in soybean breeding, a GWAS was conducted using a panel of 329 soybean accessions selected to maximize genetic diversity. Accessions were phenotyped using a 1–5 visual rating and by using image analysis to count lesion number and measure the percent of leaf area diseased. Eight novel loci on eight chromosomes were identified for three traits utilizing the FarmCPU or BLINK models, of which a locus on chromosome 11 was highly significant across all model-trait combinations. KASP markers were designed using the SoySNP50K Beadchip and variant information from 65 of the accessions that have been sequenced to target SNPs in the gene model Glyma.11g230400, a LEUCINE-RICH REPEAT RECEPTOR-LIKE PROTEIN KINASE. The association of a KASP marker, GSM990, designed to detect a missense mutation in the gene was the most significant with all three traits in a genome-wide association, and the marker may be useful to select for resistance to frogeye leaf spot in soybean breeding.
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All data generated or analysed during this study are included in this published article and its supplementary information files or are available from the corresponding author on reasonable request.
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Acknowledgements
The authors wish to acknowledge the technical support provided by Carol Picard in conducting greenhouse disease assays and Nicole Bachleda and Tatyana Nienow in conducting marker assays. Thank you to Dr. Randall Nelson (USDA, retired) for providing seeds from the USDA Soybean Germplasm Collection used in this study.
Funding
Funding for this research was provided by the University of Georgia Research Foundation, Georgia Agricultural Commodity Commission for Soybeans, and Georgia Seed Development. This research was also supported by the funds allocated to the Georgia Agricultural Experiment Stations.
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ZL conceived the project, provided oversight of the experiments, interpreted the results, and edited the manuscript. SM conducted the experiments, performed the phenotyping, analyzed the data and drafted the manuscript. JB oversaw greenhouse phenotyping and edited the manuscript. QS selected the association panel and edited the manuscript. All authors read and approved the final manuscript.
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Supplementary file1 (EPS 357 KB) Scree plot of the first 10 principal coordinates (PC) from population structure analysis using the SoySNP50K Beadchip. The y-axis on the left shows the percent of total variation that each PC accounts for, and the y-axis on the right shows the variance for each PC
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Supplementary file2 (EPS 3510 KB) Maximum likelihood estimations of individual subpopulations for each accession in the association panel calculated in ADMIXTURE. K values ranged from 2 to 10 subpopulations
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Supplementary file4 (PNG 81 KB) Genome-wide linkage disequilibrium (LD) decay plot for 329 soybean accessions based on 36,317 SNPs. r2 dropped to half of its maximum value at approximately 175 kb
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Supplementary file5 (EPS 2147 KB) Neighbor joining tree of the association panel. Sixty-five sequenced lines that were used to design KASP markers for variants in the chromosome 11 locus are colored in blue
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Supplementary file6 (EPS 1912 KB) Manhattan plots with SoySNP50K (black) and KASP (blue) markers for (a) FarmCPU model with visual rating trait, (b) FarmCPU model with lesion number trait, (c) FarmCPU model with percent of leaf area diseased trait, (d) BLINK model with visual rating trait, (e) BLINK model with lesion number trait, and (f) BLINK model with percent of leaf area diseased trait. Significant threshold for all was −log10(P) = 5.86
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Supplementary file8 (XLSX 25 KB) List of accessions in the association panel with their regions of origin, maturity groups, and BLUP values for visual rating, lesion number, and percent of leaf area diseased
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Supplementary file9 (XLSX 14 KB) List of 52 candidate genes and their annotations identified in the 8 haplotype blocks identified for their involvement in FLS resistance
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McDonald, S.C., Buck, J., Song, Q. et al. Genome-wide association study reveals novel loci and a candidate gene for resistance to frogeye leaf spot (Cercospora sojina) in soybean. Mol Genet Genomics 298, 441–454 (2023). https://doi.org/10.1007/s00438-022-01986-z
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DOI: https://doi.org/10.1007/s00438-022-01986-z