This work presents the first eight-way multi-parental advanced generation inter-cross (MAGIC) population in pepper. This interspecific MAGIC population was built with six Capsicum annuum accessions and two C. chinense accessions, selected for encompassing a representative and wide genetic diversity, and being complementary for morphological, agronomic, and fruit quality traits. The population in its third selfing generation has been phenotyped with reliable descriptors and genotyped using genotyping-by-sequencing to assess its overall diversity, homozygosity, parental contributions, and genetic structure. A great variability was found in the phenotyping study, showing many forms of recombination of all the founder lines. Moreover, new phenotypic combinations were found, as well as transgressive inheritance in quantitative traits. The S3 generation contained a balanced distribution of the parental genomes and each S3 individual seemed to contain a unique genomic combination of the founder lines, reaching high homozygosity. In this regard, a preliminary genome-wide association study (GWAS) was performed for highly heritable traits to evaluate the potential of this population for future breeding prospects. Strong associations were found for most traits analysed, like stem pubescence and fruit colour at maturity stage, with associated genes related to response to stress and defence functions; or fruit wall consistency, with associated genes related to lipid metabolism. Our results show that this first Capsicum MAGIC population is a valuable genetic resource for research and breeding purposes in peppers, by identifying genomic regions associated with traits of interest and its potential for future GWAS in more complex agronomical and fruit quality traits.

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