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

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.

Environment of origin and domestication affect morphological, physiological, and agronomic response to water deficit in chile pepper (Capsicum sp.)

Global climate change is having a significant effect on agriculture by causing greater precipitation variability and an increased risk of drought. To mitigate these effects, it is important to identify specific traits, adaptations, and germplasm that improve tolerance to soil water deficit. Local varieties, known as landraces, have undergone generations of farmer-mediated selection and can serve as sources of variation, specifically for tolerance to abiotic stress. Landraces can possess local adaptations, where accessions adapted to a particular environment will outperform others grown under the same conditions. We explore adaptations to water deficit in chile pepper landraces from across an environmental gradient in Mexico, a center of crop domestication and diversity, as well in improved varieties bred for the US. In the present study, we evaluated 25 US and Mexico accessions in a greenhouse experiment under well-watered and water deficit conditions and measured morphological, physiological, and agronomic traits. Accession and irrigation regime influenced biomass and height, while branching, CO2 assimilation, and fruit weight were all influenced by an interaction between accession and irrigation. A priori group contrasts revealed possible adaptations to water deficit for primary branching, CO 2 assimilation, and plant height associated with geographic origin, domestication level, and pepper species. Additionally, within the Mexican landraces, the number of primary branches had a strong relationship with precipitation from the environment of origin. This work provides insight into chile pepper response to water deficit and adaptation to drought and identifies possibly tolerant germplasm.

Tolerance to Virulence Phenotypes of Phytophthora capsici in Pasilla Pepper Cultivars

Phytophthora capsici is the most important limiting factor in the production of chile pepper in Mexico. This pathogen presents virulence phenotypes capable of infecting diverse cultivars of this crop. The search and development of resistance in chile pepper is an excellent alternative for the management of P. capsici. The objective of this work was to evaluate the response of four pasilla pepper cultivars to infection with five virulence phenotypes of P. capsici. Pasilla pepper landraces PAS-1, PAS-2, PAS-3, and PAS-4 were inoculated with P. capsici isolates MX-1, MX-2, MX-7, MX-8, and MX-10. Two experiments were conducted under greenhouse conditions from April through June 2017 and April through June 2018. ‘California Wonder’ was included as a susceptible control, and uninoculated plants were included as a negative control. In each experiment, groups of six 56-day-old plants from each pepper cultivar were inoculated with each virulence phenotype. Disease severity was evaluated 20 days after inoculation using an individual plant severity scale. All pepper cultivars were classified as resistant = R, moderately resistant (MR), tolerant (T), moderately tolerant (MT), or susceptible (S), according to the frequency of resistant plants (severity 0–1). ‘California Wonder’ and ‘PAS-4’ were susceptible to all five virulence phenotypes. The rest had different responses to the virulence phenotypes, but ‘PAS-2’ and ‘PAS-3’ were susceptible to only one of the five virulence phenotypes. Pasilla peppers with low severity exhibited a slow rate of infection, which is a mechanism we have called “slow wilting.” The pasilla pepper cultivars PAS-1, PAS-2, and PAS-3 could be used in plant breeding programs as sources of genetic tolerance and moderate resistance against P. capsici.

Genetic Architecture of Chile Pepper (Capsicum spp.) QTLome Revealed Using Meta-QTL Analysis

In recent years, quantitative trait loci (QTL) mapping approaches have been widely implemented to identify genomic regions affecting variation for different traits for marker-assisted selection (MAS). Meta-QTL analysis for different traits in chile peppers (Capsicum spp.) remains lacking, and therefore it would be necessary to re-evaluate identified QTL for a more precise MAS for genetic improvement. We report the first known meta-QTL analysis for diverse traits in the chile pepper QTLome. A literature survey using 29 published linkage mapping studies identified 766 individual QTL from five different trait classes. A total of 311 QTL were projected into a consensus map. Meta-analysis identified 30 meta-QTL regions distributed across the 12 chromosomes of Capsicum. MQTL5.1 and MQTL5.2 related to Phytophthora capsici fruit and root rot resistance were delimited to < 1.0 cM confidence intervals in chromosome P5. Candidate gene analysis for the P5 meta-QTL revealed functions related to histone methylation and demethylation, indicating the potential role of epigenetics for P. capsici resistance. Allele-specific markers for the meta-QTL will be developed and validated for MAS of P. capsici resistant lines. Altogether, results from meta-QTL analysis for chile pepper QTLome rendered further insights into the genetic architecture of different traits for this valuable horticultural crop.

A Study on the Feasibility of Robotic Harvesting for Chile Pepper

This paper presents a study on the robotic harvesting of New Mexico type chile pepper, in a laboratory setting, using a five degrees of freedom (DoF) serial manipulator. The end-effector of the manipulator, a scissor-type cutting mechanism, was devised and experimentally tested in a lab setup which cuts the chile stem to detach the fruit. Through a MATLAB™-based program, the location of the chile pepper is estimated in the robot’s reference frame, using Intel RealSense Depth Camera. The accuracy of the 3D location estimation system matches the maximum accuracy claimed by the manufacturer of the hardware, with a maximum error to be in Y-axis, which is 5.7 mm. The forward and inverse kinematics are developed, and the reachable and dexterous workspaces of the robot are studied. An application-based path planning algorithm is developed to minimize the travel for a specified harvesting task. The robotic harvesting system was able to cut the chile pepper from the plant based on 3D location estimated by MATLAB™ program. On the basis of harvesting operation, on 77 chile peppers, the following harvesting indicators were achieved: localization success rate of 37.7%, detachment success rate of 65.5%, harvest success rate of 24.7%, damage rate of 6.9%, and cycle time of 7 s.

A field evaluation of jalapeño and non-jalapeño chile pepper resistance to Phytophthora blight caused by Phytophthora capsici

Phytophthora capsici is a destructive soilborne pathogen, which causes Phytophthora blight in many vegetable crops including chile pepper (Capsicum sp.). Our research was aimed at evaluating the resistance of jalapeño cultivars in field conditions and identifying the factors associated with reduction of Phytophthora blight caused by P. capsici. Six jalapeño (NuMex Orange Spice, NuMex Pumpkin Spice, NuMex Jalmundo, TAM Jalapeño, Early Jalapeño, and NuMex Vaquero) and two non-jalapeño (CM-334 and NM 6-4) cultivars were inoculated with P. capsici at the fruiting stage. Disease severity index (DSI), disease incidence (DI), and area under the disease progress curve (AUDPC) for each cultivar were measured. The most susceptible jalapeño cultivars with the highest DSI, DI, and AUDPC were NuMex Orange Spice, NuMex Jalmundo and NuMex Pumpkin Spice, whereas the least susceptible jalapeño cultivars were Early Jalapeño, TAM Jalapeño, and NuMex Vaquero, with the lowest DSI, DI, and AUDPC. The identified jalapeños with reduced susceptibility to Phytophthora blight can be planted in infested fields, combined with other control methods which may help in soil disinfestation by reducing the inoculum level in soil over time.

New Mexico Chile pepper producers are affected by a diverse Verticillium dahliae population that includes many race 2 strains that break Ve1 mediated resistance.

Chile pepper is an important crop in in New Mexico both for its cultural heritage and its cash receipts. Vericillium dahliae caused wilt is one of the largest constraints on chile production in Southern NM. Identification of natural resistance sources, like the Ve locus used in commercial tomato lines, would be a significant help to NM chile growers. Understanding the diversity and race structure of V. dahliea affecting chile production in NM is a necessary first step toward identifying and deploying genetic resistance in chile peppers. Here we report race characterization and diversity studies which show that NM is affected by a diverse population of V. dahliae strains, and many of which overcome the Ve mediated resistance in tomato. The results of this work suggest that Ve like resistance, either discovered within the chile gene pool or introduced from tomato via genetic engineering, is unlikely to be useful for generating chile cultivars resistant to Verticillium wilt.

Efficacy of Pecan Husk and Shell Phenolic Extracts Against Phytophthora Blight in Chile Pepper

Phytophthora blight, caused by Phytophthora capsici, is detrimental to chile peppers (Capsicum spp.). In this study, phenolics extracted from pecan (Carya illinoinensis) husk and shell, were foliarly applied to chile pepper (Capsicum annuum L., cultivar NM 6-4) to induce a resistance response against plant infection by P. capsici. Several pecan metabolite extractions were tested, and an acetic acid (2%) in aqueous methanol (80%) solution was the best extraction solvent, yielding total polyphenolic content of 290 mg/g dry weight from husk and 641 mg/g from shell. The phenolic extracts from husk and shell were applied as foliar sprays at different concentrations to chile plants inoculated with a virulent isolate of P. capsici. Chile plants treated with 1% phenolic husk or shell extracts or 0.1% salicylic acid remained alive throughout the study while plants subjected to all other treatments (including a water control treatment) died. Analyses of the extracts through spectrophotometry and high performance liquid chromatography indicated that the phenolic content in the extracts was largely made up of proanthocyanidins also known as condensed tannins. Pecan byproducts may be used as additional options for management of Phytophthora blight.