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United States Department of Agriculture

Agricultural Research Service

Research Project: Breeding for Charcoal Rot Resistance and Pathogen Characterization

Location: Crop Genetics Research Unit

2013 Annual Report


1a.Objectives (from AD-416):
1) Continuation of the breeding program to select and release germplasm with enhanced resistance, .
2)the development of new recombinant inbred line (RIL) mapping populations designed to identify and map new resistance genes, .
3)complete the development and begin the characterization of near-isogenic lines differing only in resistance, .
4)collect and characterize Macrophomina phaseolina (M. phaseolina) isolates across a wide geographic area,.
5)the characterization of the distribution and variation of M. phaseolina within a field and across years and.
6)the comparison of M. phaseolina isolates in the soil with those found in plants.


1b.Approach (from AD-416):
Obj.1: The current recombinant inbred line (RIL) population has exhibited transgressive segregation for charcoal rot resistance and we propose to continue the selection of lines with improved resistance. We are near the release of new germplasm "DS-880" which has improved resistance to charcoal rot, resistance to cyst nematode, and moderate resistance to reniform nematode, sudden death syndrome, and stem canker; all in a competitive yield background. We expect other releases as the program progresses. Obj.2: In our 2008 field screening we identified lines that were more susceptible than the susceptible parent used in out current mapping population. This greater divergence in resistance may allow the identification of additional genetic loci involved in resistance. Using these lines, three more populations were initiated with the intent of developing new RIL mapping populations. Obj.3: Over the last few years, we have had a program of developing near-isogenic lines (NIL) that differ only in their level of resistance. We propose the complete the development, confirm differences, and initiate molecular and phenotypic characterization of the NIL. Such characterization has the potential to determine the physiological basis of charcoal rot resistance and could indicate mechanisms for enhanced resistance. Obj.4: Very little research has been conducted on the pathogen M. phaseolina. We propose to begin collecting and characterizing isolates from around the United States. Characterization will include both pathogenicity and molecular discrimination. Recently, we have completed the development of over 180 simple sequence repeat (SSR) markers specific to M. phaseolina, these will be used to fingerprint the isolates collected. This research is also critical to the breeding and molecular marker analysis described above. Currently we have no method of determining if the M. phaseolina isolates encountered in a particular field are the same or different from a field at another location, or even if isolates vary from one year to another. Characterization and molecular discrimination (fingerprinting) of isolates will allow the matching of resistance loci and resistant line/cultivars to specific isolates. Obj.5: Almost no information is available regarding the distribution and variation of M. phaseolina within a given field, including variations in pathogen aggressiveness. We propose to spatially characterize the distribution and variation of isolates within a field and to determine what changes in distribution and variation occur from year to another. The SSR markers we have developed will be used to determine the variation and distribution of isolates. Coupled with the molecular characterization of field-based variation and distribution of M. phaseolina, we will determine the pathogen aggressiveness of the various isolates identified. Obj.6: No information exists regarding the relationship between the M. phaseolina isolates that occur in the soil and those that actually infest the plant. We will use the SSR markers that we developed, to determine the relationship between isolate actually infesting plants with those isolates that occur in the soil.


3.Progress Report:

A two-year study measuring yield and the incidence of charcoal rot was conducted at Stoneville, MS, on a Sharkey clay soil, under furrow irrigation. Six soybean lines were included in the study, and there was a wide range of yield and charcoal rot. However, a combined regression analysis across the 6 lines over 2011 and 2012 (108 plots in total) indicated no significant relationship between yield and the incidence of charcoal rot. A report of a second study examining the relationship between maturity and the incidence of charcoal rot was submitted for publication. The study showed little relationship between maturity and the incidence of charcoal rot. DNA of a 271 recombinant inbred population was submitted for expanded characterization of molecular marker polymorphisms. More than 1,000 isolates have been cultured and their DNA isolated. All DNA characterized by a select group of molecular markers has been completed. The markers were designed to assay isolate diversity, and preliminary analysis indicates isolate diversity is readily identifiable by the markers. Multiple breeding lines assayed for their reaction to charcoal rot had low mean levels of colony forming units (less than 400) and were advanced to yield trials.


Last Modified: 10/31/2014
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