Marker-trait association analysis for easy fruit destemming and mechanical harvestability traits in New Mexican chile pepper (Capsicum annuum L.)

Introduction Chile pepper ( Capsicum annuum L.) mechanization is a promising alternative to traditional hand harvesting due to the costs associated with manual harvest, as well as the increasing unavailability of skilled manual chile harvesters. This study aimed to identify single nucleotide polymorphisms (SNPs) associated with mechanical harvestability (MH) and yield-related traits using multi-locus genome-wide association mapping approaches in a C. annuum association mapping population. Methods A C. annuum association mapping panel for mechanical harvest was manually direct seeded in an augmented block design in two locations. After filtration, imputation, and quality control 27,291 single nucleotide polymorphism (SNP) markers were used for association analyses. Six multi-locus GWAS models were implemented to identify marker trait association. Results and Discussion Multi-locus GWAS models identified 12 major SNP markers (R 2 > 10) across nine chromosomes associated with plant architecture, easy destemming traits, and yield parameters. The presence of a major QTL in chromosome P2, dstem2.1, identified recently to be associated with destemming force, was confirmed. Mature green and mature red yield shared three SNP markers mapped on chromosome P3, P5, and P6 explaining 11.94% to 25.15% of the phenotypic variation. Candidate gene analysis for the significant loci identified 19 candidate genes regulating different phytohormone biosynthesis/signaling, metabolic processes, transcription, methylation, DNA repair/replication, and RNA splicing, with potential roles in controlling plant architecture and morphology. The diverse positions of the associated SNPs suggest the complex nature of these quantitative traits, involvement of multiple genetic factors, and novel significant marker-trait associations. Results from this study will be relevant for genetic improvement of mechanical harvestability traits in New Mexican chile pepper using molecular markerassisted breeding and selection.