Genome-wide association analysis identifies a consistent QTL for powdery mildew resistance on chromosome 3A in Nordic and Baltic spring wheat.

KEY MESSAGE: QPm.NOBAL-3A is an important QTL providing robust adult plant powdery mildew resistance in Nordic and Baltic spring wheat, aiding sustainable crop protection and breeding. Powdery mildew, caused by the biotrophic fungal pathogen Blumeria graminis f. sp. tritici, poses a significant threat to bread wheat (Triticum aestivum L.), one of the world's most crucial cereal crops. Enhancing cultivar resistance against this devastating disease requires a comprehensive understanding of the genetic basis of powdery mildew resistance. In this study, we performed a genome-wide association study (GWAS) using extensive field trial data from multiple environments across Estonia, Latvia, Lithuania, and Norway. The study involved a diverse panel of recent wheat cultivars and breeding lines sourced from the Baltic region and Norway. We identified a major quantitative trait locus (QTL) on chromosome 3A, designated as QPm.NOBAL-3A, which consistently conferred high resistance to powdery mildew across various environments and countries. Furthermore, the consistency of the QTL haplotype effect was validated using an independent Norwegian spring wheat panel. Subsequent greenhouse seedling inoculations with 15 representative powdery mildew isolates on a subset of the GWAS panel indicated that this QTL provides adult plant resistance and is likely of race non-specific nature. Moreover, we developed and validated KASP markers for QPm.NOBAL-3A tailored for use in breeding. These findings provide a critical foundation for marker-assisted selection in breeding programs aimed at pyramiding resistance QTL/genes to achieve durable and broad-spectrum resistance against powdery mildew.

Multispectral-derived genotypic similarities from budget cameras allow grain yield prediction and genomic selection augmentation in single and multi-environment scenarios in spring wheat.

With abundant available genomic data, genomic selection has become routine in many plant breeding programs. Multispectral data captured by UAVs showed potential for grain yield (GY) prediction in many plant species using machine learning; however, the possibilities of utilizing this data to augment genomic prediction models still need to be explored. We collected high-throughput phenotyping (HTP) multispectral data in a genotyped multi-environment large-scale field trial using two cost-effective cameras to fill this gap. We tested back to back the prediction ability of GY prediction models, including genomic (G matrix), multispectral-derived (M matrix), and environmental (E matrix) relationships using best linear unbiased predictor (BLUP) methodology in single and multi-environment scenarios. We discovered that M allows for GY prediction comparable to the G matrix and that models using both G and M matrices show superior accuracies and errors compared with G or M alone, both in single and multi-environment scenarios. We showed that the M matrix is not entirely environment-specific, and the genotypic relationships become more robust with more data capture sessions over the season. We discovered that the optimal time for data capture occurs during grain filling and that camera bands with the highest heritability are important for GY prediction using the M matrix. We showcased that GY prediction can be performed using only an RGB camera, and even a single data capture session can yield valuable data for GY prediction. This study contributes to a better understanding of multispectral data and its relationships. It provides a flexible framework for improving GS protocols without significant investments or software customization. Supplementary Information: The online version contains supplementary material available at 10.1007/s11032-024-01449-w.

Grain yield and adaptation of spring wheat to Norwegian growing conditions is driven by allele frequency changes at key adaptive loci discovered by genome-wide association mapping.

KEY MESSAGE: Adaptation to the Norwegian environment is associated with polymorphisms in the Vrn-A1 locus. Historical selection for grain yield in Nordic wheat is associated with TaGS5-3A and TaCol-5 loci. Grain yields in Norwegian spring wheat increased by 18 kg ha-1 per year between 1972 and 2019 due to introduction of new varieties. These gains were associated with increments in the number of grains per spike and extended length of the vegetative period. However, little is known about the genetic background of this progress. To fill this gap, we conducted genome-wide association study on a panel consisting of both adapted (historical and current varieties and lines in the Nordics) and important not adapted accessions used as parents in the Norwegian wheat breeding program. The study concerned grain yield, plant height, and heading and maturity dates, and detected 12 associated loci, later validated using independent sets of recent breeding lines. Adaptation to the Norwegian cropping conditions was found to be associated with the Vrn-A1 locus, and a previously undescribed locus on chromosome 1B associated with heading date. Two loci associated with grain yield, corresponding to the TaGS5-3A and TaCol-5 loci, indicated historical selection pressure for high grain yield. A locus on chromosome 2A explained the tallness of the oldest accessions. We investigated the origins of the beneficial alleles associated with the wheat breeding progress in the Norwegian material, tracing them back to crosses with Swedish, German, or CIMMYT lines. This study contributes to the understanding of wheat adaptation to the Norwegian growing conditions, sheds light on the genetic basis of historical wheat improvement and aids future breeding efforts by discovering loci associated with important agronomic traits in wheat.

A major yellow rust resistance QTL on chromosome 6A shows increased frequency in recent Norwegian spring wheat cultivars and breeding lines.

KEY MESSAGE: A major yellow rust resistance QTL, QYr.nmbu.6A, contributed consistent adult plant resistance in field trials across Europe, China, Kenya and Mexico. Puccinia striiformis f. sp. tritici, causing wheat yellow rust (YR), is one of the most devastating biotrophic pathogens affecting global wheat yields. Owing to the recent epidemic of the PstS10 race group in Europe, yellow rust has become a reoccurring disease in Norway since 2014. As all stage resistances (ASR) (or seedling resistances) are usually easily overcome by pathogen evolution, deployment of durable adult plant resistance (APR) is crucial for yellow rust resistance breeding. In this study, we assessed a Nordic spring wheat association mapping panel (n = 301) for yellow rust field resistance in seventeen field trials from 2015 to 2021, including nine locations in six countries across four different continents. Nine consistent QTL were identified across continents by genome-wide association studies (GWAS). One robust QTL on the long arm of chromosome 6A, QYr.nmbu.6A, was consistently detected in nine out of the seventeen trials. Haplotype analysis of QYr.nmbu.6A confirmed significant QTL effects in all tested environments and the effect was also validated using an independent panel of new Norwegian breeding lines. Increased frequency of the resistant haplotype was found in new varieties and breeding lines in comparison to older varieties and landraces, implying that the resistance might have been selected for due to the recent changes in the yellow rust pathogen population in Europe.

Genome-wide association mapping of septoria nodorum blotch resistance in Nordic winter and spring wheat collections.

KEY MESSAGE: A new QTL for SNB, QSnb.nmbu-2AS, was found in both winter and spring wheat panels that can greatly advance SNB resistance breeding Septoria nodorum blotch (SNB), caused by the necrotrophic fungal pathogen Parastagonospora nodorum, is the dominant leaf blotch pathogen of wheat in Norway. Resistance/susceptibility to SNB is a quantitatively inherited trait, which can be partly explained by the interactions between wheat sensitivity loci (Snn) and corresponding P. nodorum necrotrophic effectors (NEs). Two Nordic wheat association mapping panels were assessed for SNB resistance in the field over three to four years: a spring wheat and a winter wheat panel (n = 296 and 102, respectively). Genome-wide association studies found consistent SNB resistance associated with quantitative trait loci (QTL) on eleven wheat chromosomes, and ten of those QTL were common in the spring and winter wheat panels. One robust QTL on the short arm of chromosome 2A, QSnb.nmbu-2AS, was significantly detected in both the winter and spring wheat panels. For winter wheat, using the four years of SNB field severity data in combination with five years of historical data, the effect of QSnb.nmbu-2AS was confirmed in seven of the nine years, while for spring wheat, the effect was confirmed for all tested years including the historical data from 2014 to 2015. However, lines containing the resistant haplotype are rare in both Nordic spring (4.0%) and winter wheat cultivars (15.7%), indicating the potential of integrating this QTL in SNB resistance breeding programs. In addition, clear and significant additive effects were observed by stacking resistant alleles of the detected QTL, suggesting that marker-assisted selection can greatly facilitate SNB resistance breeding.

Genome-wide association study and genomic prediction of resistance to stripe rust in current Central and Northern European winter wheat germplasm.

KEY MESSAGE: We found two loci on chromosomes 2BS and 6AL that significantly contribute to stripe rust resistance in current European winter wheat germplasm. Stripe or yellow rust, caused by the fungus Puccinia striiformis Westend f. sp. tritici, is one of the most destructive wheat diseases. Sustainable management of wheat stripe rust can be achieved through the deployment of rust resistant cultivars. To detect effective resistance loci for use in breeding programs, an association mapping panel of 230 winter wheat cultivars and breeding lines from Northern and Central Europe was employed. Genotyping with the Illumina® iSelect® 25 K Infinium® single nucleotide polymorphism (SNP) genotyping array yielded 8812 polymorphic markers. Structure analysis revealed two subpopulations with 92 Austrian breeding lines and cultivars, which were separated from the other 138 genotypes from Germany, Norway, Sweden, Denmark, Poland, and Switzerland. Genome-wide association study for adult plant stripe rust resistance identified 12 SNP markers on six wheat chromosomes which showed consistent effects over several testing environments. Among these, two marker loci on chromosomes 2BS (RAC875_c1226_652) and 6AL (Tdurum_contig29607_413) were highly predictive in three independent validation populations of 1065, 1001, and 175 breeding lines. Lines with the resistant haplotype at both loci were nearly free of stipe rust symptoms. By using mixed linear models with those markers as fixed effects, we could increase predictive ability in the three populations by 0.13-0.46 compared to a standard genomic best linear unbiased prediction approach. The obtained results facilitate an efficient selection for stripe rust resistance against the current pathogen population in the Northern and Central European winter wheat gene pool.

Genetic architecture of fusarium head blight disease resistance and associated traits in Nordic spring wheat.

KEY MESSAGE: This study identified a significant number of QTL that are associated with FHB disease resistance in NMBU spring wheat panel by conducting genome-wide association study. Fusarium head blight (FHB) is a widely known devastating disease of wheat caused by Fusarium graminearum and other Fusarium species. FHB resistance is quantitative, highly complex and divided into several resistance types. Quantitative trait loci (QTL) that are effective against several of the resistance types give valuable contributions to resistance breeding. A spring wheat panel of 300 cultivars and breeding lines of Nordic and exotic origins was tested in artificially inoculated field trials and subjected to visual FHB assessment in the years 2013-2015, 2019 and 2020. Deoxynivalenol (DON) content was measured on harvested grain samples, and anther extrusion (AE) was assessed in separate trials. Principal component analysis based on 35 and 25 K SNP arrays revealed the existence of two subgroups, dividing the panel into European and exotic lines. We employed a genome-wide association study to detect QTL associated with FHB traits and identify marker-trait associations that consistently influenced FHB resistance. A total of thirteen QTL were identified showing consistent effects across FHB resistance traits and environments. Haplotype analysis revealed a highly significant QTL on 7A, Qfhb.nmbu.7A.2, which was further validated on an independent set of breeding lines. Breeder-friendly KASP markers were developed for this QTL that can be used in marker-assisted selection. The lines in the wheat panel harbored from zero to five resistance alleles, and allele stacking showed that resistance can be significantly increased by combining several of these resistance alleles. This information enhances breeders´ possibilities for genomic prediction and to breed cultivars with improved FHB resistance.

Identification and cross-validation of genetic loci conferring resistance to Septoria nodorum blotch using a German multi-founder winter wheat population.

KEY MESSAGE: We identified allelic variation at two major loci, QSnb.nmbu-2A.1 and QSnb.nmbu-5A.1, showing consistent and additive effects on SNB field resistance. Validation of QSnb.nmbu-2A.1 across genetic backgrounds further highlights its usefulness for marker-assisted selection. Septoria nodorum blotch (SNB) is a disease of wheat (Triticum aestivum and T. durum) caused by the necrotrophic fungal pathogen Parastagonospora nodorum. SNB resistance is a typical quantitative trait, controlled by multiple quantitative trait loci (QTL) of minor effect. To achieve increased plant resistance, selection for resistance alleles and/or selection against susceptibility alleles must be undertaken. Here, we performed genetic analysis of SNB resistance using an eight-founder German Multiparent Advanced Generation Inter-Cross (MAGIC) population, termed BMWpop. Field trials and greenhouse testing were conducted over three seasons in Norway, with genetic analysis identifying ten SNB resistance QTL. Of these, two QTL were identified over two seasons: QSnb.nmbu-2A.1 on chromosome 2A and QSnb.nmbu-5A.1 on chromosome 5A. The chromosome 2A BMWpop QTL co-located with a robust SNB resistance QTL recently identified in an independent eight-founder MAGIC population constructed using varieties released in the United Kingdom (UK). The validation of this SNB resistance QTL in two independent multi-founder mapping populations, regardless of the differences in genetic background and agricultural environment, highlights the value of this locus in SNB resistance breeding. The second robust QTL identified in the BMWpop, QSnb.nmbu-5A.1, was not identified in the UK MAGIC population. Combining resistance alleles at both loci resulted in additive effects on SNB resistance. Therefore, using marker assisted selection to combine resistance alleles is a promising strategy for improving SNB resistance in wheat breeding. Indeed, the multi-locus haplotypes determined in this study provide markers for efficient tracking of these beneficial alleles in future wheat genetics and breeding activities.

Identification of eight QTL controlling multiple yield components in a German multi-parental wheat population, including Rht24, WAPO-A1, WAPO-B1 and genetic loci on chromosomes 5A and 6A.

KEY MESSAGE: Quantitative trait locus (QTL) mapping of 15 yield component traits in a German multi-founder population identified eight QTL each controlling ≥2 phenotypes, including the genetic loci Rht24, WAPO-A1 and WAPO-B1. Grain yield in wheat (Triticum aestivum L.) is a polygenic trait representing the culmination of many developmental processes and their interactions with the environment. Toward maintaining genetic gains in yield potential, 'reductionist approaches' are commonly undertaken by which the genetic control of yield components, that collectively determine yield, are established. Here we use an eight-founder German multi-parental wheat population to investigate the genetic control and phenotypic trade-offs between 15 yield components. Increased grains per ear was significantly positively correlated with the number of fertile spikelets per ear and negatively correlated with the number of infertile spikelets. However, as increased grain number and fertile spikelet number per ear were significantly negatively correlated with thousand grain weight, sink strength limitations were evident. Genetic mapping identified 34 replicated quantitative trait loci (QTL) at two or more test environments, of which 24 resolved into eight loci each controlling two or more traits-termed here 'multi-trait QTL' (MT-QTL). These included MT-QTL associated with previously cloned genes controlling semi-dwarf plant stature, and with the genetic locus Reduced height 24 (Rht24) that further modulates plant height. Additionally, MT-QTL controlling spikelet number traits were located to chromosome 7A encompassing the gene WHEAT ORTHOLOG OF APO1 (WAPO-A1), and to its homoeologous location on chromosome 7B containing WAPO-B1. The genetic loci identified in this study, particularly those that potentially control multiple yield components, provide future opportunities for the targeted investigation of their underlying genes, gene networks and phenotypic trade-offs, in order to underpin further genetic gains in yield.

Septoria Nodorum Blotch of Wheat: Disease Management and Resistance Breeding in the Face of Shifting Disease Dynamics and a Changing Environment.

The fungus Parastagonospora nodorum is a narrow host range necrotrophic fungal pathogen that causes Septoria nodorum blotch (SNB) of cereals, most notably wheat (Triticum aestivum). Although commonly observed on wheat seedlings, P. nodorum infection has the greatest effect on the adult crop. It results in leaf blotch, which limits photosynthesis and thus crop growth and yield. It can also affect the wheat ear, resulting in glume blotch, which directly affects grain quality. Reports of P. nodorum fungicide resistance, the increasing use of reduced tillage agronomic practices, and high evolutionary potential of the pathogen, combined with changes in climate and agricultural environments, mean that genetic resistance to SNB remains a high priority in many regions of wheat cultivation. In this review, we summarize current information on P. nodorum population structure and its implication for improved SNB management. We then review recent advances in the genetics of host resistance to P. nodorum and the necrotrophic effectors it secretes during infection, integrating the genomic positions of these genetic loci by using the recently released wheat reference genome assembly. Finally, we discuss the genetic and genomic tools now available for SNB resistance breeding and consider future opportunities and challenges in crop health management by using the wheat-P. nodorum interaction as a model.

Genetic mapping using a wheat multi-founder population reveals a locus on chromosome 2A controlling resistance to both leaf and glume blotch caused by the necrotrophic fungal pathogen Parastagonospora nodorum.

KEY MESSAGE: A locus on wheat chromosome 2A was found to control field resistance to both leaf and glume blotch caused by the necrotrophic fungal pathogen Parastagonospora nodorum. The necrotrophic fungal pathogen Parastagonospora nodorum is the causal agent of Septoria nodorum leaf blotch and glume blotch, which are common wheat (Triticum aestivum L.) diseases in humid and temperate areas. Susceptibility to Septoria nodorum leaf blotch can partly be explained by sensitivity to corresponding P. nodorum necrotrophic effectors (NEs). Susceptibility to glume blotch is also quantitative; however, the underlying genetics have not been studied in detail. Here, we genetically map resistance/susceptibility loci to leaf and glume blotch using an eight-founder wheat multiparent advanced generation intercross population. The population was assessed in six field trials across two sites and 4 years. Seedling infiltration and inoculation assays using three P. nodorum isolates were also carried out, in order to compare quantitative trait loci (QTL) identified under controlled conditions with those identified in the field. Three significant field resistance QTL were identified on chromosomes 2A and 6A, while four significant seedling resistance QTL were detected on chromosomes 2D, 5B and 7D. Among these, QSnb.niab-2A.3 for field resistance to both leaf blotch and glume blotch was detected in Norway and the UK. Colocation with a QTL for seedling reactions against culture filtrate from a Norwegian P. nodorum isolate indicated the QTL could be caused by a novel NE sensitivity. The consistency of this QTL for leaf blotch at the seedling and adult plant stages and culture filtrate infiltration was confirmed by haplotype analysis. However, opposite effects for the leaf blotch and glume blotch reactions suggest that different genetic mechanisms may be involved.

Two Main Stripe Rust Resistance Genes Identified in Synthetic-Derived Wheat Line Soru#1.

Stripe rust is a major disease constraint of wheat production worldwide. Resistance to stripe rust was analyzed using 131 F6 recombinant inbred lines (RILs) derived from a cross between synthetic derived wheat line Soru#1 and wheat cultivar Naxos. The phenotype was evaluated in Mexico and Norway at both seedling and adult plant stages. Linkage groups were constructed based on 90K single-nucleotide polymorphism (SNP), sequence-tagged site, and simple sequence repeat markers. Two major resistance loci conferred by Soru#1 were detected and located on chromosomes 1BL and 4DS. The 1BL quantitative trait loci explained 15.8 to 40.2 and 51.1% of the phenotypic variation at adult plant and seedling stages, respectively. This locus was identified as Yr24/Yr26 based on the flanking markers and infection types. Locus 4DS was flanked by molecular markers D_GB5Y7FA02JMPQ0_238 and BS00108770_51. It explained 8.4 to 27.8 and 5.5% of stripe rust variation at the adult plant and seedling stages, respectively. The 4DS locus may correspond to known resistance gene Yr28 based on the resistance source. All RILs that combine Yr24/Yr26 and Yr28 showed significantly reduced stripe rust severity in all four environments compared with the lines with only one of the genes. SNP marker BS00108770_51 was converted into a breeder-friendly kompetitive allele-specific polymerase chain reaction marker that will be useful to accelerate Yr28 deployment in wheat breeding programs.

Identification of quantitative trait loci associated with resistance to net form net blotch in a collection of Nordic barley germplasm.

KEY MESSAGE: Association mapping of resistance to Pyrenophora teres f. teres in a collection of Nordic barley germplasm at different developmental stages revealed 13 quantitative loci with mostly small effects. Net blotch, caused by the necrotrophic fungus Pyrenophora teres, is one of the major diseases in barley in Norway causing quantitative and qualitative yield losses. Resistance in Norwegian cultivars and germplasm is generally insufficient and resistance sources have not been extensively explored yet. In this study, we mapped quantitative trait loci (QTL) associated with resistance to net blotch in Nordic germplasm. We evaluated a collection of 209 mostly Nordic spring barley lines for reactions to net form net blotch (NFNB; Pyrenophora teres f. teres) in inoculations with three single conidia isolates at the seedling stage and in inoculated field trials at the adult stage in 4 years. Using 5669 SNP markers genotyped with the Illumina iSelect 9k Barley SNP Chip and a mixed linear model accounting for population structure and kinship, we found a total of 35 significant marker-trait associations for net blotch resistance, corresponding to 13 QTL, on all chromosomes. Out of these QTL, seven conferred resistance only in adult plants and four were only detectable in seedlings. Two QTL on chromosomes 3H and 6H were significant during both seedling inoculations and adult stage field trials. These are promising candidates for breeding programs using marker-assisted selection strategies. The results elucidate the genetic background of NFNB resistance in Nordic germplasm and suggest that NB resistance is conferred by a number of genes each with small-to-moderate effects, making it necessary to pyramid these genes to achieve sufficient levels of resistance.

Mapping of SnTox3-Snn3 as a major determinant of field susceptibility to Septoria nodorum leaf blotch in the SHA3/CBRD × Naxos population.

KEY MESSAGE: The effect of the SnTox3-Snn3 interaction was documented for the first time under natural infection at the adult plant stage in the field. Co-segregating SNP markers were identified. Parastagonospora nodorum is a necrotrophic pathogen of wheat, causing Septoria nodorum blotch (SNB) affecting both the leaf and glume. P. nodorum is the major leaf blotch pathogen on spring wheat in Norway. Resistance to the disease is quantitative, but several host-specific interactions between necrotrophic effectors (NEs) and host sensitivity (Snn) genes have been identified, playing a major role at the seedling stage. However, the effect of these interactions in the field under natural infection has not been investigated. In the present study, we saturated the genetic map of the recombinant inbred (RI) population SHA3/CBRD × Naxos using the Illumina 90 K SNP chip. The population had previously been evaluated for segregation of SNB susceptibility in field trials. Here, we infiltrated the population with the purified NEs SnToxA, SnTox1 and SnTox3, and mapped the Snn3 locus on 5BS based on sensitivity segregation and SNP marker data. We also conducted inoculation and culture filtrate (CF) infiltration experiments on the population with four selected P. nodorum isolates from Norway and North America. Remapping of quantitative trait loci (QTL) for field resistance showed that the SnTox3-Snn3 interaction could explain 24% of the phenotypic variation in the field, and more than 51% of the variation in seedling inoculations. To our knowledge, this is the first time the effect of this interaction has been documented at the adult plant stage under natural infection in the field.

Characterization of polyploid wheat genomic diversity using a high-density 90,000 single nucleotide polymorphism array.

High-density single nucleotide polymorphism (SNP) genotyping arrays are a powerful tool for studying genomic patterns of diversity, inferring ancestral relationships between individuals in populations and studying marker-trait associations in mapping experiments. We developed a genotyping array including about 90,000 gene-associated SNPs and used it to characterize genetic variation in allohexaploid and allotetraploid wheat populations. The array includes a significant fraction of common genome-wide distributed SNPs that are represented in populations of diverse geographical origin. We used density-based spatial clustering algorithms to enable high-throughput genotype calling in complex data sets obtained for polyploid wheat. We show that these model-free clustering algorithms provide accurate genotype calling in the presence of multiple clusters including clusters with low signal intensity resulting from significant sequence divergence at the target SNP site or gene deletions. Assays that detect low-intensity clusters can provide insight into the distribution of presence-absence variation (PAV) in wheat populations. A total of 46 977 SNPs from the wheat 90K array were genetically mapped using a combination of eight mapping populations. The developed array and cluster identification algorithms provide an opportunity to infer detailed haplotype structure in polyploid wheat and will serve as an invaluable resource for diversity studies and investigating the genetic basis of trait variation in wheat.

Molecular mapping of adult plant resistance to Parastagonospora nodorum leaf blotch in bread wheat lines 'Shanghai-3/Catbird' and 'Naxos'.

KEY MESSAGE: The field resistance to Parastagonospora nodorum leaf blotch in SHA3/CBRD is based on many genes with minor effects. Parastagonospora nodorum leaf blotch is a severe wheat disease in Norway and other regions with humid and rainy climate. It causes grain shriveling and reduced yield in years of epidemics. Shanghai-3/Catbird (SHA3/CBRD), a CIMMYT breeding line, was observed to be resistant to P. nodorum leaf blotch in the field. The objective of the current study was to map the genetic factors related to its resistance. A recombinant inbred line population from a cross between SHA3/CBRD and the susceptible German spring cv. Naxos was tested in field trials over 4 years (2010, 2011, 2012 and 2013) with natural infection supplied with mist irrigation. Leaf blotch severity was scored together with plant height, heading date and maturity date in these trials. A testing data set was also available from other field trials with the same population. Totally, two major and six minor QTL were detected for leaf blotch resistance. The major QTL on chromosome 3BL with resistance contributed by Naxos was consistent across all environments and explained up to 12 % of the phenotypic variation. Another major QTL on 3B with resistance from SHA3/CBRD was significant in 2010, 2013 and the testing data set and explained up to 12 % of the phenotypic variation. Minor QTL were detected on 1B, 3AS, 5BS, 5BL, 7A and 7B. The 5BS QTL was likely caused by Snn3-B1, with sensitivity contributed by Naxos. The 5BL QTL mapped to the Tsn1 region, but was likely caused by other mechanisms since both parents were insensitive to ToxA.

Lr67/Yr46 confers adult plant resistance to stem rust and powdery mildew in wheat.

KEY MESSAGE: We demonstrate that Lr67/Yr46 has pleiotropic effect on stem rust and powdery mildew resistance and is associated with leaf tip necrosis. Genes are designated as Sr55, Pm46 and Ltn3 , respectively. Wheat (Triticum aestivum) accession RL6077, known to carry the pleiotropic slow rusting leaf and yellow rust resistance genes Lr67/Yr46 in Thatcher background, displayed significantly lower stem rust (P. graminis tritici; Pgt) and powdery mildew (Blumeria graminis tritici; Bgt) severities in Kenya and in Norway, respectively, compared to its recurrent parent Thatcher. We investigated the resistance of RL6077 to stem rust and powdery mildew using Avocet × RL6077 F6 recombinant inbred lines (RILs) derived from two photoperiod-insensitive F3 families segregating for Lr67/Yr46. Greenhouse seedling tests were conducted with Mexican Pgt race RTR. Field evaluations were conducted under artificially initiated stem rust epidemics with Pgt races RTR and TTKST (Ug99 + Sr24) at Ciudad Obregon (Mexico) and Njoro (Kenya) during 2010-2011; and under natural powdery mildew epiphytotic in Norway at Ås and Hamar during 2011 and 2012. In Mexico, a mean reduction of 41 % on stem rust severity was obtained for RILs carrying Lr67/Yr46, compared to RILs that lacked the gene, whereas in Kenya the difference was smaller (16 %) but significant. In Norway, leaf tip necrosis was associated with Lr67/Yr46 and RILs carrying Lr67/Yr46 showed a 20 % reduction in mean powdery mildew severity at both sites across the 2 years of evaluation. Our study demonstrates that Lr67/Yr46 confers partial resistance to stem rust and powdery mildew and is associated with leaf tip necrosis. The corresponding pleiotropic, or tightly linked, genes, designated as Sr55, Pm46, and Ltn3, can be utilized to provide broad-spectrum durable disease resistance in wheat.

Utilization of deletion bins to anchor and order sequences along the wheat 7B chromosome.

KEY MESSAGE: A total of 3,671 sequence contigs and scaffolds were mapped to deletion bins on wheat chromosome 7B providing a foundation for developing high-resolution integrated physical map for this chromosome. Bread wheat (Triticum aestivum L.) has a large, complex and highly repetitive genome which is challenging to assemble into high quality pseudo-chromosomes. As part of the international effort to sequence the hexaploid bread wheat genome by the international wheat genome sequencing consortium (IWGSC) we are focused on assembling a reference sequence for chromosome 7B. The successful completion of the reference chromosome sequence is highly dependent on the integration of genetic and physical maps. To aid the integration of these two types of maps, we have constructed a high-density deletion bin map of chromosome 7B. Using the 270 K Nimblegen comparative genomic hybridization (CGH) array on a set of cv. Chinese spring deletion lines, a total of 3,671 sequence contigs and scaffolds (~7.8 % of chromosome 7B physical length) were mapped into nine deletion bins. Our method of genotyping deletions on chromosome 7B relied on a model-based clustering algorithm (Mclust) to accurately predict the presence or absence of a given genomic sequence in a deletion line. The bin mapping results were validated using three different approaches, viz. (a) PCR-based amplification of randomly selected bin mapped sequences (b) comparison with previously mapped ESTs and (c) comparison with a 7B genetic map developed in the present study. Validation of the bin mapping results suggested a high accuracy of the assignment of 7B sequence contigs and scaffolds to the 7B deletion bins.

QTL mapping of adult-plant resistance to leaf rust in a RIL population derived from a cross of wheat cultivars Shanghai 3/Catbird and Naxos.

KEY MESSAGE: Six QTL for adult plant resistance to leaf rust, including two QTL effective against additional diseases, were identified in a RIL population derived from a cross between Shanghai 3/Catbird and Naxos. Leaf rust is an important wheat disease and utilization of adult-plant resistance (APR) may be the best approach to achieve long-term protection from the disease. The CIMMYT spring wheat line Shanghai 3/Catbird (SHA3/CBRD) showed a high level of APR to Chinese Puccinia triticina pathotypes in the field. To identify APR genes in this line, a mapping population of 164 recombinant inbred lines (RILs) was developed from a cross of this line and Naxos, a moderately susceptible German cultivar. The RILs were evaluated for final disease severity (FDS) at Baoding, Hebei province, and Zhoukou, Henan province, in the 2010-2011 and 2011-2012 cropping seasons. QTL analysis detected one major QTL derived from SHA3/CBRD on chromosome 2BS explaining from 15 to 37 % of the phenotypic variance across environments. In addition one minor resistance QTL on chromosome 1AL from SHA3/CBRD and four minor QTL from Naxos on chromosomes 2DL, 5B, 7BS, and 7DS were also detected. SHA3/CBRD also possessed seedling resistance gene Lr26, and Naxos contained Lr1 based on gene postulation following tests with an array of P. triticina pathotypes and molecular marker assays. These seedling resistance and APR genes and their closely linked molecular markers are potentially useful for improving leaf rust resistance in wheat breeding programs.

Genome-wide association study reveals 18 QTL for major agronomic traits in a Nordic-Baltic spring wheat germplasm.

Spring wheat (Triticum aestivum L.) remains an important alternative to winter wheat cultivation at Northern latitudes due to high risk of overwintering or delayed sowing of winter wheat. We studied nine major agronomic traits in a set of 299 spring wheat genotypes in trials across 12-year-site combinations in Lithuania, Latvia, Estonia, and Norway for three consecutive years. The dataset analyzed here consisted of previously published phenotypic data collected in 2021 and 2022, supplemented with additional phenotypic data from the 2023 field season collected in this study. We combined these phenotypic datasets with previously published genotypic data generated using a 25K single nucleotide polymorphism (SNP) array that yielded 18,467 markers with a minor allele frequency above 0.05. Analysis of these datasets via genome-wide association study revealed 18 consistent quantitative trait loci (QTL) replicated in two or more trials that explained more than 5% of phenotypic variance for plant height, grain protein content, thousand kernel weight, or heading date. The most consistent markers across the tested environments were detected for plant height, thousand kernel weight, and days to heading in eight, five, and six trials, respectively. No beneficial effect of the semi-dwarfing alleles Rht-B1b and Rht-D1b on grain yield performance was observed across the 12 tested trials. Moreover, the cultivars carrying these alleles were low yielding in general. Based on principal component analysis, wheat genotypes developed in the Northern European region clustered separately from those developed at the southern latitudes, and markers associated with the clustering were identified. Important phenotypic traits, such as grain yield, days to heading, grain protein content, and thousand kernel weight were associated with this clustering of the genotype sets. Interestingly, despite being adapted to the Nordic environment, genotypes in the Northern set demonstrated lower grain yield performance across all tested environments. The results indicate that spring wheat germplasm harbors valuable QTL/alleles, and the identified trait-marker associations might be useful in improving Nordic-Baltic spring wheat germplasm under global warming conditions.