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ARS Home » Pacific West Area » Salinas, California » Crop Improvement and Protection Research » Research » Research Project #439290

Research Project: Host Resistance and Fumigation Alternatives for Control of Macrophomina Phaseolina in Strawberry - Strawberry Genomics

Location: Crop Improvement and Protection Research

Project Number: 2038-22000-016-048-A
Project Type: Cooperative Agreement

Start Date: Nov 1, 2020
End Date: Feb 28, 2023

Objective:
Develop tools for genomic-assisted selection of Macrophomina resistance in strawberry by screening progeny of crosses between resistant and susceptible individuals, analyzing the transcriptome of resistant and susceptible strawberry accessions, and identifying candidate genes responsible for the resistance phenotype. In addition, identify candidate virulence genes in the fungus by transcriptomics.

Approach:
The project team will use the progeny from a cross between a Macrophomina-resistant heirloom cultivar (tested in Objective 1) and a Macrophomina-susceptible parent for these experiments. Some seedlings will inherit resistance, and others will inherit susceptibility. These progenies will be tested for resistance to Macrophomina in field trials for Objective 1. From each seedling (n = 300) the project team will extract DNA and conduct genotyping with a low-cost array. DNA extraction and genotyping with an array will enable the project team to correlate genotypes with resistance or susceptibility observed in Objective 1. Then, we will conduct genome-wide association studies to test the correlation between Macrophomina resistance and specific genomic regions. If identified, these markers, or genomic signatures, can be used to accelerate selection for resistance to Macrophomina. We will conduct experiments evaluating the transcriptomic (mRNA expression) response to Macrophomina in resistant germplasm. Macrophomina resistant and susceptible accessions will be inoculated and grown under controlled conditions. RNA will be extracted from three timepoints, which correspond to increasing symptom expression. RNA will be purified and sent for library preparation (using both 3’ TagSeq and PacBio IsoSeq technology) and sequencing (Illumina NovaSeq and PacBio Sequel II sequencing platforms). We will then analyze the transcriptomic sequence data to identify genes that are differentially expressed in resistant versus susceptible strawberry plants. These data will be compared with the results of the genome wide association study to identify genes that may be responsible for the resistance phenotype. DNA analysis looks at many sites that may not be expressed (i.e. turned into RNA, then protein) during infection. The project team can refine the search for markers of resistance by also sequencing RNA, as proposed. This is a powerful approach that can improve the accuracy of markers predicted by DNA analysis alone. We will then assess the overlap between genes associated with the resistance from the transcriptome and genome-wide association study and develop molecular markers that are predictive of the resistance phenotype based on these results.