Identification of QTL associated with resistance to Phytophthora fruit rot in cucumber (Cucumis sativus L.)

Authors: LIN, YING-CHEN - Michigan State University; MANSFELD, BEN - Michigan State University; TANG, XUEMEI - Cornell University; COLLE, MARIVI - Michigan State University; CHEN, FEIFAN - University Of Wisconsin; Weng, Yiqun; FEI, ZHANGJUN - Boyce Thompson Institute; GRUMET, REBECCA - Michigan State University

Submitted to: Frontiers in Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/30/2023
Publication Date: 11/15/2023
Citation: Lin, Y., Mansfeld, B.N., Tang, X., Colle, M., Chen, F., Weng, Y., Fei, Z., Grumet, R. 2023. Identification of QTL associated with resistance to Phytophthora fruit rot in cucumber (Cucumis sativus L.). Frontiers in Plant Science. 14. https://doi.org/10.3389/fpls.2023.1281755.
DOI: https://doi.org/10.3389/fpls.2023.1281755

Interpretive Summary: Phytophthora fruit rot (PFR) is caused by the soilborne pathogen, Phytophthora capsici, that can cause severe yield loss in cucumber especially under the open field once-over machine harvest production system. Currently there is no resistant variety available in production and genetic resources are needed to develop resistant varieties. The goal of this work was to identify quantitative trait loci (QTL) associated with PFR resistance using multiple genomic approaches and populations. Two types of PFR resistances have been identified: age-related resistance (ARR) and young fruit resistance. ARR occurs at 12-16 days post pollination (dpp), coinciding with the end of exponential fruit growth of cucumber. A major QTL for ARR was discovered on chromosome 3 and a candidate gene was identified based on comparative transcriptomic analysis. Young fruit resistance, which is observed during the state of rapid fruit growth prior to harvest, is a quantitative trait for which multiple QTL were identified. The largest effect QTL, qPFR5.1, located on chromosome 5 was fine mapped to a 1-Mb region. Genome-wide association studies (GWAS) and extreme-phenotype genome-wide association study (XP-GWAS) for young fruit resistance also were performed on a cucumber core collection. From GWAS, several QTL for PFR resistance were identified including qPFR5.1. The resistant alleles were found mostly in accessions from India and South Asia. The results from this work can be applied to future disease resistance studies and marker-assisted selection for PFR resistance in cucumber breeding programs.

Technical Abstract: Phytophthora fruit rot caused by the soilborne oomycete pathogen, Phytophthora capsici, can cause severe yield loss in cucumber. With no resistant variety available, genetic resources are needed to develop resistant varieties. The goal of this work was to identify quantitative trait loci (QTL) associated with resistance to Phytophthora fruit rot using multiple genomic approaches and populations. Two types of resistances have been identified: age-related resistance (ARR) and young fruit resistance. ARR occurs at 12-16 days post pollination (dpp), coinciding with the end of exponential fruit growth. A major QTL for ARR was discovered on chromosome 3 and a candidate gene identified based on comparative transcriptomic analysis. Young fruit resistance, which is observed during the state of rapid fruit growth prior to harvest, is a quantitative trait for which multiple QTL were identified. The largest effect QTL, qPFR5.1, located on chromosome 5 was fine mapped to a 1-Mb region. Genome-wide association studies (GWAS) and extreme-phenotype genome-wide association study (XP-GWAS) for young fruit resistance also were performed on a cucumber core collection representing > 96% of the genetic diversity of the USDA cucumber germplasm. Several SNPs overlapped with the QTL identified from QTL-seq analysis on biparental populations. In addition, novel SNPs associated with the resistance were identified from the germplasm. The resistant alleles were found mostly in accessions from India and South Asia, the center of origin for cucumber. The results from this work can be applied to future disease resistance studies and marker-assisted selection in breeding programs.