Date of Graduation


Document Type


Degree Name

Doctor of Philosophy in Crop, Soil & Environmental Sciences (PhD)

Degree Level



Crop, Soil & Environmental Sciences


Andy Pereira

Committee Member

Richard E. Mason

Second Committee Member

Burt H. Bluhm

Third Committee Member

John C. Rupe

Fourth Committee Member

Lisa Wood


Charcoal rot, Disease, QTL, QTL-seq, Resistance, Soybean


Charcoal rot of soybean (Glycine max (L.), caused by Macrophomina phaseolina is a disease of economic significance in the United States. The identification and quantification of the resistance is difficult, and very little is known about the genetics and markers linked to the charcoal rot (CR) resistance genes. Current assay methods can be time consuming, and data may vary between tests. The objectives of this study were to 1) create a robust seed plate assay (SPA) for CR resistance by comparing results with cut-stem and CFUI assays; 2) correlate and compare field data disease assessments with SPA; 3) identify QTLs for CR resistance using SNP markers; 4) identify genetic loci and candidate genes for resistance using next-generation sequencing (NGS)-based bulked-segregant analysis. For objective one, seeds of eight differential soybean genotypes inoculated with an isolate of M. phaseolina on water agar plates were evaluated for germination, and showed correspondence to results from the cut-stem and CFUI assays. In the second objective, nineteen differential genotypes were used to assess disease resistance to M. phaseolina using the SPA, and results were correlated with field disease assessment data from Rohwer and Stuttgart, AR. Disease assessments were significant, and correlated with SPA between different years and locations. For the third objective, an F2-3 mapping population was developed from a cross between PI 567562A and PI 567437, the lines genotyped with 5403 single nucleotide polymorphism (SNP) markers covering 20 chromosomes, and the population phenotyped with the cut-stem assay. Composite Interval Mapping analysis indicated three QTLs for resistance to M. phaseolina. In the fourth objective, two extreme phenotypic bulks were generated from the same F2-3 population by pooling equal amounts of DNA from 10 plants of each bulk, and the bulks along with parents were sequenced using Illumina HiSeqTM. A SNP-index was calculated at each SNP position for both bulks, and the average distributions of the SNP-index and Δ SNP-index were estimated using sliding window analysis. Three genomic regions on chromosomes 5, 8 and 14 were identified with positive values of Δ SNP-index plots that potentially indicate QTLs governing the difference between the R-bulk and S-bulk.