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United States Department of Agriculture

Agricultural Research Service

Research Project: Population Dynamics and Disease Management of Soybean Root Pathogens

Location: Crop Production and Pest Control Research

2012 Annual Report


1a.Objectives (from AD-416):
This project plan describes the hypothesis-based research to be conducted for two root rot diseases of soybean, PRR and SDS. The aim of this project is to mitigate the impact of these diseases on yield by improving our understanding of pathogen biology, disease development, and host-pathogen interactions. To this end, we propose:

Objective 1: Evaluate the outcrossing and diversity of Phytophthora sojae populations and host plant interactions. In this objective, this research group will look into the role of outcrossing in diversifying populations of P. sojae, which may be contributing to the rapid adaptation of this pathogen to deployed R-genes (resistance genes). The research group will also screen for race-specific and partial resistance, which minimizes colonization as well as symptom development, to P. sojae in germplasm with resistance to other root-infecting pathogens.

Objective 2: Evaluate the population dynamics of Fusarium virguliforme, sudden death syndrome disease cycle, and host plant interactions. For this objective, the research group will study the effect of the isolate of F. virguliforme on SDS foliar and/or root rot resistance to determine if known quantitative trait loci (QTL) are isolate-specific. In addition, the research group will also examine the early stages of the disease cycle to determine the cause, timing, and mechanism of initial infection by F. virguliforme.

Objective 3: Organize, manage, and conduct the Northern Uniform Soybean Tests. The goal of this non-hypothesis based component of the project is to provide public breeders with information needed to determine if a breeding line is to be released as a new variety. Although the aim of Objective 3 differs from that of Objectives 1 and 2, the Uniform Soybean Tests (USTs) serve a key role in advancing soybean production in the U.S.


1b.Approach (from AD-416):
Established cultural techniques and markers linked to known avir genes will be used to evaluate the role of outcrossing in diversifying populations of Phytophthora sojae. Soybean germplasm will be evaluated for race-specific (hypocotyl test) and partial (percent root rot-layer test and colonization-qPCR) resistance to P. sojae. QTLs for resistance to SDS will be evaluated for isolate specificity using multiple RIL and NIL populations and isolates of Fusarium virguliforme that are genetically (DNA fingerprinting) and geographically diverse. Soybean hairy roots and a GFP-expressing isolate of F. virguliforme will be used to study the infection process and to assess morphological differences between SDS-resistant and susceptible varieties. Publically developed lines will be evaluated for agronomic qualities and disease resistance in multiple field environments to determine their release as a variety.


3.Progress Report:
Objective 1. Soils samples from soybean production fields throughout Indiana have been collected and processed for obtaining isolates of Phytophthora sojae. Protocols to improve the efficiency and efficacy of determining pathotypes for isolates of P. sojae where tested and are currently being used for pathotyping isolates from Indiana fields. These protocols are also being used to evaluate soybean germplasm (varieties, breeding lines, plant introductions) for race-specific resistance to Phytophthora root rot (PRR). Protocols for improving the quality and quantity of DNA from isolates of P. sojae have been tested and have enabled us to obtain DNA from Indiana isolates suitable for genetic analysis using twenty-one, polymorphic microsatellite markers, and primers specific to avirulence genes Avr1a, -1k, -3a, -3c, and -4/6.

Objective 2. Three populations of recombinant inbreed lines (RILs), containing one or more quantitative trait loci (QTLs) for resistance to soybean sudden death syndrome (SDS), were obtained from breeders at the Southern Illinois University at Carbondale. Concurrently, a diverse collection of isolates of Fusarium virguliforme, the fungus that causes SDS in the U.S., is being obtained, which will be used to evaluate these RILs to determine if known QTLs are isolate specific. Sequences for fungal mating-type genes (MAT1 and MAT.
2)were identified from the sequenced genomes of F. virguliforme and F. tucumaniae (the main species of Fusarium causing SDS in South America) by collaborators at Iowa State University. Along with ARS scientists at Peoria, IL, sequences are being used to develop conserved primers for MAT 1 and MAT 2, to determine presence of these two loci among U.S. and South American populations of F. virguliforme and to assess the phylogenetic relationship among the species of Fusarium associated with SDS and the closely related disease, brown root rot. Protocols are being adapted or developed to study the genetics of host resistance to SDS and the process by which F. virguliforme infects soybean roots.

Objective 3. A total of 385 soybean breeding lines in maturity groups 00 to IV were submitted by public breeders in the U.S. and Canada for evaluation in 2012. Based on maturity group, lines were evaluated for agronomic performance and disease development in as many as 18 field locations throughout the U.S. and Canada with the collaborative support of university and ARS scientists. In conjunction with scientists at the University of Illinois at Urbana-Champaign and The Ohio State University, entries were evaluated for resistance to the soybean cyst nematode, as well as race-specific and partial resistance to PRR, under greenhouse conditions. Data collected will be used by breeders to determine if a line is to be maintained or dropped from a program or release as a new variety for public use.


4.Accomplishments
1. Identification of the model legume, Medicago truncatula, as a host for Fusarium virguliforme. Host resistance, conferred by the presence of quantitative trait loci (QTLs-large areas of DNA that contains numerous genes), is the most effective way to manage yield loss due to soybean sudden death syndrome (SDS). However, in order to understand the host-pathogen interaction and to expedite crop improvement it is essential to identify and delineate the gene(s) within a given QTL responsible for the resistant reaction. Although this has been done for a number of traits in several crops through the candidate gene approach, it has been difficult to do in soybean, which is recalcitrant to transformation. Medicago truncatula, or barrel medic, is a relative of soybean that possesses a number of key characteristics (small genome, amenable to transformation, short lifecycle, large collection of available mutants), which make it an ideal model for studying legume biology. ARS scientists in West Lafayette, Indiana completed Koch’s postulates and identified M. truncatula as a host for Fusarium virguliforme, the fungus that causes SDS. Based on this information, soybean pathologists can effectively use the candidate gene approach, adopting M. truncatula as a host, to study the genetics underlying resistance to SDS. Identifying the exact gene(s) that specifically confer resistance to SDS will assist breeders in developing more effective SDS-resistant soybean varieties, which growers can use to reduce yield loss associated with this disease.


Last Modified: 11/22/2014
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