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IntroductionChile 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.MethodsA 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 DiscussionMulti-locus GWAS models identified 12 major SNP markers (R2 > 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.

Increasing global temperature has adverse effects on crop health and productivity at both seedling and reproductivity stages. It is paramount to develop heat tolerant wheat cultivars able to sustain under high and fluctuating temperature conditions. An experiment was conducted to characterize 194 historical wheat cultivars of Pakistan under high temperature at seedling stage to identify loci associated with heat tolerance using genome-wide association studies (GWAS). A quantitative trait locus, TaHST1, on chr4A was also characterized to identify the haplotypes at this locus associated with heat tolerance in wheat from Pakistan. Initially, the diversity panel was planted under control conditions (25°C/20°C day and night temperature) in a glass house. At three leaf stage, plants were subjected to heat stress (HS) by increasing temperature (40°C/35°C day and night), while one treatment was kept at control condition. After 7 days of HS, data were collected for seedling morphology. Heat stress reduced these traits by 25% (root weight) to 40% (shoot weight), and shoot biomass was largely affected by heat stress. A GWAS model, fixed and random model circulating probability unification (FarmCPU), identified 43 quantitative trait nucleotides (QTNs) on all chromosomes, except chr7B, were associated under both HS and control conditions. Thirteen QTNs were identified in control, while 30 QTNs were identified in HS condition. In total, 24 haplotypes were identified at TaHST1 locus, and most of the heat tolerant genotypes were assigned to Hap-20 and Hap-21. Eleven QTNs were identified within 0.3–3.1 Mb proximity of heat shock protein (HSP). Conclusively, this study provided a detailed genetic framework of heat tolerance in wheat at the seedling stage and identify potential genetic regions associated with heat tolerance which can be used for marker assisted selection (MAS) in breeding for heat stress tolerance.