Optimising the genetic resources of a Capsicum spp. (peppers) proprietary collection through effective pre-breeding approaches

the relationships among genotypes within germplasm collections is crucial for genetic improvement and the management of genetic resources. The objective of this study was to introduce the latest advancements in marker development and deployment for the molecular characterization of the company’s germplasm collection of Capsicum spp. (peppers), and to enhance its breeding strategy for releasing new, superior, and resistant varieties. To enhance the exploration of genetic variability and subsequent selection in pepper species, the inter-crossing scheme allowed for the multiple accumulation of favourable genes in a single genotype with improved accuracy and efficiency through gene pyramiding. This approach facilitated multi-trait and multi-environment selection, thereby improving genotype adaptability. Inter-crossing selection generated superior elite genotypes with diverse genetic backgrounds, leading to the development of new advanced elite materials. These materials confer adaptability “plasticity” to hybrids, enabling them to thrive under varying growing conditions. The availability of next-generation sequencing (NGS) technologies and the Capsicum annuum (L.) reference genome provides an opportunity to employ resequencing strategies to address specific and practical issues in genome-assisted breeding schemes. This approach also aids in identifying new markers for genes of interest. A restricted panel of private SNPs distributed across most chromosomes, which result in codon stop gains or losses (leading to truncated or highly modified proteins with altered functions), was identified for application in the company for traceability and variety identification, with potential for patent application. Notably, a stable number of 8-10 private SNPs causing stop gains or losses were consistently identified in all genotypes. Our work demonstrates how, with current resequencing costs, seed companies can easily characterize the complete genomic profiles of their varieties, mining these data for genes and markers useful for breeding programs and protecting their intellectual property.