ArticleBMC genomics2015
SNP identification and marker assay development for high-throughput selection of soybean cyst nematode resistance.
Article in BMC genomics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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Who cites it
41 citing papers in PubMed.
- Genetic Diversity and SNP-Based Fingerprinting of 94 Pumpkin Cultivars: Database Establishment and Population Analysis.Plants (Basel, Switzerland) · 2026Article
- Non-destructive seed genotyping via microneedle-based DNA extraction.Plant biotechnology journal · 2025Article
- Multi-omics analysis identified the GmUGT88A1 gene, which coordinately regulates soybean resistance to cyst nematode and isoflavone content.Plant biotechnology journal · 2025Article
- Breeding SCN-resistant soybean lines with improved oil and protein contents.Frontiers in plant science · 2025Article
- SNP loci identification and KASP marker development system for genetic diversity, population structure, and fingerprinting in sweetpotato (Ipomoea batatas L.).BMC genomics · 2024Article
- Allele-tagged TaqManMolecular biology reports · 2024Article
- The elite variations in germplasms for soybean breeding.Molecular breeding : new strategies in plant improvement · 2023Article
- Identification of resistant sources fromFrontiers in plant science · 2023Article
- The Key to the Future Lies in the Past: Insights from Grain Legume Domestication and Improvement Should Inform Future Breeding Strategies.Plant & cell physiology · 2022Review
- Breeding for disease resistance in soybean: a global perspective.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2022Review
- Quantitative trait loci and gene-specific markers associated with resistance to soybean cyst nematode HG type 2.5.7.Molecular breeding : new strategies in plant improvement · 2022Article
- Molecular sexual determinants in Pistacia genus by KASP assay.Molecular biology reports · 2022Article
- Detection of rare nematode resistance Rhg1 haplotypes in Glycine soja and a novel Rhg1 α-SNAP.The plant genome · 2022Article
- Development and Validation of SNP and InDel Markers for Pod-Shattering Tolerance in Soybean.International journal of molecular sciences · 2022Article
- Article
- Identification of Candidate Genes Controlling Soybean Cyst Nematode Resistance in "Handou 10" Based on Genome and Transcriptome Analyzes.Frontiers in plant science · 2022Article
- Developing and deploying an efficient genotyping workflow for accelerating maize improvement in developing countries.Gates open research · 2022Article
- Incorporation of Soil-Derived Covariates in Progeny Testing and Line Selection to Enhance Genomic Prediction Accuracy in Soybean Breeding.Frontiers in genetics · 2022Article
- TheFrontiers in plant science · 2022Article
- The Spatial Distribution and Genetic Diversity of the Soybean Cyst Nematode,Frontiers in plant science · 2022Article
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Authors and funding
6 authors.
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No grant is acknowledged in the PubMed record.
Abstract
backgroundSoybean cyst nematode (SCN) is the most economically devastating pathogen of soybean. Two resistance loci, Rhg1 and Rhg4 primarily contribute resistance to SCN race 3 in soybean. Peking and PI 88788 are the two major sources of SCN resistance with Peking requiring both Rhg1 and Rhg4 alleles and PI 88788 only the Rhg1 allele. Although simple sequence repeat (SSR) markers have been reported for both loci, they are linked markers and limited to be applied in breeding programs due to accuracy, throughput and cost of detection methods. The objectives of this study were to develop robust functional marker assays for high-throughput selection of SCN resistance and to differentiate the sources of resistance.
resultsBased on the genomic DNA sequences of 27 soybean lines with known SCN phenotypes, we have developed Kompetitive Allele Specific PCR (KASP) assays for two Single nucleotide polymorphisms (SNPs) from Glyma08g11490 for the selection of the Rhg4 resistance allele. Moreover, the genomic DNA of Glyma18g02590 at the Rhg1 locus from 11 soybean lines and cDNA of Forrest, Essex, Williams 82 and PI 88788 were fully sequenced. Pairwise sequence alignment revealed seven SNPs/insertion/deletions (InDels), five in the 6th exon and two in the last exon. Using the same 27 soybean lines, we identified one SNP that can be used to select the Rhg1 resistance allele and another SNP that can be employed to differentiate Peking and PI 88788-type resistance. These SNP markers have been validated and a strong correlation was observed between the SNP genotypes and reactions to SCN race 3 using a panel of 153 soybean lines, as well as a bi-parental population, F5-derived recombinant inbred lines (RILs) from G00-3213xLG04-6000.
conclusionsThree functional SNP markers (two for Rhg1 locus and one for Rhg4 locus) were identified that could provide genotype information for the selection of SCN resistance and differentiate Peking from PI 88788 source for most germplasm lines. The robust KASP SNP marker assays were developed. In most contexts, use of one or two of these markers is sufficient for high-throughput marker-assisted selection of plants that will exhibit SCN resistance.
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