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Lin YC, Mansfeld BN, Tang X, Colle M, Chen F, Weng Y, Fei Z, Grumet R. Identification of QTL associated with resistance to Phytophthora fruit rot in cucumber ( Cucumis sativus L.). FRONTIERS IN PLANT SCIENCE 2023; 14:1281755. [PMID: 38046614 PMCID: PMC10693349 DOI: 10.3389/fpls.2023.1281755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 10/30/2023] [Indexed: 12/05/2023]
Abstract
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.
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Affiliation(s)
- Ying-Chen Lin
- Department of Horticulture, Graduate Program in Plant Breeding, Genetics and Biotechnology, Michigan State University, East Lansing, MI, United States
| | - Ben N. Mansfeld
- Department of Horticulture, Graduate Program in Plant Breeding, Genetics and Biotechnology, Michigan State University, East Lansing, MI, United States
| | - Xuemei Tang
- Boyce Thompson Institute, Cornell University, Ithaca, NY, United States
| | - Marivi Colle
- Department of Horticulture, Graduate Program in Plant Breeding, Genetics and Biotechnology, Michigan State University, East Lansing, MI, United States
| | - Feifan Chen
- Department of Plant and Agroecosystem Sciences, University of Wisconsin, Madison, WI, United States
| | - Yiqun Weng
- Department of Plant and Agroecosystem Sciences, University of Wisconsin, Madison, WI, United States
- Vegetable Crops Research Unit, United States Department of Agriculture-Agriculture Research Service (USDA-ARS), Madison, WI, United States
| | - Zhangjun Fei
- Boyce Thompson Institute, Cornell University, Ithaca, NY, United States
- Robert W. Holley Center for Agriculture and Health, United States Department of Agriculture-Agriculture Research Service (USDA-ARS), Ithaca, NY, United States
| | - Rebecca Grumet
- Department of Horticulture, Graduate Program in Plant Breeding, Genetics and Biotechnology, Michigan State University, East Lansing, MI, United States
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Kushalappa AC, Hegde NG, Yogendra KN. Metabolic pathway genes for editing to enhance multiple disease resistance in plants. JOURNAL OF PLANT RESEARCH 2022; 135:705-722. [PMID: 36036859 DOI: 10.1007/s10265-022-01409-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 08/22/2022] [Indexed: 06/15/2023]
Abstract
Diseases are one of the major constraints in commercial crop production. Genetic diversity in varieties is the best option to manage diseases. Molecular marker-assisted breeding has produced hundreds of varieties with good yields, but the resistance level is not satisfactory. With the advent of whole genome sequencing, genome editing is emerging as an excellent option to improve the inadequate traits in these varieties. Plants produce thousands of antimicrobial secondary metabolites, which as polymers and conjugates are deposited to reinforce the secondary cell walls to contain the pathogen to an initial infection area. The resistance metabolites or the structures produced from them by plants are either constitutive (CR) or induced (IR), following pathogen invasion. The production of each resistance metabolite is controlled by a network of biosynthetic R genes, which are regulated by a hierarchy of R genes. A commercial variety also has most of these R genes, as in resistant, but a few may be mutated (SNPs/InDels). A few mutated genes, in one or more metabolic pathways, depending on the host-pathogen interaction, can be edited, and stacked to increase resistance metabolites or structures produced by them, to achieve required levels of multiple pathogen resistance under field conditions.
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Affiliation(s)
- Ajjamada C Kushalappa
- Plant Science Department, McGill University, Ste.-Anne-de-Bellevue, QC, H9X 3V9, Canada.
| | - Niranjan G Hegde
- Plant Science Department, McGill University, Ste.-Anne-de-Bellevue, QC, H9X 3V9, Canada
| | - Kalenahalli N Yogendra
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, Telangana, India
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