Consumers within the Spicy Pepper Supply Chain

“Spicy pepper” is a term used to describe a variety of “pungent” peppers, sometimes referred to as hot, chili, or chile. The USDA reports that the per capita availability of chile peppers has increased more than 100% since the early 1980s. While the availability of spicy peppers has increased, easily accessible data regarding which varieties are consumed, how they are used by households, and who is most likely to consume them is not available. This paper provides insights into U.S. spicy pepper production and consumption as provided by a review of existing trade data and a survey of U.S. consumers.

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.

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.

Single nucleotide polymorphisms reveal genetic diversity in New Mexican chile peppers (Capsicum spp.)

Background Chile peppers (Capsicum spp.) are among the most important horticultural crops in the world due to their number of uses. They are considered a major cultural and economic crop in the state of New Mexico in the United States. Evaluating genetic diversity in current New Mexican germplasm would facilitate genetic improvement for different traits. This study assessed genetic diversity, population structure, and linkage disequilibrium (LD) among 165 chile pepper genotypes using single nucleotide polymorphism (SNP) markers derived from genotyping-by-sequencing (GBS). Results A GBS approach identified 66,750 high-quality SNP markers with known map positions distributed across the 12 chromosomes of Capsicum. Principal components analysis revealed four distinct clusters based on species. Neighbor-joining phylogenetic analysis among New Mexico State University (NMSU) chile pepper cultivars showed two main clusters, where the C. annuum genotypes grouped together based on fruit or pod type. A Bayesian clustering approach for the Capsicum population inferred K = 2 as the optimal number of clusters, where the C. chinense and C. frutescens grouped in a single cluster. Analysis of molecular variance revealed majority of variation to be between the Capsicum species (76.08 %). Extensive LD decay (~ 5.59 Mb) across the whole Capsicum population was observed, demonstrating that a lower number of markers would be required for implementing genome wide association studies for different traits in New Mexican type chile peppers. Tajima’s D values demonstrated positive selection, population bottleneck, and balancing selection for the New Mexico Capsicum population. Genetic diversity for the New Mexican chile peppers was relatively low, indicating the need to introduce new alleles in the breeding program to broaden the genetic base of current germplasm. Conclusions Genetic diversity among New Mexican chile peppers was evaluated using GBS-derived SNP markers and genetic relatedness on the species level was observed. Introducing novel alleles from other breeding programs or from wild species could help increase diversity in current germplasm. We present valuable information for future association mapping and genomic selection for different traits for New Mexican chile peppers for genetic improvement through marker-assisted breeding.

Single Nucleotide Polymorphisms Reveal Genetic Diversity in New Mexican Chile Peppers (Capsicum Spp.)

Background: Chile peppers (Capsicum spp.) are among the most important horticultural crops in the world due to their number of uses. They are considered a major cultural and economic crop in the state of New Mexico in the United States. Evaluating genetic diversity in current New Mexican germplasm would facilitate genetic improvement for different traits. This study assessed genetic diversity, population structure, and linkage disequilibrium (LD) among 165 chile pepper genotypes using single nucleotide polymorphism (SNP) markers derived from genotyping-by-sequencing (GBS). Results: A GBS approach identified 66,750 high-quality SNP markers with known map positions distributed across the 12 chromosomes of Capsicum. Principal components analysis revealed four distinct clusters based on species. Neighbor-joining phylogenetic analysis among New Mexico State University (NMSU) chile pepper varieties showed two main clusters, where the C. annuum genotypes grouped together based on fruit or pod type. A Bayesian clustering approach for the Capsicum population inferred K= 2 as the optimal number of clusters, where the C. chinense and C. frutescens grouped in a single cluster. Analysis of molecular variance revealed majority of variation to be between the Capsicum species (76.08%). Extensive LD decay (~5.59 Mb) across the whole Capsicum population was observed, demonstrating that a lower number of markers would be required for implementing genomewide association studies for different traits in New Mexican type chile peppers. Tajima’s D values demonstrated positive selection, population bottleneck, and balancing selection for the New Mexico Capsicum population. Genetic diversity for the New Mexican chile peppers was relatively low, indicating the need to introduce new alleles in the breeding program to broaden the genetic base of current germplasm. Conclusions: Analysis of genetic diversity among New Mexican chile peppers were evaluated using GBS-derived SNP markers and genetic relatedness on the species level was observed. Introducing novel alleles from other breeding programs or from wild species could help increase diversity in current germplasm. We present valuable information for future association mapping and genomic selection for different traits for New Mexican chile peppers for genetic improvement through marker-assisted breeding.

Bacterial Spot of Pepper

Bacterial spot, caused by three species of Xanthomonas, is a limiting disease problem on all peppers. This new 4-page fact sheet provides information on symptoms, causal organism and host resistance, disease cycle and epidemiology, and disease management (including cultural and sanitation practices, chemical control measures and the use of Actigard® in chile peppers). Written by Camille McAvoy, Pamela Roberts, and Jeffrey Jones, and published by the UF/IFAS Plant Pathology Department.https://edis.ifas.ufl.edu/pp362

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

Chile peppers (Capsicum spp.) are among the most important vegetable crops in the world due to their health-related, economic, and industrial uses. 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) in peppers. Meta-QTL analysis for different traits in Capsicum 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 flanking sequences for the P5 meta-QTL revealed biological functions related to DNA repair and transcription regulation. Moreover, epigenetic mechanisms such as histone and RNA methylation and demethylation were predicted, indicating the potential role of epigenetics for P. capsici resistance. Allele specific SNP markers for the meta-QTL will be developed and validated using different breeding populations of Capsicum 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.

Germination response of diverse wild and landrace chile peppers (Capsicum spp.) under drought stress simulated with polyethylene glycol

Responses to drought within a single species may vary based on plant developmental stage, drought severity, and the avoidance or tolerance mechanisms employed. Early drought stress can restrict emergence and seedling growth. Thus, in areas where water availability is limited, rapid germination leading to early plant establishment may be beneficial. Alternatively, germination without sufficient water to support the seedling may lead to early senescence, so reduced germination under low moisture conditions may be adaptive at the level of the population. We studied the germination response to osmotic stress of diverse chile pepper germplasm collected in southern Mexico from varied ecozones, cultivation systems, and of named landraces. Drought stress was simulated using polyethylene glycol solutions. Overall, survival time analysis revealed delayed germination at the 20% concentration of PEG across all ecozones. The effect was most pronounced in the genotypes from hotter, drier ecozones. Additionally, accessions from wetter and cooler ecozones had the fastest rate of germination. Moreover, accessions of the landraces Costeño Rojo and Tusta germinated more slowly and incompletely if sourced from a drier ecozone than a wetter one, indicating that slower, reduced germination under drought stress may be an adaptive avoidance mechanism. Significant differences were also observed between named landraces, with more domesticated types from intensive cultivation systems nearly always germinating faster than small-fruited backyard- or wild-types, perhaps due to the fact that the smaller-fruited accessions may have undergone less selection. Thus, we conclude that there is evidence of local adaptation to both ecozone of origin and source cultivation system in germination characteristics of diverse chile peppers.