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ARS Home » Plains Area » Fargo, North Dakota » Edward T. Schafer Agricultural Research Center » Sunflower and Plant Biology Research » Research » Research Project #438720

Research Project: Developing Knowledge and Tools to Optimize Sunflower Breeding for Sclerotinia Resistance and Improved Microbiome-Related Traits

Location: Sunflower and Plant Biology Research

Project Number: 3060-21000-043-030-S
Project Type: Non-Assistance Cooperative Agreement

Start Date: Aug 1, 2020
End Date: Sep 30, 2022

Objective:
Objective 1: Whole genome assembly and annotation of culturable OTUs for the development of high throughput qPCR tests of microbial presence and abundance. Objective 2: Quantify environmental variation in sunflower - rhizosphere microbiome. Objective 3: Greenhouse based in-vivo assessment of combinations of bacterial and fungal isolates with probiotic potential. Objective 4: High throughput genotyping of the plants using novel targeted sequencing.

Approach:
To better understand this mechanism and enhance it for breeders and producers, we propose four main objectives. The first is to culture the OTUs of interest, that have a demonstrated statistical significance in disease resistance, and perform whole genome sequencing, assembly and annotation. These detailed genetic data will enable us to design specific qPCR primers for use in a high-throughput assay for microbial presence and abundance. Even if the the OTUs of interest fail to be culturable, we can still perform whole genome sequencing on the soil samples of interest and bioinformatically filter for the desired bacterial or fungal genome sequence, which will again yield the necessary data for qPCR primer design. Our high-throughput assay will allow for farmers to quickly determine their crops’ rhizosphere community and whether the OTUs that confer resistance are present and to what degree. Objective two is to quantify the environmental variation in the sunflower - rhizosphere interaction. Our previous results are based off of direct soil collection from one field (Carrington, ND) and correlation to four other field and two greenhouse environments. We would like to expand the number of fields to cover the sunflower growing region to bolster our initial analyses. These data will provide valuable information on the ubiquity of the taxa-of-interest. The third objective provides a greenhouse assay for validation of field studies or proof-of-concept for the roles of individual or combinations of cultured taxa on Sclerotinia basal stalk rot resistance. The new assay will allow us to assess the ideal combination of bacterial and fungal OTU isolates that may have potential probiotic properties promoting Sclerotina disease resistance. The final objective is to develop an easy, high-throughput pipeline to assess plant genotype. We plan to develop long, specific probes for sequencing-based methods that will not require the cost nor time consuming step of library preparation.