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ARS Home » Southeast Area » Stoneville, Mississippi » Crop Genetics Research » Research » Research Project #437472

Research Project: Molecular and Bioinformatic Analyses of Soybean Biotic/Abiotic Interactions and Physiology

Location: Crop Genetics Research

Project Number: 6066-21220-014-018-N
Project Type: Non-Funded Cooperative Agreement

Start Date: Jan 1, 2020
End Date: Dec 31, 2024

The objective of this research is to conduct molecular, bioinformatic, pathological, and physiological analysis of soybean abiotic and biotic interactions in order to identify important genetic relationships.

Isolates of soybean fungal pathogens Cercospora (C.) sojina (frogeye leaf spot) and Macrophomina (M.) phaseolina (charcoal rot) have been collected and maintained at the USDA, ARS, Crop Genetics Research Unit in Stoneville, Mississippi. Some of the isolates have been comparatively analyzed pathologically and have also been sequenced and/or genotyped. In this component of the research, new isolates will be added to the collection, pathologically characterized, genotyped and/or sequenced and the molecular data comparatively analyzed to identify genetic relationships. Part of this component is to develop a standard set of “fingerprint” molecular markers to differentiate among C. sojina isolates and among M. phaseolina isolates. In the second component of the research, soybean genetic populations segregating for C. sojina resistance have been developed at Stoneville, Mississippi, from a cross of a resistant soybean line (PI 458175B) and a Stoneville agronomically sound soybean breeding line. The population has been advanced to the F2 generation and the parents are in the process of being sequenced. Tissue of individual F2 plants have been collected and DNA isolated. F2-3 plants will be phenotyped for resistance to specific C. sojina isolates. Molecular markers will be applied to the population to identify genetic loci associated with resistance as well as to determine if the resistance is novel. Additionally, where appropriate, agronomically sound resistant lines from the segregating population will be advanced as part of the breeding program. Ultimately, a germplasm release with novel C. sojina resistance is anticipated. In the third component of the research, the breeding program at Stoneville, has developed a set of breeding lines with various combinations of Phakopsora (P.) pachyrhizi (soybean rust) resistance genes. The genomes of these lines and control soybean rust resistant germplasm have been sequenced (22 lines). An additional four rust-related breeding and germplasm lines are currently being sequenced. The breeding lines have also been phenotyped with individual P. pachyrhizi isolates and different responses among the breeding lines elucidated. Upon completion of the sequencing, a comparative bioinformatic analysis will be conducted to elucidate the relationship among the seven known P. pachyrhizi resistance genes as well as to identify the nature of resistance in the breeding lines. It is expected that several of the resistant breeding lines are unique and/or have stacked resistance. All data will be released to the soybean community. The final component of the research is to use a comparative bioinformatic analysis of the genomic sequence of highly isogenic soybean breeding lines developed at Stoneville to identify putative genes responsible for differential responses to abiotic and/or biotic conditions between the isolines. Currently, the genomic sequence of three sets of highly isogenic lines has been generated and the sequencing of a fourth set is underway. It is anticipated that at least two different sets of highly near isogenic lines will be released to the soybean community along with relevant genomic information.