Abstract
BackgroundPhytophthora 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.ResultsDevelopment 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.ConclusionsResults 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.
Highlights
Phytophthora root rot, caused by Phytophthora capsici, is a major disease affecting Capsicum production worldwide
The present study aimed to develop a linkage map based on GBS-derived single nucleotide polymorphism (SNP) markers and determine the genetic basis of P. capsici root rot resistance in chile pepper using Quantitative trait loci (QTL) mapping and candidate gene analysis
A QTL mapping approach was implemented to dissect the genetic architecture of Phytophthora capsici root rot resistance using a chile pepper recombinant inbred line (RIL) population
Summary
Phytophthora root rot, caused by Phytophthora capsici, is a major disease affecting Capsicum production worldwide. Phytophthora root rot, caused by the soil-borne oomycete Phytophthora capsici, is one of the most devastating diseases affecting Capsicum annuum (2n=2x=24) production across the globe [1,2,3,4]. Crop rotation, and irrigation management can circumvent the effects of P. capsici in chile pepper [3], identifying sources of resistance alleles and using resistant cultivars remains the most eco-friendly and cost-effective approaches to minimize the effect of this pathogen [7, 8]. The presence of a single dominant inhibitor gene affecting P. capsici resistance (Ipcr) in chile pepper has been observed, where susceptibility of individuals cannot be explained by the absence of resistance genes, but, instead, results from the action of the Ipcr inhibitor interfering with the host-specific defense mechanism [18]. The Phytophthora–Capsicum pathosystem is more complex than what was initially thought, and breeding strategies that incorporate more diverse germplasm and novel genomics and sequencing approaches must be utilized to achieve local and global success in breeding for disease resistance [4]
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