The evolutionary patterns of barley pericentromeric chromosome regions, as shaped by linkage disequilibrium and domestication.

The distribution of recombination events along large cereal chromosomes is uneven and is generally restricted to gene-rich telomeric ends. To understand how the lack of recombination affects diversity in the large pericentromeric regions, we analysed deep exome capture data from a final panel of 815 Hordeum vulgare (barley) cultivars, landraces and wild barleys, sampled from across their eco-geographical ranges. We defined and compared variant data across the pericentromeric and non-pericentromeric regions, observing a clear partitioning of diversity both within and between chromosomes and germplasm groups. Dramatically reduced diversity was found in the pericentromeres of both cultivars and landraces when compared with wild barley. We observed a mixture of completely and partially differentiated single-nucleotide polymorphisms (SNPs) between domesticated and wild gene pools, suggesting that domesticated gene pools were derived from multiple wild ancestors. Patterns of genome-wide linkage disequilibrium, haplotype block size and number, and variant frequency within blocks showed clear contrasts among individual chromosomes and between cultivars and wild barleys. Although most cultivar chromosomes shared a single major pericentromeric haplotype, chromosome 7H clearly differentiated the two-row and six-row types associated with different geographical origins. Within the pericentromeric regions we identified 22 387 non-synonymous SNPs, 92 of which were fixed for alternative alleles in cultivar versus wild accessions. Surprisingly, only 29 SNPs found exclusively in the cultivars were predicted to be 'highly deleterious'. Overall, our data reveal an unconventional pericentromeric genetic landscape among distinct barley gene pools, with different evolutionary processes driving domestication and diversification.

Genome-Wide Association Mapping of Bacterial Leaf Streak Resistance in Two Elite Barley Breeding Panels.

Bacterial leaf streak (BLS), caused chiefly by the pathogen Xanthomonas translucens pv. translucens, is becoming an increasingly important foliar disease of barley in the Upper Midwest. The deployment of resistant cultivars is the most economical and practical method of control. To identify sources of BLS resistance, we evaluated two panels of breeding lines from the University of Minnesota (UMN) and Anheuser-Busch InBev (ABI) barley improvement programs for reaction to strain CIX95 in the field at St. Paul and Crookston, MN, in 2020 and 2021. The percentage of resistant lines in the UMN and ABI panels with mid-season maturity was 1.8% (6 of 333 lines) and 5.2% (13 of 251 lines), respectively. Both panels were genotyped with the barley 50K iSelect SNP array, and then a genome-wide association study was performed. A single, highly significant association was identified for BLS resistance on chromosome 6H in the UMN panel. This association was also identified in the ABI panel. Seven other significant associations were detected in the ABI panel: two each on chromosomes 1H, 2H, and 3H and one on chromosome 5H. Of the eight associations identified in the panels, five were novel. The discovery of resistance in elite breeding lines will hasten the time needed to develop and release a BLS-resistant cultivar.

Sources of Bacterial Leaf Streak Resistance Identified in a Diverse Collection of Barley Germplasm.

Bacterial leaf streak (BLS) is a sporadic yet damaging disease of cereals that is growing in importance across the Upper Midwest production region. In barley (Hordeum vulgare ssp. vulgare), this disease is caused primarily by the bacterium Xanthomonas translucens pv. translucens. Accessions resistant to BLS have been reported in past studies, but few have been rigorously validated in the field. To identify accessions carrying diverse resistance alleles to BLS, a largescale germplasm screening study was undertaken against strain CIX95 of X. translucens pv. translucens in St. Paul and Crookston, Minnesota, in 2020 and 2021. The germplasm screened was diverse and included adapted breeding lines from two improvement programs, two landrace panels (one global and one from Ethiopia/Eritrea), introgression lines from wild barley (H. vulgare ssp. spontaneum) in the genetic background of barley cultivar 'Rasmusson', and an assemblage of accessions previously reported to carry BLS resistance. Of the 2,094 accessions evaluated in this study, 32 (1.5%) exhibited a consistently high level of resistance across locations and years and had heading dates similar to standard cultivars grown in the region. Accessions resistant to BLS were identified from all germplasm panels tested, providing genetically diverse sources for barley improvement programs focused on breeding for resistance to this important bacterial disease.

Development of first linkage map for Silphium integrifolium (Asteraceae) enables identification of sporophytic self-incompatibility locus.

Silphium integrifolium (Asteraceae) has been identified as a candidate for domestication as a perennial oilseed crop and is assumed to have sporophytic self-incompatibility system-the genetic basis of which is not well understood in the Asteraceae. To address this gap, we sought to map the genomic location of the self-recognition locus (S-locus) in this species. We used a biparental population and genotyping-by-sequencing to create the first genetic linkage map for this species, which contained 198 SNP markers and resolved into the correct number of linkage groups. Then we developed a novel crossing scheme and set of analysis methods in order to infer S-locus genotypes for a subset of these individuals, allowing us to map the trait. Finally, we evaluated potential genes of interest using synteny analysis with the annual sunflower (Helianthus annuus) and lettuce (Lactuca sativa) genomes. Our results confirm that S. integrifolium does indeed have a sporophytic self-incompatibility system. Our method is effective and efficient, allowed us to map the S. integrifolium S-locus using fewer resources than existing methods, and could be readily applied to other species.

Effects of interrupting daily sedentary behavior on children's glucose metabolism: A 6-day randomized controlled trial.

BACKGROUND: Metabolic disease risk in youth is influenced by sedentary behaviors. Acute in-lab studies show that, during a single day, interrupting a sedentary period with short bouts of physical activity improves glucometabolic outcomes. OBJECTIVE: To determine if acutely improved glucose metabolism persists after multi-day interruptions of sitting with walking brief bouts. We hypothesized that children who underwent interrupting sitting on multiple days would demonstrate lower insulin area under the curve during an oral glucose tolerance test compared to uninterrupted sitting. METHODS: Healthy, normoglycemic children (N = 109) ages 7-11 years were randomized to one of two conditions: Control (3 h of daily Uninterrupted Sitting) or Interrupted Sitting (3-min of moderate-intensity walking every 30 min for 3 h daily); with dietary intake controlled through provision of foodstuffs for the entire experiment. Participants attended six consecutive daily visits at a research ambulatory unit. The primary outcome was insulin area under the curve during the oral glucose tolerance test on day 6 during interrupted or uninterrupted sitting; secondary outcomes included glucose and c-peptide area under the curve, energy intake at a buffet meal on day 6, and free-living activity. RESULTS: Among 93 children (42 uninterrupted sitting, 51 interrupted sitting), daily interrupted sitting resulted in 21% lower insulin (ß = 0.102 CI:0.032-0.172, p = 0.005) and a 10% lower C-peptide (ß = 0.043, CI:0.001-0.084, p = 0.045) area under the curve. Matsuda and Glucose Effectiveness Indices were also improved (p's < 0.05). There were no group differences in energy intake or expenditure. CONCLUSIONS: Sustained behavioral change by interrupting sedentary behaviors is a promising intervention strategy for improving metabolic risk in children.

Oat Crown Rust Disease Severity Estimated at Many Time Points Using Multispectral Aerial Photos.

All plant breeding programs are dependent on plant phenotypic and genotypic data, but the development of phenotyping technology has been slow relative to that of genotyping. Crown rust (Puccinia coronata f. sp. avenae Erikss.) is the most important disease of cultivated oat (Avena sativa L.), making the development of disease-resistant oat cultivars an important breeding objective. Visual observation is the most common scoring method, but it can be laborious and subjective. We visually scored a diverse collection of 256 oat lines at a total of 27 time points in three disease nursery environments. Multispectral aerial photos were collected using an unmanned aerial vehicle at the same time points as the visual observations. The photos were analyzed, and subsets of the spectral properties of each plot were measured. Random forest modeling was used to model the relationship between the spectral properties of the plots and visually observed disease severity. The ability of the photo data and the random forest model to estimate visually observed disease severity was evaluated using three different cross-validation analyses. We specifically addressed the issue of assessing phenotyping accuracy across and within time points. The accuracy of the photo estimates was greatest for adult plants shortly before they began to senesce. Accuracy outside of that time frame was generally low but statistically significant. Unmanned aerial vehicle-mounted sensors could increase disease scoring efficiency, but additional investigation into the spectral signature of disease severity at all plant growth stages may be necessary to automate accurate full-season measurements.

Genetic loci mediating circadian clock output plasticity and crop productivity under barley domestication.

Circadian clock rhythms are shown to be intertwined with crop adaptation. To realize the adaptive value of changes in these rhythms under crop domestication and improvement, there is a need to compare the genetics of clock and yield traits. We compared circadian clock rhythmicity based on Chl leaf fluorescence and transcriptomics among wild ancestors, landraces, and breeding lines of barley under optimal and high temperatures. We conducted a genome scan to identify pleiotropic loci regulating the clock and field phenotypes. We also compared the allelic diversity in wild and cultivated barley to test for selective sweeps. We found significant loss of thermal plasticity in circadian rhythms under domestication. However, transcriptome analysis indicated that this loss was only for output genes and that temperature compensation in the core clock machinery was maintained. Drivers of the circadian clock (DOC) loci were identified via genome-wide association study. Notably, these loci also modified growth and reproductive outputs in the field. Diversity analysis indicated selective sweep in these pleiotropic DOC loci. These results indicate a selection against thermal clock plasticity under barley domestication and improvement and highlight the importance of identifying genes underlying for understanding the biochemical basis of crop adaptation to changing environments.

Transpiration increases under high-temperature stress: Potential mechanisms, trade-offs and prospects for crop resilience in a warming world.

The frequency and intensity of high-temperature stress events are expected to increase as climate change intensifies. Concomitantly, an increase in evaporative demand, driven in part by global warming, is also taking place worldwide. Despite this, studies examining high-temperature stress impacts on plant productivity seldom consider this interaction to identify traits enhancing yield resilience towards climate change. Further, new evidence documents substantial increases in plant transpiration rate in response to high-temperature stress even under arid environments, which raise a trade-off between the need for latent cooling dictated by excessive temperatures and the need for water conservation dictated by increasing evaporative demand. However, the mechanisms behind those responses, and the potential to design the next generation of crops successfully navigating this trade-off, remain poorly investigated. Here, we review potential mechanisms underlying reported increases in transpiration rate under high-temperature stress, within the broader context of their impact on water conservation needed for crop drought tolerance. We outline three main contributors to this phenomenon, namely stomatal, cuticular and water viscosity-based mechanisms, and we outline research directions aiming at designing new varieties optimized for specific temperature and evaporative demand regimes to enhance crop productivity under a warmer and dryer climate.

Genetic dissection of a pericentromeric region of barley chromosome 6H associated with Fusarium head blight resistance, grain protein content and agronomic traits.

KEY MESSAGE: Fine mapping of barley 6H pericentromeric region identified FHB QTL with opposite effects, and high grain protein content was associated with increased FHB severity. Resistance to Fusarium head blight (FHB), kernel discoloration (KD), deoxynivalenol (DON) accumulation and grain protein content (GPC) are important traits for breeding malting barley varieties. Previous work mapped a Chevron-derived FHB QTL to the pericentromeric region of 6H, coinciding with QTL for KD resistance and GPC. The Chevron allele reduced FHB and KD, but unfavorably increased GPC. To determine whether the correlations are caused by linkage or pleiotropy, a fine mapping approach was used to dissect the QTL underlying these quality and disease traits. Two populations, referred to as Gen10 and Gen10/Lacey, derived from a recombinant near-isogenic line (rNIL) were developed. Recombinants were phenotyped for FHB, KD, DON, GPC and other agronomic traits. Three FHB, two DON and two KD QTLs were identified. One of the three FHB QTLs, one DON QTL and one KD QTL were coincident with the GPC QTL, which contains the Hv-NAM1 locus affecting grain protein accumulation. The Chevron allele at the GPC QTL increased GPC and FHB and decreased DON and KD. The other two FHB QTL and the other DON and KD QTL were identified in the regions flanking the Hv-NAM1 locus, and the Chevron alleles decreased FHB, DON and KD. Our results suggested that the QTL associated with FHB, KD, DON and GPC in the pericentromeric region of 6H was controlled by both pleiotropy and tightly linked loci. The rNILs identified in this study with low FHB severity and moderate GPC may be used for breeding malting barley cultivars.

Multi-omics prediction of oat agronomic and seed nutritional traits across environments and in distantly related populations.

KEY MESSAGE: Integration of multi-omics data improved prediction accuracies of oat agronomic and seed nutritional traits in multi-environment trials and distantly related populations in addition to the single-environment prediction. Multi-omics prediction has been shown to be superior to genomic prediction with genome-wide DNA-based genetic markers (G) for predicting phenotypes. However, most of the existing studies were based on historical datasets from one environment; therefore, they were unable to evaluate the efficiency of multi-omics prediction in multi-environment trials and distantly related populations. To fill those gaps, we designed a systematic experiment to collect omics data and evaluate 17 traits in two oat breeding populations planted in single and multiple environments. In the single-environment trial, transcriptomic BLUP (T), metabolomic BLUP (M), G + T, G + M, and G + T + M models showed greater prediction accuracy than GBLUP for 5, 10, 11, 17, and 17 traits, respectively, and metabolites generally performed better than transcripts when combined with SNPs. In the multi-environment trial, multi-trait models with omics data outperformed both counterpart multi-trait GBLUP models and single-environment omics models, and the highest prediction accuracy was achieved when modeling genetic covariance as an unstructured covariance model. We also demonstrated that omics data can be used to prioritize loci from one population with omics data to improve genomic prediction in a distantly related population using a two-kernel linear model that accommodated both likely casual loci with large-effect and loci that explain little or no phenotypic variance. We propose that the two-kernel linear model is superior to most genomic prediction models that assume each variant is equally likely to affect the trait and can be used to improve prediction accuracy for any trait with prior knowledge of genetic architecture.

Measurements of lethal and nonlethal inbreeding depression inform the de novo domestication of Silphium integrifolium.

PREMISE: Inbreeding depression, or the reduction in fitness of progeny with related parents, has the potential to adversely affect the long-term viability of both wild and captive plant populations. Silphium integrifolium, a prairie plant native to the central United States, has been identified as a potential candidate for domestication as a perennial oilseed crop. Little is known about the potential for inbreeding depression in this species, but it is expected to be nonnegligible because S. integrifolium is both perennial and self-incompatible. Here, we measure lethal inbreeding depression expressed through embryo deaths, and nonlethal inbreeding depression expressed through changes in vigor and fitness phenotypes of progeny. METHODS: First, we made controlled crosses among related and unrelated individuals to determine the effect of two different levels of inbreeding on seed production. Then, we grew inbred and outbred progeny from this population to reproductive maturity and measured 11 key traits. RESULTS: We found that within an improved S. integrifolium population, individuals carried an average of slightly less than one lethal allele per gamete. In progeny, significant inbreeding depression was observed in at least one family for eight of the 11 measured traits. CONCLUSIONS: Inbreeding depression is likely to be an important challenge to S. integrifolium domestication, reducing overall population fecundity and values for important phenotypes. These effects may grow worse as selection reduces effective population size. We recommend several strategies for S. integrifolium breeding to help mitigate these problems.

Identification of quantitative trait loci for net form net blotch resistance in contemporary barley breeding germplasm from the USA using genome-wide association mapping.

KEY MESSAGE: Association mapping study conducted in a population of 3490 elite barley breeding lines from ten barley breeding programs of the USA identified 12 QTLs for resistance/susceptibility to net form of net blotch. Breeding resistant varieties is the best management strategy for net form of net blotch (NFNB) in barley (Hordeum vulgare L.) caused by Pyrenophora teres f. teres (Ptt). Several resistance QTL have been previously identified in barley via linkage mapping and genome-wide association studies (GWAS). A GWAS conducted in a collection of advanced breeding lines (n = 3490) representing elite germplasm from ten barley breeding programs of the USA identified 42 unique marker-trait associations (MTA) for NFNB resistance. The lines were genotyped with 3072 SNP markers and phenotyped with four Ptt isolates in controlled environment. The lines were used to construct 13 different GWAS panels. Efficient mixed model association method with principal components and kinship was used for GWAS. Significance threshold for MTA was set at a false discovery rate of 0.05. Two, eight, six, one and 25 MTA were identified in chromosomes 1H, 3H, 4H, 5H and 6H, respectively. Based on genetic positions and linkage disequilibrium, these MTA's correspond to two, three, two, one and four QTLs in chromosome 1H, 3H, 4H, 5H and 6H, respectively. A comparison with previous linkage and GWAS studies revealed several previously identified and novel QTLs. Moreover, different genomic regions were found to be responsible for NFNB resistance in two-row versus six-row germplasm. The germplasm-specific SNP markers with additive effects and allelic distribution is reported to facilitate breeders in selection of markers for MAS to introgress novel net blotch resistance.

The Effects of Interrupting Sitting Time on Affect and State Anxiety in Children of Healthy Weight and Overweight: A Randomized Crossover Trial.

PURPOSE: Sedentary time relates to higher anxiety and more negative affect in children. This study assessed whether interrupting sitting over 3 hours is sufficient to influence state anxiety, positive affect, or negative affect, and tested weight status as a moderator. METHODS: Analyses were the second (preplanned) purpose of a larger study. Children (N = 61; age: mean [SD] = 9.5 [1.3]; 43% healthy weight) completed 2 experimental conditions: continuous sitting for 3 hours and sitting for 3 hours interrupted with walking for 3 minutes in every 30 minutes. State anxiety, positive affect, and negative affect were reported at pretest and posttest. Multilevel models for repeated measures assessed whether experimental condition predicted posttest scores. RESULTS: Experimental condition was unrelated to posttest state anxiety or positive affect. Weight status moderated how experimental condition influenced posttest negative affect (P = .003). Negative affect was lower in the children of healthy weight after interrupted sitting (vs continuous sitting; ß = -0.8; 95% confidence interval, -1.5 to 0.0, P = .05), but it was higher in the children with overweight/obesity after interrupted sitting (vs continuous sitting; ß = 0.6; 95% confidence interval, 0.0 to 1.2, P = .06). CONCLUSIONS: Interrupting sitting acutely reduced negative affect in children of healthy weight, but not in children with overweight. Further research is needed to better understand the potential emotional benefits of sitting interruptions in youth.

Connecting Data to Insight: A Pan-Canadian Study on AI in Healthcare.

Across Canada, healthcare leaders are exploring the potential of artificial intelligence and advanced analytics to transform the healthcare system. This report shares a summary of the current state of healthcare analytics across major hospitals and public healthcare agencies in Canada. We present information on the current level of investment, data governance maturity, analytics talent and tools and models being leveraged across the nation. The findings point to an opportunity for enhanced collaboration in advanced analytics and the adoption of nascent artificial intelligence technologies in healthcare. The recommendations will help drive adoption in Canada, ultimately improving the patient experience and promoting better health outcomes for Canadians.

The Role of Deleterious Substitutions in Crop Genomes.

Populations continually incur new mutations with fitness effects ranging from lethal to adaptive. While the distribution of fitness effects of new mutations is not directly observable, many mutations likely either have no effect on organismal fitness or are deleterious. Historically, it has been hypothesized that a population may carry many mildly deleterious variants as segregating variation, which reduces the mean absolute fitness of the population. Recent advances in sequencing technology and sequence conservation-based metrics for inferring the functional effect of a variant permit examination of the persistence of deleterious variants in populations. The issue of segregating deleterious variation is particularly important for crop improvement, because the demographic history of domestication and breeding allows deleterious variants to persist and reach moderate frequency, potentially reducing crop productivity. In this study, we use exome resequencing of 15 barley accessions and genome resequencing of 8 soybean accessions to investigate the prevalence of deleterious single nucleotide polymorphisms (SNPs) in the protein-coding regions of the genomes of two crops. We conclude that individual cultivars carry hundreds of deleterious SNPs on average, and that nonsense variants make up a minority of deleterious SNPs. Our approach identifies known phenotype-altering variants as deleterious more frequently than the genome-wide average, suggesting that putatively deleterious variants are likely to affect phenotypic variation. We also report the implementation of a SNP annotation tool BAD_Mutations that makes use of a likelihood ratio test based on alignment of all currently publicly available Angiosperm genomes.

Differential transcriptomic responses to Fusarium graminearum infection in two barley quantitative trait loci associated with Fusarium head blight resistance.

BACKGROUND: Fusarium graminearum causes Fusarium head blight (FHB), a major disease problem worldwide. Resistance to FHB is controlled by quantitative trait loci (QTL) of which two are located on barley chromosomes 2H bin8 and 6H bin7. The mechanisms of resistance mediated by FHB QTL are poorly defined. RESULTS: Near-isogenic lines (NILs) carrying Chevron-derived resistant alleles for the two QTL were developed and exhibited FHB resistance in field trials. To understand the molecular responses associated with resistance, transcriptomes of the NILs and recurrent parents (M69 and Lacey) were investigated with RNA sequencing (RNA-Seq) after F. graminearum or mock inoculation. A total of 2083 FHB-responsive transcripts were detected and provide a gene expression atlas for the barley-F. graminearum interaction. Comparative analysis of the 2Hb8 resistant (R) NIL and M69 revealed that the 2Hb8 R NIL exhibited an elevated defense response in the absence of fungal infection and responded quicker than M69 upon fungal infection. The 6Hb7 R NIL displayed a more rapid induction of a set of defense genes than Lacey during the early stage of fungal infection. Overlap of differentially accumulated genes were identified between the two R NILs, suggesting that certain responses may represent basal resistance to F. graminearum and/or general biotic stress response and were expressed by both resistant genotypes. Long noncoding RNAs (lncRNAs) have emerged as potential key regulators of transcription. A total of 12,366 lncRNAs were identified, of which 604 were FHB responsive. CONCLUSIONS: The current transcriptomic analysis revealed differential responses conferred by two QTL during F. graminearum infection and identified genes and lncRNAs that were associated with FHB resistance.

A genome-wide association study of malting quality across eight U.S. barley breeding programs.

KEY MESSAGE: We report malt quality QTLs relevant to breeding with greater precision than previous mapping studies. The distribution of favorable alleles suggests strategies for marker-assisted breeding and germplasm exchange. This study leverages the breeding data of 1,862 barley breeding lines evaluated in 97 field trials for genome-wide association study of malting quality traits in barley. The mapping panel consisted of six-row and two-row advanced breeding lines from eight breeding populations established at six public breeding programs across the United States. A total of 4,976 grain samples were subjected to micro-malting analysis and mapping of nine quality traits was conducted with 3,072 SNP markers distributed throughout the genome. Association mapping was performed for individual breeding populations and for combined six-row and two-row populations. Only 16% of the QTL we report here had been detected in prior bi-parental mapping studies. Comparison of the analyses of the combined two-row and six-row panels identified only two QTL regions that were common to both. In total, 108 and 107 significant marker-trait associations were identified in all six-row and all two-row breeding programs, respectively. A total of 102 and 65 marker-trait associations were specific to individual six-row and two-row breeding programs, respectively indicating that most marker-trait associations were breeding population specific. Combining datasets from different breeding program resulted in both the loss of some QTL that were apparent in the analyses of individual programs and the discovery of new QTL not identified in individual programs. This suggests that simply increasing sample size by pooling samples with different breeding history does not necessarily increase the power to detect associations. The genetic architecture of malting quality and the distribution of favorable alleles suggest strategies for marker-assisted selection and germplasm exchange.

Genetic Characterization of Resistance to Wheat Stem Rust Race TTKSK in Landrace and Wild Barley Accessions Identifies the rpg4/Rpg5 Locus.

Race TTKSK of the wheat stem rust pathogen (Puccinia graminis f. sp. tritici) threatens the production of wheat and barley worldwide because of its broad-spectrum virulence on many widely grown cultivars. Sources of resistance against race TTKSK were recently identified in several barley landraces (Hordeum vulgare subsp. vulgare) and wild barley accessions (H. vulgare subsp. spontaneum). The objectives of this study were to characterize the inheritance of resistance to wheat stem rust race TTKSK in four barley landraces (Hv501, Hv545, Hv602, and Hv612) and two wild barley (WBDC213 and WBDC345) accessions, map the resistance genes, and determine the allelic relationships among the genes in these accessions and the previously described rpg4/Rpg5 locus. Resistant accessions were crossed with the susceptible cv. Steptoe and resulting F3 populations were evaluated for resistance to race TTKSK at the seedling stage. Segregation of F3 families in populations involving the resistance sources of Hv501, Hv545, Hv612, WBDC213, and WBDC345 fit a 1:2:1 ratio for homozygous resistant (HR)/segregating (SEG)/homozygous susceptible (HS) progenies (with χ2=2.27 to 5.87 and P=0.053 to 0.321), indicating that a single gene confers resistance to race TTKSK. Segregation of F3 families in cross Steptoe/Hv602 did not fit a 1:2:1 ratio (HR/SEG/HS of 20:47:43 with χ2=11.95 and P=0.003), indicating that more than one gene is involved in imparting resistance to race TTKSK. Bulked segregant analysis using >1,500 single-nucleotide polymorphism markers positioned a resistance locus in all six populations on chromosome 5HL in very close proximity to the known location of the rpg4/Rpg5 complex locus. Allelism tests were conducted by making crosses among resistant accessions Hv501, Hv545, and Hv612 and also Q21861 with the rpg4/Rpg5 complex. No segregation was observed in F2 families inoculated with race TTKSK, demonstrating that all Hv lines carry the same allele for resistance and that it resides at or very near the rpg4/Rpg5 locus. Phenotype evaluations of the six barley accessions with wheat stem rust race QCCJ revealed resistant infection types (ITs) at a low incubation temperature and susceptible ITs at a high incubation temperature, similar to Q21861, which carries the temperature-sensitive gene rpg4. The accessions also exhibited low ITs against the rye stem rust isolate 92-MN-90, suggesting that they also carry Rpg5. This result was confirmed through molecular analysis, which revealed that all six barley accessions contain the serine threonine protein kinase domain that confers Rpg5 resistance. These results indicate that cultivated barley is extremely vulnerable to African stem rust races such as TTKSK because even these diverse selections of landrace and wild barley accessions carry only one locus for resistance.

Using near-isogenic barley lines to validate deoxynivalenol (DON) QTL previously identified through association analysis.

Fusarium head blight (FHB) and its associated mycotoxin, deoxynivalenol (DON), are the major biotic factors limiting cereal production in many parts of the world. A recent association mapping (AM) study of US six-row spring barley identified several modest effect quantitative trait loci (QTL) for DON and FHB. To date, few studies have attempted to verify the results of association analyses, particularly for complex traits such as DON and FHB resistance in barley. While AM methods use measures to control for the effects of population structure and multiple testing, false positive associations may still occur. A previous AM study used elite breeding germplasm to identify QTL for FHB and DON. To verify the results of that study, we evaluated the effects of the nine DON QTL using near-isogenic lines (NILs). We created families of contrasting homozygous haplotypes from lines in the original AM populations that were heterozygous for the DON QTL. Seventeen NIL families were evaluated for FHB and DON in three field experiments. Significant differences between contrasting NIL haplotypes were detected for three QTL across environments and/or genetic backgrounds, thereby confirming QTL from the original AM study. Several explanations for those QTL that were not confirmed are discussed, including the effect of genetic background and incomplete sampling of relevant haplotypes.

Haplotype diversity and population structure in cultivated and wild barley evaluated for Fusarium head blight responses.

Fusarium head blight (FHB) is a threat to barley (Hordeum vulgare L.) production in many parts of the world. A number of barley accessions with partial resistance have been reported and used in mapping experiments to identify quantitative trait loci (QTL) associated with FHB resistance. Here, we present a set of barley germplasm that exhibits FHB resistance identified through screening a global collection of 23,255 wild (Hordeum vulgare ssp. spontaneum) and cultivated (Hordeum vulgare ssp. vulgare) accessions. Seventy-eight accessions were classified as resistant or moderately resistant. The collection of FHB resistant accessions consists of 5, 27, 46 of winter, wild and spring barley, respectively. The population structure and genetic relationships of the germplasm were investigated with 1,727 Diversity Array Technology (DArT) markers. Multiple clustering analyses suggest the presence of four subpopulations. Within cultivated barley, substructure is largely centered on spike morphology and growth habit. Analysis of molecular variance indicated highly significant genetic variance among clusters and within clusters, suggesting that the FHB resistant sources have broad genetic diversity. The haplotype diversity was characterized with DArT markers associated with the four FHB QTLs on chromosome 2H bin8, 10 and 13 and 6H bin7. In general, the wild barley accessions had distinct haplotypes from those of cultivated barley. The haplotype of the resistant source Chevron was the most prevalent in all four QTL regions, followed by those of the resistant sources Fredrickson and CIho4196. These resistant QTL haplotypes were rare in the susceptible cultivars and accessions grown in the upper Midwest USA. Some two- and six-rowed accessions were identified with high FHB resistance, but contained distinct haplotypes at FHB QTLs from known resistance sources. These germplasm warrant further genetic studies and possible incorporation into barley breeding programs.