From Genebank to Field: Exploiting Italian Pepper Landraces for Breeding Through Genomic and Phenotypic Characterization

Abstract

Italian sweet pepper landraces represent an important reservoir of genetic diversity, although their practical exploitation in breeding programmes remains limited. Historical germplasm collections preserve variation accumulated through centuries of farmer selection, but their organization into resources suitable for pre-breeding and parental selection has rarely been investigated. In this study, 35 historical Piedmont sweet pepper accessions conserved in the DISAFA Genebank and five historical breeding reference lines were characterized through quantitative fruit phenotyping and genome-wide SNP genotyping. A total of 190 individuals were genotyped by ddRADseq, yielding a final dataset of 1925 filtered SNP markers. Phenotypic characterization confirmed the major historical fruit morphotypes, while genome-wide analyses revealed genetic relationships broadly consistent with traditional morphotype classification and the history of conservative selection. Comparison between historical accessions and the corresponding sampled reference lines identified complementary private variation in all comparable genomic groups, although private variation was also detected in the reference materials. On this basis, we propose Historical Breeding Pools as a breeding-oriented interpretive framework integrating genomic relationships, traditional morphotypes and historical breeding reference lines to organize conserved diversity for future pre-breeding and parental selection. These results show how historical genebank collections can be characterized beyond conservation alone and used to prioritize genetic resources for further breeding-oriented evaluation.