Powdery mildew is one of the devastating wheat diseases and is caused by the biotrophic fungus Blumeria graminis f.sp. tritici. The identification of natural sources of resistance and breeding for resistant varieties is the most effective way to control this disease, as chemical control is expensive. To date, more than 40 Pm resistance genes have been characterized, while only one of these genes, Pm3, has been cloned. Pm3 is localized on the short arm of wheat chromosome 1A and is present in 17 functional allelic forms (Pm3a to Pm3g, Pm3k to Pm3t). The Pm3 alleles confer race-specific resistance to different wheat powdery mildew races. The objectives of this work were to study the behaviour of powdery mildew resistance Pm3 gene in a collection of tetraploid wheats and to isolate the complete genomic sequence of Pm3 gene in susceptible and resistant genotypes in order to identify new functional alleles. The search for new Pm3 alleles was carried out on a collection of 233 tetraploid wheat genotypes (Triticum turgidum L.). The collection comprises 128 cultivars of durum wheat (ssp. durum), as well as 19 accessions of ssp. turgidum, 20 of ssp. turanicum, 20 of ssp. polonicum, 12 of ssp. carthlicum, 20 of ssp. dicoccum, and 14 of ssp. dicoccoides. The entire set of these accessions was phenotypically characterized for resistance against wheat powdery mildew by screening with one powdery mildew isolate (O2). This screening led to the identification of 34 resistant accessions (14,6% of the total set). The tetraploid wheat collection was analysed for the Pm3 haplotype by screening for the presence of a Pm3-like gene with a STS marker. This STS marker amplifies a 946 bp fragment from the 5' non- coding region of Pm3b and is diagnostic for the presence of a Pm3-like gene. A total of 129 accessions, both resistant and susceptible, out of 233 (55.4%) tested were identified with a likely presence of a Pm3 gene. Subsequently a set of 21 resistant and susceptible lines showing the presence of a Pm3-like gene was screened for the presence of Pm3a to Pm3g alleles. A positive PCR reaction was observed for the Pm3b allele. Five of these lines, either resistant and susceptible, were further analysed with 11 PCR primer combination covering all the Pm3b sequence. Pm3b allele from tetraploid wheat had a size of 4,442 bp, comprising two exons of 4,156 and 86 bp respectively, and an intron of 200 bp. Sequences alignment compared with the Pm3b sequence, used as reference, indicated that the Pm3 genes from the five tetraploid wheat lines contain several “indels” and SNPs in the form of highly polymorphic sequence blocks. The present study demonstrates that allelic variation occurs in functional genes and represents the first step for the identification and sequencing of new functional Pm3 alleles in tetraploid wheat genotypes.

In the present study, a detailed deletion map for wheat chromosomes 5A and 5B is reported, as well as an integrated genetic linkage map of chromosome 5A enriched with single nucleotide polymorphism (SNP) markers, useful both for comparison studies with other existing maps and for mapping major genes and quantitative trait loci (QTLs). Physical mapping of 5,011 SNP markers was obtained using Chinese Spring bin deletion lines for the homoeologous chromosomes of group 5; 509 SNPs were also genetically mapped in a recombinant inbred line population segregating for chromosome 5A only, obtained by crossing the cultivar Chinese Spring and the disomic substitution line Chinese Spring-5A dicoccoides. The whole 5A genetic map, containing 572 markers, covered a total length of 248.7 cM distributed among three linkage groups of 83.5, 117.8 and 47.4, respectively. The majority of SNP markers physically mapped on 5A were mapped to a unique bin, while a small percentage was assigned a double location, suggesting the presence of a segment of 5A short arm which may have undergone a duplication followed by an insertion into the long arm of the same chromosome. A QTL analysis for yield components was performed, identifying a major QTL in the subtelomeric region of chromosome 5A, corresponding to the 5AL15-0.67-0.78 bin; the chromosome segment was 23.5 cM long and included 111 markers. Candidate genes for yield components on chromosome 5A were identified through a syntenic genomic approach by comparison with genomes of model species. Putative function analysis revealed genes involved in basic metabolism and in stress condition responses, including heat shock proteins, chaperones, serine/ threonine protein kinases and membrane transporters, located in the region of the QTL. This information represents an important step for map-based and candidate gene-based cloning of yield QTLs.

Wheat is the most widely grown crop in the world and provides 20% of the daily protein and food calories for 4.5 billion people. Together with rice, it is the most important food crop in the developing world. In the last decades, various symptoms have been recorded across the population due to the consumption of wheat products, also summarized as “wheat allergy.” Wheat allergy is usually reported as a food allergy but can also be a contact allergy as a result of exposure to wheat. Several important wheat allergens have been characterized in the last years through biochemical, immunological, and molecular biological techniques. In the present work, the identification of allelic variation of genes involved in wheat allergy was reported. A collection of wheat genotypes was screened in order to identify new alleles. A total of 14 new alleles were identified for profilin, triosephosphateisomerase, dehydrin, glyceraldehyde-3-phosphate-dehydrogenase, / gliadin, GluB3-23, and Glutathione transferase allergen genes (located on chromosomes 1B, 3B, 6A, and homoelogous groups 5 and 7), potentially related to a minor allergenicity and useful in breeding program

Background: In higher plants, inorganic nitrogen is assimilated via the glutamate synthase cycle or GS-GOGAT pathway. GOGAT enzyme occurs in two distinct forms that use NADH (NADH-GOGAT) or Fd (Fd-GOGAT) as electron carriers. The goal of the present study was to characterize wheat Fd-GOGAT genes and to assess the linkage with grain protein content (GPC), an important quantitative trait controlled by multiple genes. Results: We report the complete genomic sequences of the three homoeologous A, B and D Fd-GOGAT genes from hexaploid wheat (Triticum aestivum) and their localization and characterization. The gene is comprised of 33 exons and 32 introns for all the three homoeologues genes. The three genes show the same exon/intron number and size, with the only exception of a series of indels in intronic regions. The partial sequence of the Fd-GOGAT gene located on A genome was determined in two durum wheat (Triticum turgidum ssp. durum) cvs Ciccio and Svevo, characterized by different grain protein content. Genomic differences allowed the gene mapping in the centromeric region of chromosome 2A. QTL analysis was conducted in the Svevo6Ciccio RIL mapping population, previously evaluated in 5 different environments. The study co-localized the Fd-GOGAT-A gene with the marker GWM-339, identifying a significant major QTL for GPC. Conclusions: The wheat Fd-GOGAT genes are highly conserved; both among the three homoeologous hexaploid wheat genes and in comparison with other plants. In durum wheat, an association was shown between the Fd-GOGAT allele of cv Svevo with increasing GPC - potentially useful in breeding programs.

High-density genetic linkage maps of crop species are particularly useful in detecting qualitative and quantitative trait loci (QTLs) for agronomically important traits and in improving the power of classical approaches to identify candidate genes. The aim of this study was to develop a high-density genetic linkage map in a durum wheat recombinant inbred lines population derived from two elite wheat cultivars and to identify and characterize QTLs for yellow pigment content (YPC). A dense map was constructed by genotyping with the wheat 90K iSelect array and consisted of 5,670 loci, comprising 5,019 single nucleotide polymorphism (SNP), 467 DArT, 182 SSR markers and eight genes distributed in 35 linkage groups. Data for yellow pigment content were obtained from four replicated trials conducted at two locations in southern Italy for 2 years. A total of seven QTLs on different chromosome regions (1B, 2A, 2B, 5A, 5B, 7A and 7B) were identified, three of which were consistent in three or four environments and across environments. The genome scan for QTLs and the SNP homology prediction against annotated proteins in wheat and Brachypodium genomes identified two candidate genes of the carotenoid biosynthesis pathway (aldehyde oxidase, AO1, and diphosphomevalonate decarboxylase, DMAPD) significantly associated with YPC. This study provides a basis for further genetic QTL dissection and tools for marker-assisted breeding programs, because SNP markers and some carotenoid candidate genes were found to be tightly linked to major QTLs for YPC.

Background: Nitrogen uptake and the efficient absorption and metabolism of nitrogen are essential elements in attempts to breed improved cereal cultivars for grain or silage production. One of the enzymes related to nitrogen metabolism is glutamine-2-oxoglutarate amidotransferase (GOGAT). Together with glutamine synthetase (GS), GOGAT maintains the flow of nitrogen from NH4 + into glutamine and glutamate, which are then used for several aminotransferase reactions during amino acid synthesis. Results: The aim of the present work was to identify and analyse the structure of wheat NADH-GOGAT genomic sequences, and study the expression in two durum wheat cultivars characterized by low and high kernel protein content. The genomic sequences of the three homoeologous A, B and D NADH-GOGAT genes were obtained for hexaploid Triticum aestivum and the tetraploid A and B genes of Triticum turgidum ssp. durum. Analysis of the gene sequences indicates that all wheat NADHGOGAT genes are composed of 22 exons and 21 introns. The three hexaploid wheat homoeologous genes have high conservation of sequence except intron 13 which shows differences in both length and sequence. A comparative analysis of sequences among di- and mono-cotyledonous plants shows both regions of high conservation and of divergence. qRT-PCR performed with the two durum wheat cvs Svevo and Ciccio (characterized by high and low protein content, respectively) indicates different expression levels of the two NADH-GOGAT-3A and NADH-GOGAT-3B genes. Conclusion: The three hexaploid wheat homoeologous NADH-GOGAT gene sequences are highly conserved – consistent with the key metabolic role of this gene. However, the dicot and monocot amino acid sequences show distinctive patterns, particularly in the transit peptide, the exon 16–17 junction, and the C-terminus. The lack of conservation in the transit peptide may indicate subcellular differences between the two plant divisions - while the sequence conservation within enzyme functional domains remains high. Higher expression levels of NADH-GOGAT are associated with higher grain protein content in two durum wheats.

arget region amplification polymorphism (TRAP) is a relatively new PCR-based technique that detects large numbers of loci in a single reaction without extensive pre-PCR processing of samples. The aim of this study was to integrate TRAP markers in an EST-derived SSR linkage map of a RIL mapping population from the cross of the durum wheat cultivars Ciccio and Svevo, for a more general purpose of establishing a high-throughput system for genetic map saturation. Primer combinations producing PCR products with at least 4-5 polymorphic bands were selected and analyzed across the mapping population. The PCR reactions produced a total of 2,881 fragments with an average of 52 peaks per reaction. A total of 142 new TRAP markers were mapped and found to be randomly distributed in the genome. The total length of the map was 2,043.0 cM, with an average chromosome length of 145.9 cM. Homoeologous group one had the highest number of TRAP markers (38 loci) and the longest map length (407.9 cM) for a total of 87 markers, while the homoeologous group five had the lowest TRAP marker number (5 loci) and the shortest map length (232.5 cM). The distribution of markers among the seven homoeologous groups was random. The results indicate that TRAP is highly efficient in genetic mapping, generating a large number of markers scattered across the genome. This closes many existing gaps in marker coverage and may join otherwise separate linkage groups