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ARS Home » Pacific West Area » Pullman, Washington » Plant Germplasm Introduction and Testing Research » Research » Research Project #434981

Research Project: Evaluation and Association Analysis of Soybean Cyst Nematode Resistance in USDA Common Bean (Phaseolus vulgaris) Germplasm

Location: Plant Germplasm Introduction and Testing Research

Project Number: 2090-21000-032-011-S
Project Type: Non-Assistance Cooperative Agreement

Start Date: Aug 1, 2018
End Date: Dec 31, 2021

1. Evaluate 300 USDA common bean accessions for their resistance to Soybean Cyst Nematode (SCN), and 2. Conduct genome-wide association study of SCN resistance in USDA common bean germplasm.

Three hundred of common bean accessions will be evaluated for soybean cyst nematode (SCN) resistance in greenhouse condition. The phenotypic data (female index) of the 300 common bean accessions will be used as the association set for association mapping of SCN resistance. Genomic DNA will be extracted from freeze-dried leaves of bean plants using the CTAB method. Each DNA sample will be sequenced by Illumina HiSeq X Ten or NovaSeq platforms. The short-read sequences data will be analyzed using SOAP family software for SNP discovery. Population structure will be built using the model-based program STRUCTURE 2.3.4 (Pritchard et al. 2010) and the genetic diversity will be assessed using the MEGA 7 (Kumar et al., 2016) based on the Maximum Likelihood tree method. Genome-wide association study (GWAS) will be conducted with the mixed linear model method as described in TASSEL 5 (Bradbury et al., 2007) and the analysis will be also performed with compressed mixed linear model (Zhang et al., 2010) implemented in the GAPIT R package (Lipka et al., 2012) and in FarmCPU (Liu et al., 2016). For those SNPs associated with SCN resistance postulated from association analysis, KASP single nucleotide polymorphism (SNP) genotyping will be used to validate each SNP marker associated with SCN resistance.