Genome-Wide Association Study of Resistance to Phytophthora capsici in the Pepper (Capsicum spp.) Collection

Abstract

One of the most serious pepper diseases is Phytophthora blight, which is caused by Phytophthora capsici. It is crucial to assess the resistance of pepper genetic resources to Phytophthora blight, understand the genetic resistances, and develop markers for selecting resistant pepper materials in breeding programs. In this study, the resistance of 342 pepper accessions to P. capsici was evaluated. The disease severity score method was used to evaluate the phenotypic responses of pepper accessions inoculated with the KCP7 isolate. A genome-wide association study (GWAS) was performed to identify single nucleotide polymorphisms (SNPs) linked to P. capsici (isolate KCP7) resistance. The pepper population was genotyped using the genotype-by-sequencing (GBS) method, and 45,481 SNPs were obtained. A GWAS analysis was performed using resistance evaluation data and SNP markers. Significantly associated SNPs for P. capsici resistance at 4 weeks after inoculation of the GWAS pepper population were selected. These SNPs for Phytophthora blight resistance were found on all chromosomes except Chr.05, Chr.09, and Chr.11. One of the SNPs found on Chr.02 was converted into a high-resolution melting (HRM) marker, and another marker (QTL5-1) from the previous study was applied to pepper accessions and breeding lines for validation and comparison. This SNP marker was selected because the resistance phenotype and the HRM marker genotype matched well. The selected SNP was named Chr02-1126 and was located at 112 Mb on Chr.02. The Chr02-1126 marker predicted P. capsici resistance with 78.5% accuracy, while the QTL5-1 marker predicted resistance with 80.2% accuracy. Along with the marker for major quantitative traits loci (QTLs) on Chr.05, this Chr02-1126 marker could be used to accurately predict Phytophthora blight resistance in pepper genetic resources. Therefore, this study will assist in the selection of resistant pepper plants in order to breed new phytophthora blight-resistant varieties.

Insights into the genetic architecture of Phytophthora capsici root rot resistance in chile pepper (Capsicum spp.) from multi-locus genomewide association study

“…The previously identi ed QTL.Pc9 was also ~ 1.91 Mb upstream to the signi cant SNP, S9_237909149 detected on chromosome 9 in the present work [8]. In another GWAS, signi cant SNPs were identi ed at 9.14 Mb and 208.4 Mb on chromosomes 7 and 12 respectively, which were ~ 0.11 Mb and ~ 0.91 Mb upstream to the SNPs, S7_9249493 and S12_209274913 detected in this study [30]. A novel major SNP marker, S6_705421 was discovered in this study which accounted for up to 54.4% of the phenotypic variation.…”

“…Most of the signi cant SNPs identi ed in this research represent potential novel resistance loci which can be targeted in breeding toward resistance. Though chromosome 5 has been known to be the major region with disease resistance loci against P. capsici, this study as well as previous studies have detected genomic regions on other chromosomes which demonstrates the complexity of Phytophthora root rot resistance in chile peppers [8,9,27,30,68,74].…”

“…Genomewide association study (GWAS) is an e cient tool that can be utilized to identify genetic loci linked with various complex traits using natural populations [29] and can be used to complement biparental mapping. Previously, a total of 117 and 30 signi cant SNP markers were identi ed across the entire Capsicum genome using single-locus GWAS for P. capsici resistance using 352 [9] and 342 accessions [30].…”

Evaluation of Inhibitory Effect and Mechanism of Euphorbia Factor L3 against Phytophthora capsici

“…Phytophthora capsici Leonian is a notoriously harmful pathogen that can infect more than 60 species of vegetable crops (e.g., pepper, tomato, eggplant, and some melon crops) in the Solanaceous, Cucurbitaceous, and Fabaceous families [ 1 , 2 , 3 ]. Typical symptoms caused by P. capsici on vegetables include stem and fruit rot, wilting, stunting, damping off, and plant death, along with stem and leaf blight [ 4 , 5 ]. It is estimated that P. capsici -induced diseases are responsible for at least $200 million in losses each year [ 6 ].…”

Multi‐environment association study highlights candidate genes for robust agronomic quantitative trait loci in a novel worldwide Capsicum core collection

“…High‐throughput single nucleotide polymorphism (SNP) technologies such as genotyping‐by‐sequencing (GBS) have recently been used to describe the genetic structure of the pepper germplasm (Colonna et al., 2019; Hill et al., 2013; Lee, Ro, et al., 2020; Lozada et al., 2022; Ro et al., 2022; Tamisier et al., 2020; Taranto et al., 2016; Wu et al., 2019). Most recently, the G2P‐SOL project produced a comprehensive survey of pepper diversity, describing the genetic structure of over 10 000 wild and cultivated accessions housed in 10 genebanks (Tripodi et al., 2021).…”