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Abstract Recently, there has been a substantial increase in high‐throughput technologies that generate highly complex large datasets for use in the sciences. Plant breeding and genetics have benefited from this data explosion where many public and private institutions now implement genomic and phenomic data to predict performance thus informing germplasm selection. However, the multitude of methodologies and data generates a situation of strategic uncertainty. We set out to compare different methods of genomic and phenomic selection in the Capsicum core collection, developed through the G2P‐SOL project, producing a combination of unique and similar selected genotypes for heat tolerance. Combined, the methods tested identified a total of 33 genotypes that show tremendous promise for use as parents in heat tolerance breeding: with 13 of these being present in more than 1 selection method. Combining classical and multispectral phenotyping methods produced better selection results than either method alone. When each method was conducted without being informed by the other, similar results were obtained. Our weighted rank‐sum selection index identified 10 entries across environments that show heat tolerance, 8 of which are also selected within heat environments. This suggests that different breeding programs can reach similar results despite having different logistical constraints. Our case study within pepper germplasm using phenomic and genomic data exhibits the potential to compensate for the dearth of germplasm knowledge with high‐throughput data as well as the converse, to compensate for logistical or financial constraint to new technologies with breeder knowledge.

Phenolic acids and flavonoids are large groups of secondary metabolites ubiquitous in the plant kingdom. They are currently in the spotlight due to the numerous health benefits associated with their consumption, as well as for their vital roles in plant biological processes and in plant-environment interaction. Tomato, eggplant and pepper are in the top ten most consumed vegetables in the world, and their fruit accumulation profiles have been extensively characterized, showing substantial differences. A broad array of genetic and genomic tools has helped to identify QTLs and candidate genes associated with the fruit biosynthesis of phenolic acids and flavonoids. The aim of this review was to synthesize the available information making it easily available for researchers and breeders. The phenylpropanoid pathway is tightly regulated by structural genes, which are conserved across species, along with a complex network of regulatory elements like transcription factors, especially of MYB family, and cellular transporters. Moreover, phenolic compounds accumulate in tissue-specific and developmental-dependent ways, as different paths of the metabolic pathway are activated/deactivated along with fruit development. We retrieved 104 annotated putative orthologues encoding for key enzymes of the phenylpropanoid pathway in tomato (37), eggplant (29) and pepper (38) and compiled 267 QTLs (217 for tomato, 16 for eggplant and 34 for pepper) linked to fruit phenolic acids, flavonoids and total phenolics content. Combining molecular tools and genetic variability, through both conventional and genetic engineering strategies, is a feasible approach to improve phenolics content in tomato, eggplant and pepper. Finally, although the phenylpropanoid biosynthetic pathway has been well-studied in the Solanaceae, more research is needed on the identification of the candidate genes behind many QTLs, as well as their interactions with other QTLs and genes.