Transcriptome profile of pecan scab resistant and susceptible trees from a pecan provenance collection

Authors: Brungardt, Jordan; ALARCON, YANINA - University Of Texas Southwestern Medical Center; SHILLER, JASON - New Zealand Institute Of Plant & Food Research; MONTEROS, MARIA - Bayer Cropscience; YOUNG, CAROLYN - North Carolina State University; RANDALL, JENNIFER - New Mexico State University; Bock, Clive

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/12/2024
Publication Date: 2/15/2024
Citation: Brungardt, J.J., Alarcon, Y., Shiller, J., Monteros, M., Young, C., Randall, J.J., Bock, C.H. 2024. Transcriptome profile of pecan scab resistant and susceptible trees from a pecan provenance collection. BMC Genomics. 25:180. https://doi.org/10.1186/s12864-024-10010-0.
DOI: https://doi.org/10.1186/s12864-024-10010-0

Interpretive Summary: Pecan scab, caused by the fungus Ventura effusa (V. effusa), is the most important disease affecting pecan production in the southeast United States. The need to apply costly fungicides at regular intervals for managing the disease, in addition to reduced yields, affects profitability of the crop for farmers. The biological nature of V. effusa allows the pathogen to become resistance to fungicides. Natural, genetic-based resistance to wild populations of V. effusa is present in uncultivated pecan. Such trees can be found in the pecan provenance collection at the USDA-ARS Byron, Georgia location. Genome-wide expression of genes were evaluated from pecan scab resistant and susceptible trees from this provenance collection. This work identifies a number of potential targets for increasing resistance to V. effusa in cultivated pecan varieties through the use of traditional breeding or biotechnology-based methods.

Technical Abstract: Pecan scab is a devastating disease that causes damage to pecan (Carya illinoinensis (Wangenh.) K. Koch) fruit and leaves. The disease is caused by the fungus Venturia effusa (G. Winter) and the main management practice for controlling the disease is by application of fungicides at 2-to-3-week intervals throughout the growing season. Besides disease-related yield loss, application of fungicides can result in considerable cost and increases chances of fungicide resistance developing in the pathogen. Resistant cultivars are available for pecan growers; although, in several cases resistance has been overcome as the pathogen adapts to infect resistant hosts. Despite the importance of host resistance in scab management, there is little information regarding the molecular basis of genetic resistance to pecan scab. The purpose of this study was to elucidate mechanisms of natural resistance by analyzing transcripts that are differentially expressed in pecan leaf samples from scab resistant and susceptible trees. The leaf samples were collected from trees in a provenance collection orchard that represents the natural range of pecan in the US and Mexico. Trees in the orchard have been exposed to natural scab infections since planting in 1989, and scab ratings were collected over three seasons. Based on this data, ten susceptible trees and ten resistant trees were selected for analysis. RNA-seq data was collected and analyzed for diseased and non-diseased susceptible trees as well as for resistant trees. Three hundred and thirteen genes were found to be differentially expressed when comparing resistant and susceptible trees without disease. For susceptible trees showing scab symptoms, 1,454 genes were identified as differentially expressed compared to non-diseased susceptible trees. Many genes involved in pathogen recognition, defense responses, and signal transduction were up-regulated in diseased samples of susceptible trees, whereas down-regulation of the overall transcriptome seems to be responsible for resistance to pecan scab. Our results provide the first account of candidate genes involved in resistance/susceptibility to pecan scab under natural conditions in a pecan orchard. This information can be used to aid pecan breeding programs and development of biotechnology-based approaches for generating pecan cultivars with more durable scab resistance.