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

Abstract

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.

Ridge regression and deep learning models for genomewide selection of complex traits in New Mexican chile peppers

“…Varying levels of LD were previously observed across different populations of chile peppers indicating the in uence of different factors such as population structure, recombination hotspots, and selective sweeps on the patterns of LD [36][37][38][39]. The extent of LD for this population has been reported at ~ 2.82 Mb [30], which can potentially explain why a lower number of markers was su cient to capture the large LD blocks present, resulting in an overall improvement in prediction accuracy across several traits. For populations with larger extent of LD, lesser number of markers can be used for performing predictions, whereas for panels with rapid LD decay, more loci should be included in the prediction models [40].…”

Widely Targeted Metabolomics Reveals Metabolite Diversity in Jalapeño and Serrano Chile Peppers (Capsicum annuum L.)

“…Correlation analyses within sample treatments were significant ( p < 0.0001), demonstrating clustering based on the cultivars. Genomic information using 66,650 single nucleotide polymorphism markers, nonetheless, previously classified ‘NuMex LotaLutein’ and ‘NuMex Pumpkin Spice’ in the same cluster [ 33 ], indicating high genetic relatedness; yet, implementing a metabolomic approach can resolve differences between the cultivars.…”

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

“…In another study, SSR marker-based genetic diversity of 32 Phytophthora capsici resistant accessions of C. annuum from Ethiopia and India were evaluated and the genotypes clustered into three genetic resistance groups ( Rabuma et al, 2020 ). Recently, genotyping using 66,000 GBS-derived SNP markers demonstrated that genetic structure was related to fruit (pod) architecture and morphology across the different species ( Lozada et al, 2021a ). Nevertheless, genetic diversity was relatively low; hence, there is a need to introduce new beneficial alleles to increase genetic diversity in current New Mexican chile pepper germplasm by introducing genes from other breeding programs and from wild relatives or domesticated species.…”

“…For example, the “NuMex Heritage Big Jim” ( Bosland and Coon, 2013 ) and “NuMex Sandia Select” ( Bosland and Coon, 2014 ) derived from the heirlooms “NuMex Big Jim” ( Nakayama, 1975 ) and “NuMex Sandia” ( Harper, 1950 ) respectively, formed separate clusters with their parental lines. This could be a consequence of extensive and multiple cycles of breeding and phenotypic single-plant selections in the breeding program ( Lozada et al, 2021a ). Genetic improvement of current germplasm, then, can be linked to the differences and variation in the alleles and genes present that were selected on each cycle of phenotypic selection in the breeding program.…”