- 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. - A Bayesian clustering approach for the Capsicum population inferred K = 2 as the optimal number of clusters, where the C. - 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.. - Chile peppers belonging to the genus Capsicum are one of the most important vegetable crops in the world. - [6] evaluated a Mexican chile pepper collection using SNP markers and observed that genetic diversity was related to the cultiva- tion techniques used for the different landraces.. - Genetic diversity studies are important for the gen- etic fingerprinting of varietal types, identification of gen- etic relatedness among different genotypes for breeding programs, genetic resource conservation, and develop- ment of non-redundant core collections [21].. - Chile peppers are among the major crops in the State of New Mexico, with the official state question, “Red or Green?” referring to these valuable crops. - DNA profiling could identify beneficial alleles and their combinations that could be introduced in different chile pepper breed- ing programs for the genetic improvement of current germplasm. - Sequencing using Illumina NovaSeq™ 6000 generated an average of 4.31 million high-quality read tags for the 165 chile pepper genotypes. - www.https://doi.org/10.6084/m9.figshare.14447526) have known map positions in the Zunla-1 reference genome [8]. - Average frequency of minor allele for the 66,750 SNP loci was 0.21, and the proportion of heterozygotes was 0.05. - Results from the PCA were consistent with clustering based on a neighbor-joining (NJ) phylogenetic analysis for the Capsicum population (Fig. - Genetic diversity. - Inbreeding coefficient for the Capsicum population was 0.54. - Expected nucleotide diversity (θ) for the whole Capsicum panel was 0.18. - baccatum and C.chacoense complex (0.55) (Additional file 2, Table S1). - Table 1 Analysis of molecular variance using genome wide SNP markers for the Capsicum populations. - chacoense) and 0.12 (C. - Tajima’s D statistic for the Capsicum population across all chromosomes was D = 2.85 (Fig. - Negative values for D were observed for the individual species. - Inference for the best number of clusters, K using the Evanno criterion revealed K = 2 (ΔK Fig. - chinense (N = 44 geno- types), whereas cluster 2 consisted of the C. - In addition, K = 9 and K = 4 showed high ΔK relative to the other clusters, which indicates that these can also serve as alternative values to describe the gen- etic differentiation in the Capsicum population. - 1 a Principal component (PC) biplot derived from genome wide SNP marker data for the Capsicum population showing four major clusters based on species. - Group I comprised of the C. - b Neighbor-joining tree for the Capsicum population showing differentiation based on species. - chacoense formed a separate group (Group II), similar with what was observed in the PC plot. - 2 Neighbor joining (NJ) phylogenetic tree for the NMSU. - Note that the official names for the NMSU chile pepper cultivars include the designation ‘ NuMex ’ before the actual name, e.g. - For convenience, the name was omitted in the NJ tree presented herein. - Table 2 Genetic diversity indices for the Capsicum population. - Analysis of LD decay by plotting r 2 against distance revealed an extensive LD for the whole population, where LD starts to decay at ~ 5.59 Mb (Fig. - LD starts to decay at 0.07 and 0.38 Mb for the C. - This panel included at least 50 different cul- tivars previously released by the NMSU Chile Pepper Breeding Program, regarded as the longest continuous program for Capsicum improvement in the world.. - 3 Tajima ’ s D statistics for each chromosome for the whole Capsicum population and representative species. - 4 Bar plots for the admixture indices for each individual in the Capsicum population for K= 2 a and K= 4 c clusters. - b Inference for the best number of clusters using the Evanno method revealed the optimal number of clusters to be K= 2. - d Linkage disequilibrium (LD) decay plot for the Capsicum population. - Genomic information from this study would be useful for the genome wide selection and association studies for trait improvement in chile peppers.. - annuum genotypes in the population and the reference genome used. - in the Capsi- cum population that could be attributed to the inbreeding nature of the Capsicum spp. - annuum in the PCA biplot. - In the current study, the wild species C. - A relatively large marker dataset, such as the one used in the current study, might result in a more precise and robust cluster- ing based on species in the PCA plot. - The efficiency of utilizing a smaller subset of markers (i.e., 48 SNP loci) with high polymorphism content in combination with 32 different phenotypic traits, nevertheless, was previ- ously demonstrated for the construction of a core collec- tion of chile pepper germplasm [35]. - Breeding and selection for improvement of heirloom cultivars including ‘NuMex Big Jim’ and ‘NuMex Sandia’. - have resulted in the release of the ‘NuMex Heritage Big Jim’ and the ‘NuMex Sandia Select’, with both cultivars having increased consumer and horticultural value [38, 39]. - Neighbor- joining analysis based on SNP loci showed ‘NuMex Heri- tage Big Jim’ and ‘NuMex Sandia Select’ forming a group, whereas ‘NuMex Big Jim’ and ‘NuMex Sandia’. - Selective sweeps in the chile pepper genome. - The presence of potential selective sweeps in the chile pepper population and across the different Capsicum species was assessed using the Tajima’s D statistic. - observed a positive value for Tajima’s D statistic (D = 2.85) for the whole population, demonstrating an abun- dance of intermediate frequency alleles and can result from population structure, bottlenecks, and/or balancing selection [40]. - Low (negative) values for the Taji- ma’s coefficient were nevertheless observed within the representative Capsicum species evaluated, demonstrat- ing that minor alleles were less frequent than would be predicted in a neutrally evolving population, suggesting the potential occurrence of genes or gene clusters under strong purifying selection, population expansions, or positive selection [6, 40]. - The varying values of Tajima’s D could signify that breeding and selection for the development of new cultivars across the different Capsicum species resulted in differences in the allele frequency. - Positive D values were noted across individual chromosomes for the C. - annuum cultivars might explain genetic diversity and recovery from genetic bottleneck effects in the individual chromo- some level [41]. - Population stratification in the Capsicum population Analysis of population structure using a Bayesian model- based clustering algorithm revealed K = 2 as the optimal number of clusters for the Capsicum population. - Knowledge of the LD decay across populations is rele- vant for the identification of significant marker-trait as- sociations and implementation of marker-assisted selection [45, 46]. - In the current study, analyses revealed varying levels of LD decay across the different chromo- somes for the Capsicum population. - Extensive LD was observed for the whole population, with LD reaching to. - 5.59 Mb, whereas a rapid LD decay was noted for the C. - chinense (0.38 Mb) com- plexes for the evaluated Capsicum population. - Our re- sults for the C. - Conversely, for the C. - Information on genetic diversity is relevant for the gen- omic improvement of current germplasm. - bottleneck, and balancing selection has been observed in the Capsicum population. - The extensive LD observed for the Capsicum panel indicates that a lower number of markers can be used for genome wide association map- ping. - The relatively low genetic diversity in the current New Mexican Capsicum population could be improved by introducing novel alleles from other breeding pro- grams or from wild germplasm. - A collection of Capsicum lines consisting of 165 diverse ge- notypes of chile peppers from five Capsicum species was evaluated in the current study (Additional file 1, Table S6).. - chacoense, was included in the study.. - The New Mexican types included ‘NuMex Joe E.. - Parker’ [48], ‘NuMex Heritage Big Jim’ [38], ‘NuMex Big Jim’. - [49], and ‘NuMex Sandia Select’ [39], whereas the cayenne type included ‘NuMex Las Cruces’ [50]. - The paprika type consisted of ‘NuMex Garnet’ [51], and the jalapenos com- prised of ‘NuMex Jalmundo’ [52], ‘NuMex Vaquero’ [53],. - and ‘NuMex Piñata’ [54]. - ‘NuMex Twilight’ [55], ‘NuMex Christmas’, and ‘NuMex. - chinense comprised of the. - ‘NuMex Suave Red’ and ‘NuMex Suave Orange’ [58],. - frutescens consisted of the ‘NuMex Nobasco’. - Finally, the Capsicum population also included some of the. - puckerbuttpeppercompany.com), regarded as the hottest chile pepper in the world.. - Genotyping-by-sequencing (GBS) for the Capsicum population was conducted through the University of Minnesota Genomics Center (https://genomics.umn.. - the ‘GeneticSubsetter’ package [74] in R.. - Genetic stratification for the chile pepper population was evaluated using the program STRUCTURE [44]. - Inference on the true number of K that best represent the genotypes was conducted with the Evanno criterion that employs an ad hoc statistic ΔK based on the degree of changes in the log probability of data between values of K [75] implemented in STRUCTURE HARVESTER [76]. - Flanking sequences for the 66,750 SNP markers identified in the Capsicum population.. - Inference on the best number of clusters K for the Capsicum population using Evanno criterion. - disequilibrium for the intrachromosomal marker pairs in the Capsicum population. - The datasets generated and/or analyzed during the current study are available in the FigShare repository, www.https://doi.org/10.6084/m9.figshare.. - L.) in the Americas. - Austin, Published for the Robert S. - Multiple lines of evidence for the origin of domesticated chili pepper, Capsicum annuum, in Mexico. - In: The Recent Topics in Genetic Polymorphisms. - Taxonomy and genetic diversity of domesticated Capsicum species in the Andean region. - Notice of the Naming and Release of ‘ NuMex Big Jim. - NuMex Centennial ’ and ’ NuMex Twilight ’ Ornamental Chiles. - NuMex suave red ’ and ‘ NuMex suave orange ’ mild Capsicum chinense cultivars. - genodive version 3.0: Easy-to ‐ use software for the analysis of genetic data of diploids and polyploids. - Structure of linkage disequilibrium and phenotypic associations in the maize genome
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