Construction and genetic characterization of an interspecific raspberry hybrids panel aiming resistance to late leaf rust and adaptation to tropical regions

Raspberries (Rubus spp) are temperate climate fruits with profitable high returns and have the potential for diversification of fruit growing in mid to low-latitude regions. However, there are still no cultivars adapted to climatic conditions and high pressure of diseases that occurs in tropical areas. In this context, our objective was to evaluate the genetic diversity from a 116 raspberry genotypes panel obtained from interspecific crosses in a testcross scheme with four cultivars already introduced in Brazil. The panel was genotyped via genotyping-by-sequencing. 28,373 and 27,281 SNPs were obtained, using the species R. occidentalis and R. idaeus genomes as references, respectively. A third marker dataset was constructed consisting of 41,292 non-coincident markers. Overall, there were no differences in the results when using the different marker sets for the subsequent analyses. The mean heterozygosity was 0.54. The average effective population size was 174, indicating great genetic variability. The other analyses revealed that the half-sibling families were structured in three groups. It is concluded that the studied panel has great potential for breeding and further genetic studies. Moreover, only one of the three marker matrices is sufficient for diversity studies.

Optimizing Genomic-Enabled Prediction in Small-Scale Maize Hybrid Breeding Programs: A Roadmap Review

The usefulness of genomic prediction (GP) for many animal and plant breeding programs has been highlighted for many studies in the last 20 years. In maize breeding programs, mostly dedicated to delivering more highly adapted and productive hybrids, this approach has been proved successful for both large- and small-scale breeding programs worldwide. Here, we present some of the strategies developed to improve the accuracy of GP in tropical maize, focusing on its use under low budget and small-scale conditions achieved for most of the hybrid breeding programs in developing countries. We highlight the most important outcomes obtained by the University of São Paulo (USP, Brazil) and how they can improve the accuracy of prediction in tropical maize hybrids. Our roadmap starts with the efforts for germplasm characterization, moving on to the practices for mating design, and the selection of the genotypes that are used to compose the training population in field phenotyping trials. Factors including population structure and the importance of non-additive effects (dominance and epistasis) controlling the desired trait are also outlined. Finally, we explain how the source of the molecular markers, environmental, and the modeling of genotype-environment interaction can affect the accuracy of GP. Results of 7 years of research in a public maize hybrid breeding program under tropical conditions are discussed, and with the great advances that have been made, we find that what is yet to come is exciting. The use of open-source software for the quality control of molecular markers, implementing GP, and envirotyping pipelines may reduce costs in an efficient computational manner. We conclude that exploring new models/tools using high-throughput phenotyping data along with large-scale envirotyping may bring more resolution and realism when predicting genotype performances. Despite the initial costs, mostly for genotyping, the GP platforms in combination with these other data sources can be a cost-effective approach for predicting the performance of maize hybrids for a large set of growing conditions.

Tolerance of tomato to cadmium-induced stress: analyzing cultivars with different fruit colors

The objective of the present study was to assess the response of tomato cultivars with different fruit colors to exposure to increasing Cd levels in the substrate by measuring the impacts of Cd on the oxidative stress indicators and physicochemical features of fruits, as well as plant development and yield components. A completely randomized experiment in a 3 × 3 factorial design [tomato cultivar (which produces purple, red, or white fruits) vs Cd level in the substrate (0, 3.6, or 12 mg kg^-1)] was performed. The cultivation of plants in substrate containing 3.6 mg kg^-1 Cd did not affect yield, but fruits exhibited nonpermissive Cd concentrations in both peel and mesocarp across all cultivars. By contrast, yield was decreased in plants with red and white fruits after their cultivation in substrate containing 12 mg kg^-1 Cd, while the productivity of plants with purple fruits was maintained under such conditions. The hydrogen peroxide content in the fruit mesocarp depended only on cultivar. However, an increased lipid peroxidation level was detected in the mesocarp of purple fruits at the highest Cd concentration. No parameters of fruit quality [i.e., diameter, length, °Brix, pH, titratable acidity, color (L*, a*, and b*), and concentrations of lycopene and β-carotene in mesocarp] were affected by long-term exposure to Cd at 12 mg kg^-1. In conclusion, the results of this study suggested that the potential Cd side effects on diverse tomato quality features can be buffered at the fruit level because these features were maintained at the usual values despite high Cd concentrations in tomato peel and pulp. Moreover, these buffering mechanisms are independent of lycopene and β-carotene concentrations in fruit peel, since the three tomato cultivars that were evaluated in the present study (white fruits, possessing no or negligible concentrations of these carotenoids, and red and purple tomato, possessing high lycopene and β-carotene concentrations) were able to sustain several fruit quality parameters after long-term exposure to high Cd concentrations in the substrate.

Quantitative proteomic analysis of tomato genotypes with differential cadmium tolerance

This is a report on comprehensive characterization of cadmium (Cd)-exposed root proteomes in tomato using label-free quantitative proteomic approach. Two genotypes differing in Cd tolerance, Pusa Ruby (Cd-tolerant) and Calabash Rouge (Cd-sensitive), were exposed during 4 days to assess the Cd-induced effects on root proteome. The overall changes in both genotypes in terms of differentially accumulated proteins (DAPs) were mainly associated to cell wall, redox, and stress responses. The proteome of the sensitive genotype was more responsive to Cd excess, once it presented higher number of DAPs. Contrasting protein accumulation in cellular component was observed: Cd-sensitive enhanced intracellular components, while the Cd-tolerant increased proteins of extracellular and envelope regions. Protective and regulatory mechanisms were different between genotypes, once the tolerant showed alterations of various protein groups that lead to a more efficient system to cope with Cd challenge. These findings could shed some light on the molecular basis underlying the Cd stress response in tomato, providing fundamental insights for the development of Cd-safe cultivars. Graphical abstract.

Cadmium toxicity degree on tomato development is associated with disbalances in B and Mn status at early stages of plant exposure

Cadmium (Cd) toxicity is frequently coupled to its accumulation in plants, but not always the highest Cd concentration triggers the worst damages, indicating that additional events influence the magnitude of Cd side-effects. We investigated the early mechanisms behind the differential Cd-induced impacts on plant development of four tomato accessions with contrasting tolerance to Cd toxicity. At organ level, the highest Cd concentration was not associated with the largest biomass losses. In leaves, changes in superoxide dismutase and catalase activities were not related to differences in Cd concentration, which was unable to provoke H₂O₂ overproduction on the sixth day of plant exposure to this metal. Further investigation in the mineral profile revealed that magnitude of Cd toxicity depends probably on synergic effects from increased B status, in addition to the own Cd accumulation. Furthermore, disbalances in Mn status (i.e., excess in leaves and deficiency in roots) may enhance Cd toxicity degree. According to data, however, the low magnesium (Mg) status can be linked to tomato tolerance against Cd toxicity. In conclusion, the tomato tolerance degree under short-Cd exposure depends on actively, finely regulation of mineral homeostasis that results in different development of plant organs. The better understanding on the mode of action of Cd toxicity in plants can help in the establishment of strategies to mitigate its impacts on crop yield.

Temporal dynamic responses of roots in contrasting tomato genotypes to cadmium tolerance

Despite numerous studies on cadmium (Cd) uptake and accumulation in crops, relatively little is available considering the temporal dynamic of Cd uptake and responses to stress focused on the root system. Here we highlighted the responses to Cd-induced stress in roots of two tomato genotypes contrasting in Cd-tolerance: the tolerant Pusa Ruby and the sensitive Calabash Rouge. Tomato genotypes growing in the presence of 35 μM CdCl₂ exhibited a similar trend of Cd accumulation in tissues, mainly in the root system and overall plants exhibited reduction in the dry matter weight. Both genotypes showed similar trends for malondialdehyde and hydrogen peroxide accumulation with increases when exposed to Cd, being this response more pronounced in the sensitive genotype. When the antioxidant machinery is concerned, in the presence of Cd the reduced glutathione content was decreased in roots while ascorbate peroxidase (APX), glutathione reductase (GR) and glutathione S-transferase (GST) activities were increased in the presence of Cd in the tolerant genotype. Altogether these results suggest APX, GR and GST as the main players of the antioxidant machinery against Cd-induced oxidative stress.