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.

This study established the heat levels for several high-heat chile pepper (Capsicum chinense) varieties (Trinidad Moruga Scorpion, Bhut Jolokia, Trinidad Scorpion, Douglah Trinidad Chocolate, and Trinidad 7-pot Jonah) to determine which variety has the highest average measured heat level and the relatedness of the chile peppers using molecular analysis. In replicated trials with appropriate controls at Las Cruces, NM, results show two ‘Trinidad Moruga Scorpion’ chile pepper plants reached more than two million Scoville heat units (SHU). This is the first confirmation of chile pepper fruit measuring more than two million SHU. A large range of heat levels was observed among the field plots—further supporting strong environmental effects on chile pepper pungency. ‘Trinidad Moruga Scorpion’ was significantly hotter than ‘Bhut Jolokia’, but ‘Trinidad 7-pot Jonah’, ‘Douglah Trinidad Chocolate’, and ‘Trinidad Scorpion’ did not differ significantly from ‘Bhut Jolokia’. Molecular analysis with randomly amplified polymorphic DNA (RAPD) markers confirmed that the accessions are genetically unique. ‘Trinidad Moruga Scorpion’ belongs to the species C. chinense and is not the same chile pepper as ‘Bhut Jolokia’.

Chile peppers (Capsicum sp.) are one of the most important spices in the world and a significant vegetable, providing substantial amounts of vitamins A and C. Chile peppers are also used as a medicinal and lachrymator plant because of the characteristic burning sensation they cause when consumed by mammals. This sensation is caused by capsaicinoids that are alkaloids produced in vesicles inside the fruit. A novel class of chile peppers known as “super-hots” having greater than 1 million Scoville heat units have generated much interest. We compared the morphological structure of fruit pericarp and placental tissue of “super-hot” chile peppers to those of jalapeno and bell pepper. Most chile peppers including jalapenos, only produce the capsaicinoids in secreting vesicles found on the placenta. We report on the novel discovery that these “super-hot” chile peppers have developed accessorial vesicles on the pericarp tissue in addition to the vesicles on the placental tissue, thus leading to exceedingly high Scoville heat units for these plants.

Pepper Breeding and Genetics Program announces the release of 'NuMex Heritage Big Jim' chile pepper (Capsicum annuum L.). 'NuMex Heritage Big Jim' is an openpollinated, improved, New Mexican pod-type cultivar. The name was chosen to distinguish the newly selected cultivar from the original cultivar, NuMex Big Jim, while retaining its association. 'NuMex Heritage Big Jim' has superior flavor, a uniform and higher heat level, greater plant and pod uniformity, and higher yield as compared with the current commercially available 'NuMex Big Jim' chile pepper. There is a renewed interest in heirloom vegetables in the United States because of the variety of shapes, sizes, colors, and, most importantly, the flavor they provide (Creasy, 1999; McLaughlin, 2010). There is no official definition for what constitutes an heirloom vegetable. Most sources agree that heirloom cultivars, also called heritage or vintage cultivars, should be open-pollinated and have a well-established history (Harris, 2007; Iannotti, 2012). One such heirloom legacy is 'NuMex Big Jim'. The New Mexican-type chile pepper cultivar, NuMex Big Jim, was released by New Mexico State University in 1975 (Nakayama, 1975). It is listed in the Guinness Book of Records as producing the world's largest pepper pod at 33.75 cm (13.5 inches) long (Coon et al., 2008). Because of the large pods, the cultivar is a favorite of home gardeners and chefs for making chile relleno, a stuffed chile pepper pod. Changes have occurred to the original 'NuMex Big Jim' that includes yield, maturity date, plant habit, and fruit characteristics. Growers state that 'NuMex Big Jim' fruit is much milder than it was in the past. Also, when released in 1975, one of the complaints about the original 'NuMex Big Jim' was that

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