2013 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.
Objective 1. A total of 598 isolates of Phytophthora sojae were obtained from soils collected throughout Indiana during the first 12 months of this project. Each isolate has been or is currently being pathotyped and tested for sensitivity to fungicides metalaxyl and mefenoxam (90% complete). In addition, DNA has been or is currently being obtained from each isolate for determining genotype (85% complete). Along with soybean geneticists at Purdue University, predominate pathotypes of P. sojae present in Indiana were used to evaluate two novel, race-specific resistance genes (Rps-Resistance to Phytophthora sojae) identified in plant introduction (PI) 567139B. In addition, RNAseq was used to study the transcriptomes of nine soybean near isogenic lines, each containing a single Rps gene, to determine the genetics involved in resistance to PRR.
Objective 2. Seed for three populations of recombinant inbreed lines (RILs), containing one or more quantitative trait loci (QTL) for resistance to sudden death syndrome (SDS), were initially increased in 2012 and again in 2013. Protocols for evaluating SDS disease severity under greenhouse conditions were tested and an assay for examining the probability of isolate-specific QTLs was selected. Along with ARS scientists at Peoria, IL, conserved primers for mating loci MAT 1 and MAT 2 were developed and used to determine presence of these two loci among U.S. and South American populations of the seven Fusarium species known to cause SDS and brown root rot (BRR), F. virguliforme, F. tucumaniae, F. brasilenese, F. cuneirostrum, F. phaseoli, F. crassistipatum, and F. azukicola. In collaboration with scientists at Purdue University, field experiments were established on university research farms to evaluate SDS symptom development in soybean varieties containing different sources of resistance to the soybean cyst nematode. Modification of the soybean silencing vector pSM103 to carry the red fluorescent protein reporter gene, which will be used to study the genetics of host resistance to SDS, is in progress.
Objective 3. A total of 386 soybean breeding lines in maturity groups 00 to IV were submitted by public breeders in the U.S. and Canada for evaluation in 2013. Along with University and ARS scientists, lines were evaluated for agronomic performance and disease development in as many as 20 field locations throughout the U.S. and Canada. In collaboration with plant pathologists at The Ohio State University and the University of Illinois at Urbana-Champaign, entries were evaluated under greenhouse conditions for resistance to the soybean cyst nematode and for race-specific and partial resistance to Phytophthora root rot (PRR). Data collected will be used by breeders to determine if a line is to be advanced, dropped, or released as a new variety for public and private use.
Two novel, race-specific resistance genes for Phytophthora root rot in PI 567139B.
Phytophthora root rot is a disease that impacts soybean production on average by 44.5 million bushels, equating to approximately $640 million annually. The primary means of controlling Phytophthora root rot is through the use of soybean varieties with race-specific (qualitative, single gene) resistance or Rps genes. Although this form of resistance is effective in controlling this disease, populations of the causal agent, Phytopthora sojae, are highly diverse and quick to adapt to deployed Rps genes. As such, it is important to identify new Rps genes for the development of resistant varieties. In collaboration with soybean geneticists at Purdue University, ARS scientists in West Lafayette, Indiana identified and mapped two novel genes in a soybean plant introduction from Indonesia. Together, these genes confer complete resistance to all contemporary isolates of P. sojae present in Indiana. The development of molecular markers linked to these genes will expedite the breeding of this resistance into commercial varieties, which can then be used by growers to significantly reduce yield loss associated with Phytophthora root rot.
Cook, D.E., Lee, T., Guo, X., Melito, S., Bayless, A., Hughes, T.J., Willis, D.K., Clemente, T., Diers, B.W., Jiang, J., Hudson, M., Ben, A.F. 2012. Copy number variation of multiple genes at Rhg1 mediates nematode resistance in soybean. Science. 338:1206-1209.
Lin, F., Zhao, M., Ping, J., Johnson, A., Zhang, B., Abney, T.S., Hughes, T.J., Ma, J. 2013. Molecular mapping and characterization of two genes conferring resistance to Phytophthora sojae in a soybean landrace PI 567139B. Theoretical and Applied Genetics. 126:2177-2185.