Soybean cyst nematode (SCN) infects and feeds on soybean roots and can reduce soybean yields by up to 50%. Soybean varieties with resistance from the PI 88788 become less effective in controlling this pest due to widespread virulent SCN populations being able to overcome the resistance and leading to high egg numbers at the end of soybean growing season. Non-host crop rotation has been utilized to reduce SCN densities because SCN juveniles hatching from eggs cannot feed on roots of non-host plants and eventually die in the soil. However, the high SCN egg numbers at the end of soybean growing season can compromise efficacies of non-host crop rotation to control SCN, because some SCN populations can stay dormant and do not hatch when corns (a typical non-host of SCN) are grown and only hatch when soybeans are grown in the next season. Hence, it is necessary to evaluate the SCN hatch potential to predict if a non-host crop rotation will be effective in reducing SCN populations. The regular SCN hatch assay takes three weeks and is very labor-consuming. Here we propose to develop a molecular assay to evaluate hatch potentials of SCN populations which can be finished within 8 hours. The SCN hatch molecular assay and the re-designed SCN HG test developed by the PI’s lab will provide integrated and field-specific data that is informative for growers to make decisions on using non-host crop rotation and selection of soybean resistant varieties to effectively control SCN in their fields.

The progress of the project will be evaluated by monitoring the number of SCN genes found associated with SCN hatch potential and the number of SCN populations collected from growers and tested for SCN hatch potential using the molecular assay. We expect to finish the proposed project in a year (October 1, 2022 to September 30, 2023). The aim 1 will take about five months, from October 2022 to February 2023. The aim 2 will be conducted the following seven months, from March to September of 2023.
Aim 1:
The status of SCN hatch potential as a trait of SCN is determined by differently expressed nematode genes in response to temperature and availability of host roots. We aim to identifying SCN genes responsible for SCN hatch potential by analysis of gene expression using RNA-sequencing (RNA-seq) on SCN eggs treated with low temperature (4oC) or exposed to soybean root exudates. RNA-seq is a nextgeneration sequencing technique commonly used to identify genes potentially involved in a specific biological process (Wang et al., 2009). We will determine SCN genes highly expressed in active SCN eggs stimulated by soybean root exudates or low temperature-induced dormant eggs. We expect to select at least 20 SCN genes as candidate marker genes of nematode hatch potential. The SCN candidate genes
selected here will be tested using SCN populations from soybean fields in Aim 2.
Aim 2:
We will contact at least 50 soybean growers in Indiana in the spring of 2023 who previously submitted soil samples to us in 2020 and 2021 to get more soil samples on fields where the previous crop is soybean. The eggs of SCN populations will be isolated from the soil samples, and egg numbers will be counted and returned to growers free-of-charge. We plan to implement a molecular diagnostic assay to evaluate hatch potentials of the 50 SCN populations using quantitative PCR (qPCR) by measuring expression of the 20 candidate SCN marker genes selected in Aim 1. In the meantime, the traditional SCN hatch assay will be performed on the SCN populations. We will set up the traditional hatch assay in lab and monitor hatch of SCN eggs in a 3-week-period to determine the hatch rate of a SCN population. Statistical association studies between the molecular assay and regular SCN hatch assay will be conducted to narrow down to 2 to 3 nematode genes that are able to serve as reliable markers of SCN hatch potential. We will notify growers about the SCN hatch potentials and summarize the data to develop a fast and reliable molecular assay to evaluate hatch potential of SCN populations. The molecular diagnostic assay for SCN hatch potential developed here can be completed within 8 hours and less expressive in comparison to the three-week time needed by a regular SCN hatch assay.

We expect to develop a molecular assay to evaluate SCN hatch potential. It is a fast and economical method that can be completed in 8 hours, and provide field-specific data on SCN hatch potentials and hence is useful for growers to make decision on SCN management using non-host crop rotation. The payment schedule follows the Master Research
Agreement.
The results of project such as SCN hatch potential, egg counts and recommendation of SCN management will be returned to growers who submit soil samples in the spring of 2023. The summary of results will be made available to ISA and distributed to farmers at extension meetings and field days.

Update:

View uploaded report

We plan to work with the Plant and Pest Diagnostic Lab (PPDL) at Purdue to provide commercial service of the molecular SCN hatch assay. In addition to SCN egg counts and HG types, the information on SCN hatch is useful for growers to make decisions on non-host crop rotation and selection of appropriate soybean resistant varieties for effective SCN control.