Transcriptomic response to nitrogen availability reveals signatures of adaptive plasticity during tetraploid wheat domestication

: The domestication of crops, coupled with agroecosystem development, is associated with major environmental changes and provides an ideal model of phenotypic plasticity. Here, we examined 32 genotypes of three tetraploid wheat (Triticum turgidum L.) subspecies, wild emmer, emmer and durum wheat, which are representative of the key stages in the domestication of tetraploid wheat. We developed a pipeline that integrates RNA-Seq data and population genomics to assess gene expression plasticity and identify selection signatures under diverse nitrogen availability conditions. Our analysis revealed differing gene expression responses to nitrogen availability across primary (wild emmer to emmer) and secondary (emmer to durum wheat) domestication. Notably, nitrogen triggered the expression of twice as many genes in durum wheat compared to that in emmer and wild emmer. Unique selection signatures were identified at each stage: primary domestication mainly influenced genes related to biotic interactions, whereas secondary domestication affected genes related to amino acid metabolism, in particular lysine. Selection signatures were found in differentially expressed genes, notably those associated with nitrogen metabolism, such as the gene encoding glutamate dehydrogenase. Overall, our study highlights the pivotal role of nitrogen availability in the domestication and adaptive responses of a major food crop, with varying effects across different traits and growth conditions

Metabolic Profiling of a Mapping Population Exposes New Insights in the Regulation of Seed Metabolism and Seed, Fruit, and Plant Relations

To investigate the regulation of seed metabolism and to estimate the degree of metabolic natural variability, metabolite profiling and network analysis were applied to a collection of 76 different homozygous tomato introgression lines (ILs) grown in the field in two consecutive harvest seasons. Factorial ANOVA confirmed the presence of 30 metabolite quantitative trait loci (mQTL). Amino acid contents displayed a high degree of variability across the population, with similar patterns across the two seasons, while sugars exhibited significant seasonal fluctuations. Upon integration of data for tomato pericarp metabolite profiling, factorial ANOVA identified the main factor for metabolic polymorphism to be the genotypic background rather than the environment or the tissue. Analysis of the coefficient of variance indicated greater phenotypic plasticity in the ILs than in the M82 tomato cultivar. Broad-sense estimate of heritability suggested that the mode of inheritance of metabolite traits in the seed differed from that in the fruit. Correlation-based metabolic network analysis comparing metabolite data for the seed with that for the pericarp showed that the seed network displayed tighter interdependence of metabolic processes than the fruit. Amino acids in the seed metabolic network were shown to play a central hub-like role in the topology of the network, maintaining high interactions with other metabolite categories, i.e., sugars and organic acids. Network analysis identified six exceptionally highly co-regulated amino acids, Gly, Ser, Thr, Ile, Val, and Pro. The strong interdependence of this group was confirmed by the mQTL mapping. Taken together these results (i) reflect the extensive redundancy of the regulation underlying seed metabolism, (ii) demonstrate the tight co-ordination of seed metabolism with respect to fruit metabolism, and (iii) emphasize the centrality of the amino acid module in the seed metabolic network. Finally, the study highlights the added value of integrating metabolic network analysis with mQTL mapping

Metabolomics Provides Valuable Insight for the Study of Durum Wheat: A Review

Metabolomics is increasingly being applied in various fields offering a highly informative tool for high-throughput diagnostics. However, in plant sciences, metabolomics is underused, even though plant studies are relatively easy and cheap when compared to those on humans and animals. Despite their importance for human nutrition, cereals, and especially wheat, remain understudied from a metabolomics point of view. The metabolomics of durum wheat has been essentially neglected, although its genetic structure allows the inference of common mechanisms that can be extended to other wheat and cereal species. This review covers the present achievements in durum wheat metabolomics highlighting the connections with the metabolomics of other cereal species (especially bread wheat). We discuss the metabolomics data from various studies and their relationships to other "-omics" sciences, in terms of wheat genetics, abiotic and biotic stresses, beneficial microbes, and the characterization and use of durum wheat as feed, food, and food ingredient

Protein Hydrolysates from <i>Crambe abyssinica</i> Seed Cake as Potential Biostimulants for Root Development

Crambe abyssinica Hochst defatted seed meals were used to produce protein hydrolysates through a mild enzymatic two-step hydrolysis process. The resulting hydrolysates were rich in free amino acids, low-molecular-weight peptides, and potential bioactive compounds such as phenols, glucosinolates, or their derivatives. These hydrolysates were tested in bioassays, performed under controlled conditions, on mung bean (Vigna radiata) cuttings, to investigate a possible auxin effect, and on maize (Zea mays L.) in an aeroponic/hydroponic system during the first two weeks of growth. In both assays, crambe hydrolysates revealed a stimulating effect on root development at a dose corresponding to nitrogen concentration of 4.8 mM, promoting lateral root formation and altering root architecture. Furthermore, they exhibited a positive impact on nitrogen content in both maize roots and shoots, along with an increase in the chlorophyll SPAD index. Notably, the observed effects were similar to those induced by a commercial biostimulant based on an animal-derived hydrolysate, tested under the same conditions on maize. The present work underscores the potential of crambe seed by-products for new sustainable and environmentally safe agro-inputs aimed at enhancing crop performance within the framework of a circular economy

Evolution of the Crop Rhizosphere: Impact of Domestication on Root Exudates in Tetraploid Wheat (Triticum turgidum L.)

Domestication has induced major genetic changes in crop plants to satisfy human needs and as a consequence of adaptation to agroecosystems. This adaptation might have affected root exudate composition, which can influence the interactions in the rhizosphere. Here, using two different soil types (sand, soil), we provide an original example of the impact of domestication and crop evolution on root exudate composition through metabolite profiling of root exudates for a panel of 10 wheat genotypes that correspond to the key steps in domestication of tetraploid wheat (wild emmer, emmer, durum wheat). Our data show that soil type can dramatically affect the composition of root exudates in the rhizosphere. Moreover, the composition of the rhizosphere metabolites is associated with differences among the genotypes of the wheat domestication groups, as seen by the high heritability of some of the metabolites. Overall, we show that domestication and breeding have had major effects on root exudates in the rhizosphere, which suggests the adaptive nature of these changes

Variability of Nutritional, Antioxidant, and Textural Traits of a Collection of Snap Beans of Different Colors

A set of 54 snap bean lines grown under organic farming was characterized for different traits: pod color, pod cross-section shape, pod section width (PSW), protein content (PC), and sugar content (S). After cooking, the lines were analyzed for firmness and color parameters (CIE-L*, a*, b*). The snap bean lines were grouped based on pod cross-section shape and pod color into eight groups, and significant differences were observed among lines and groups for all the traits investigated. In particular, the yellow pods were harder than the other snap beans and less sweet due to the negative correlation between firmness and sugar content. Fourteen selected lines with contrasting firmness and belonging to different color groups were investigated for their phenolic composition and antioxidant activity (TEAC) before and after domestic cooking. A general decrease was observed only for vanillic acid, quercetin, and apigenin-8-C-glucoside. Quercetin-3-O-rutinoside and kaempferol-3-O-rutinoside were detected in all samples with the highest values in the SBP042 line in both raw and cooked samples. Antioxidant activity decreased with cooking (average of 39%), but purple line SBP053 showed the lowest and no significant loss (3.1%). The results reported in this study could be useful to design specific varieties for different markets and purposes

Relationship between Seed Morphological Traits and Ash and Mineral Distribution along the Kernel Using Debranning in Durum Wheats from Different Geographic Sites

Debranning was applied to durum wheat to the study the relationship between kernel shape and size, and ash and mineral distribution having implications for semolina yield. To this aim four durum wheat genotypes carried out over three environments were selected to determine the morphological and yield traits as well as the distribution along the kernel of the ash, macro- (Na, K, P, Ca, and Mg), and micro-elements (Mn, Fe, Cu, Zn, and Mo). A descendent ash gradient within the kernel reflects the decreases in the minerals that occurred during debranning. Perciasacchi with high seed weight (TKW) and greater thickness followed by Cappelli showed a more uniform distribution of ash content along the kernels. High r Pearson coefficient (p &lt; 0.01) showed an inverse relationship between thickness and ash decay. Since thickness was strongly affected by the genotype, it could represent a useful trait for breeding programs to predict the milling quality