Bulked Segregant Analysis Using the GoldenGate Assay to Locate the Rpp3 Locus that Confers Resistance to Soybean Rust in Soybean

Few resistance loci to soybean rust (SBR), caused by Phakopsora pachyrhizi Syd., have been genetically mapped and linked to molecular markers that can be used for marker assisted selection. New technologies are available for single nucleotide polymorphism (SNP) genotyping that can be used to rapidly map traits controlled by single loci such as resistance to SBR. Our objective was to demonstrate that the highthroughput SNP genotyping method known as the GoldenGate assay can be used to perform bulked segregant analysis (BSA) to fi nd candidate regions to facilitate effi cient mapping of a dominant resistant locus to SBR designated Rpp3. We used a 1536 SNP GoldenGate assay to perform BSA followed by simple sequence repeat (SSR) mapping in an F 2 population segregating for SBR resistance conditioned by Rpp3. A 13-cM region on linkage group C2 was the only candidate region identifi ed with BSA. Subsequent F 2 mapping placed Rpp3 between SSR markers BARC_Satt460 and BARC_Sat_263 on linkage group C2 which is the same region identifi ed by BSA. These results suggest that the GoldenGate assay was successful at implementing BSA, making it a powerful tool to quickly map qualitative traits since the GoldenGate assay is capable of screening 1536 SNPs on 192 DNA samples in three days.

• Publication year

  2009

• Venue

  Crop Science

• Publication date

  Unknown publication date

• Fields of study

  Agricultural and Food Sciences, Biology

• Identifiers
  DOI 10.2135/CROPSCI2008.08.0511
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar

• No claims are published for this paper.

• No concepts are published for this paper.

• Molecular mapping of soybean rust (Phakopsora pachyrhizi) resistance genes: discovery of a novel locus and alleles

  2008influential reference
• Molecular mapping of two loci that confer resistance to Asian rust in soybean

  2008influential reference
• High-throughput genotyping with the GoldenGate assay in the complex genome of soybean

  2008cited by this paper
• Soybean rust found in Iowa

  2007cited by this paper
• Late Season Occurrence of Soybean Rust Caused by Phakopsora pachyrhizi on Soybean in Illinois.

  2007cited by this paper
• A Soybean Transcript Map: Gene Distribution, Haplotype and Single-Nucleotide Polymorphism Analysis

  2007cited by this paper
• Mapping and Confirmation of the ‘Hyuuga’ Red-Brown Lesion Resistance Gene for Asian Soybean Rust

  2007influential reference
• Map Location of the Rpp1 Locus That Confers Resistance to Soybean Rust in Soybean

  2007cited by this paper
• SNP-PHAGE – High throughput SNP discovery pipeline

  2006cited by this paper
• Illumina universal bead arrays.

  2006cited by this paper
• Impacts of genetic bottlenecks on soybean genome diversity

  2006cited by this paper
• First Report of Soybean Rust Caused by Phakopsora pachyrhizi in the Continental United States.

  2005cited by this paper
• Epidemics of Soybean Rust (Phakopsora pachyrhizi) in Brazil and Paraguay from 2001 to 2003.

  2005cited by this paper
• Single-nucleotide polymorphisms in soybean.

  2003cited by this paper
• A Low-Cost, High-Throughput Polyacrylamide Gel Electrophoresis System for Genotyping with Microsatellite DNA Markers

  2003cited by this paper
• Highly parallel SNP genotyping.

  2003cited by this paper
• Map Manager QTX, cross-platform software for genetic mapping

  2001cited by this paper
• Primer3 on the WWW for general users and for biologist programmers.

  2000cited by this paper
• An Integrated Genetic Linkage Map of the Soybean Genome

  1999cited by this paper
• Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.

  1997cited by this paper
• Sequence mapping by electronic PCR

  1997influential reference
• Identification of markers linked to disease-resistance genes by bulked segregant analysis: a rapid method to detect markers in specific genomic regions by using segregating populations.

  1991cited by this paper
• A rapid protocol for isolating soybean DNA

  1988cited by this paper
• Identification of a Fourth Major Gene Conferring Resistance to Soybean Rust1

  1986cited by this paper
• The Plant Pathogen Containment Facility at Frederick, Maryland

  1983cited by this paper
• Relationships Among Three Genes Conferring Specific Resistance to Rust in Soybeans1

  1983cited by this paper
• Resistance to soybean rust and mode of inheritance.

  1980cited by this paper
• Inheritance of resistance to rust (Phakopsora pachyrhizi) in soybeans.

  1980cited by this paper

• Transcriptome Profiling of Resistance Genes Analogs in Soybean’s Cross-Tolerance to Water Limitation and Rust Stress

  2025influential citation
• Advancing Soybean Rust Resistance: Strategies, Mechanisms, and Innovations in Gene Pyramiding

  2025cites this paper
• Fine mapping of the unique Ur-11 gene conferring broad resistance to the rust pathogen of common bean

  2025cites this paper
• Review of Plant Genetic Resources, Utilization and Conservation of Genetic Resources

  2024cites this paper
• Allelic variability in the Rpp1 locus conferring resistance to Asian soybean rust revealed by genome-wide association

  2024cites this paper
• Advanced biotechnology techniques for disease resistance in soybean: a comprehensive review

  2024cites this paper
• Mapping of a soybean rust resistance in PI 594756 at the Rpp1 locus

  2023cites this paper
• Rpp genes conferring resistance to Asian soybean rust in F2 population in the field conditions

  2023cites this paper
• Soybean‐ Phakopsora pachyrhizi interactions: towards the development of next‐generation disease‐resistant plants

  2023cites this paper
• Genetic Diversity, Conservation, and Utilization of Plant Genetic Resources

  2023cites this paper
• Molecular mapping of two recessive genes controlling resistance to bacterial leaf pustule disease in soybean ( Glycine max )

  2023cites this paper
• Mapping of a soybean rust resistance in PI 594756 at the Rpp1 locus

  2023cites this paper
• Simultaneously mapping loci related to two plant architecture traits by phenotypic recombination BSA/BSR in peanut (Arachis hypogaea L.)

  2023cites this paper
• Genetic Mapping of Seven Kinds of Locus for Resistance to Asian Soybean Rust

  2023influential citation
• RNA-Seq and Comparative Transcriptomic Analyses of Asian Soybean Rust Resistant and Susceptible Soybean Genotypes Provide Insights into Identifying Disease Resistance Genes

  2023cites this paper
• Genomic regions associated with resistance to soybean rust (Phakopsora pachyrhizi) under field conditions in soybean germplasm accessions from Japan, Indonesia and Vietnam

  2022cites this paper
• Reactions of 52 soybean germplasm accessions with Rpp3 alleles to a panel of 13 Phakopsora pachyrhizi (soybean rust) isolates from the southern United States

  2021cites this paper
• Selection of functional EPHB2 genotypes from ENU mutated grass carp treated with GCRV

  2021cites this paper
• Reactions of 52 soybean germplasm accessions with Rpp3 alleles to a panel of 13 Phakopsora pachyrhizi (soybean rust) isolates from the southern United States

  2021cites this paper
• Selection of functional EPHB2 genotype in ENU mutated grass carp response to GCRV by the method of BSA Sequence Analysis

  2021cites this paper
• Phenotypic reactions of 53 soybean genotypes to infection with each of 16 isolates of Phakopsora pachyrhizi

  2021cites this paper
• Confirmation of Rpp Genes Conferring Resistance to Asian Soybean Rust and Mapping of Rpp1 Allele from PI 594723

  2021cites this paper
• Inheritance and mapping of drought tolerance in soybean at seedling stage using bulked segregant analysis

  2020cites this paper
• Characterization of three soybean landraces resistant to Asian soybean rust disease

  2020cites this paper
• Mapping and confirmation of two genes conferring resistance to soybean rust (Phakopsora pachyrhizi) in the soybean line UG‐5 (Glycine max)

  2020cites this paper
• Whole Genome Re-sequencing of Soybean Accession EC241780 Providing Genomic Landscape of Candidate Genes Involved in Rust Resistance

  2020cites this paper
• Legume Crops and Biotrophic Pathogen Interactions: A Continuous Cross-Talk of a Multilayered Array of Defense Mechanisms

  2020cites this paper
• Near-isogenic soybean lines carrying Asian soybean rust resistance genes for practical pathogenicity validation

  2020cites this paper
• Prospects for Durable Resistance Against an Old Soybean Enemy: A Four-Decade Journey from Rpp1 (Resistance to Phakopsora pachyrhizi) to Rpp7

  2019cites this paper
• Common Bean Genetics, Breeding, and Genomics for Adaptation to Changing to New Agri-environmental Conditions

  2019cites this paper
• Single-plant GWAS coupled with bulk segregant analysis allows rapid identification and corroboration of plant-height candidate SNPs

  2019cites this paper
• Screening of Kenyan Soybean Cultivars for Resistance to Different Races of Phakopsora Pachyrhizi (Soybean Rust) and Determination of Molecular Basis for Rust Resistance

  2019cites this paper
• Molecular markers linked to bacterial wilt (Ralstonia solanacearum) resistance gene loci in eggplant (Solanum melongena L.)

  2019cites this paper
• Pyramiding three rust‐resistance genes confers a high level of resistance in soybean ( Glycine max )

  2019cites this paper
• Identification and mapping of quantitative trait loci associated with soybean rust (Phakopsora pachyrhizi) resistance in genotype UG 5

  2018influential citation
• Microsatellite molecular marker-assisted gene pyramiding for resistance to Asian soybean rust (ASR)

  2018influential citation
• A new leaf rust resistance gene Lr79 mapped in chromosome 3BL from the durum wheat landrace Aus26582

  2018cites this paper
• Pathogenic variation of Asian soybean rust pathogen in Bangladesh

  2018cites this paper
• Breeding soybeans with resistance to soybean rust (Phakopsora pachyrhizi)

  2018cites this paper
• Molecular mapping of quantitative trait loci for agronomical traits in soybean under Asian soybean rust infection

  2018cites this paper
• Genetic Analysis Using RNA‐Seq: Bulk Segregant RNA‐Seq

  2017cites this paper
• Assessing the numbers of SNPs needed to establish molecular IDs and characterize the genetic diversity of soybean cultivars derived from Tokachi nagaha

  2017cites this paper
• Dark period transcriptomic and metabolic profiling of two diverse Eutrema salsugineum accessions

  2017cites this paper
• Evaluation of soybean cyst nematode (SCN) resistance in perennial glycine species and genome-wide association mapping and genomic prediction study for SCN resistance in common bean and prediction of the short distance movement of soybean rust urediniospores through machine learning

  2017cites this paper
• A new soybean rust resistance allele from PI 423972 at the Rpp4 locus

  2017cites this paper
• Discovery of a seventh Rpp soybean rust resistance locus in soybean accession PI 605823

  2017cites this paper
• Fine-mapping and identification of a novel locus Rsc15 underlying soybean resistance to Soybean mosaic virus

  2017cites this paper
• High density mapping and quantitative trait loci analysis for fungal diseases in vitis aestivalis-derived 'Norton' and breeding for low palmitic acid in glycine max

  2017influential citation
• Asian soybean rust in Brazil: past, present, and future

  2016cites this paper
• Molecular Soybean-Pathogen Interactions.

  2016cites this paper
• VIRUS-SOYBEAN INTERACTIONS : THE SOYBEAN MOSAIC VIRUS PATHOSYSTEM

  2016cites this paper
• A novel Phakopsora pachyrhizi resistance allele (Rpp) contributed by PI 567068A

  2016influential citation
• Molecular Characterization of Resistance to Soybean Rust (Phakopsora pachyrhizi Syd. & Syd.) in Soybean Cultivar DT 2000 (PI 635999)

  2016cites this paper
• A pigeonpea gene confers resistance to Asian soybean rust in soybean

  2016cites this paper
• Characterization of Disease Resistance Loci in the USDA Soybean Germplasm Collection Using Genome-Wide Association Studies.

  2016cites this paper
• Soybean (Glycine max) Mutant and Germplasm Resources: Current Status and Future Prospects.

  2016cites this paper
• Soybean production in eastern and southern Africa and threat of yield loss due to soybean rust caused by Phakopsora pachyrhizi

  2016cites this paper
• Chapter 12 – Soybean

  2016cites this paper
• Registration of Four Near‐Isogenic Soybean Lines of G00‐3213 for Resistance to Asian Soybean Rust

  2016cites this paper
• Identification of a new stripe rust resistance gene in Chinese winter wheat Zhongmai 175

  2016cites this paper
• Ferrugem-asiática da soja no Brasil: passado, presente e futuro

  2016cites this paper
• The locus for resistance to Asian soybean rust in PI 587855

  2016cites this paper
• IDENTIFICATION OF MOLECULAR MARKERS LINKED TO YELLOW MOSAIC VIRUS RESISTANCE IN BLACKGRAM (Vigna mungo (L.) Hepper)

  2016cites this paper
• Prevention of leaf yellowing in Asian soybean rust infected plants is associated with green cotyledon color and the infection index

  2015cites this paper
• Genetic analysis and molecular mapping of resistance gene to Phakopsora pachyrhizi in soybean germplasm SX6907

  2015cites this paper
• Molecular marker associated with a deleterious recessive anomaly in Eucalyptus grandis seedlings

  2015cites this paper
• A haplotype map of allohexaploid wheat reveals distinct patterns of selection on homoeologous genomes

  2015cites this paper
• Genetic Characterization of Resistance to Wheat Stem Rust Race TTKSK in Landrace and Wild Barley Accessions Identifies the rpg4/Rpg5 Locus.

  2015cites this paper
• Molecular tagging of Asiatic soybean rust resistance in exotic genotype EC 241780 reveals complementation of two genes

  2015cites this paper
• Multiple Rpp-gene pyramiding confers resistance to Asian soybean rust isolates that are virulent on each of the pyramided genes

  2015cites this paper
• A SNARE-Like Protein and Biotin Are Implicated in Soybean Cyst Nematode Virulence

  2015cites this paper
• Plant Genetic Resources, Traditional Knowledge and Their Use in Crop Improvement

  2015cites this paper
• Comparison of Pathogenic Variation among Phakopsora pachyrhizi Isolates Collected from the United States and International Locations, and Identification of Soybean Genotypes Resistant to the U.S. Isolates.

  2015cites this paper
• Molecular mapping of Asian soybean rust resistance in soybean landraces PI 594767A, PI 587905 and PI 416764

  2015cites this paper
• Identification of unique genetic sources of soybean rust resistance from the USDA soybean germplasm collection.

  2015cites this paper
• Shared Genomic Regions Between Derivatives of a Large Segregating Population of Maize Identified Using Bulked Segregant Analysis Sequencing and Traditional Linkage Analysis

  2015cites this paper
• Empowering breeding programs with new approaches to overcome constraints for selecting superior quality traits of rice

  2015cites this paper
• Molecular mapping of Asian soybean rust resistance in Chinese and Japanese soybean lines, Xiao Jing Huang, Himeshirazu, and Iyodaizu B

  2015cites this paper
• Inheritance of Enzymatic Activities Related to Asian Rust Resistance in Soybean [Glycine max (L.) Merrill]

  2015cites this paper
• Resistance to Phakopsora pachyrhizi in Soybean PI 587905 Maps to the Rpp1 Locus and Exhibits Variable Dominance Associated with Plant Ontogeny

  2015cites this paper
• Gaining insight into soybean defense responses using functional genomics approaches.

  2015cites this paper
• From Select Agent to an Established Pathogen: The Response to Phakopsora pachyrhizi (Soybean Rust) in North America.

  2015cites this paper
• Plant Genetic Resources and Traditional/Indigenous Knowledge: Potentials and Challenges

  2015cites this paper
• Diversidade de características agronômicas e moleculares em cultivares de soja com diferentes graus de resistência à Phakopsora Pachyrhizi = Diversity of agronomic and molecular traits of the soybean cultivars with diferent levels of Phakopsora ...

  2015cites this paper
• Development of a SNP marker assay for the Lr67 gene of wheat using a genotyping by sequencing approach

  2014cites this paper
• Fine mapping of the Asian soybean rust resistance gene Rpp2 from soybean PI 230970

  2014cites this paper
• Plantes resistantes aux champignons exprimant ein2

  2014cites this paper
• Registration of Eight Soybean Germplasm Lines Resistant to Soybean Rust

  2014cites this paper
• Non-toxic and efficient DNA extractions for soybean leaf and seed chips for high-throughput and large-scale genotyping

  2014cites this paper
• Application of Bioinformatics in Crop Improvement: Annotating the Putative Soybean Rust resistance gene Rpp3 for Enhancing Marker Assisted Selection

  2014influential citation
• Marker-assisted introgression of a QTL region to improve rust resistance in three elite and popular varieties of peanut (Arachis hypogaea L.)

  2014cites this paper
• Application of the ASLP technology to a novel platform for rapid and noise-free multiplexed SNP genotyping.

  2014cites this paper
• Genotyping and development of single-nucleotide polymorphism (SNP) markers associated with blast resistance genes in rice using GoldenGate assay

  2014cites this paper
• Identical Substitutions in Magnesium Chelatase Paralogs Result in Chlorophyll-Deficient Soybean Mutants

  2014influential citation
• Identification of novel QTL for leaf traits in soybean

  2014cites this paper
• Genomics of plant genetic resources: a gateway to a new era of global food security

  2014cites this paper
• QTL for resistance to root lesion nematode (Pratylenchus thornei) from a synthetic hexaploid wheat source

  2014cites this paper
• Identification and utility of sequence related amplified polymorphism (SRAP) markers linked to bacterial wilt resistance genes in potato

  2014cites this paper
• Characterizing the host response and genetic control of resistance in 'Honeycrisp' to apple scab (Venturia inaequalis)

  2014cites this paper
• Evaluation of Soybean Germplasm Accessions for Resistance to Phakopsora pachyrhizi Populations in the Southeastern United States, 2009-2012

  2014cites this paper