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Identification of genomic loci conferring broad-spectrum resistance to multiple nematode species in exotic soybean accession PI 567305

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Abstract

Key Message

Genetic analysis identified a unique combination of major QTL for resistance to important soybean nematodes concurrently present in a single soybean accession, which has not been reported earlier.

Abstract

An exotic soybean [Glycine max (L.) Merr.] accession, PI 567305, was reported to be highly resistant to three important nematode species, soybean cyst (SCN), root-knot (RKN), and reniform (RN) nematodes. However, genetic basis controlling broad-spectrum resistance in this germplasm has not been investigated. We report results of genetic analysis to identify genomic loci conferring resistance to these nematode species. A bi-parental population consisting of 242 F8-derived recombinant inbred lines (RILs) was developed from a cross of a nematode susceptible cultivar, Magellan, and resistant accession, PI 567305. The RILs were phenotyped for nematode resistance to three SCN HG types. They were genotyped using the Infinium SoySNP6K BeadChips and genotype-by-sequencing (GBS) methods in an attempt to evaluate the cost-effectiveness and efficiency of these two genotyping platforms. Genetic analysis confirmed the major QTL on chromosomes (Chrs) 10 and 18 with broad-spectrum resistance to the three nematodes present in this germplasm. Haplotype and copy number variation analyses of SCN resistance QTL indicated that PI 567305 has a different haplotype, which is associated with likely a unique SCN resistance mechanism different from Peking- or PI 88788-type resistance. The evaluations of both Infinium Beadchip- and GBS-based genotyping technologies provided comprehensive insights for researchers to choose a cost-effective and efficient platform for QTL mapping and for other genomic studies in soybeans.

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Acknowledgements

This research was partially funded by the United States Department of Agriculture—National Institute of Food and Agriculture (USDA-NIFA) grant 2019-67013-29370—and the USDA-NIFA Hatch/Multistate grant MO-MSPS0002. The authors would like to thank undergraduate students for their technical assistance in field and laboratory work.

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Author notes

  1. H. Sonah

    Present address: National Agri-Food Biotechnology Institute, Sector 81, Mohali-140306, P.O. Manauli, Punjab, India

  2. K. S. Kim

    Present address: LG Chem-FarmHannong, Ltd, Daejeon, 34115, Republic of Korea

Authors and Affiliations

  1. Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA

    T. D. Vuong, C. Meinhardt, M. Usovsky, K. S. Kim, J. G. Shannon & H. T. Nguyen

  2. Département de Phytologie, Faculté Des Sciences de L’Agriculture Et de L’Alimentation, Centre de Recherche en Horticulture, Université Laval, Québec, Canada

    H. Sonah

  3. Institute of Genomics for Crop Abiotic Stress Tolerance (IGCAST), Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, 79409, USA

    G. Patil

  4. Département de Phytologie, Université Laval, Pavillon Charles-Eugène Marchand 1030, Avenue de la Médecine, Québec, Canada

    F. Belzile

  5. Institute of Plant Breeding, Genetics, Genomics and Department of Crop and Soil Sciences, University of Georgia, Athens, GA, 30602, USA

    Z. Li

  6. Department of Plant Pathology, University of Arkansas, Fayetteville, AR, 72701, USA

    R. Robbins

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Contributions

TDV and HTN conceptualized the study; TDV led the investigation, performed data analysis, drafted the manuscript; HS and FB carried out GBS and data analysis; GP performed haplotype and CNV analysis; CM carried SCN phenotyping assay; MU and KSK contributed to the original draft; ZL coordinated RKN phenotyping assay; RR coordinated RN phenotyping assay; JGS provided technical discussion. All authors contributed their critical reviews of the manuscript during the preparation.

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Correspondence to T. D. Vuong or H. T. Nguyen.

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Communicated by Istvan Rajcan.

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Vuong, T.D., Sonah, H., Patil, G. et al. Identification of genomic loci conferring broad-spectrum resistance to multiple nematode species in exotic soybean accession PI 567305. Theor Appl Genet 134, 3379–3395 (2021). https://doi.org/10.1007/s00122-021-03903-1

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  • DOI: https://doi.org/10.1007/s00122-021-03903-1

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