Genomic regions and candidate genes linked with Phytophthora capsici root rot resistance in chile pepper (Capsicum annuum L.)

Abstract

Background Phytophthora root rot, caused by Phytophthora capsici, is a major disease affecting Capsicum production worldwide. A recombinant inbred line (RIL) population derived from the hybridization between ‘Criollo de Morellos-334’ (CM-334), a resistant landrace from Mexico, and ‘Early Jalapeno’, a susceptible cultivar was genotyped using genotyping-by-sequencing (GBS)-derived single nucleotide polymorphism (SNP) markers. A GBS-SNP based genetic linkage map for the RIL population was constructed. Quantitative trait loci (QTL) mapping dissected the genetic architecture of P. capsici resistance and candidate genes linked to resistance for this important disease were identified. Results Development of a genetic linkage map using 1,973 GBS-derived polymorphic SNP markers identified 12 linkage groups corresponding to the 12 chromosomes of chile pepper, with a total length of 1,277.7 cM and a marker density of 1.5 SNP/cM. The maximum gaps between consecutive SNP markers ranged between 1.9 (LG7) and 13.5 cM (LG5). Collinearity between genetic and physical positions of markers reached a maximum of 0.92 for LG8. QTL mapping identified genomic regions associated with P. capsici resistance in chromosomes P5, P8, and P9 that explained between 19.7 and 30.4% of phenotypic variation for resistance. Additive interactions between QTL in chromosomes P5 and P8 were observed. The role of chromosome P5 as major genomic region containing P. capsici resistance QTL was established. Through candidate gene analysis, biological functions associated with response to pathogen infections, regulation of cyclin-dependent protein serine/threonine kinase activity, and epigenetic mechanisms such as DNA methylation were identified. Conclusions Results support the genetic complexity of the P. capsici–Capsicum pathosystem and the possible role of epigenetics in conferring resistance to Phytophthora root rot. Significant genomic regions and candidate genes associated with disease response and gene regulatory activity were identified which allows for a deeper understanding of the genomic landscape of Phytophthora root rot resistance in chile pepper.

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

“…The major effect QTLs for P. capsici root rot resistance was found on pepper chromosomes P5, P8, and P9. These QTLs were named QTL.Pc5, QTL.Pc8.1, and QTL.Pc9 ( Lozada et al, 2021 ). Regardless of the resistance sources or P. capsici isolates, major resistance QTLs for P. capsici have been consistently detected in the close vicinity of chromosome P5 in several studies ( Bonnet et al, 2007 ; Kim et al, 2008 ; Mallard et al, 2013 ; Liu et al, 2014 ; Rehrig et al, 2014 ).…”

Chile Pepper (Capsicum) Breeding and Improvement in the “Multi-Omics” Era

“…While management practices can help mitigate the effects of P. capsici on chile pepper production ( Sanogo and Ji, 2012 ), breeding and selection for disease-resistant cultivars are still the most cost-effective approach ( Xu et al, 2016 ; Siddique et al, 2019 ). The short arm of chromosome P5 is a major genetic hotspot containing QTL for P. capsici resistance ( Mallard et al, 2013 ; Rehrig et al, 2014 ; Siddique et al, 2019 ; Du et al, 2021 ; Lozada et al, 2021b , c ), and this information facilitates breeding efforts for resistance to P. capsici . A set of New Mexico recombinant inbred lines (NMRIL) derived from the hybridization between the resistant landrace, CM-334, and the susceptible cultivar “Early Jalapeno” was previously developed at NMSU to facilitate a better understanding of the complex inheritance of P. capsici root rot resistance and the characterization of different races for breeding resistant cultivars ( Sy et al, 2008 ).…”

“…A set of New Mexico recombinant inbred lines (NMRIL) derived from the hybridization between the resistant landrace, CM-334, and the susceptible cultivar “Early Jalapeno” was previously developed at NMSU to facilitate a better understanding of the complex inheritance of P. capsici root rot resistance and the characterization of different races for breeding resistant cultivars ( Sy et al, 2008 ). Recently, large main effect and QTL interaction in chromosomes P5 and P8 that can be used as a basis for marker-assisted selection were identified using the NMRIL ( Lozada et al, 2021b ). Genetic mapping further mapped SNP loci related to other diseases in chile pepper, such as anthracnose on chromosomes 2 and 4, where three major QTLs for resistance were located between two SNP markers within 17 cM distance in chromosome 4 ( Mahasuk et al, 2016 ).…”

“…There has been growing evidence on the potential involvement of epigenetic factors, such as DNA methylation, histone acetylation, and chromatin remodeling, specifically on conferring P. capsici resistance in chile pepper ( Du et al, 2021 ; Lozada et al, 2021b , 2021c ). Examining the chile pepper epigenome using various techniques, such as DNA methylation PCR-based bisulfite sequencing and chromatin immunoprecipitation assays ( Cazaly et al, 2019 ; Li, 2021 ), could therefore be relevant in breeding and selection for P. capsici resistant lines.…”

Genetic basis of maize kernel protein content revealed by high-density bin mapping using recombinant inbred lines

“…Consequently, there are contrasting reports on QTL number, genetic effects, and distribution ( Yang et al., 2016 ). Molecular marker development and the implementation of fine gene mapping to genetically improve traits could also not be achieved due to the absence of stable markers ( Lozada et al., 2018 ; Ren et al., 2019 ; Ma et al., 2020 ; Lozada et al., 2021 ; Yepuri et al., 2022 ).…”