Meta-QTL analysis and candidate genes for quality traits, mineral content, and abiotic-related traits in wild emmer.

Wild emmer (Triticum turgidum ssp. dicoccoides) genotypes were studied for their high-nutritional value and good tolerance to various types of stress; for this reason, several QTL (quantitative trait loci) studies have been conducted to find favorable alleles to be introgressed into modern wheat cultivars. Given the complexity of the QTL nature, their interaction with the environment, and other QTLs, a small number of genotypes have been used in wheat breeding programs. Meta-QTL (MQTL) analysis helps to simplify the existing QTL information, identifying stable genomic regions and possible candidate genes for further allele introgression. The study aimed to identify stable QTL regions across different environmental conditions and genetic backgrounds using the QTL information of the past 14 years for different traits in wild emmer based upon 17 independent studies. A total of 41 traits were classified as quality traits (16), mineral composition traits (11), abiotic-related traits (13), and disease-related traits (1). The analysis revealed 852 QTLs distributed across all 14 chromosomes of wild emmer, with an average of 61 QTLs per chromosome. Quality traits had the highest number of QTLs (35%), followed by mineral content (33%), abiotic-related traits (28%), and disease-related traits (4%). Grain protein content (GPC) and thousand kernel weight (TKW) were associated with most of the QTLs detected. A total of 43 MQTLs were identified, simplifying the information, and reducing the average confidence interval (CI) from 22.6 to 4.78 cM. These MQTLs were associated with multiple traits across different categories. Nine candidate genes were identified for several stable MQTLs, potentially contributing to traits such as quality, mineral content, and abiotic stress resistance. These genes play essential roles in various plant processes, such as carbohydrate metabolism, nitrogen assimilation, cell wall biogenesis, and cell wall extensibility. Overall, this study underscores the importance of considering MQTL analysis in wheat breeding programs, as it identifies stable genomic regions associated with multiple traits, offering potential solutions for improving wheat varieties under diverse environmental conditions.

Exploring Aegilops caudata: A Comprehensive Study of the CslF6 Gene and ß-Glucan.

In the quest for sustainable and nutritious food sources, exploration of ancient grains and wild relatives of cultivated cereals has gained attention. Aegilops caudata, a wild wheatgrass species, stands out as a promising genetic resource due to its potential for crop enhancement and intriguing nutritional properties. This manuscript investigates the CslF6 gene sequence and protein structure of Aegilops caudata, employing comparative analysis with other grass species to identify potential differences impacting ß-glucan content. The study involves comprehensive isolation and characterization of the CslF6 gene in Ae. caudata, utilizing genomic sequence analysis, protein structure prediction, and comparative genomics. Comparisons with sequences from diverse monocots reveal evolutionary relationships, highlighting high identities with wheat genomes. Specific amino acid motifs in the CslF6 enzyme sequence, particularly those proximal to key catalytic motifs, exhibit variations among monocot species. These differences likely contribute to alterations in ß-glucan composition, notably impacting the DP3:DP4 ratio, which is crucial for understanding and modulating the final ß-glucan content. The study positions Ae. caudata uniquely within the evolutionary landscape of CslF6 among monocots, suggesting potential genetic divergence or unique functional adaptations within this species. Overall, this investigation enriches our understanding of ß-glucan biosynthesis, shedding light on the role of specific amino acid residues in modulating enzymatic activity and polysaccharide composition.

The Role of Glutamine Synthetase (GS) and Glutamate Synthase (GOGAT) in the Improvement of Nitrogen Use Efficiency in Cereals.

Cereals are the most broadly produced crops and represent the primary source of food worldwide. Nitrogen (N) is a critical mineral nutrient for plant growth and high yield, and the quality of cereal crops greatly depends on a suitable N supply. In the last decades, a massive use of N fertilizers has been achieved in the desire to have high yields of cereal crops, leading to damaging effects for the environment, ecosystems, and human health. To ensure agricultural sustainability and the required food source, many attempts have been made towards developing cereal crops with a more effective nitrogen use efficiency (NUE). NUE depends on N uptake, utilization, and lastly, combining the capability to assimilate N into carbon skeletons and remobilize the N assimilated. The glutamine synthetase (GS)/glutamate synthase (GOGAT) cycle represents a crucial metabolic step of N assimilation, regulating crop yield. In this review, the physiological and genetic studies on GS and GOGAT of the main cereal crops will be examined, giving emphasis on their implications in NUE.

Dataset from RNAseq analysis of bud differentiation in Ficus carica.

The presented data regards the transcriptome profiling and differential analysis with RNA-Seq approach with the following goals: de novo transcriptome assembly and genome annotation of Ficus carica and the differential expression analysis of parthenocarpic and non-partenocarpic varieties in order to identify candidate genes for the production of seedless fig. Two fig varieties Dottato and Petrelli and the caprifig were grown at the fig repository at the 'P. Martucci' experimental station in Valenzano (Bari) of University of Bari 'Aldo Moro'. The data included: RNA-seq data obtained from fruits of parthenocarpic and non-parthenocarpic varieties, gene expression in the different genetic materials; genes up and down regulated. The data in this article support information presented in the research article "I. Marcotuli, A. Mazzeo, P. Colasuonno, R. Terzano, D. Nigro, C. Porfido, A. Tarantino, R. Aiese Cigliano, W. Sanseverino, A. Gadaleta, G. Ferrara, Fruit Development in Ficus carica L.: Morphological and Genetic Approaches to Fig Buds for an Evolution From Monoecy Toward Dioecy. Front. Plant Sci.(2020) 11:1208. doi: 10.3389/fpls.2020.01208.

Datasets for genetic diversity assessment in a collection of wild and cultivated pomegranates (Punica granatum L.) by microsatellite markers.

Data described in this article refer to molecular characterization and assessment of genetic diversity within a wide collection of pomegranate genotypes including both selections and cultivars from different geographical origin/disseminations by using microsatellite (SSR, Simple Sequence Repeats) markers. Supplied datasets refer to a set of 63 genotypes including 55 accessions (landraces) from Italy, Turkmenistan, Japan, and USA and 8 cultivars from Israel, established at the pomegranate repository of the Fruit Tree Unit of the Department of Soil, Plant and Food Science at University of Bari "Aldo Moro", Italy. Pomegranate accessions differed for end-use purpose (edible, ornamental) and some morpho-pomological traits including juice taste, inner tegmen hardness, and skin/seed color. Molecular data were opportunely employed to build a similarity matrix to establish phylogenetic relationships (genetic similarity and distances) among pomegranate accessions and compare genetic clustering to morpho-pomological classification. The present data article provides detailed information and methodological protocols on SSR markers, PCR amplification and banding profiling aimed to molecular characterization of pomegranate collection. This latter was conducted by amplifying a set of informative polymorphic SSR markers on the genomic DNA of each pomegranate accession, and then comparing the different molecular profiles by capillary electrophoresis. The banding patterns obtained from microsatellite markers were used to build a binary matrix containing the scores for each individual SSR fragment, which was transformed into a similarity matrix and finally used for cluster analysis and dendrogram building based on the UPGMA algorithm. This paper supplies data potentially useful for the identification of polymorphic markers suitable for varietal identification and traceability, or discrimination between tightly related pomegranate accessions with very high morphological similarity and/or geographical identity. Data described in this paper support the published original research article titled "Exploiting DNA-based molecular tools to assess genetic diversity in pomegranate (Punica granatum L.) selections and cultivars" [1].

Metabolomics and genetics of reproductive bud development in Ficus carica var. sativa (edible fig) and in Ficus carica var. caprificus (caprifig): similarities and differences.

In figs, reproductive biology comprises cultivars requiring or not pollination, with female trees (edible fig) and male trees (caprifig) bearing different types of fruits. Metabolomic and genetic studies may clarify bud differentiation mechanisms behind the different fruits. We used a targeted metabolomic analysis and genetic investigation through RNA sequence and candidate gene investigation to perform a deep analysis of buds of two fig cultivars, 'Petrelli' (San Pedro type) and 'Dottato' (Common type), and one caprifig. In this work, proton nuclear magnetic resonance (1H NMR-based metabolomics) has been used to analyze and compare buds of the caprifig and the two fig cultivars collected at different times of the season. Metabolomic data of buds collected on the caprifig, 'Petrelli', and 'Dottato' were treated individually, building three separate orthogonal partial least squared (OPLS) models, using the "y" variable as the sampling time to allow the identification of the correlations among metabolomic profiles of buds. The sampling times revealed different patterns between caprifig and the two edible fig cultivars. A significant amount of glucose and fructose was found in 'Petrelli', differently from 'Dottato', in the buds in June, suggesting that these sugars not only are used by the ripening brebas of 'Petrelli' but also are directed toward the developing buds on the current year shoot for either a main crop (fruit in the current season) or a breba (fruit in the successive season). Genetic characterization through the RNA-seq of buds and comparison with the literature allowed the identification of 473 downregulated genes, with 22 only in profichi, and 391 upregulated genes, with 21 only in mammoni.

New Breeding Technologies in Grasses.

Plant breeding is continuously evolving to develop new cultivars with the desired traits in the most efficient way [...].

Mushroom-Based Supplements in Italy: Let's Open Pandora's Box.

Mushrooms and derivates are well known to the scientific community for having different health benefits and exhibit a wide range of pharmacological activities, including lipid-lowering, antihypertensive, antidiabetic, antimicrobic, antiallergic, anti-inflammatory, anticancer, immunomodulating, neuroprotective and osteoprotective actions. In Europe, medical mushrooms are mainly marketed in the form of food supplements as single components or combined with other nutraceuticals. In this context, the first peculiarity that distinguishes it is the safety established through the "history of consumption" that characterizes that mushroom. However, the cultivation of medicinal mushrooms on a large scale is performed mainly in China, where most of the production facilities do not have internationally recognized good manufacturing practices, despite that many European companies that sell myotherapies are supplied by Chinese manufacturers. This is particularly evident in Italy, where an arsenal of mushroom products is marketed in the form of powders and extracts not always of ascertained origin and sometimes of doubtful taxonomic identification, and thus not meeting the quality criteria required. The growing interest in mycotherapy involves a strong commitment from the scientific community to propose supplements of safe origin and genetic purity as well as to promote clinical trials to evaluate its real effects on humans. The purpose of this research is to analyze different mushroom-based dietary supplements used in medicine as monotherapy on the Italian market and to evaluate their composition and quality. The molecular identification of the sequences with those deposited in GenBank allowed for identifying 6 out of 19 samples, matching with those deposited belonging to the species indicated in the label, i.e., Lentinula edodes (samples 1, 4, 12 and 18) and Ganoderma lucidum (samples 5 and 10). Samples containing Ganoderma, labeled in the commercial product as G. lucidum, showed sequences that showed homology of 100% and 99% with G. resinaceum and G. sichuanense. An additional investigation was carried out in order to determine the active fungal ingredients, such as ergosterol, aflatoxins, heavy metals, nicotine and total glucan. The results obtained and shown in the manuscript highlight how the data were not only in line with what is expected with respect to what is indicated in the labels.

Discovering Loci for Breeding Prospective and Phenology in Wheat Mediterranean Landraces by Environmental and eigenGWAS.

Knowledge of the genetic basis of traits controlling phenology, differentiation patterns, and environmental adaptation is essential to develop new cultivars under climate change conditions. Landrace collections are an appropriate platform to study the hidden variation caused by crop breeding. The use of genome-wide association analysis for phenology, climatic data and differentiation among Mediterranean landraces led to the identification of 651 marker-trait associations that could be grouped in 46 QTL hotspots. A candidate gene analysis using the annotation of the genome sequence of the wheat cultivar 'Chinese Spring' detected 1097 gene models within 33 selected QTL hotspots. From all the gene models, 42 were shown to be differentially expressed (upregulated) under abiotic stress conditions, and 9 were selected based on their levels of expression. Different gene families previously reported for their involvement in different stress responses were found (protein kinases, ras-like GTP binding proteins and ethylene-responsive transcription factors). Finally, the synteny analysis in the QTL hotspots regions among the genomes of wheat and other cereal species identified 23, 21 and 7 ortho-QTLs for Brachypodium, rice and maize, respectively, confirming the importance of these loci.

Genome-wide association study of common resistance to rust species in tetraploid wheat.

Rusts of the genus Puccinia are wheat pathogens. Stem (black; Sr), leaf (brown; Lr), and stripe (yellow; Yr) rust, caused by Puccinia graminis f. sp. tritici (Pgt), Puccinia triticina (Pt), and Puccinia striiformis f. sp. tritici (Pst), can occur singularly or in mixed infections and pose a threat to wheat production globally in terms of the wide dispersal of their urediniospores. The development of durable resistant cultivars is the most sustainable method for controlling them. Many resistance genes have been identified, characterized, genetically mapped, and cloned; several quantitative trait loci (QTLs) for resistance have also been described. However, few studies have considered resistance to all three rust pathogens in a given germplasm. A genome-wide association study (GWAS) was carried out to identify loci associated with resistance to the three rusts in a collection of 230 inbred lines of tetraploid wheat (128 of which were Triticum turgidum ssp. durum) genotyped with SNPs. The wheat panel was phenotyped in the field and subjected to growth chamber experiments across different countries (USA, Mexico, Morocco, Italy, and Spain); then, a mixed linear model (MLM) GWAS was performed. In total, 9, 34, and 5 QTLs were identified in the A and B genomes for resistance to Pgt, Pt, and Pst, respectively, at both the seedling and adult plant stages. Only one QTL on chromosome 4A was found to be effective against all three rusts at the seedling stage. Six QTLs conferring resistance to two rust species at the adult plant stage were mapped: three on chromosome 1B and one each on 5B, 7A, and 7B. Fifteen QTLs conferring seedling resistance to two rusts were mapped: five on chromosome 2B, three on 7B, two each on 5B and 6A, and one each on 1B, 2A, and 7A. Most of the QTLs identified were specific for a single rust species or race of a species. Candidate genes were identified within the confidence intervals of a QTL conferring resistance against at least two rust species by using the annotations of the durum (cv. 'Svevo') and wild emmer wheat ('Zavitan') reference genomes. The 22 identified loci conferring resistance to two or three rust species may be useful for breeding new and potentially durable resistant wheat cultivars.

Influence of Some Spaghetti Processing Variables on Technological Attributes and the In Vitro Digestion of Starch.

Durum semolina spaghetti is known to have a low-moderate glycaemic index but the impact of various processing variables during the manufacture and cooking of pasta does affect pasta structure and potentially could alter starch digestion. In this study, several process variables were investigated to see if they can impact the in vitro starch digestion in spaghetti while also monitoring the pasta's technological quality. Cooking time had a large impact on pasta starch digestion and reducing cooking from fully cooked to al dente and using pasta of very high protein content (17%), reduced starch digestion extent. The semolina particle size distribution used to prepare pasta impacted pasta quality and starch digestion to a small extent indicating a finer semolina particle size (<180 µm) may promote a more compact structure and help to reduce starch digestion. The addition of a structural enzyme, Transglutaminase in the pasta formulae improved overcooking tolerance in low protein pasta comparable to high protein pasta with no other significant effects and had no effect on starch digestion over a wide protein range (8.6−17%). While cold storage of cooked pasta was expected to increase retrograded starch, the increase in resistant starch was minor (37%) with no consequent improvement in the extent of starch digestion. Varying three extrusion parameters (die temperature, die pressure, extrusion speed) impacted pasta technological quality but not the extent of starch digestion. Results suggest the potential to subtly manipulate the starch digestion of pasta through some processing procedures.

QTL Mapping of Stem Rust Resistance in Populations of Durum Wheat.

Stem rinfectionust, caused by the fungus Puccinia graminis f. sp. tritici (Pgt), is one of the most devastating fungal diseases of durum and common wheat worldwide. The identification of sources of resistance and the validation of QTLs identified through genome-wide association studies is of paramount importance for reducing the losses caused by this disease to wheat grain yield and quality. Four segregating populations whose parents showed contrasting reactions to some Pgt races were assessed in the present study, and 14 QTLs were identified on chromosomes 3A, 4A, 6A, and 6B, with some regions in common between different segregating populations. Several QTLs were mapped to chromosomal regions coincident with previously mapped stem rust resistance loci; however, their reaction to different Pgt races suggest that novel genes or alleles could be present on chromosomes 3A and 6B. Putative candidate genes with a disease-related functional annotation have been identified in the QTL regions based on information available from the reference genome of durum cv. 'Svevo'.

A consensus map for quality traits in durum wheat based on genome-wide association studies and detection of ortho-meta QTL across cereal species.

The present work focused on the identification of durum wheat QTL hotspots from a collection of genome-wide association studies, for quality traits, such as grain protein content and composition, yellow color, fiber, grain microelement content (iron, magnesium, potassium, selenium, sulfur, calcium, cadmium), kernel vitreousness, semolina, and dough quality test. For the first time a total of 10 GWAS studies, comprising 395 marker-trait associations (MTA) on 57 quality traits, with more than 1,500 genotypes from 9 association panels, were used to investigate consensus QTL hotspots representative of a wide durum wheat genetic variation. MTA were found distributed on all the A and B genomes chromosomes with minimum number of MTA observed on chromosome 5B (15) and a maximum of 45 on chromosome 7A, with an average of 28 MTA per chromosome. The MTA were equally distributed on A (48%) and B (52%) genomes and allowed the identification of 94 QTL hotspots. Synteny maps for QTL were also performed in Zea mays, Brachypodium, and Oryza sativa, and candidate gene identification allowed the association of genes involved in biological processes playing a major role in the control of quality traits.

A comprehensive meta-QTL analysis for yield-related traits of durum wheat (Triticum turgidum L. var. durum) grown under different water regimes.

Abiotic stress strongly affects yield-related traits in durum wheat, in particular drought is one of the main environmental factors that have effect on grain yield and plant architecture. In order to obtain new genotypes well adapted to stress conditions, the highest number of desirable traits needs to be combined in the same genotype. In this context, hundreds of quantitative trait loci (QTL) have been identified for yield-related traits in different genetic backgrounds and environments. Meta-QTL (MQTL) analysis is a useful approach to combine data sets and for creating consensus positions for the QTL detected in independent studies for the reliability of their location and effects. MQTL analysis is a useful method to dissect the genetic architecture of complex traits, which provide an extensive allelic coverage, a higher mapping resolution and allow the identification of putative molecular markers useful for marker-assisted selection (MAS). In the present study, a complete and comprehensive MQTL analysis was carried out to identify genomic regions associated with grain-yield related traits in durum wheat under different water regimes. A total of 724 QTL on all 14 chromosomes (genomes A and B) were collected for the 19 yield-related traits selected, of which 468 were reported under rainfed conditions, and 256 under irrigated conditions. Out of the 590 QTL projected on the consensus map, 421 were grouped into 76 MQTL associated with yield components under both irrigated and rainfed conditions, 12 genomic regions containing stable MQTL on all chromosomes except 1A, 4A, 5A, and 6B. Candidate genes associated to MQTL were identified and an in-silico expression analysis was carried out for 15 genes selected among those that were differentially expressed under drought. These results can be used to increase durum wheat grain yields under different water regimes and to obtain new genotypes adapted to climate change.

Datasets for grain protein content, yield-related traits, and candidate genes in a durum wheat RIL population derived from a "hexaploid × tetraploid" interspecific cross.

Data described in this article refer to the evaluation of genetic variability for quantity (grain protein content, GPC) and composition (HMW-glutenin subunits and gliadins) of seed storage proteins, and two yield components (grain yield per spike, GYS, and thousand-kernel weight, TKW) in a durum wheat recombinant inbred line (RIL) population derived by an interspecific cross between the common wheat accession 02-5B-318 and the durum cv. Saragolla. This article provides datasets relative to GPC, GYS and TKW collected in the two parents and in 135 durum RIL progenies from plants grown in field trials conducted in Valenzano (Metropolitan City of Bari, BA, Italy) by a randomized complete block design with three replicates. Data on GPC were acquired from Near-Infrared Reflectance on whole-meal flour and are expressed as percentage of proteins on a dry weight basis. Data relative to composition of seed storage proteins refer to high molecular weight glutenin subunits (encoded by Glu-A1 and Glu-B1 loci) and gliadins (encoded by Gli-B1 locus) extracted from whole-grain samples and identified based on their electrophoretic relative mobility on SDS-PAGE. This paper also provides datasets for the detection of quantitative trait loci (QTLs) for GPC, GYS, TKW on a durum wheat genetic linkage map previously developed in the same durum population genotyped with the Illumina 90 K iSelect SNP array. The present article finally supports information for the identification of candidate genes related to wheat grain quantity, composition, and yield by providing data relative to all the SNP markers mapped in the QTL confidence intervals for each trait of interest (GPC, GYS, TKW). Data described in this paper support the published original research article titled "Genetic variation for protein content and yield-related traits in a durum population derived from an inter-specific cross between hexaploid and tetraploid wheat cultivars" (Giancaspro et al., 2019).

Identification of New QTLs for Dietary Fiber Content in Aegilops biuncialis.

Grain dietary fiber content is an important health-promoting trait of bread wheat. A dominant dietary fiber component of wheat is the cell wall polysaccharide arabinoxylan and the goatgrass Aegilops biuncialis has high ß-glucan content, which makes it an attractive gene source to develop wheat lines with modified fiber composition. In order to support introgression breeding, this work examined genetic variability in grain ß-glucan, pentosan, and protein content in a collection of Ae. biuncialis. A large variation in grain protein and edible fiber content was revealed, reflecting the origin of Ae. biuncialis accessions from different eco-geographical habitats. Association analysis using DArTseq-derived SNPs identified 34 QTLs associated with ß-glucan, pentosan, water-extractable pentosan, and protein content. Mapping the markers to draft chromosome assemblies of diploid progenitors of Ae. biuncialis underlined the role of genes on chromosomes 1Mb, 4Mb, and 5Mb in the formation of grain ß-glucan content, while other QTLs on chromosome groups 3, 6, and 1 identified genes responsible for total- and water-extractable pentosan content. Functional annotation of the associated marker sequences identified fourteen genes, nine of which were identified in other monocots. The QTLs and genes identified in the present work are attractive targets for chromosome-mediated gene transfer to improve the health-promoting properties of wheat-derived foods.

Abscisic Acid-Stress-Ripening Genes Involved in Plant Response to High Salinity and Water Deficit in Durum and Common Wheat.

In the dry and hot Mediterranean regions wheat is greatly susceptible to several abiotic stresses such as extreme temperatures, drought, and salinity, causing plant growth to decrease together with severe yield and quality losses. Thus, the identification of gene sequences involved in plant adaptation to such stresses is crucial for the optimization of molecular tools aimed at genetic selection and development of stress-tolerant varieties. Abscisic acid, stress, ripening-induced (ASR) genes act in the protection mechanism against high salinity and water deficit in several plant species. In a previous study, we isolated for the first time the TtASR1 gene from the 4A chromosome of durum wheat in a salt-tolerant Tunisian landrace and assessed its involvement in plant response to some developmental and environmental signals in several organs. In this work, we focused attention on ASR genes located on the homoeologous chromosome group 4 and used for the first time a Real-Time approach to "in planta" to evaluate the role of such genes in modulating wheat adaptation to salinity and drought. Gene expression modulation was evaluated under the influence of different variables - kind of stress, ploidy level, susceptibility, plant tissue, time post-stress application, gene chromosome location. ASR response to abiotic stresses was found only slightly affected by ploidy level or chromosomal location, as durum and common wheat exhibited a similar gene expression profile in response to salt increase and water deficiency. On the contrary, gene activity was more influenced by other variables such as plant tissue (expression levels were higher in roots than in leaves), kind of stress [NaCl was more affecting than polyethylene glycol (PEG)], and genotype (transcripts accumulated differentially in susceptible or tolerant genotypes). Based on such experimental evidence, we confirmed Abscisic acid, stress, ripening-induced genes involvement in plant response to high salinity and drought and suggested the quantification of gene expression variation after long salt exposure (72 h) as a reliable parameter to discriminate between salt-tolerant and salt-susceptible genotypes in both Triticum aestivum and Triticum durum.

A durum wheat recombinant inbred line (RIL) population: Data on ß-glucans, grain protein content, grain yield per spike, and heading time.

Data presented are on genetic variation of quality trait and production in a recombinant inbred line (RIL) population derived from a cross between two elite durum wheat cultivars grown in two different locations (Valenzano, metropolitan city of Bari -Italy) and Policoro (metropolitan city of Matera - Italy). The data of the two environment include: 1. ß-glucan content; 2. grain protein content; 3. grain yield per spike; 4. heading time. In addition data on high-density SNP-based genetic linkage map and linkage analysis are reported. The data in this article support and augment information presented in the research article "Development of a high-density SNP-based linkage map and detection of QTL for ß-glucans, protein content, grain yield per spike and heading time in durum wheat" (Int J Mol Sci. 18(6):1329, 2017, https://doi.org/10.3390/ijms18061329).