Fine-mapping and characterization of qSCN18 , a novel QTL controlling soybean cyst nematode resistance in PI 567516C
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ORIGINAL ARTICLE
Fine‑mapping and characterization of qSCN18, a novel QTL controlling soybean cyst nematode resistance in PI 567516C Mariola Usovsky1 · Heng Ye1 · Tri D. Vuong1 · Gunvant B. Patil2 · Jinrong Wan1 · Lijuan Zhou1 · Henry T. Nguyen1 Received: 27 March 2020 / Accepted: 27 October 2020 © Springer-Verlag GmbH Germany, part of Springer Nature 2020
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. 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
Communicated by Brian Diers.
Introduction
Electronic supplementary material The online version of this article (https://doi.org/10.1007/s00122-020-03718-6) contains supplementary material, which is available to authorized users. * Henry T. Nguyen [email protected] 1
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