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Introduction: Heat 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. Methods: We 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). Results: Over 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. Discussion: We 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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Consensus linkage maps are important tools in crop genomics. We have assembled a high-density tetraploid wheat consensus map by integrating 13 data sets from independent biparental populations involving durum wheat cultivars (Triticum turgidum ssp. durum), cultivated emmer (T. turgidum ssp. dicoccum) and their ancestor (wild emmer, T. turgidum ssp. dicoccoides). The consensus map harboured 30 144 markers (including 26 626 SNPs and 791 SSRs) half of which were present in at least two component maps. The final map spanned 2631 cM of all 14 durum wheat chromosomes and, differently from the individual component maps, all markers fell within the 14 linkage groups. Marker density per genetic distance unit peaked at centromeric regions, likely due to a combination of low recombination rate in the centromeric regions and even gene distribution along the chromosomes. Comparisons with bread wheat indicated fewer regions with recombination suppression, making this consensus map valuable for mapping in the A and B genomes of both durum and bread wheat. Sequence similarity analysis allowed us to relate mapped gene-derived SNPs to chromosome-specific transcripts. Dense patterns of homeologous relationships have been established between the A- and B-genome maps and between nonsyntenic homeologous chromosome regions as well, the latter tracing to ancient translocation events. The gene-based homeologous relationships are valuable to infer the map location of homeologs of target loci/QTLs. Because most SNP and SSR markers were previously mapped in bread wheat, this consensus map will facilitate a more effective integration and exploitation of genes and QTL for wheat breeding purposes.

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. [ABSTRACT FROM AUTHOR]

Wheat, being the third largest U.S. crop and the principal food grain, faces significant risks from climate extremes such as drought. This necessitates identifying and developing methods for early water-stress detection to prevent yield loss and improve water-use efficiency. This study investigates the potential of hyperspectral imaging to detect the early stages of drought stress in wheat. The goal is to utilize this technology as a tool for screening and selecting drought-tolerant wheat genotypes in breeding programs. Additionally, this research aims to systematically evaluate the effectiveness of various existing sensors and methods for detecting early stages of water stress. The experiment was conducted in a durum wheat experimental field trial in Maricopa, Arizona, in the spring of 2019 and included well-watered and water-limited treatments of a panel of 224 replicated durum wheat genotypes. Spectral indices derived from hyperspectral imagery were compared against other plant-level indicators of water stress such as Photosystem II (PSII) and relative water content (RWC) data derived from proximal sensors. Our findings showed a 12% drop in photosynthetic activity in the most affected genotypes when compared to the least affected. The Leaf Water Vegetation Index 1 (LWVI1) highlighted differences between drought-resistant and drought-susceptible genotypes. Drought-resistant genotypes retained 43.36% more water in leaves under well-watered conditions compared to water-limited conditions, while drought-susceptible genotypes retained only 15.69% more. The LWVI1 and LWVI2 indices, aligned with the RWC measurements, revealed a strong inverse correlation in the susceptible genotypes, underscoring their heightened sensitivity to water stress in earlier stages. Several genotypes previously classified based on their drought resistance showed spectral indices deviating from expectations. Results from this research can aid farmers in improving crop yields by informing early management practices. Moreover, this research offers wheat breeders insights into the selection of drought-tolerant genotypes, a requirement that is becoming increasingly important as weather patterns continue to change. [ABSTRACT FROM AUTHOR]

Chlorophyll fluorescence (ChlF) is a powerful non‐invasive technique for probing photosynthesis. Although proposed as a method for drought tolerance screening, ChlF has not yet been fully adopted in physiological breeding, mainly due to limitations in high‐throughput field phenotyping capabilities. The light‐induced fluorescence transient (LIFT) sensor has recently been shown to reliably provide active ChlF data for rapid and remote characterisation of plant photosynthetic performance. We used the LIFT sensor to quantify photosynthesis traits across time in a large panel of durum wheat genotypes subjected to a progressive drought in replicated field trials over two growing seasons. The photosynthetic performance was measured at the canopy level by means of the operating efficiency of Photosystem II (Fq′/Fm′) and the kinetics of electron transport measured by reoxidation rates (Fr1′ and Fr2′). Short‐ and long‐term changes in ChlF traits were found in response to soil water availability and due to interactions with weather fluctuations. In mild drought, Fq′/Fm′ and Fr2′ were little affected, while Fr1′ was consistently accelerated in water‐limited compared to well‐watered plants, increasingly so with rising vapour pressure deficit. This high‐throughput approach allowed assessment of the native genetic diversity in ChlF traits while considering the diurnal dynamics of photosynthesis. Photosynthetic performance of a large durum wheat panel under progressive drought in the field was quantified using the light‐induced fluorescence transient (LIFT) sensor for high‐throughput phenotyping. Photosynthesis traits showed high genetic variability, aiding physiological crop breeding. [ABSTRACT FROM AUTHOR]

Keywords: durum wheat; germplasm collections; drought resistance; disease resistance; genome-wide association study (GWAS); quantitative trait locus (QTL); yield sustainability; grain quality EN durum wheat germplasm collections drought resistance disease resistance genome-wide association study (GWAS) quantitative trait locus (QTL) yield sustainability grain quality N.PAG N.PAG 4 05/17/21 20210409 NES 210409 This Special Issue of Frontiers in Plant Science collects 14 manuscripts presented at the Congress "From Seed to Pasta 3" (www.fromseedtopasta.com/). Giancaspro et al.reviewed the genetic variability for quantity and composition of grain protein content (GPC), together with grain yield/spike (GYS) and thousand-kernel weight (TKW) in a durum wheat population obtained from an interspecific cross between a common wheat accession and the durum cv. Crosses with CIMMYT durum lines all produced soft kernel progeny, showing that soft durum can be considered a "tetraploid soft white spring wheat"; notably, excellent bread making potential was achieved by introgressing Dx2+Dy12 I Glu-D1 i alleles in the Soft Svevo background. Durum wheat, germplasm collections, drought resistance, disease resistance, genome-wide association study (GWAS), quantitative trait locus (QTL), yield sustainability, grain quality. [Extracted from the article]

Background: Genetic improvement of root system architecture is essential to improve water and nutrient use efficiency of crops or to boost their productivity under stress or non-optimal soil conditions. One hundred ninety-two Ethiopian durum wheat accessions comprising 167 historical landraces and 25 modern cultivars were assembled for GWAS analysis to identify QTLs for root system architecture (RSA) traits and genotyped with a high-density 90 K wheat SNP array by Illumina. Results: Using a non-roll, paper-based root phenotyping platform, a total of 2880 seedlings and 14,947 seminal roots were measured at the three-leaf stage to collect data for total root length (TRL), total root number (TRN), root growth angle (RGA), average root length (ARL), bulk root dry weight (RDW), individual root dry weight (IRW), bulk shoot dry weight (SDW), presence of six seminal roots per seedling (RT6) and root shoot ratio (RSR). Analysis of variance revealed highly significant differences between accessions for all RSA traits. Four major (− log10P ≥ 4) and 34 nominal (− log10P ≥ 3) QTLs were identified and grouped in 16 RSA QTL clusters across chromosomes. A higher number of significant RSA QTL were identified on chromosome 4B particularly for root vigor traits (root length, number and/or weight). Conclusions: After projecting the identified QTLs on to a high-density tetraploid consensus map along with previously reported RSA QTL in both durum and bread wheat, fourteen nominal QTLs were found to be novel and could potentially be used to tailor RSA in elite lines. The major RGA QTLs on chromosome 6AL detected in the current study and reported in previous studies is a good candidate for cloning the causative underlining sequence and identifying the beneficial haplotypes able to positively affect yield under water- or nutrient-limited conditions. [ABSTRACT FROM AUTHOR]

Durum wheat (Triticum turgidum L. ssp. durum) is one of the top crops in Kazakhstan, where it is cultivated in different ecological niches, mainly at higher latitudes in the steppe zone of the northern region. Therefore, local breeding programs for durum wheat are primarily focused on selection for high productivity in Northern Kazakhstan based on the introduction of promising foreign germplasm and the adoption of marker-assisted selection. In this study, a world tetraploid wheat collection consisted of 184 primitive and domesticated accessions, which were previously genotyped using 16,425 polymorphic SNP markers, was field-tested in Northern and South-eastern Kazakhstan. The field tests have allowed the identification of 80 durum wheat promising lines in Northern Kazakhstan in comparison with a local standard cultivar. Also, GGE (Genotype and Genotype by Environment) biplot analyses for yield performance revealed that accessions of T. dicoccum, T. carthlicum, and T. turanicum also have potential to improve durum wheat yield in the region. The genome-wide association study (GWAS) has allowed the identification of 83 MTAs (marker-trait associations) for heading date, seed maturation time, plant height, spike length, number of fertile spikes, number of kernels per spike, and thousand kernel weight. The comparison of the 83 identified MTAs with those previously reported in GWAS for durum wheat suggests that 38 MTAs are presumably novel, while the co-localization of a large number of MTAs with those previously published confirms the validity of the results of this study. The MTAs reported herewith will provide the opportunity to implement marker-assisted selection in ongoing durum wheat breeding projects targeting higher productivity in the region. [ABSTRACT FROM AUTHOR]

Although durum wheat (Triticum turgidum var. durum Desf.) is a minor cereal crop representing just 5–7% of the world's total wheat crop, it is a staple food in Mediterranean countries, where it is used to produce pasta, couscous, bulgur and bread. In this paper, we cover multi-trait prediction of grain yield (GY), days to heading (DH) and plant height (PH) of 270 durum wheat lines that were evaluated in 43 environments (country–location–year combinations) across a broad range of water regimes in the Mediterranean Basin and other locations. Multi-trait prediction analyses were performed by implementing a multi-trait deep learning model (MTDL) with a feed-forward network topology and a rectified linear unit activation function with a grid search approach for the selection of hyper-parameters. The results of the multi-trait deep learning method were also compared with univariate predictions of the genomic best linear unbiased predictor (GBLUP) method and the univariate counterpart of the multi-trait deep learning method (UDL). All models were implemented with and without the genotype × environment interaction term. We found that the best predictions were observed without the genotype × environment interaction term in the UDL and MTDL methods. However, under the GBLUP method, the best predictions were observed when the genotype × environment interaction term was taken into account. We also found that in general the best predictions were observed under the GBLUP model; however, the predictions of the MTDL were very similar to those of the GBLUP model. This result provides more evidence that the GBLUP model is a powerful approach for genomic prediction, but also that the deep learning method is a practical approach for predicting univariate and multivariate traits in the context of genomic selection. [ABSTRACT FROM AUTHOR]

Carotenoid pigment content is an important quality trait as it confers a natural bright yellow color to pasta preferred by consumers (whiteness vs. yellowness) and nutrients, such as provitamin A and antioxidants, essential for human diet. The main goal of the present review is to summarize the knowledge about the genetic regulation of the accumulation of pigment content in durum wheat grain and describe the genetic improvements obtained by using breeding approaches in the last two decades. Although carotenoid pigment content is a quantitative character regulated by various genes with additive effects, its high heritability has facilitated the durum breeding progress for this quality trait. Mapping research for yellow index and yellow pigment content has identified quantitative trait loci (QTL) on all wheat chromosomes. The major QTL, accounting for up to 60%, were mapped on 7L homoeologous chromosome arms, and they are explained by allelic variations of the phytoene synthase (PSY) genes. Minor QTL were detected on all chromosomes and associated to significant molecular markers, indicating the complexity of the trait. Despite there being currently a better knowledge of the mechanisms controlling carotenoid content and composition, there are gaps that require further investigation and bridging to better understand the genetic architecture of this important trait. The development and the utilization of molecular markers in marker-assisted selection (MAS) programs for improving grain quality have been reviewed and discussed. [ABSTRACT FROM AUTHOR]

Key message: Genomic selection had a higher selection response for FHB resistance than phenotypic selection, while association mapping identified major QTL on chromosome 3B unaffected by plant height and flowering date. Fusarium head blight (FHB) is one of the most destructive diseases of durum wheat. Hence, minimizing losses in yield, quality and avoiding contamination with mycotoxins are of pivotal importance, as durum wheat is mostly used for human consumption. While growing resistant varieties is the most promising approach for controlling this fungal disease, FHB resistance breeding in durum wheat is hampered by the limited variation in the elite gene pool and difficulties in efficiently combining the numerous small-effect resistance quantitative trait loci (QTL) in the same line. We evaluated an international collection of 228 genotyped durum wheat cultivars for FHB resistance over 3 years to investigate the genetic architecture and potential of genomic-assisted breeding for FHB resistance in durum wheat. Plant height was strongly positively correlated with FHB resistance and led to co-localization of plant height and resistance QTL. Nevertheless, a major QTL on chromosome 3B independent of plant height was identified in the same chromosomal interval as reported for the prominent hexaploid resistance QTL Fhb1, though haplotype analysis highlighted the distinctiveness of both QTL. Comparison between phenotypic and genomic selection for FHB resistance revealed a superior prediction ability of the former. However, simulated selection experiments resulted in higher selection responses when using genomic breeding values for early generation selection. An earlier identification of the most promising lines and crossing parents was feasible with a genomic selection index, which suggested a much faster short-term population improvement than previously possible in durum wheat, complementing long-term strategies with exotic resistance donors. [ABSTRACT FROM AUTHOR]

Stripe rust of wheat, caused by Puccinia striiformis f. sp. tritici (Pst), is a global concern for wheat production and has been increasingly destructive in Ethiopia, as well as in the United States and in many other countries. As Ethiopia has a long history of stripe rust epidemics, its native wheat germplasm harbors potentially valuable resistance loci. Moreover, the Ethiopian germplasm has been historically underutilized in breeding of modern wheat worldwide and thus the resistance alleles from the Ethiopian germplasm represent potentially novel sources. The objective of this study was to identify loci conferring resistance to predominant Pst races in Ethiopia and the United States. Using a high-density 90 K wheat single nucleotide polymorphism array, a genome-wide association analysis (GWAS) was conducted on 182 durum wheat landrace accessions and contemporary varieties originating from Ethiopia. Landraces were detected to be more resistant at the seedling stage while cultivars were more resistant at the adultplant stages. GWAS identified 68 loci associated with seedling resistance to one or more races. Six loci on chromosome arms 1AS, 1BS, 3AS, 4BL and 5BL were associated with resistance against at least two races at the seedling stage and five loci were previously undocumented. GWAS analysis of field resistance reactions identified 12 loci associated with resistance on chromosomes 1A, 1B, 2BS, 3BL, 4AL, 4B and 5AL, which were detected in at least two of six field screening nurseries at the adult-plant stage. Comparison with previously mapped resistance loci indicates that six of the 12 resistance loci are newly documented. This study reports effective sources of resistance to contemporary races in Ethiopia and the United States and reveals that Ethiopian durum wheat landraces are abundant in novel Pst resistance loci that may be transferred into adapted cultivars to provide resistance against Pst. [ABSTRACT FROM AUTHOR]

The marker x environment interaction (MxE) genomic model can be used to generate predictions for untested individuals and identify genomic regions in which effects are stable across environments and others that show environmental specificity. The objectives of this study were (i) to extend the MxE model using priors that produce shrinkage and variable selection such as Bayesian ridge regression (BRR) and BayesB (BB), respectively, and (ii) to evaluate the genomic prediction accuracy of MxE, single-environment, and across-environment models using a multiparental durum wheat (Triticum turgidum L. spp. duram) population characterized for grain yield (GY), grain volume weight (GVW), 1000-kernel weight (GWT), and heading date (HD) in four environments. Breeding value predictions were generated for two prediction problems: cross-validation problem 1 (CV1) and cross-validation problem 2 (CV2). In general, results showed that the MxE model performed better than the single-environment and across-environment models, in terms of minimizing the model residual variance, for both CV1 and CV2. The improved data-fitting gain over the other models was more evident for GWT and HD (up to twofold differences) than to GY and GVW, which showed more complex genetic bases and smaller single-marker effects. Considering the Bayesian models used, BB showed better overall prediction accuracy than BRR. As proof-of-concept for the MxE model, the major controllers of HD--Ppd and FT on chromosomes 2A, 2B, and 7A--showed stable effects across environments as well as environment-specific effects. For GY, besides the regions on chromosomes 2B and 7A, additional chromosome regions with large marker effects were detected in all chromosome groups. [ABSTRACT FROM AUTHOR]

Optimization of root system architecture (RSA) traits is an important objective for modern wheat breeding. Linkage and association mapping for RSA in two recombinant inbred line populations and one association mapping panel of 183 elite durum wheat (Triticum turgidum L. var. durum Desf.) accessions evaluated as seedlings grown on filter paper/polycarbonate screening plates revealed 20 clusters of quantitative trait loci (QTLs) for root length and number, as well as 30 QTLs for root growth angle (RGA). Divergent RGA phenotypes observed by seminal root screening were validated by root phenotyping of field-grown adult plants. QTLs were mapped on a high-density tetraploid consensus map based on transcriptassociated Illumina 90K single nucleotide polymorphisms (SNPs) developed for bread and durum wheat, thus allowing for an accurate cross-referencing of RSA QTLs between durum and bread wheat. Among the main QTL clusters for root length and number highlighted in this study, 15 overlapped with QTLs for multiple RSA traits reported in bread wheat, while out of 30 QTLs for RGA, only six showed co-location with previously reported QTLs in wheat. Based on their relative additive effects/significance, allelic distribution in the association mapping panel, and co-location with QTLs for grain weight and grain yield, the RSA QTLs have been prioritized in terms of breeding value. Three major QTL clusters for root length and number (RSA_QTL_cluster_5#, RSA_QTL_cluster_6#, and RSA_QTL_cluster_12#) and nine RGA QTL clusters (QRGA.ubo- 2A.1, QRGA.ubo-2A.3, QRGA.ubo-2B.2/2B.3, QRGA.ubo-4B.4, QRGA.ubo-6A.1, QRGA.ubo-6A.2, QRGA.ubo-7A.1, QRGA. ubo-7A.2, and QRGA.ubo-7B) appear particularly valuable for further characterization towards a possible implementation of breeding applications in marker-assisted selection and/or cloning of the causal genes underlying the QTLs. [ABSTRACT FROM AUTHOR]

Multiparental cross designs for mapping quantitative trait loci ( QTL) provide an efficient alternative to biparental populations because of their broader genetic basis and potentially higher mapping resolution. We describe the development and deployment of a recombinant inbred line ( RIL) population in durum wheat ( Triticum turgidum ssp. durum) obtained by crossing four elite cultivars. A linkage map spanning 2664 cM and including 7594 single nucleotide polymorphisms ( SNPs) was produced by genotyping 338 RILs. QTL analysis was carried out by both interval mapping on founder haplotype probabilities and SNP bi-allelic tests for heading date and maturity date, plant height and grain yield from four field experiments. Sixteen QTL were identified across environments and detection methods, including two yield QTL on chromosomes 2 BL and 7 AS, with the former mapped independently from the photoperiod response gene Ppd- B1, while the latter overlapped with the vernalization locus VRN- A3. Additionally, 21 QTL with environment-specific effects were found. Our results indicated a prevalence of environment-specific QTL with relatively small effect on the control of grain yield. For all traits, functionally different QTL alleles in terms of direction and size of genetic effect were distributed among parents. We showed that QTL results based on founder haplotypes closely matched functional alleles at known heading date loci. Despite the four founders, only 2.1 different functional haplotypes were estimated per QTL, on average. This durum wheat population provides a mapping resource for detailed genetic dissection of agronomic traits in an elite background typical of breeding programmes. [ABSTRACT FROM AUTHOR]

Association mapping provides useful insights on the genetic architecture of quantitative traits across a large number of unrelated genotypes, which in turn allows an informed choice of the lines to be crossed for a more accurate characterization of major QTLs in a biparental genetic background. In this study, seedlings of 183 durum wheat elite accessions were evaluated in order to identify QTLs for root system architecture (RSA). The QTLs identified were compared with QTLs detected for grain yield and its component traits, plant height and peduncle length measured in a previous study where the same accessions were evaluated in 15 field trials with a broad range of soil moisture availability and productivity (Maccaferri et al. in J Exp Bot 62:409-438, ). The following RSA features were investigated in seedlings at the four-leaf stage: seminal root angle, primary root length, total root length, average root length, root number and shoot length. Highly significant differences among accessions were detected for all traits. The highest repeatability ( h = 0.72) was observed for seminal root angle. Out of the 48 QTLs detected for RSA, 15 overlapped with QTLs for agronomic traits and/or grain yield in two or more environments. The congruency of the effects of RSA traits and agronomic traits was evaluated. Seminal root angle and root number appear the most promising traits for further studies on the adaptive role of RSA plasticity on field performance in environments differing for water availability. Our results provide novel insights on the genetic control of RSA and its implications on field performance of durum wheat. [ABSTRACT FROM AUTHOR]

Durum wheat is susceptible to terminal drought which can greatly decrease grain yield. Breeding to improve crop yield is hampered by inadequate knowledge of how the physiological and metabolic changes caused by drought are related to gene expression. To gain better insight into mechanisms defining resistance to water stress we studied the physiological and transcriptome responses of three durum breeding lines varying for yield stability under drought. Parents of a mapping population (Lahn x Cham1) and a recombinant inbred line (RIL2219) showed lowered flag leaf relative water content, water potential and photosynthesis when subjected to controlled water stress time transient experiments over a six-day period. RIL2219 lost less water and showed constitutively higher stomatal conductance, photosynthesis, transpiration, abscisic acid content and enhanced osmotic adjustment at equivalent leaf water compared to parents, thus defining a physiological strategy for high yield stability under water stress. Parallel analysis of the flag leaf transcriptome under stress uncovered global trends of early changes in regulatory pathways, reconfiguration of primary and secondary metabolism and lowered expression of transcripts in photosynthesis in all three lines. Differences in the number of genes, magnitude and profile of their expression response were also established amongst the lines with a high number belonging to regulatory pathways. In addition, we documented a large number of genes showing constitutive differences in leaf transcript expression between the genotypes at control non-stress conditions. Principal Coordinates Analysis uncovered a high level of structure in the transcriptome response to water stress in each wheat line suggesting genome-wide co-ordination of transcription. Utilising a systems-based approach of analysing the integrated wheat’s response to water stress, in terms of biological robustness theory, the findings suggest that each durum line transcriptome responded to water stress in a genome-specific manner which contributes to an overall different strategy of resistance to water stress. [ABSTRACT FROM AUTHOR]

Marker development for marker-assisted selection in plant breeding is increasingly based on next-generation sequencing ( NGS). However, marker development in crops with highly repetitive, complex genomes is still challenging. Here we applied sequence-based genotyping ( SBG), which couples AFLP®-based complexity reduction to NGS, for de novo single nucleotide polymorphisms ( SNP) marker discovery in and genotyping of a biparental durum wheat population. We identified 9983 putative SNPs in 6372 contigs between the two parents and used these SNPs for genotyping 91 recombinant inbred lines ( RILs). Excluding redundant information from multiple SNPs per contig, 2606 (41%) markers were used for integration in a pre-existing framework map, resulting in the integration of 2365 markers over 2607 cM. Of the 2606 markers available for mapping, 91% were integrated in the pre-existing map, containing 708 SSRs, DAr T markers, and SNPs from CRo PS technology, with a map-size increase of 492 cM (23%). These results demonstrate the high quality of the discovered SNP markers. With this methodology, it was possible to saturate the map at a final marker density of 0.8 cM/marker. Looking at the binned marker distribution (Figure 2), 63 of the 268 10- cM bins contained only SBG markers, showing that these markers are filling in gaps in the framework map. As to the markers that could not be used for mapping, the main reason was the low sequencing coverage used for genotyping. We conclude that SBG is a valuable tool for efficient, high-throughput and high-quality marker discovery and genotyping for complex genomes such as that of durum wheat. [ABSTRACT FROM AUTHOR]

Puccinia graminis f. sp. tritici, the causative agent of stem rust in wheat, is a devastating disease of durum wheat. While more than 50 stem rust resistance ( Sr) loci have been identified in wheat, only a few of them have remained effective against Ug99 (TTKSK race) and other durum-specific Ethiopian races. An association mapping (AM) approach based on 183 diverse durum wheat accessions was utilized to identify resistance loci for stem rust response in Ethiopia over four field-evaluation seasons and artificial inoculation with Ug99 and a mixture of durum-specific races. The panel was profiled with simple sequence repeat, Diversity Arrays Technology and sequence-tagged site markers (1,253 in total). The resistance turned out to be oligogenic, with twelve QTL-tagging markers that were significant ( P < 0.05) across three or four seasons. R values ranged from 1.1 to 11.3 %.Twenty-four additional single-marker/QTL regions were found to be significant over two seasons. The AM results confirmed the role of Sr13, previously described in bi-parental mapping studies, and the role of chromosome regions putatively harbouring Sr9, Sr14, Sr17 and Sr28. Three minor QTLs were coincident with those reported in hexaploid wheat and five overlapped with those recently reported in the Sebatel × Kristal durum mapping population. Thirteen single-marker/QTL regions were located in chromosome regions where no Sr genes/QTLs have been previously reported. The allelic variation identified in this study is readily available and can be exploited for marker-assisted selection, thus providing additional opportunities for a more durable stem rust resistance under field conditions. [ABSTRACT FROM AUTHOR]

Leaf rust ( Puccinia triticina Eriks. & Henn.) is a major disease affecting durum wheat production. The Lr14a-resistant gene present in the durum wheat cv. Creso and its derivative cv. Colosseo is one of the best characterized leaf-rust resistance sources deployed in durum wheat breeding. Lr14a has been mapped close to the simple sequence repeat markers gwm146, gwm344 and wmc10 in the distal portion of the chromosome arm 7BL, a gene-dense region. The objectives of this study were: (1) to enrich the Lr14a region with single nucleotide polymorphisms (SNPs) and high-resolution melting (HRM)-based markers developed from conserved ortholog set (COS) genes and from sequenced Diversity Array Technology (DArT) markers; (2) to further investigate the gene content and colinearity of this region with the Brachypodium and rice genomes. Ten new COS-SNP and five HRM markers were mapped within an 8.0 cM interval spanning Lr14a. Two HRM markers pinpointed the locus in an interval of <1.0 cM and eight COS-SNPs were mapped 2.1-4.1 cM distal to Lr14a. Each marker was tested for its capacity to predict the state of Lr14a alleles (in particular, Lr14- Creso associated to resistance) in a panel of durum wheat elite germplasm including 164 accessions. Two of the most informative markers were converted into KASPar markers. Single assay markers ubw14 and wPt- 4038- HRM designed for agarose gel electrophoresis/KASPar assays and high-resolution melting analysis, respectively, as well as the double-marker combinations ubw14/ubw18, ubw14/ubw35 and wPt- 4038- HRM- ubw35 will be useful for germplasm haplotyping and for molecular-assisted breeding. [ABSTRACT FROM AUTHOR]

Genetic analysis of Soil- Borne Cereal Mosaic Virus (SBCMV) resistance in durum wheat was carried out using a population of 180 recombinant inbred lines (RILs) obtained from Simeto (susceptible) × Levante (resistant). The RILs were characterized for SBCMV response in the field under severe and uniform SBCMV infection in two growing seasons and genotyped with simple sequence repeat (SSR) and Diversity Arrays Technology markers. Transgressive segregation was observed for disease reaction as estimated by symptom severity scores and virus concentration in leaves. Heritability of the disease response was high, with h values consistently above 80%. A major quantitative trait locus (QTL) ( QSbm.ubo- 2BS) in the distal telomeric region of chromosome 2BS accounted for 60-70% of the phenotypic variation for symptom severity, 40-55% for virus concentration and 15-30% for grain yield. The favorable allele was contributed by Levante. Seven additional QTL influenced SBCMV resistance, with the low-susceptibility allele contributed by Levante at five QTL and by Simeto at the remaining two. The meta-QTL analysis carried out using the data from two mapping populations (Simeto × Levante and Meridiano × Claudio) suggests that in both populations SBCMV resistance is likely controlled by QSbm.ubo- 2BS. Our results confine QSbm.ubo- 2BS to a c. 2-cM-wide interval flanked by SSR markers that are already being used for marker-assisted selection. [ABSTRACT FROM AUTHOR]

We describe the application of complexity reduction of polymorphic sequences (CRoPS) technology for the discovery of SNP markers in tetraploid durum wheat ( Triticum durum Desf.). A next-generation sequencing experiment was carried out on reduced representation libraries obtained from four durum cultivars. SNP validation and minor allele frequency (MAF) estimate were carried out on a panel of 12 cultivars, and the feasibility of genotyping these SNPs in segregating populations was tested using the Illumina Golden Gate (GG) technology. A total of 2,659 SNPs were identified on 1,206 consensus sequences. Among the 768 SNPs that were chosen irrespective of their genomic repetitiveness level and assayed on the Illumina BeadExpress genotyping system, 275 (35.8%) SNPs matched the expected genotypes observed in the SNP discovery phase. MAF data indicated that the overall SNP informativeness was high: a total of 196 (71.3%) SNPs had MAF >0.2, of which 76 (27.6%) showed MAF >0.4. Of these SNPs, 157 were mapped in one of two mapping populations (Meridiano × Claudio and Colosseo × Lloyd) and integrated into a common genetic map. Despite the relatively low genotyping efficiency of the GG assay, the validated CRoPS-derived SNPs showed valuable features for genomics and breeding applications such as a uniform distribution across the wheat genome, a prevailing single-locus codominant nature and a high polymorphism. Here, we report a new set of 275 highly robust genome-wide Triticum SNPs that are readily available for breeding purposes. [ABSTRACT FROM AUTHOR]

Association mapping was used to dissect the genetic basis of drought-adaptive traits and grain yield (GY) in a collection of 189 elite durum wheat accessions evaluated in 15 environments highly different for water availability during the crop cycle (from 146 to 711 mm) and GY (from 9.9 to 67.3 q ha−1). For highly heritable traits (e.g. heading date, kernel weight, etc.) several significant experiment-wise marker-trait associations were detected across five or more (up to 13 for kernel weight) environments, with R2 values ranging from ca. 5 to 10%. As to GY, significant associations (R2 from 2.5 to 4.2%) were mostly detected in one environment only (56 markers), while decreasing rapidly from two to five environments (from 20 to three markers, respectively) and with only one marker (Xbarc197 on chr. 5A) found significant in six environments (ranging from low- to high-yielding). These results are probably due to the complex genetic basis of GY and its interaction with environmental conditions. The number of markers significantly affecting GY decreased considerably under drought conditions, suggesting a limited effectiveness of association mapping to identify loci for GY under low-moisture conditions, most likely because different genotypes can attain similar phenotypes via different morpho-physiological traits and corresponding gene networks. Our study confirmed the role of major loci for phenology previously described in biparental mapping populations, highlighted a novel set of loci for drought-adaptive traits, and provided information on the agronomic value of the alleles at such loci across a broad range of soil moisture conditions. [ABSTRACT FROM PUBLISHER]

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. [ABSTRACT FROM AUTHOR]

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The cover image is based on the Original Article High‐throughput field phenotyping reveals genetic variation in photosynthetic traits in durum wheat under drought by Nícolas Zendonadi dos Santos et al., https://doi.org/10.1111/pce.14136. [ABSTRACT FROM AUTHOR]

Flowering time is a critical stage for crop development as it regulates the ability of plants to adapt to an environment. To understand the genetic control of flowering time, a genome-wide association study (GWAS) was conducted to identify the genomic regions associated with the control of this trait in durum wheat (Triticum durum Desf.). A total of 96 landraces and 288 modern lines were evaluated for days to heading, growing degree days, and accumulated day length at flowering across 13 environments spread across Morocco, Lebanon, Mauritania, and Senegal. These environments were grouped into four pheno-environments based on temperature, day length, and other climatic variables. Genotyping with a 35K Axiom array generated 7652 polymorphic single nucleotide polymorphisms (SNPs) in addition to 3 KASP markers associated with known flowering genes. In total, 32 significant QTLs were identified in both landraces and modern lines. Some QTLs had a strong association with already known regulatory photoperiod genes, Ppd-A and Ppd-B, and vernalization genes Vrn-A1 and VrnA7. However, these loci explained only 5% to 20% of variance for days to heading. Seven QTLs overlapped between the two germplasm groups in which Q.ICD.Eps-03 and Q.ICD.Vrn-15 consistently affected flowering time in all the pheno-environments, while Q.ICD.Eps-09 and Q.ICD.Ppd-10 were significant only in two pheno-environments and the combined analysis across all environments. These results help clarify the genetic mechanism controlling flowering time in durum wheat and show some clear distinctions to what is known for common wheat (Triticum aestivum L.). [ABSTRACT FROM AUTHOR]

High-throughput phenotyping platforms provide valuable opportunities to investigate biomass and drought-adaptive traits. We explored the capacity of traits associated with drought adaptation such as aerial measurements of the Normalized Difference Vegetation Index (NDVI) and carbon isotope composition (δ13C) determined at the leaf level to predict genetic variation in biomass. A panel of 248 elite durum wheat accessions was grown at the Maricopa Phenotyping platform (US) under well-watered conditions until anthesis, and then irrigation was stopped and plot biomass was harvested about three weeks later. Globally, the δ13C values increased from the first to the second sampling date, in keeping with the imposition of progressive water stress. Additionally, δ13C was negatively correlated with final biomass, and the correlation increased at the second sampling, suggesting that accessions with lower water-use efficiency maintained better water status and, thus, performed better. Flowering time affected NDVI predictions of biomass, revealing the importance of developmental stage when measuring the NDVI and the effect that phenology has on its accuracy when monitoring genotypic adaptation to specific environments. The results indicate that in addition to choosing the optimal phenotypic traits, the time at which they are assessed, and avoiding a wide genotypic range in phenology is crucial. [ABSTRACT FROM AUTHOR]

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 Tscl and Tsc2 were associated with susceptibility to Ptr ToxC- and Ptr ToxB-producing isolates, respectively, but Tsnl was not associated with tan spot caused by Ptr ToxA-producing isolates, which further validates that the Tsnl--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, Tscl, Tsc2, and the chromosome 2AS loci to obtain broad resistance to tan spot. [ABSTRACT FROM AUTHOR]

Highlights • Th. ponticum 7AgL introgressions onto durum wheat 7AL improve yield-related traits. • 7AgL chromatin significantly increases grain number across contrasting environments. • A major QTL for grain number increase was confirmed in the 28–40% 7AgL interval. • Results validate the use of chromosome engineering for targeted wheat improvement. Abstract Introgressions of Thinopyrum ponticum 7AgL chromosome segments, spanning 23%, 28% and 40% of the distal end of durum wheat 7AL arm, were previously shown to contain multiple beneficial gene(s)/QTL for yield-related traits, in addition to effective disease resistance (Lr19, Sr25) and quality (Yp) genes. In the present study, durum wheat near isogenic recombinant lines (NIRLs), harbouring each of the three introgressions, were included for the first time in multi-location field trials, to evaluate general and environment-specific effects of the alien chromatin on 26 yield-related traits. Results from nine different trials across contrasting environments of Italy, Morocco and South Australia over four years revealed that the overall impact of 7AgL introgressions into the tetraploid wheat background did not incur, except in one environment, a major yield penalty. The effect of the three 7AgL segments on individual yield-contributing traits resulted in significant increases of biomass m−2 (+9%), spike number m−2 (+13%), grain number m−2 (+11%) and spikelet-1 (+8%), as well as a significant decrease in grain weight (−8%). When the separate NIRLs were analysed, each of the three 7AgL segments were associated with specific yield component variation. The effects of the 40%-long segment proved to be the most stably expressed across environments and involved significant increases of spike and grain number m−2 (13% and 15%, respectively), grain number spike-1 (10%) and spike fertility index (46%), though accompanied by a significant decrease in thousand grain weight (−23%). In spite of this trade-off between grain number and grain weight, their interplay was such that in four trials, including drier environments, a grain yield advantage was observed. This evidence, and comparison with the two other NIRLs, substantiates the hypothesized existence of major gene(s)/QTL for grain number in the most proximal 28–40% 7AgL region, exclusive to the 40%-long 7AgL introgression. The present study represents an important validation of the use of chromosomally engineered genetic stocks for durum wheat improvement, targeting not only disease resistance and quality traits but also relevant yield components. [ABSTRACT FROM AUTHOR]

Soil-borne cereal mosaic (SBCM) is a viral disease, which seriously affects hexaploid as well as tetraploid wheat crops in Europe. In durum wheat ( Triticum durum Desf.), the elite germplasm is characterized by a wide range of responses to SBCMV, from susceptibility to almost complete resistance. In this study, the genetic analysis of SBCMV resistance was carried out using a population of 181 durum wheat recombinant inbred lines (RILs) obtained from Meridiano (resistant) × Claudio (moderately susceptible), which were profiled with SSR and DArT markers. The RILs were characterized for SBCMV response in the field under severe and uniform SBCMV infection during 2007 and 2008. A wide range of disease reactions (as estimated by symptom severity and DAS-ELISA) was observed. A large portion of the variability for SBCMV response was explained by a major QTL ( QSbm.ubo- 2BS) located in the distal telomeric region of chromosome 2BS near the marker triplet Xbarc35- Xwmc661- Xgwm210, with R values ranging from 51.6 to 91.6%. The favorable allele was contributed by Meridiano. Several QTLs with minor effects on SBCMV response were also detected. Consistently with the observed transgressive segregation, the resistance alleles at minor QTLs were contributed by both parents. The presence and effects of QSbm.ubo- 2BS were validated through association mapping in a panel of 111 elite durum wheat accessions. [ABSTRACT FROM AUTHOR]