TY - JOUR
T1 - Identification of QTL associated with resistance to Phytophthora fruit rot in cucumber (Cucumis sativus L.)
AU - Lin, Ying Chen
AU - Mansfeld, Ben N.
AU - Tang, Xuemei
AU - Colle, Marivi
AU - Chen, Feifan
AU - Weng, Yiqun
AU - Fei, Zhangjun
AU - Grumet, Rebecca
N1 - Publisher Copyright:
Copyright © 2023 Lin, Mansfeld, Tang, Colle, Chen, Weng, Fei and Grumet.
PY - 2023
Y1 - 2023
N2 - Phytophthora fruit rot (PFR) 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 PFR 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 commercial 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 were also 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 diversity for cucumber. The results from this work can be applied to future disease resistance studies and marker-assisted selection in breeding programs.
AB - Phytophthora fruit rot (PFR) 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 PFR 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 commercial 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 were also 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 diversity for cucumber. The results from this work can be applied to future disease resistance studies and marker-assisted selection in breeding programs.
KW - age-related resistance
KW - cucumber core collection
KW - disease resistance
KW - GWAS
KW - Phytophthora capsici
KW - QTL-seq
KW - XP-GWAS
UR - http://www.scopus.com/inward/record.url?scp=85178177134&partnerID=8YFLogxK
U2 - 10.3389/fpls.2023.1281755
DO - 10.3389/fpls.2023.1281755
M3 - Article
C2 - 38046614
AN - SCOPUS:85178177134
SN - 1664-462X
VL - 14
JO - Frontiers in Plant Science
JF - Frontiers in Plant Science
M1 - 1281755
ER -