Update:
During the 2019 growing season, we have collected leaves found growing in several Iowa counties from late summer through the fall. Combined with the 2018 growing season, we now have a total of 46 plant samples that were collected from different Iowa counties and stored at minus 80 degrees Celsius. The samples represent a wide spectrum of different symptoms that included diseases that could be tentatively identified and those that could not be identified. Samples that were collected displayed an array of symptoms including: Virus-like symptoms with discoloration or mosaic patterns and vein necrosis, Phyllosticta-like lesions with water-soaking (3 “zone” lines), brown veins and necrosis, stunted plants with heavily chlorotic leaves, big brown spots on pods, complete chlorosis and necrosis on leaves, unknown spots, several with “top die back” symptoms, and several with unknown symptoms.

We are trying to determine if there are biotic causes of leaf tissues with virus-like symptoms. A sample from Bruner farm tested positive for TRSV using TRSV ImmunoStrip test (Agdia). Leaf samples collected from North of LaPorte city on S. Canfield Rd with Top Dieback symptoms with numerous yellow patch on leaves tested positive for TRSV. Leaf samples collected from North of Dysart on county Rd, V37 with Top Dieback symptoms and leaf samples collected from Nevada-Pioneer (2 varieties) with Top Dieback symptoms both were positive for TSV using TSV ImmunoStrip test (Agdia). We had previously found TRSV and/or TSV in some plants that had top die back symptoms, but the results of these tests from 2019 samples suggest that the cause may not be either of these two viruses since we cannot find a 100% correlation between symptoms and a particular virus. We completed RNA sequencing of the 46 samples for 2018 and 2019 in late December. We are currently analyzing the RNA sequencing data using our established sequencing analysis pipeline to identify viruses, bacteria or fungal pathogens present in the samples. To test our ideas about the need for more soybean pathogen genomes, we also generated the DNA sequencing data need to construct draft genome sequence of the fungal soybean pathogens Septoria glycines, Cercospora sojina, and Cercospora flagellaris. Once the draft genomes are assembled, we will use it to reanalyze our RNA sequencing data from the 2016, 2017, 2018, and 2019 field samples to determine if we can now better identify the pathogens.

The RNA sequencing platform has been very useful in identifying and characterizing viruses present in plant samples displaying virus-like symptoms. Major results from this work are:
1. We have discovered and validated a virus that is new to soybean fields in Iowa, Clover yellow vein virus.
2. Tobacco ring spot virus and tobacco streak virus are commonly occurring in Iowa soybean fields.
3. We used RNA sequencing to assist in identifying the cause of a disease tentatively called top die back. The results are inconclusive as far as the cause being biotic, abiotic, or some combination.

The RNA sequencing platform was used to identify some bacterial and fungal pathogens present in field-grown soybean samples. However, there currently are limitations and assumptions that need to be overcome by adding more reference genome sequences for soybean pathogens to public databases that were used to make identifications. We will use the data generated in this project to test our ideas for improving identification of bacterial and fungal pathogens.