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Fine-mapping and characterization of qSCN18, a novel QTL controlling soybean cyst nematode resistance in PI 567516C

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Abstract

Key message

The qSCN18 QTL from PI 56756C was confirmed and fine-mapped to improve soybean resistance to the SCN population HG Type 2.5.7 using near-isogenic lines carrying recombination crossovers within the QTL region. The QTL underlying resistance was fine-mapped to a 166-Kbp region on chromosome 18, and the candidate genes were selected based on genomic analyses.

Abstract

Soybean cyst nematode (SCN, Heterodera glycines, Ichinohe) is the most devastating pathogen of soybean. Understanding the genetic basis of SCN resistance is crucial for managing this parasite in the field. Two major loci, rhg1 and Rhg4, were previously characterized as valuable resources for SCN resistance. However, their continuous use has caused shifts in the virulence of SCN populations, which can overcome the resistance conferred by these two major loci. Reduced effectiveness became a major concern in the soybean industry due to continuous use of rhg1 for decades. Thus, it is imperative to identify sources of SCN resistance for durable SCN management. A novel QTL qSCN18 was identified in PI567516C. To fine-map qSCN18 and identify resistance genes, a large backcross population was developed. Nineteen near-isogenic lines (NILs) carrying recombination crossovers within the QTL region were identified. The first phase of fine-mapping narrowed the QTL region to 549-Kbp, whereas the second phase confined the region to 166-Kbp containing 23 genes. Two flanking markers, MK-1 and MK-6, were developed and validated to detect the presence of the qSCN18 resistance allele. Haplotype analysis clustered the fine-mapped qSCN18 region from PI 567516C with the cqSCN-007 locus previously mapped in the wild soybean accession PI 468916. The NILs were developed to further characterize the causal gene(s) harbored in this QTL. This study also confirmed the previously identified qSCN18. The results will facilitate marker-assisted selection (MAS) introducing the qSCN18 locus from PI 567516C into high-yielding soybean cultivars with durable resistance to SCN.

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Abbreviations

ANOVA:

Analysis of variance

FI:

Female index

HSD:

Tukey’s honestly significant difference test

KASP:

Kompetitive allele specific PCR

MAS:

Marker-assisted selection

NIL:

Near-isogenic line

RCBD:

Randomized complete block design

QTL:

Quantitative trait loci

SCN:

Soybean cyst nematode

SNP:

Single nucleotide polymorphism

WGRS:

Whole genome re-sequencing

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Acknowledgements

This research was funded by the United States Department of Agriculture—National Institute of Food and Agriculture (USDA-NIFA) grant 2019-67013-29370. The authors would like to thank Dr. J. Grover Shannon for his scientific suggestions and careful proofreading of the manuscript.

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Authors and Affiliations

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

    Mariola Usovsky, Heng Ye, Tri D. Vuong, Jinrong Wan, Lijuan Zhou & Henry T. Nguyen

  2. Institute for Genomics of Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, 79415, USA

    Gunvant B. Patil

Authors
  1. Mariola Usovsky
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  2. Heng Ye
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  3. Tri D. Vuong
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  4. Gunvant B. Patil
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  5. Jinrong Wan
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  6. Lijuan Zhou
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  7. Henry T. Nguyen
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Contributions

MU carried out the experiments, developed KASP markers and recombinant NILs, performed phenotyping, analyzed data, and wrote the manuscript. HY analyzed data and contributed to the interpretation of the results. TDV developed backcross population, contributed to the design and implementation of the research. GBP performed haplotype and synteny analyses. JW and LZ contributed to phenotyping preparation and sample processing. HTN conceived the original idea and supervised the project. All authors discussed the results and contributed to the final manuscript.

Corresponding author

Correspondence to Henry T. Nguyen.

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The authors declare that they have no conflict of interest.

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Communicated by Brian Diers.

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Usovsky, M., Ye, H., Vuong, T.D. et al. Fine-mapping and characterization of qSCN18, a novel QTL controlling soybean cyst nematode resistance in PI 567516C. Theor Appl Genet 134, 621–631 (2021). https://doi.org/10.1007/s00122-020-03718-6

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