Justyna Milc

Durum wheat productivity in Mediterranean regions faces growing challenges from drought and heat stress. Understanding the genetic architecture of diverse germplasm is therefore essential to support pre-breeding efforts and enhance stress adaptation. In this context, 125 durum wheat genotypes were evaluated for agro-morphological traits across two contrasting Algerian locations over two growing seasons. A subset of 94 genotypes, selected on the basis of phenotypic characterization, was genotyped using the Illumina 7K SNP array. Population structure analysis revealed two to four subgroups, with linkage disequilibrium decaying at 4.09 Mb. Genome-wide association analysis identified 27 distinct significant SNPs associated with eight traits, with most associations detected for spike length, thousand-kernel weight, and plant height. The marker TGWA25K-TG0010 on chromosome 4A showed pleiotropic effects on plant height and peduncle length and co-localized with the Dwarf8 and gibberellic-acid-insensitive genes. Additionally, wsnp_Ex_c2033_3814035 on chromosome 2A was associated with heading earliness and the number of fertile spikelets per spike, and wsnp_Ku_c51039_56457361 on chromosome 5A with plant height and peduncle length in a single site and season. Several other environment-specific associations were also identified. These results support future studies in which the identified markers may be deployed in breeding strategies aimed at improving yield stability and stress adaptability in durum wheat under Algerian conditions.

In marginal mountain areas, farm management presents challenges, particularly the sustainable improvement of yield and quality. To ensure this agronomic result, it is crucial to select appropriate varieties and apply sustainable agricultural practices, such as the use of plant biostimulants. To address these challenges a two-year field study was conducted using three potato varieties (Désirée, Kennebec and Spunta) in the Tuscan-Emilian Apennines. These varieties were treated with two plant biostimulants: one based on hydrolyzed proteins from animal epithelial tissue (Fitostim^®) and another based on seaweed extracts (FitostimAlga^®). Agronomic and biochemical traits were used to evaluate the development of plants, yield and tubers quality. Significant interactions among factors were found, resulting in higher or lower efficiency of the plant biostimulant treatment depending on weather conditions and potato genotype. Furthermore, results demonstrated that plant biostimulant treatments increased the leaf chlorophyll content (+ 11.5%), the number of leaves per plant (+ 13.3%) and the height of potato plants (+ 6.5%), while no effects were observed on yield. The Désirée variety achieved the highest yield (0.54 kg plant^-1), whereas Kennebec was shown as the best variety to use for production of French fries due to a lower tuber quantity of reducing sugars, which were reduced also by plant biostimulants treatment (-18%). Moreover, Spunta tubers had the highest content of polyphenols, and the best value was achieved by Spunta variety treated with Fitostim^® alga in the second year. Our finding have proven that plant biostimulant treatments can increase the quality of potato tuber without compromising yield.

The pivotal role of CBF/DREB1 transcriptional factors in Triticeae crops involved in the abiotic stress response has been highlighted. The CBFs represent an important hub in the ICE-CBF-COR pathway, which is one of the most relevant mechanisms capable of activating the adaptive response to cold and drought in wheat, barley, and rye. Understanding the intricate mechanisms and regulation of the cluster of CBF genes harbored by the homoeologous chromosome group 5 entails significant potential for the genetic improvement of small grain cereals. Triticeae crops seem to share common mechanisms characterized, however, by some peculiar aspects of the response to stress, highlighting a combined landscape of single-nucleotide variants and copy number variation involving CBF members of subgroup IV. Moreover, while chromosome 5 ploidy appears to confer species-specific levels of resistance, an important involvement of the ICE factor might explain the greater tolerance of rye. By unraveling the genetic basis of abiotic stress tolerance, researchers can develop resilient varieties better equipped to withstand extreme environmental conditions. Hence, advancing our knowledge of CBFs and their interactions represents a promising avenue for improving crop resilience and food security.

Inoculation with plant growth promoting rhizobacteria (PGPR) might be a sustainable practice to increase nutrients use efficiency of crops. In order to elucidate the mechanisms underlying the beneficial interaction, an RNA-Seq transcriptional profiling of tomato leaves was performed after roots’ inoculation with Azospirillum baldaniorum (AB) or Paraburkholderia graminis (PG). Overall, 427 and 512 differentially expressed tomato genes were retrieved for AB and PB inoculation, respectively, and in both cases, the number of up-regulated genes exceeded the number of those down-regulated. Expression profiles suggest that the interactions between tomato seedlings and microorganisms are species-specific. The common activated pathways involved genes coding for proteins related to water and nutrients uptake, defense responses to biotic and abiotic stresses and hormonal regulation of fruit-set and ripening. While AB induced genes coding for MYB transcription factors known to be involved in response to biotic and abiotic stresses, PG upregulated 5 genes coding for putative late blight resistance protein homolog. Auxin responsive molecules and gibberellins involved in the fruit-set and early fruit growth in tomato were mainly induced by AB correlating to higher fruit number obtained in a previous field study. On the other hand, ERF transcription factors involved in ripening were induced mainly by PG treatment.

Key message: Exome sequencing-based allele mining for frost tolerance suggests HvCBF14 rather than CNV at Fr-H2 locus is the main responsible of frost tolerance in barley. Wild relatives, landraces and old cultivars of barley represent a reservoir of untapped and potentially important genes for crop improvement, and the recent sequencing technologies provide the opportunity to mine the existing genetic diversity and to identify new genes/alleles for the traits of interest. In the present study, we use frost tolerance and vernalization requirement as case studies to demonstrate the power of allele mining carried out on exome sequencing data generated from > 400 barley accessions. New deletions in the first intron of VRN-H1 were identified and linked to a reduced vernalization requirement, while the allelic diversity of HvCBF2a, HvCBF4b and HvCBF14 was investigated by combining the analysis of SNPs and read counts. This approach has proven very effective to identify gene paralogs and copy number variants of HvCBF2 and the HvCBF4b-HvCBF2a segment. A multiple linear regression model which considers allelic variation at these genes suggests a major involvement of HvCBF14, rather than copy number variation of HvCBF4b-HvCBF2a, in controlling frost tolerance in barley. Overall, the present study provides powerful resource and tools to discover novel alleles at relevant genes in barley.

Plant secondary metabolic pathways are finely regulated by the activity of transcription factors, among which members of the bHLH and MYB subfamilies play a main role. Cannabis sativa L. is a unique officinal plant species with over 600 synthesized phytochemicals having diverse scale-up industrial and pharmaceutical usage. Despite comprehensive knowledge of cannabinoids’ metabolic pathways, very little is known about their regulation, while the literature on flavonoids’ metabolic pathways is still scarce. In this study, we provide the first genome-wide analysis of bHLH and MYB families in C. sativa reference cultivar CBDRx and identification of candidate coding sequences for these transcription factors. Cannabis sativa bHLHs and MYBs were then classified into functional subfamilies through comparative phylogenetic analysis with A. thaliana transcription factors. Analyses of gene structure and motif distribution confirmed that CsbHLHs and CsMYBs belonging to the same evolutionary clade share common features at both gene and amino acidic level. Candidate regulatory genes for key metabolic pathways leading to flavonoid and cannabinoid synthesis in Cannabis were also retrieved. Furthermore, a candidate gene approach was used to identify structural enzyme-coding genes for flavonoid and cannabinoid synthesis. Taken as a whole, this work represents a valuable resource of candidate genes for further investigation of the C. sativa cannabinoid and flavonoid metabolic pathways for genomic studies and breeding programs.

While durum wheat is a major food source in Mediterranean countries, storage (i.e., gluten) proteins are however responsible for celiac disease (CD), a serious autoimmune disease that occurs in genetically predisposed subjects. Different gluten epitopes—defined as “immunogenic” (IP) and “toxic” (TP) peptides—are involved in the pathology and their content in wheat grain depends on environmental and genetic factors. Detection of IP and TP is not trivial, and no work has been conducted so far to identify the genomic regions associated with their accumulation in wheat. In the present study, a genome-wide association study was performed on a durum wheat collection to identify marker–trait associations (MTAs) between 5730 high quality SNPs and the accumulation of CD-related peptides and gluten protein composition measured in two consecutive cropping seasons (2015/2016 and 2016/2017). High-molecular-weight glutenin subunits (HMW-GS) were more stable between the two years, and differences in total gluten proteins were mainly due to low-molecular-weight glutenin subunits (LMW-GS) and accumulation of gliadins. In the first instance, association tests were conducted on yellow pigment content (YP), a highly inheritable trait with a well-known genetic basis, and several significant MTAs were found corresponding to loci already known for being related to YP. These findings showed that MTAs found for the rest of the measured traits were reliable. In total, 28 significant MTAs were found for gluten composition, while 14 were found to be associated with IP and TP. Noteworthy, neither significant (−log10p > 4.7) nor suggestive (−log10p > 3.3) MTAs for the accumulation of CD-triggering epitopes were found on Gli-A1/Glu-A3 and Gli-B1/Glu-B3 loci, thus suggesting regulatory rather than structural gene effect. A PBF transcription factor on chromosome 5B, known to be involved in the regulation of the expression of CD-related peptides, was identified among the positional candidate genes in the LD-decay range around significant SNPs. Results obtained in the present study provide useful insights and resources for the long-term objective of selecting low-toxic durum wheat varieties while maintaining satisfactory gluten quality.

Cadmium (Cd) and lead (Pb) are two toxic heavy metals (HMs) whose presence in soil is generally low. However, industrial and agricultural activities in recent years have significantly raised their levels, causing progressive accumulations in plant edible tissues, and stimulating research in this field. Studies on toxic metals are commonly focused on a single metal, but toxic metals occur simultaneously. The understanding of the mechanisms of interaction between HMs during uptake is important to design agronomic or genetic strategies to limit contamination of crops. To study the single and combined effect of Cd and Pb on durum wheat, a hydroponic experiment was established to examine the accumulation of the two HMs. Moreover, the molecular mechanisms activated in the roots were investigated paying attention to transcription factors (bHLH family), heavy metal transporters and genes involved in the biosynthesis of metal chelators (nicotianamine and mugineic acid). Cd and Pb are accumulated following different molecular strategies by durum wheat plants, even if the two metals interact with each other influencing their respective uptake and translocation. Finally, we demonstrated that some genes (bHLH 29, YSL2, ZIF1, ZIFL1, ZIFL2, NAS2 and NAAT) were induced in the durum wheat roots only in response to Cd.

Several environmental factors, such as drought, salinity, and extreme temperatures, negatively affect plant growth and development, which leads to yield losses. The tolerance or sensitivity to abiotic stressors are the expression of a complex machinery involving molecular, biochemical, and physiological mechanisms. Here, a meta-analysis on previously published RNA-Seq data was performed to identify the genes conferring tolerance to chilling, osmotic, and salt stresses, by comparing the transcriptomic changes between tolerant and susceptible rice genotypes. Several genes encoding transcription factors (TFs) were identified, suggesting that abiotic stress tolerance involves upstream regulatory pathways. A gene co-expression network defined the metabolic and signalling pathways with a prominent role in the differentiation between tolerance and susceptibility: (i) the regulation of endogenous abscisic acid (ABA) levels, through the modulation of genes that are related to its biosynthesis/catabolism, (ii) the signalling pathways mediated by ABA and jasmonic acid, (iii) the activity of the “Drought and Salt Tolerance” TF, involved in the negative regulation of stomatal closure, and (iv) the regulation of flavonoid biosynthesis by specific MYB TFs. The identified genes represent putative key players for conferring tolerance to a broad range of abiotic stresses in rice; a fine-tuning of their expression seems to be crucial for rice plants to cope with environmental cues.