For new varieties to be sold, they must first pass assessment using a set of phenotypic criteria that test for distinctness, uniformity, and stability (DUS) and which serve as the basis for the awarding of plant breeders' rights. The objective of this study was to use historical DUS phenotypic data to investigate the genetic architecture of DUS characteristics in wheat (Triticum aestivum L.). Using a panel of 334 varieties, genome-wide association studies (GWAS) identified significant marker-trait associations for 18 of the 33 wheat DUS characteristics investigated. The most significant was the genetic locus P22_3B_821 for stem pith thickness, located between 818 and 830 Mb on chromosome 3B. Haplotype analysis informed conversion of three genetic markers selected from the genotyping array to the KASP genotyping platform, allowing alleles associated with low-medium versus thick pith thickness to be easily tracked. Subsequent genomic and molecular analysis found evidence that TaDof-B copy number variation (CNV) may underlie control of pith thickness in wheat, whereby CNV ≥3 was associated with the solid stem phenotype, analogous to that previously observed for TdDof-B in durum wheat (T. turgidum subsp. durum) and lower CNV with hollow stems. Finally, correlations between DUS characteristics with yield, grain quality traits, and year of release indicated that reduced ear density is under breeder selection and that this has a beneficial effect on the quality traits 'grain test weight' and 'Hagberg falling number'. Collectively, these findings and molecular tools will help inform commercial, DUS regulatory and scientific advances in future wheat research and development programmes.

We assembled a European bread wheat (Triticum aestivum L.) association mapping panel (n = 480) genotyped using a 90,000 feature single nucleotide polymorphism array, with the aim of identifying genetic loci controlling resistance to four fungal diseases: yellow (stripe) rust (YR), brown (leaf) rust (BR), Septoria tritici blotch (ST) and powdery mildew (PM). Simulations showed our panel to have good power to detect genetic loci, with > 50% probability of identifying loci controlling as little as 5% of the variance when heritability was 0.6 or more. Using disease infection data collected across 31 trials undertaken in five European countries, genome-wide association studies (GWAS) identified 34 replicated genetic loci (20 for YR, 12 for BR, two for PM, 0 for ST), with seven loci associated with resistance to two or more diseases. Construction and analysis of eight bi-parental populations enabled two selected genetic loci, yellow rust resistance locus YR_2A010 (chromosome 2A) and YR_6A610 (6A), to be independently cross-validated, along with the development of genetic markers to track resistance alleles at these loci. Notably, the chromosome 2A yellow and brown rust resistance locus corresponds to the 2NvS introgression from the wild wheat species, Aegilops ventricosa. We found evidence of strong selection for 2NvS over recent breeding history, being present in 48% of the most recent cultivars in our panel. Collectively, we define the genetic architectures controlling resistance to major fungal diseases of wheat under European field environments, and provide resources to exploit these for the development of new wheat cultivars with improved disease resistance.

Harnessing genetic diversity in major staple crops through the development of new breeding capabilities is essential to ensure food security1. Here we examined the genetic and phenotypic diversity of the A. E. Watkins landrace collection2 of bread wheat (Triticum aestivum), a major global cereal, by whole-genome re-sequencing of 827 Watkins landraces and 208 modern cultivars and in-depth field evaluation spanning a decade. We found that modern cultivars are derived from two of the seven ancestral groups of wheat and maintain very long-range haplotype integrity. The remaining five groups represent untapped genetic sources, providing access to landrace-specific alleles and haplotypes for breeding. Linkage disequilibrium-based haplotypes and association genetics analyses link Watkins genomes to the thousands of identified high-resolution quantitative trait loci and significant marker-trait associations. Using these structured germplasm, genotyping and informatics resources, we revealed many Watkins-unique beneficial haplotypes that can confer superior traits in modern wheat. Furthermore, we assessed the phenotypic effects of 44,338 Watkins-unique haplotypes, introgressed from 143 prioritized quantitative trait loci in the context of modern cultivars, bridging the gap between landrace diversity and current breeding. This study establishes a framework for systematically utilizing genetic diversity in crop improvement to achieve sustainable food security.

Wheat ( Triticum aestivum L.) is a major source of nutrients for populations across the globe, but the amino acid composition of wheat grain does not provide optimal nutrition. The nutritional value of wheat grain is limited by low concentrations of lysine (the most limiting essential amino acid) and high concentrations of free asparagine (precursor to the processing contaminant acrylamide). There are currently few available solutions for asparagine reduction and lysine biofortification through breeding. In this study, we investigated the genetic architecture controlling grain free amino acid composition and its relationship to other traits in a Robigus × Claire doubled haploid population. Multivariate analysis of amino acids and other traits showed that the two groups are largely independent of one another, with the largest effect on amino acids being from the environment. Linkage analysis of the population allowed identification of quantitative trait loci (QTL) controlling free amino acids and other traits, and this was compared against genomic prediction methods. Following identification of a QTL controlling free lysine content, wheat pangenome resources facilitated analysis of candidate genes in this region of the genome. These findings can be used to select appropriate strategies for lysine biofortification and free asparagine reduction in wheat breeding programs.

Summary The wheat flag leaf is the main contributor of photosynthetic assimilates to developing grains. Understanding how canopy architecture strategies affect source strength and yield will aid improved crop design. We used an eight‐founder population to investigate the genetic architecture of flag leaf area, length, width and angle in European wheat. For the strongest genetic locus identified, we subsequently created a near‐isogenic line (NIL) pair for more detailed investigation across seven test environments. Genetic control of traits investigated was highly polygenic, with colocalisation of replicated quantitative trait loci (QTL) for one or more traits identifying 24 loci. For QTL QFll.niab‐5A.1 (FLL5A), development of a NIL pair found the FLL5A+ allele commonly conferred a c. 7% increase in flag and second leaf length and a more erect leaf angle, resulting in higher flag and/or second leaf area. Increased FLL5A‐mediated flag leaf length was associated with: (1) longer pavement cells and (2) larger stomata at lower density, with a trend for decreased maximum stomatal conductance (Gsmax) per unit leaf area. For FLL5A, cell size rather than number predominantly determined leaf length. The observed trade‐offs between leaf size and stomatal morphology highlight the need for future studies to consider these traits at the whole‐leaf level.

Genomic selection has recently become an established part of breeding strategies in cereals. However, a limitation of linear genomic prediction models for complex traits such as yield is that these are unable to accommodate Genotype by Environment effects, which are commonly observed over trials on multiple locations. In this study, we investigated how this environmental variation can be captured by the collection of a large number of phenomic markers using high-throughput field phenotyping and whether it can increase GS prediction accuracy. For this purpose, 44 winter wheat (Triticum aestivum L.) elite populations, comprising 2,994 lines, were grown on two sites over 2 years, to approximate the size of trials in a practical breeding programme. At various growth stages, remote sensing data from multi- and hyperspectral cameras, as well as traditional ground-based visual crop assessment scores, were collected with approximately 100 different data variables collected per plot. The predictive power for grain yield was tested for the various data types, with or without genome-wide marker data sets. Models using phenomic traits alone had a greater predictive value (R-2 = 0.39-0.47) than genomic data (approximately R-2 = 0.1). The average improvement in predictive power by combining trait and marker data was 6%-12% over the best phenomic-only model, and performed best when data from one full location was used to predict the yield on an entire second location. The results suggest that genetic gain in breeding programmes can be increased by utilisation of large numbers of phenotypic variables using remote sensing in field trials, although at what stage of the breeding cycle phenomic selection could be most profitably applied remains to be answered.

Yellow rust (YR), or stripe rust, is a fungal infection of wheat (Triticum aestivum L.) caused by the pathogen Puccinia striiformisWestend f. sp. tritici (Pst). Although much research has focused on YR leaf infection, we are not aware of studies investigating the genetic control of YR resistance in the wheat ear. Using an eight-founder multiparent advanced generation intercross (MAGIC) population, we identified five quantitative trait loci (QTL) controlling glume YR resistance in wheat ears. Of these, three (QYrg.niab-2D.2, QYrg.niab-4D.1, and QYrg.niab-5A.1) collocated with leaf YR resistance QTL previously identified in the same population. We find evidence that QYrg.niab-5A.1 likely corresponds to the adult plant resistance locus Yr34 introgressed from einkorn wheat (T. monococcum L. subsp. monococcum), and that resistance at QYrg.niab-2D.2 also likely originated from a chromosomal introgression from a wheat relative. The two remaining glume YR resistance QTL were linked to genetic loci controlling flowering time, with early flowering alleles conferring reduced glume YR resistance. The association between earlier flowering and increased glume infection is likely due to the emergence of the ear during environmental conditions more favorable for Pst infection. Collectively, these first insights into the genetic control of YR resistance in glumes provides specific genetic targets for the control of YR resistance in both the leaves and the glumes and will be especially relevant to wheat grown in Pst- prone agricultural environments where earlier flowering is favored.

Yellow rust (YR), or stripe rust, is a major fungal disease of wheat ( Triticum aestivum ) caused by Puccinia striiformis f. sp. tritici ( Pst ). Since 2011, the historically clonal European Pst races have been superseded by the rapid incursion of genetically diverse lineages, reducing the resistance of varieties that previously showed durable resistance. Identification of sources of genetic resistance to such races is a high priority for wheat breeding. Here we use a wheat eight-founder multi-parent population genotyped with a 90,000 feature single nucleotide polymorphism array to genetically map adult plant YR resistance to such new Pst races. Analysis of five trials, at three sites in the UK, consistently identified four highly significant quantitative trait loci (QTL) across all test environments, located on chromosomes 1A ( QYr.niab-1A.1 ), 2A ( QYr.niab-2A.1 ), 2B ( QYr.niab-2B.1 ) and 2D ( QYr.niab-2D.1 ). Together these explained ~ 50% of the phenotypic variation, and genetic markers were developed that distinguished resistant and susceptible alleles. Analysis of these QTL in two-way and three-way combinations showed combinations conferred greater resistance than single QTL. Four additional major-effect QTL were detected in two or more trials, together explaining 15–20% of the phenotypic variation, as well as six minor QTL. Genomic analysis found the median physical interval size of these eight QTL to be 19.8 Mbp, and QYr.niab-2A.1 and QYr.niab-2D.1 to be at homoeologous locations on the group-2 chromosomes. Notably, the QYr.niab-2B.1 physical interval contained five nucleotide-binding leucine-rich repeat (NLR) candidate genes with integrated BED domains, of which two corresponded to the cloned resistance genes Yr7 and Yr5/YrSp .

Key message Analysis of a wheat multi-founder population identified 14 yellow rust resistance QTL. For three of the four most significant QTL, haplotype analysis indicated resistance alleles were rare in European wheat. Abstract Stripe rust, or yellow rust (YR), is a major fungal disease of wheat ( Triticum aestivum ) caused by Puccinia striiformis Westend f. sp. tritici ( Pst ). Since 2011, the historically clonal European Pst races have been superseded by the rapid incursion of genetically diverse lineages, reducing the resistance of varieties previously showing durable resistance. Identification of sources of genetic resistance to such races is a high priority for wheat breeding. Here we use a wheat eight-founder multi-parent population genotyped with a 90,000 feature single nucleotide polymorphism array to genetically map YR resistance to such new Pst races. Genetic analysis of five field trials at three UK sites identified 14 quantitative trait loci (QTL) conferring resistance. Of these, four highly significant loci were consistently identified across all test environments, located on chromosomes 1A ( QYr.niab-1A.1 ), 2A ( QYr.niab-2A.1 ), 2B ( QYr.niab-2B.1 ) and 2D ( QYr.niab-2D.1 ), together explaining ~ 50% of the phenotypic variation. Analysis of these four QTL in two-way and three-way combinations showed combinations conferred greater resistance than single QTL, and genetic markers were developed that distinguished resistant and susceptible alleles. Haplotype analysis in a collection of wheat varieties found that the haplotypes associated with YR resistance at three of these four major loci were rare (≤ 7%) in European wheat, highlighting their potential utility for future targeted improvement of disease resistance. Notably, the physical interval for QTL QYr.niab-2B.1 contained five nucleotide-binding leucine-rich repeat candidate genes with integrated BED domains, of which two corresponded to the cloned resistance genes Yr7 and Yr5/YrSp . Graphical abstract

Crop height (Ht), heading date (Hd), and grain yield (GY) are inter-related in wheat. Independent manipulation of each is important for adaptation and performance. Validated quantitative trait loci (QTLs) for all three co-locate on chromosome 3A in the Avalon×Cadenza population, with increased Ht, Hd, and GY contributed by Cadenza. We asked if these are linked or pleiotropic effects using recombinant lines, and showed that Ht and Hd effects are independent. The Chinese Spring equivalent to the newly defined Ht interval contained a gene cluster involved in cell wall growth and displaying high levels of differential transcript expression. The Hd locus is larger and rearranged compared with the reference genome, but FT2 (Flowering Locus T2) is of particular interest. The Hd effect acted independently of photoperiod and vernalization, but did exhibit seasonal genotype×environment interaction. Recombinants were phenotyped for GY in replicated field experiments. GY was most associated with Cadenza alleles for later Hd, supporting physiological studies using the same lines proposing that 'late' alleles at this locus increase spike fertility and grain number (GN). The work has uncoupled height from heading and yield, and shown that one of very few validated GY QTLs in wheat is probably mediated by phenological variation.

Background Little is known about the initial, symptomless (latent) phase of the devastating wheat disease Septoria tritici blotch. However, speculations as to its impact on fungal success and disease severity in the field have suggested that a long latent phase is beneficial to the host and can reduce inoculum build up in the field over a growing season. The winter wheat cultivar Stigg is derived from a synthetic hexaploid wheat and contains introgressions from wild tetraploid wheat Triticum turgidum subsp. dicoccoides , which contribute to cv. Stigg’s exceptional STB resistance, hallmarked by a long latent phase. We compared the early transcriptomic response to Zymoseptoria tritici of cv. Stigg to a susceptible wheat cultivar, to elucidate the mechanisms of and differences in pathogen recognition and disease response in these two hosts. Results The STB-susceptible cultivar Longbow responds to Z. tritici infection with a stress response, including activation of hormone-responsive transcription factors, post translational modifications, and response to oxidative stress. The activation of key genes associated with these pathways in cv. Longbow was independently observed in a second susceptible wheat cultivar based on an independent gene expression study. By comparison, cv. Stigg is apathetic in response to STB, and appears to fail to activate a range of defence pathways that cv. Longbow employs. Stigg also displays some evidence of sub-genome bias in its response to Z. tritici infection, whereas the susceptible cv. Longbow shows even distribution of Z. tritici responsive genes across the three wheat sub-genomes. Conclusions We identify a suite of disease response genes that are involved in early pathogen response in susceptible wheat cultivars that may ultimately lead to susceptibility. In comparison, we hypothesise that rather than an active defence response to stave off disease progression, cv. Stigg’s defence strategy is molecular lethargy, or a lower-amplitude of pathogen recognition that may stem from cv. Stigg’s wild wheat-derived ancestry. Overall, we present insights into cv. Stigg’s exceptional resistance to STB, and present key biological processes for further characterisation in this pathosystem.

Yield penalty and increased grain protein content traits associated with Aegilops ventricosa 7D introgression have been mapped for the first time, and they are physically distinct from the eyespot resistance locus Pch1. Wheat wild relatives represent an important source of genetic variation, but introgression of agronomically relevant genes, such as for disease resistance, may lead to the simultaneous introduction of genetically linked deleterious traits. Pch1 is a dominant gene, conferring resistance to eyespot and was introgressed to wheat from Aegilops ventricosa as part of a large segment of the 7DV chromosome. This introgression has been associated with a significant yield reduction and a concomitant increase in grain protein content. In this study, we evaluated both traits and their relationship to the location of the Pch1 gene. We found that both QTLs were clearly distinct from the Pch1 gene, being located on a different linkage group to Pch1. In addition, we found that the QTL for increased grain protein content was strong and consistent across field trials, whereas the yield penalty QTL was unstable and environmentally dependent. The yield and grain protein content QTLs were genetically linked and located in the same linkage group. This finding is due in part to the small size of the population, and to the restricted recombination between wheat 7D and Ae. ventricosa 7Dv chromosomes. Although recombination in this interval is rare, it does occur. A recombinant line containing Pch1 and 7D_KASP6, the marker associated with increase in grain protein content, but not Xwmc221, the marker associated with the yield penalty effect, was identified.

SummaryWheat contains abundant xylan in cell walls of all tissues, but in endosperm, there is an unusual form of xylan substituted only by arabinose (arabinoxylan; AX) that has long chains and low levels of feruloylation, a fraction of which is extractable in water (WE‐AX). WE‐AX acts as soluble dietary fibre but also gives rise to viscous extracts from grain, a detrimental trait for some non‐food uses of wheat. Here, we show that a glycosyl transferase family 43 wheat gene abundantly expressed in endosperm complements the Arabidopsis irx9 mutant and so name the three homoeologous genes TaIRX9b. We generated wheat lines with a constitutive knockout of TaIRX9b by stacking loss‐of‐function alleles for these homeologues from a mutagenized hexaploid wheat population resulting in decreases in grain extract viscosity of 50%–80%. The amount and chain length of WE‐AX molecules from grain of these triple‐stack lines was decreased accounting for the changes in extract viscosity. Imaging of immature wheat grain sections of triple‐stacks showed abolition of immunolabelling in endosperm with LM11 antibody that recognizes epitopes in AX, but also showed apparently normal cell size and shape in all cell types, including endosperm. We identified differentially expressed genes from endosperm of triple‐stacks suggesting that compensatory changes occur to maintain this endosperm cell wall integrity. Consistent with this, we observed increased ferulate dimerization and increased cross‐linking of WE‐AX molecules in triple‐stacks. These novel wheat lines lacking functional TaIRX9b therefore provide insight into control of wheat endosperm cell walls.

Genomic selection offers several routes for increasing the genetic gain or efficiency of plant breeding programmes. In various species of livestock, there is empirical evidence of increased rates of genetic gain from the use of genomic selection to target different aspects of the breeder’s equation. Accurate predictions of genomic breeding value are central to this, and the design of training sets is in turn central to achieving sufficient levels of accuracy. In summary, small numbers of close relatives and very large numbers of distant relatives are expected to enable predictions with higher accuracy. To quantify the effect of some of the properties of training sets on the accuracy of genomic selection in crops, we performed an extensive field-based winter wheat trial. In summary, this trial involved the construction of 44 F 2:4 bi- and tri-parental populations, from which 2992 lines were grown on four field locations and yield was measured. For each line, genotype data were generated for 25 K segregating SNP markers. The overall heritability of yield was estimated to 0.65, and estimates within individual families ranged between 0.10 and 0.85. Genomic prediction accuracies of yield BLUEs were 0.125–0.127 using two different cross-validation approaches and generally increased with training set size. Using related crosses in training and validation sets generally resulted in higher prediction accuracies than using unrelated crosses. The results of this study emphasise the importance of the training panel design in relation to the genetic material to which the resulting prediction model is to be applied.

Crop diseases reduce wheat yields by ~25% globally and thus pose a major threat to global food security 1 . Genetic resistance can reduce crop losses in the field and can be selected through the use of molecular markers. However, genetic resistance often breaks down following changes in pathogen virulence, as experienced with the wheat yellow (stripe) rust fungus Puccinia striiformis f. sp. tritici ( Pst ) 2 . This highlights the need to (1) identify genes that, alone or in combination, provide broad-spectrum resistance, and (2) increase our understanding of the underlying molecular modes of action. Here we report the isolation and characterization of three major yellow rust resistance genes ( Yr7 , Yr5 and YrSP ) from hexaploid wheat ( Triticum aestivum ), each having a distinct recognition specificity. We show that Yr5 , which remains effective to a broad range of Pst isolates worldwide, is closely related yet distinct from Yr7 , whereas YrSP is a truncated version of Yr5 with 99.8% sequence identity. All three Yr genes belong to a complex resistance gene cluster on chromosome 2B encoding nucleotide-binding and leucine-rich repeat proteins (NLRs) with a non-canonical N-terminal zinc-finger BED domain 3 that is distinct from those found in non-NLR wheat proteins. We developed diagnostic markers to accelerate haplotype analysis and for marker-assisted selection to expedite the stacking of the non-allelic Yr genes. Our results provide evidence that the BED-NLR gene architecture can provide effective field-based resistance to important fungal diseases such as wheat yellow rust.

The precocious germination of cereal grains before harvest, also known as pre-harvest sprouting, is an important source of yield and quality loss in cereal production. Pre-harvest sprouting is a complex grain defect and is becoming an increasing challenge due to changing climate patterns. Resistance to sprouting is multi-genic, although a significant proportion of the sprouting variation in modern wheat cultivars is controlled by a few major quantitative trait loci, including Phs-A1 in chromosome arm 4AL. Despite its importance, little is known about the physiological basis and the gene(s) underlying this important locus. In this study, we characterized Phs-A1 and show that it confers resistance to sprouting damage by affecting the rate of dormancy loss during dry seed after-ripening. We show Phs-A1 to be effective even when seeds develop at low temperature (13 °C). Comparative analysis of syntenic Phs-A1 intervals in wheat and Brachypodium uncovered ten orthologous genes, including the Plasma Membrane 19 genes (PM19-A1 and PM19-A2) previously proposed as the main candidates for this locus. However, high-resolution fine-mapping in two bi-parental UK mapping populations delimited Phs-A1 to an interval 0.3 cM distal to the PM19 genes. This study suggests the possibility that more than one causal gene underlies this major pre-harvest sprouting locus. The information and resources reported in this study will help test this hypothesis across a wider set of germplasm and will be of importance for breeding more sprouting resilient wheat varieties.

SNP markers were developed for the OWBM resistance gene Sm1 that will be useful for MAS. The wheat Sm1 region is collinear with an inverted syntenic interval in B. distachyon.

Sunflower (Helianthus annuus L.) seed oil with high palmitic acid content has enhanced thermo-oxidative stability, which makes it well suited to high-temperature uses. CAS-5 is a sunflower mutant line that accumulates over 25 % palmitic acid in its seed oil, compared to 5–8 % in conventional cultivars. The objective of this study was to investigate the molecular basis of the high-palmitic acid trait in CAS-5 through both candidate gene and QTL mapping approaches. An F2 population derived from the cross between CAS-5 and the conventional line HA-89 was developed. A 3-ketoacyl-ACP synthase II (KASII) locus on a telomeric region of linkage group (LG) 9 of the sunflower genetic map was found to co-segregate with palmitic acid content in this population. The KASII locus explained the vast majority of the phenotypic variation (98 %) of the trait. Two minor QTL affecting palmitic acid content were also found on the lower half of LG 9 and on LG 17. Additionally, QTL associated with other major fatty acids (stearic, oleic, and linoleic acid) were identified on LG 1, 6, and 10. This result may reflect untapped genetic variation that could exist among sunflower cultivars for genes determining fatty acid composition. In addition to demonstrating the major role of a KASII locus in the accumulation of high levels of palmitic acid in CAS-5 seeds, this study stressed the importance of characterizing genes with minor effects on fatty acid profile in order to establish optimal breeding strategies for modifying fatty acid composition in sunflower seed oil.

A genetic analysis of plant characters associated with lodging resistance, yield and other agronomic traits was made on two doubled haploid winter wheat populations grown at two UK locations in the 2004/2005, 2005/2006 and 2006/2007 seasons. Wide genetic variation was found for traits that affect lodging, including plant height, components of stem strength (stem diameter, wall width and material strength), components of anchorage strength (spread and depth of the root plate), ear area and shoot number per plant. Heritabilities were estimated for each of the key lodging traits, with plant height having the highest heritability and anchorage traits the lowest values. Six quantitative trait loci (QTL) controlling plant height had individual height effects (2 × the additive effect) of 3–9 cm and taken together, could potentially increase plant height by up to 34 cm. Three of the height QTL were also associated with greater yield or greater thousand grain weight, and three were associated with components of stem strength or anchorage strength. QTL were also identified for each of the measured lodging traits, which were unrelated to height. Individual QTL with the largest estimated effects on lodging resistance were for height, stem diameter, stem material strength, stem failure moment, root plate spread and root plate depth. Diagnostic genetic markers for the most important QTL regions are now required to enable breeders to efficiently combine multiple traits together in a single variety that will increase lodging resistance and yield simultaneously.