Advancements in plant genome sequencing and assembly have enabled the production of increasingly accurate and contiguous genome sequences. Here, we present the chromosome-level assembly of the durum wheat (Triticum turgidum L. ssp. durum, cv. Svevo) reference genome produced using accurate long-reads, optical mapping and Hi-C. The new assembly (Svevo Rel.2.0) comprises 263 hybrid scaffolds with an N50 value of 112.3 Mb, arranged into 14 contiguous pseudomolecules spanning 10.4 Gb. The Svevo Rel.2.0 genome assembly was annotated using extensive short- and long-read RNA sequencing data obtained from 60 tissue/treatment combinations. The resulting annotation comprises 68 154 high-confidence protein-coding genes, which have been integrated into a comprehensive transcriptome atlas accessible through an eFP browser. Annotation was manually curated for storage protein gene families and for Leucine-Rich Repeat-Containing Receptor genes yielding 3763 LRR-CR loci. The genome assembly's accuracy and completeness were demonstrated by the correct reconstruction of the physical map of Tg1-B (Tenacious glumes 1), a locus controlling the free threshing trait located on chromosome 2B that was not assembled in the previous genome release (Svevo Rel.1.0). A wealth of 6621 QTLs/MTAs from the literature were mapped onto Svevo Rel.2.0 to identify QTL hotspots and trait-specific candidate genes. The ancestry of the durum genome to representative wild emmer populations from North-Eastern and Southern-Levant Fertile Crescent assessed by tracing haplotype transmission patterns revealed a clear mosaic pattern. This new durum reference genome, enhanced with advanced annotation and an expression atlas linked to QTLome data, is the most comprehensive tool available for durum wheat genomics.

Wild emmer wheat (Triticum turgidum subsp. dicoccoides, WEW) was one of the first crops domesticated in the Neolithic revolution that shifted humanity to agrarian societies. Understanding its population genomics has both evolutionary significance and direct relevance to wheat improvement. Leveraging whole-genome sequencing (WGS) data from 291 accessions ( 9.5x coverage), we identified 3.4 million high-quality SNPs for population genomics, evolutionary analysis, and genome-wide association studies (GWAS) of seedling-stage resistance to five races each of the stem, leaf, and stripe rust pathogens. Phylogenetic, principal component, and population structure analyses revealed three distinct WEW subgroups: the Northern Population (NP), Southern Levant (SL), and a highly differentiated judaicum subgroup consisting of accessions near the Sea of Galilee. Diversity and pairwise FST analyses highlighted varying divergence among these subpopulations. The SL accessions exhibited higher resistance to all races of the three rust pathogens compared to the judaicum and NP. The SL accessions also exhibited the highest frequency of resistance to all rust pathogens, whereas NP lacked stem rust resistance but retained resistance to some leaf and stripe rust races. GWAS identified 27, 26, and 41 significant loci associated with stem, leaf, and stripe rust resistance, respectively, most of which were novel. A major resistance hotspot was identified on chromosome 1BS ( 50–100 Mb), associated with multiple races of different rust pathogens, suggesting the presence of shared or tightly linked resistance factors in the region. The most significant loci explained up to 73

Abstract Grain yield in wheat is frequently driven by pre-anthesis growth and how carbon is directed to reproductive parts, determining the potential size of the grain-producing sink. However, the genetic mechanisms controlling this carbon allocation remain unclear. In this study we discovered a series of loci in tetraploid and hexaploid wheats that, when combined, confer an average grain yield advantage in hexaploid winter wheat of approx. 5-7% under high-input farming while approx. 10-15% under low-input conditions. The responsible gene is GRAIN NUMBER INCREASE 2 ( GNI2 ), ancestral to its duplicate GNI1 , and represented by the homoeo-allelic series GNI-A2 , GNI-B2 , and GNI-D2 . GNI1 and all GNI2 copies additively affect floral growth and fertility by modulating reproductive allocation and harvest index. Herewith, we describe a series of grain yield-relevant GNI2 homoeo-alleles with a proven track record for being beneficial in both high- and low-input environments. Their deployment offers a sustainable pathway to raise global grain yields in the future.

Over the past 10,000 years, the development of civilization has been enabled by the domestication of plants and animals tailored to human needs. The Triticeae tribe, including barley and wheat, has emerged as one of the most important sources of staple foods worldwide. Here, comparing genomes of wheat and barley genotypes from around the world, we unveiled genomic footprints of convergent selection affecting genes involved in crop adaptation and productivity, as well as a lack of parallel selection for diverse genes delivering genetic diversity specific to particular geographic and associated environmental conditions. We demonstrate that studying convergent selection between crops can help to identify genes crucial for adaptation and sources of diversity for improving cultivated species—forming the basis of the proposed concept of inter-crop translational research for breeding. Convergent selection between crops can help to identify genetic variants with important roles in adaptation as a source of diversity for the improvement of cultivated species through the concept of inter-crop translational research for breeding.

AbstractFusarium head blight (FHB), mainly caused by Fusarium graminearum and Fusarium culmorum, is a major wheat disease. Significant efforts have been made to improve resistance to FHB in bread wheat (Triticum aestivum), but more work is needed for durum wheat (Triticum turgidum spp. durum). Bread wheat has ample genetic variation for resistance breeding, which can be readily exploited, while durum wheat is characterized by higher disease susceptibility and fewer valuable resistance sources. The Wheat Initiative – Expert Working Group on Durum Wheat Genomics and Breeding has promoted a scientific discussion to define the key actions that should be prioritized for achieving resistance in durum wheat comparable to that found in bread wheat. Here, a detailed state of the art and novel tools to improve FHB resistance in durum are presented, together with a perspective on the next steps forward. A meta‐analysis grouping all quantitative trait loci (QTL) associated with FHB resistance in both bread and durum wheat has been conducted to identify hotspot regions that do not overlap with Rht alleles, which are known to negatively correlate with FHB resistance. A detailed list of QTL related to FHB resistance and deoxynivalenol contamination and durum lines carrying different sources of FHB resistance are provided as a strategic resource. QTL, closely linked markers and durum wheat lines carrying the useful alleles, can be selected to design an effective breeding program. Finally, we highlight the priority actions that should be implemented to achieve satisfactory resistance to FHB in durum wheat.

Septoria nodorum blotch (SNB) is an important disease of both durum and hard red spring wheat (HRSW) worldwide. The disease is caused by the necrotrophic fungal pathogen Parastagonospora nodorum when compatible gene-for-gene interactions occur between pathogen-produced necrotrophic effectors (NEs) and corresponding host sensitivity genes. To date, nine sensitivity gene-NE interactions have been identified, but there is little information available regarding their overall frequency in durum and HRSW. Here, we infiltrated a global HRSW panel (HRSWP) and the Global Durum Panel (GDP) with P. nodorum NEs SnToxA, SnTox1, SnTox267, SnTox3, and SnTox5. Frequencies of sensitivity to SnTox1 and SnTox5 were higher in durum compared with HRSW and vice versa for SnTox267 and SnTox3. Strong associations for the known sensitivity loci Tsn1, Snn1, Snn2, Snn3, Snn5, and Snn7 along with potentially novel sensitivity loci on chromosome arms 7DS and 3BL, associated with SnToxA and SnTox267, respectively, were identified in the HRSWP. In the GDP, Snn1, Snn3, and Snn5 were identified along with novel loci associated with sensitivity to SnTox267 on chromosome arms 2AS, 2AL, and 6AS and with SnTox5 sensitivity on 2BS and 7BL. These results reveal additional NE sensitivity loci beyond those previously described, demonstrating a higher level of genetic complexity of the wheat-P. nodorum system than was previously thought. Knowledge regarding the prevalence and genomic locations of SNB susceptibility genes in HRSW and durum will prove useful for developing efficient breeding strategies and improving varieties for SNB resistance.

Root system architecture (RSA), shoot architecture, and shoot‐to‐root biomass allocation are critical for optimizing crop water and nutrient capture and ultimately grain yield. Nevertheless, only a few studies adequately dissected the genetic basis of RSA and its relationship to shoot development. Herein, we dissected at a high level of details the RSA–shoot QTLome in a panel of 194 elite durum wheat ( Triticum turgidum ssp. durum Desf.) varieties from worldwide adopting high‐throughput phenotyping platform (HTPP) and genome‐wide association study (GWAS). Plants were grown in controlled conditions up to the seventh leaf appearance (late tillering) in the GROWSCREEN‐Rhizo, a rhizobox platform integrated with automated monochrome camera for root imaging, which allowed us to phenotype the panel for 35 shoot and root architectural traits, including seminal, nodal, and lateral root traits, width and depth, leaf area, leaf, and tiller number on a time‐course base. GWAS identified 180 quantitative trait loci (QTLs) (−log p ‐value ≥ 4) grouped in 39 QTL clusters. Among those, 10, 11, and 10 QTL clusters were found for seminal, nodal, and lateral root systems. Deep rooting, a key trait for adaptation to water limiting conditions, was controlled by three major QTLs on chromosomes 2A, 6A, and 7A. Haplotype distribution revealed contrasting selection patterns between the ICARDA rainfed and CIMMYT irrigated breeding programs, respectively. These results provide valuable insights toward a better understanding of the RSA QTLome and a more effective deployment of beneficial root haplotypes to enhance durum wheat yield in different environmental conditions.

Abiotic stress strongly affects yield-related traits in durum wheat. In particular drought is one of the main environmental factors reducing grain yield. Hundreds of quantitative trait loci (QTL) have been identified for yield-related traits across different genetic backgrounds and environments. Meta-QTL (MQTL) analysis is a useful approach to combine data sets and for creating consensus positions for QTL detected in individual studies. MQTL analysis makes it possible to dissect the genetic architecture of complex traits, provide a higher mapping resolution and allow the identification of putative molecular markers useful for marker assisted selection (MAS). This chapter provides an overview of the use of MQTL analysis in identification of genomic regions associated with grain-yield related traits in durum wheat under different water regimes.

IntroductionHeat stress negatively affects wheat production in several ways, mainly by reducing growth rate, photosynthetic capacity and reducing spike fertility. Modeling stress response means analyzing simultaneous relationships among traits affecting the whole plant response and determinants of grain yield. The aim of this study was to dissect the diverse impacts of heat stress on key yield traits and to identify the most promising sources of alleles for heat tolerance.MethodsWe evaluated a diverse durum wheat panel of 183 cultivars and breeding lines from worldwide, for their response to long-term heat stress under field conditions (HS) with respect to non stress conditions (NS), considering phenological traits, grain yield (GY) and its components as a function of the timing of heat stress and climatic covariates. We investigated the relationships among plant and environmental variables by means of a structural equation model (SEM) and Genetic SEM (GSEM). ResultsOver two years of experiments at CENEB, CIMMYT, the effects of HS were particularly pronounced for the normalized difference vegetation index, NDVI (-51.3%), kernel weight per spike, KWS (-40.5%), grain filling period, GFP (-38.7%), and GY (-56.6%). Average temperatures around anthesis were negatively correlated with GY, thousand kernel weight TKW and test weight TWT, but also with spike density, a trait determined before heading/anthesis. Under HS, the correlation between the three major determinants of GY, i.e., fertile spike density, spike fertility and kernel size, were of noticeable magnitude. NDVI measured at medium milk-soft dough stage under HS was correlated with both spike fertility and grain weight while under NS it was less predictive of grain weight but still highly correlated with spike fertility. GSEM modeling suggested that the causal model of performance under HS directly involves genetic effects on GY, NDVI, KWS and HD.DiscussionWe identified consistently suitable sources of genetic resistance to heat stress to be used in different durum wheat pre-breeding programs. Among those, Desert Durums and CIMMYT’80 germplasm showed the highest degree of adaptation and capacity to yield under high temperatures and can be considered as a valuable source of alleles for adaptation to breed new HS resilient cultivars.

Context As global temperatures increase, heat waves of >30°C for at least 3 days are projected to become more frequent during reproductive development of wheat, causing reductions in grain yield. Breeding for tolerance is difficult under field conditions owing to the unpredictable timing and intensity of natural heat events and the narrow developmental windows of sensitivity. Aims We report on a series of experiments designed to explore genetic variability for floret sterility induced by natural heat waves in the field by targeting a sensitive development stage. Methods Our method involved sowing late, and the use of auricle distance to identify main tillers exposed to heat events at a sensitive developmental stage (booting). Key results Substantial genetic variation was found for tolerance of grain set to natural heat waves, with a broad-sense heritability estimate of 0.94 for heat-exposed stems compared with 0.72 for non-stressed controls. An auricle distance of 1–3 cm was established as a phenotypic marker for tagging stems at the sensitive stage of development, and the optimal number of spikes to assess was determined as 10–15 per plot. A validation study with durum lines previously classified as tolerant/intolerant under glasshouse conditions showed agreement in ranking of genotypes at the extremes of tolerance. Conclusions We demonstrate that it is possible to screen wheat genotypes for stage-specific tolerance to natural heat waves in the field. Implications The protocol described could provide a low-cost method for evaluating heat tolerance in wheat, with relevance to commercial field production conditions. The approach allows tolerance to be assessed at a single stage of reproductive development, which should allow greater heritability in field assessments.

In the context of climate change, high temperature is one of the main abiotic stresses hampering durum wheat production. Through the characterization of an international panel of 271 genotypes, this study investigates the effects of heat stress on quality traits and identifies which glutenins (Glu-1, Glu-2 and Glu-3 loci) alleles are the most important to obtain high gluten strength under optimal and high temperature conditions. In parallel with the wide variability observed in the panel, the genotype and environmental effects, including their interaction, showed highly significant effect on test weight, thousand kernel weight, grain protein content (GPC), sodium dodecyl sulphate sedimentation volume (SDSS) and SDSS index. Only one genotype maintained test weight and thousand kernel weight under heat-stress conditions whereas for GPC, SDSS and SDSS index, most genotypes increased values. All Glu loci had significant effects on grain protein content (with the exception of Glu-B2), SDSS and SDSS Index. None of the Glu loci interacted with the environment or years under study. Among the identified alleles, Glu-A1b, Glu-B1an, Glu-B1a, Glu-B2a, Glu-A3a.x, Glu-A3d, Glu-B3a and Glu-B3ax (including the LMW-2 pattern) were associated with high values for SDSS and SDSS Index. Genotypes identified in this study, with good performances under optimal and high temperature growing conditions, could be useful for breeding programs. The non-interaction of the Glu loci with the environment facilitates the introgression of desired alleles regardless of high growing temperatures.

This chapter discusses some of the latest findings related to the genetics of drought resistance of the world's most widely grown cereals. The chapter starts with rice because of its key role as an ancestral founder species and phylogenetically pivotal role for cereal evolution. The chapter then reviews barley, second in phylogeny after rice, durum wheat, bread wheat, sorghum and maize.

Durum wheat (Triticum turgidum L. ssp. durum) landraces, traditional local varieties representing an intermediate stage in domestication, are gaining attention due to their high genetic variability and performance in challenging environments. While major kernel metabolites have been examined, limited research has been conducted on minor bioactive components like lipids, despite their nutritional benefits. To address this, we analyzed twenty-two tetraploid accessions, comprising modern elite cultivars and landraces, to (i) verify if the selection process for yield-related traits carried out during the Green Revolution has influenced lipid amount and composition; (ii) uncover the extent of lipid compositional variability, giving evidence that lipid fingerprinting effectively identifies evolutionary signatures; and (iii) identify genotypes interesting for breeding programs to improve yield and nutrition. Interestingly, total fat did not correlate with kernel weight, indicating lipid composition as a promising trait for selection. Tri- and di-acylglycerol were the major lipid components along with free fatty acids, and their relative content varied significantly among genotypes. In particular, landraces belonging to T. turanicum and carthlicum ecotypes differed significantly in total lipid and fatty acid profiles. Our findings provide evidence that landraces can be a genetically relevant source of lipid variability, with potential to be exploited for improving wheat nutritional quality.

Soil-borne cereal mosaic virus (SBCMV), the causative agent of wheat mosaic, is a Furovirus challenging wheat production all over Europe. Differently from bread wheat, durum wheat shows greater susceptibility and stronger yield penalties, so identification and genetic characterization of resistance sources are major targets for durum genetics and breeding. The Sbm1 locus providing high level of resistance to SBCMV was mapped in bread wheat to the 5DL chromosome arm (Bass in Genome 49:1140–1148, 2006). This excluded the direct use of Sbm1 for durum wheat improvement. Only one major QTL has been mapped in durum wheat, namely QSbm.ubo-2B, on the 2BS chromosome region coincident with Sbm2, already known in bread wheat as reported (Bayles in HGCA Project Report, 2007). Therefore, QSbm.ubo-2B = Sbm2 is considered a pillar for growing durum in SBCMV-affected areas. Herein, we report the fine mapping of Sbm2 based on bi-parental mapping and GWAS, using the Infinium 90 K SNP array and high-throughput KASP®. Fine mapping pointed out a critical haploblock of 3.2 Mb defined by concatenated SNPs successfully converted to high-throughput KASP® markers coded as KUBO. The combination of KUBO-27, wPt-2106-ASO/HRM, KUBO-29, and KUBO-1 allows unequivocal tracing of the Sbm2-resistant haplotype. The interval harbors 52 high- and 41 low-confidence genes, encoding 17 cytochrome p450, three receptor kinases, two defensins, and three NBS-LRR genes. These results pave the way for Sbm2 positional cloning. Importantly, the development of Sbm2 haplotype tagging KASP® provides a valuable case study for improving efficacy of the European variety testing system and, ultimately, the decision-making process related to varietal characterization and choice.

Tan spot, caused by the necrotrophic fungal pathogen Pyrenophora tritici-repentis (Ptr), is an important disease of durum and common wheat worldwide. Compared with common wheat, less is known about the genetics and molecular basis of tan spot resistance in durum wheat. We evaluated 510 durum lines from the Global Durum Wheat Panel (GDP) for sensitivity to the necrotrophic effectors (NEs) Ptr ToxA and Ptr ToxB and for reaction to Ptr isolates representing races 1 to 5. Overall, susceptible durum lines were most prevalent in South Asia, the Middle East, and North Africa. Genome-wide association analysis showed that the resistance locus Tsr7 was significantly associated with tan spot caused by races 2 and 3, but not races 1, 4, or 5. The NE sensitivity genes Tsc1 and Tsc2 were associated with susceptibility to Ptr ToxC- and Ptr ToxB-producing isolates, respectively, but Tsn1 was not associated with tan spot caused by Ptr ToxA-producing isolates, which further validates that the Tsn1-Ptr ToxA interaction does not play a significant role in tan spot development in durum. A unique locus on chromosome arm 2AS was associated with tan spot caused by race 4, a race once considered avirulent. A novel trait characterized by expanding chlorosis leading to increased disease severity caused by the Ptr ToxB-producing race 5 isolate DW5 was identified, and this trait was governed by a locus on chromosome 5B. We recommend that durum breeders select resistance alleles at the Tsr7, Tsc1, Tsc2, and the chromosome 2AS loci to obtain broad resistance to tan spot.

AbstractDurum and bread wheat are two related species with different ploidy levels but a high similarity between the common A and B genomes. This feature, which allows a continuous gene flow between the two species, can be exploited in breeding programs to improve key traits in both crops. Therefore, durum wheat, despite covering only 5% of cultivated wheat worldwide, also represents an asset for the genetic improvement of bread wheat. Tetraploid wheat, with a very large availability of wild and domesticated accessions, durum landraces, and cultivars, offers a large gene reservoir to increase the genetic diversity of A and B genomes in bread wheat. Moreover, thanks to the possibility of crossing durum wheat with Aegilops tauschii, synthetic hexaploid lines are generated which show a much larger genetic diversity also in the D genome compared to common wheat. The genome sequences of wild emmer, durum, and bread wheat provide power tools for gene cloning and comparative genomics that will also facilitate the shuttling of genes between tetraploid and hexaploid wheats.

Osmotic adjustment (OA) is a major component of drought resistance in crops. The genetic basis of OA in wheat and other crops remains largely unknown. In this study, 248 field-grown durum wheat elite accessions grown under well-watered conditions, underwent a progressively severe drought treatment started at heading. Leaf samples were collected at heading and 17 days later. The following traits were considered: flowering time (FT), leaf relative water content (RWC), osmotic potential (ψs), OA, chlorophyll content (SPAD), and leaf rolling (LR). The high variability (3.89-fold) in OA among drought-stressed accessions resulted in high repeatability of the trait (h2 = 72.3%). Notably, a high positive correlation (r = 0.78) between OA and RWC was found under severe drought conditions. A genome-wide association study (GWAS) revealed 15 significant QTLs (Quantitative Trait Loci) for OA (global R2 = 63.6%), as well as eight major QTL hotspots/clusters on chromosome arms 1BL, 2BL, 4AL, 5AL, 6AL, 6BL, and 7BS, where a higher OA capacity was positively associated with RWC and/or SPAD, and negatively with LR, indicating a beneficial effect of OA on the water status of the plant. The comparative analysis with the results of 15 previous field trials conducted under varying water regimes showed concurrent effects of five OA QTL cluster hotspots on normalized difference vegetation index (NDVI), thousand-kernel weight (TKW), and/or grain yield (GY). Gene content analysis of the cluster regions revealed the presence of several candidate genes, including bidirectional sugar transporter SWEET, rhomboid-like protein, and S-adenosyl-L-methionine-dependent methyltransferases superfamily protein, as well as DREB1. Our results support OA as a valuable proxy for marker-assisted selection (MAS) aimed at enhancing drought resistance in wheat.

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.

COPYRIGHT © 2022 Cowger, Bulli, Chen, Lillemo and Maccaferri. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. TYPE Editorial PUBLISHED 16 September 2022 DOI 10.3389/fpls.2022.1034506