BACKGROUND The consumers' perception of the importance of healthy food has promoted the interest towards fruit, vegetables and spices rich in antioxidants. Moreover, changing in eating habits has encouraged the diffusion of ready‐to‐eat commodities with specific merceological standards. In the present study, 12 hot pepper varieties devoted to powder production, canned processing, blister packaging have been evaluated for morpho‐agronomic traits and bioactive compounds in replicated trials in three locations and two growing seasons. RESULTS For all traits, the genotypic component (G) and the genotype × location interaction (G×L) were significant (P < 0.05). Morphological fruit traits evidenced a strong effect of the genotype (> 95%) while yield and biochemical traits showed a variable response to environmental effects. Capsaicin and the yellow fraction of carotenoids were the only nutraceutical compounds showing a relatively high G effect, contrariwise, ascorbic acid, carotenoids and tocopherols were more influenced by location (L) and year of cultivation (Y). Results showed how breeding for quality traits in chilli is still challenging. Multivariate analysis allowed to identify pairs of traits distinguishing the different market typologies: powder types exhibited a lower productivity and higher pungency while those for blister packaging had a remarkable antioxidant capacity. CONCLUSIONS A comprehensive approach was used to study the plasticity of agronomic and nutritional traits in chilli pepper. The set of cultivars analysed produced fruits with considerable levels of several health‐related metabolites, including capsaicin, carotenoids and antioxidant phytochemicals. This information is useful for precision breeding of novel varieties. © 2019 Society of Chemical Industry

Background Opportunity and challenges of the agriculture scenario of the next decades will face increasing demand for secure food through approaches able to minimize the input to cultivations. Large panels of tomato varieties represent a valuable resource of traits of interest under sustainable cultivation systems and for genome-wide association studies (GWAS). For mapping loci controlling the variation of agronomic, fruit quality, and root architecture traits, we used a heterogeneous set of 244 traditional and improved tomato accessions grown under organic field trials. Here we report comprehensive phenotyping and GWAS using over 37,300 SNPs obtained through double digest restriction-site associated DNA (dd-RADseq). Results A wide range of phenotypic diversity was observed in the studied collection, with highly significant differences encountered for most traits. A variable level of heritability was observed with values up to 69% for morphological traits while, among agronomic ones, fruit weight showed values above 80%. Genotype by environment analysis highlighted the strongest genotypic effect for aboveground traits compared to root architecture, suggesting that the hypogeal part of tomato plants has been a minor objective for breeding activities. GWAS was performed by a compressed mixed linear model leading to 59 significantly associated loci, allowing the identification of novel genes related to flower and fruit characteristics. Most genomic associations fell into the region surrounding SUN, OVATE, and MYB gene families. Six flower and fruit traits were associated with a single member of the SUN family (SLSUN31) on chromosome 11, in a region involved in the increase of fruit weight, locules number, and fruit fasciation. Furthermore, additional candidate genes for soluble solids content, fruit colour and shape were found near previously reported chromosomal regions, indicating the presence of synergic and multiple linked genes underlying the variation of these traits. Conclusions Results of this study give new hints on the genetic basis of traits in underexplored germplasm grown under organic conditions, providing a framework for the development of markers linked to candidate genes of interest to be used in genomics-assisted breeding in tomato, in particular under low-input and organic cultivation conditions.

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