Abstract
Key message
We identified cryptic early blight resistance introgressions in tomato breeding lines and demonstrated efficient genotypic selection for resistance in the context of a tomato breeding program.
Early blight is a widespread and problematic disease affecting tomatoes (Solanum lycopersicum). Caused by the fungal pathogen Alternaria linariae (syn. A. tomatophila), symptoms include lesions on tomato stems, fruit, and foliage, often resulting in yield losses. Breeding tomatoes with genetic resistance would enhance production sustainability. Using cross-market breeding populations, we identified several quantitative trait loci (QTL) associated with early blight resistance. Early blight resistance putatively derived from ‘Campbell 1943′ was confirmed in modern fresh market tomato breeding lines. This resistance offered substantial protection against early blight stem lesions (collar rot) and moderate protection from defoliation. A distinctive and potentially novel form of early blight foliar resistance was discovered in a processing tomato breeding line and is probably derived from S. pimpinellifolium via ‘Hawaii 7998’. Additional field trials validated the three most promising large-effect QTL, EB-1.2, EB-5, and EB-9. Resistance effects for EB-5 and EB-9 were consistent across breeding populations and environments, while EB-1.2’s effect was population specific. Using genome-wide marker-assisted backcrossing, we developed fresh market tomato lines that were near-isogenic for early blight QTL. Resistance in these lines was largely mediated by just two QTL, EB-5 and EB-9, that together captured 49.0 and 68.7% of the defoliation and stem lesion variance, respectively. Our work showcases the value of mining cryptic introgressions in tomato lines, and across market classes, for use as additional sources of disease resistance.
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Acknowledgements
Thanks to Dr. Michael Allen Gore, Professor at Cornell University and Dr. Deniz Akdemir, Statistical Consultant at the Cornell Statistical Consulting Unit for their advice on statistical methods. Dr. Tom Zitter, Emeritus Professor of Plant Pathology at Cornell University, provided Alternaria isolates and recommended the most virulent isolate (that he was aware of) for use in our study. Dr. Randolph Gardner, Emeritus Professor of Horticultural Science at North Carolina State University, supplied the seed of NC 1 CELBR, NC84-173, and C1943. Thanks to Dr. Zitter and Dr. Gardner, as well as Dr. Christine Smart and Dr. Margaret Smith of Cornell University for critically reviewing the manuscript.
Funding
This work was supported by USDA/NIFA/NY specialty crops grant SCG17-001 and grant no. 12680140 from the USDA National Institute of Food and Agriculture.
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TAA conceptualized laboratory and field experiments, completed formal analysis and investigation, acquired research funding, and wrote the manuscript. SMZ completed preliminary experiments and helped to develop pathology protocols. DMD assisted with genotyping and marker design. DMF provided sequence data for KASP maker development. DMF and MAM supervised and advised TAA and acquired research funding. All authors reviewed, edited, and approved the final manuscript.
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All data generated or analyzed during this study are included in electronic supplementary materials (ESM_5). Seed of tomato germplasm are available by request.
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Anderson, T.A., Zitter, S.M., De Jong, D.M. et al. Cryptic introgressions contribute to transgressive segregation for early blight resistance in tomato. Theor Appl Genet 134, 2561–2575 (2021). https://doi.org/10.1007/s00122-021-03842-x
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DOI: https://doi.org/10.1007/s00122-021-03842-x