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.
Highlights
Soybean [Glycine max (L.) Merrill] is one of the most economically important crops due to its potential as an oilseed crop and major source of plant protein used for both livestock and human consumption
The aims of this study were to (1) identify new sources of Charcoal rot (CR) resistance in 459 diverse soybean plant introduction (PI) lines from MG I, II, and III through field and greenhouse screening, and (2) conduct Genome-wide association studies (GWAS) to increase our understanding of the resistance mechanisms and identify genetic markers associated with resistance that will contribute to the future selection of genotypes for breeding programs and genetic studies for CR resistance
The current study is the first effort to apply GWAS to understand and explain the genetic mechanisms underlying resistance to charcoal rot in soybean
Summary
Soybean [Glycine max (L.) Merrill] is one of the most economically important crops due to its potential as an oilseed crop and major source of plant protein used for both livestock and human consumption. The United States (US) is responsible for 33% of the world production with a record 106.96 million ton in 2015, grown on 33.5 million ha and prices range from $296 to $351 per ton (http://www.usda.gov). Production can be strongly compromised by abiotic stresses, pests, and pathogens (Hartman et al, 2015). Charcoal rot (CR), a disease caused by Macrophomina phaseolina, can reduce both yield and seed quality (Smith and Wyllie, 1999). Charcoal rot is distributed worldwide in the tropics and subtropics, as well as in the US north central and southern regions (Wyllie, 1988), and M. phaseolina is known to infect over 500 plant species of economic importance including maize, sorghum (Adeyanju et al, 2015), and sunflower (Pawlowski et al, 2015). CR is a greater concern in the southern US due to frequent hot and dry conditions that tend to occur during important soybean developmental growth stages
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