Towards genomic-assisted breeding in sweet pepper: Fruit morphology and selective sweep analysis in MAGIC founders

Abstract

Sweet pepper (Capsicum annuum L.) holds significant economic and nutritional value, with fruit shape being a key trait influencing marketability and consumer preferences. Traditional breeding approaches for improving fruit morphology are labor-intensive, requiring novel strategies to accelerate genetic gains. A Multiparent Advanced Generation Inter-Cross (MAGIC) population was developed from eight diverse C. annuum accessions to capture extensive genetic diversity. At present, the population is in the G₆ developmental stage. To characterize the variability captured by the crossings, whole-genome sequencing of parental lines was performed, identifying ∼39.3 million polymorphisms, including single nucleotide polymorphisms (SNPs) and structural variants (SVs). A preliminary selective sweep (SS) analysis based on sequencing data of the 8 parentals lines, together with 8 Italian landraces, was conducted, leading to the identification of genomic regions associated with fruit morphology. In these regions, candidate genes involved in transcription regulation and hormone response pathways were highlighted, and SNP variants across the genotypes identified. Among them, a set of polymorphisms on CaOFP20 (Caz10g08850), a transcriptional repressor associated with fruit elongation, phylogenetically clustered together the elongated-fruit accessions, reinforcing the putative role of the ovate-family transcription factor in fruit morphology regulation. Additional candidate genes, auxin response factors, and NAC domain proteins, were present in the selective sweep regions related to fruit weight, diameter, and length. These findings provide a valuable genomic framework that can be leveraged in marker-assisted selection to improve fruit shape traits in sweet pepper, contributing to more efficient and targeted breeding strategies.