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Mapping QTL associated with partial resistance to Aphanomyces root rot in pea (Pisum sativum L.) using a 13.2 K SNP array and SSR markers

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Abstract

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A stable and major QTL, which mapped to an approximately 20.0 cM region on pea chromosome 4, was identified as the most consistent region conferring partial resistance to Aphanomyces euteiches.

Abstract

Aphanomyces root rot (ARR), caused by Aphanomyces euteiches Drechs., is a destructive soilborne disease of field pea (Pisum Sativum L.). No completely resistant pea germplasm is available, and current ARR management strategies rely on partial resistance and fungicidal seed treatments. In this study, an F8 recombinant inbred line population of 135 individuals from the cross ‘Reward’ (susceptible) × ‘00-2067’ (tolerant) was evaluated for reaction to ARR under greenhouse conditions with the A. euteiches isolate Ae-MDCR1 and over 2 years in a field nursery in Morden, Manitoba. Root rot severity, foliar weight, plant vigor and height were used as estimates of tolerance to ARR. Genotyping was conducted with a 13.2 K single-nucleotide polymorphism (SNP) array and 222 simple sequence repeat (SSR) markers. Statistical analyses of the phenotypic data indicated significant (P < 0.001) genotypic effects and significant G × E interactions (P < 0.05) in all experiments. After filtering, 3050 (23.1%) of the SNP and 30 (13.5%) of the SSR markers were retained for linkage analysis, which distributed 2999 (2978 SNP + 21 SSR) of the markers onto nine linkage groups representing the seven chromosomes of pea. Mapping of quantitative trait loci (QTL) identified 8 major-effect (R2 > 20%), 13 moderate-effect (10% < R2 < 20%) effect and 6 minor-effect (R2 < 10%) QTL. A genomic region on chromosome 4, delimited by the SNP markers PsCam037549_22628_1642 and PsCam026054_14999_2864, was identified as the most consistent region responsible for partial resistance to A. euteiches isolate Ae-MDCR1. Other genomic regions important for resistance were of the order chromosome 5, 6 and 7.

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Heritability of each trait, marker information, linkage information and QTL profiles are available in the main manuscript or as supplementary data.

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Acknowledgements

The Canadian Agricultural Partnership (CAP) provided financial support for this research under project # 1000210132. The University of Alberta and Alberta Agriculture and Forestry (Crop Diversification Centre North) provided in-kind support, including access to greenhouse facilities and molecular laboratory equipment. Waldo C. Penner and Dennis B. Stoesz provided technical help, while Dr. Kenneth B. McRae helped in field designs and provided statistical advice on the analysis of the field research results.

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Institutions supporting this project are indicated in the acknowledgements section.

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  1. Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2P5, Canada

    Longfei Wu, Rudolph Fredua-Agyeman, Sheau-Fang Hwang & Stephen E. Strelkov

  2. Alberta Agriculture and Forestry, Crop Diversification Centre North, 17507 Fort Road, Edmonton, AB, T5Y 6H3, Canada

    Kan-Fa Chang

  3. Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB, R6M 1Y5, Canada

    Robert L. Conner

  4. Brandon Research and Development Centre, Agriculture and Agri-Food Canada, Brandon, MB, R7A 5Y3, Canada

    Debra L. McLaren

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Contributions

LFW contributed to isolation of Aphanomyces euteiches isolate Ae-MRDC1, inoculum preparation, greenhouse screening of RIL population and parents for resistance to Aphanomyces root rot, disease rating, measurement of foliar weight, vigor and plant height, phenotypic data analysis, DNA extraction, PCR, genotyping with SSR markers and writing of the manuscript. RFA contributed to supervision of the molecular marker work, molecular data analysis, linkage map construction, QTL mapping and writing of the manuscript. SFH was the principal investigator and contributed to grant application, supervision and provision of technical support to the graduate student for RIL population screening in the greenhouse and revision of the manuscript. RLC contributed to development of the RIL population, field evaluation of RIL, disease evaluation, measurement of vigor and foliar weight and revision of the manuscript. KFC contributed to grant application, supervision and provision of technical support to the graduate student for RIL population screening in the greenhouse. DLM contributed to grant application and the provision of technical support to the graduate student. SES was the principal investigator and contributed to grant application, supervision and provision of technical support to the graduate student and revision of the manuscript.

Corresponding author

Correspondence to Stephen E. Strelkov.

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On behalf of all authors, the corresponding author states that all experiments in this study complied with the ethical standards in Canada.

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Communicated by Janila Pasupuleti.

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Wu, L., Fredua-Agyeman, R., Hwang, SF. et al. Mapping QTL associated with partial resistance to Aphanomyces root rot in pea (Pisum sativum L.) using a 13.2 K SNP array and SSR markers. Theor Appl Genet 134, 2965–2990 (2021). https://doi.org/10.1007/s00122-021-03871-6

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  • DOI: https://doi.org/10.1007/s00122-021-03871-6

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