Genetic Architecture of Charcoal Rot (Macrophomina phaseolina) Resistance in Soybean Revealed Using a Diverse Panel

Abstract

Charcoal rot (CR) disease caused by Macrophomina phaseolina is responsible for significant yield losses in soybean production. Among the methods available for controlling this disease, breeding for resistance is the most promising. Progress in breeding efforts has been slow due to the insufficient information available on the genetic mechanisms related to resistance. Genome-wide association studies (GWAS) enable unraveling the genetic architecture of resistance and identification of causal genes. The aims of this study were to identify new sources of resistance to CR in a collection of 459 diverse plant introductions from the USDA Soybean Germplasm Core Collection using field and greenhouse screenings, and to conduct GWAS to identify candidate genes and associated molecular markers. New sources for CR resistance were identified from both field and greenhouse screening from maturity groups I, II, and III. Five significant single nucleotide polymorphism (SNP) and putative candidate genes related to abiotic and biotic stress responses are reported from the field screening; while greenhouse screening revealed eight loci associated with eight candidate gene families, all associated with functions controlling plant defense response. No overlap of markers or genes was observed between field and greenhouse screenings suggesting a complex molecular mechanism underlying resistance to CR in soybean with varied response to different environments; but our findings provide useful information for advancing breeding for CR resistance as well as the genetic mechanism of resistance.

Keywords: GWAS; Macrophomina phaseolina; breeding; charcoal rot; resistance; soybean.

Figure 1

(A) Classes of charcoal rot resistance where resistant (values of 1), moderately resistant (values >1 and ≤2), moderately susceptible (values >2 and <3), and susceptible (values 3–5). (B) Split stem showing symptoms associated with the scores: 1, no microsclerotia visible in vascular tissue; 2, very few microsclerotia visible and vascular tissue is not discolored; 3, microsclerotia partially covering the vascular tissue and there is minimal discoloration; 4, numerous microsclerotia in the tissue and also visible under the outside epidermis, and discolored vascular tissue; 5, darkened vascular tissue due to high numbers of microsclerotia both inside and outside of the stem. (C) Distribution of the 459 PI lines and checks for resistance classification. (D) Class of location of the resistant check in accessions distribution.

Figure 2

(A) Variation of disease lesion length (mm) for charcoal rot from disease screening in greenhouse. (B) Distribution of the 459 PI lines and checks for resistance classification based on AUDPC. (C) Classes of distribution of the AUDPC. (D) Class of location of the resistant checks in the distribution of the accessions.