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As genotyping-by-sequencing (GBS) is widely used in barley genetic studies, the translation of the physical position of GBS-derived SNPs into accurate genetic positions has become relevant. The main aim of this study was to develop a high-resolution consensus linkage map based on GBS-derived SNPs. The construction of this integrated map involved 11 bi-parental populations composed of 3743 segregating progenies. We adopted a uniform set of SNPcalling and filtering conditions to identify 50 875 distinct SNPs segregating in at least one population. These SNPs were grouped into 18 580 non-redundant SNPs (bins). The resulting consensus linkage map spanned 1050.1 cM, providing an average density of 17.7 bins and 48.4 SNPs per cM. The consensus map is characterized by the absence of large intervals devoid of marker coverage (significant gaps), the largest interval between bins was only 3.7 cM and the mean distance between adjacent bins was 0.06 cM. This high-resolution linkage map will contribute to several applications in genomic research, such as providing useful information on the recombination landscape for QTLs/genes identified via GWAS or ensuring a uniform distribution of SNPs when developing low-cost genotyping tools offering a limited number of markers. Key words: barley, genotyping-by-sequencing, single-nucleotide polymorphism, bi-parental population, recombination event, linkage map, consensus map, genetic position. Comme le genotypage par sequen age (GBS) est largement utilise pour les analyses genetiques chez l'orge, la correspondance entre la position physique des marqueurs SNP derives du GBS et leur position genetique precise est importante a etablir. Le but principal de ce travail etait de produire une carte genetique consensus a haute resolution fondee sur des marqueurs SNP derives du GBS. La production de cette carte integree repose sur 11 populations biparentales totalisant 3743 individus en segregation. Les auteurs ont employe une serie de parametres uniformes pour l'appel et la filtration des SNP ce qui a permis d'identifier 50 875 marqueurs distincts qui etaient en segregation au sein d'au moins une population. Ces SNP ont ensuite ete groupes en 18 580 SNP non-redondants ([much less than] bins [much greater than]). La carte genetique consensus ainsi produite s'etend sur 1050,1 cM, offrant ainsi une densite moyenne de 17,7 bins et 48,4 SNP par cM. La carte consensus ne presente aucun grand intervalle depourvu de marqueurs ([much less than] gaps [much greater than] significatifs), l'intervalle le plus grand entre bins etant de seulement 3,7 cM et la distance moyenne entre bins etant de 0,06 cM. Cette carte a haute resolution trouvera de nombreuses applications en genomique tel que des informations utiles sur le niveau de recombinaison a proximite de QTL/genes identifies au terme d'analyses GWAS ou pour assurer une distribution uniforme des marqueurs SNP lors du developpement d'outils de genotypage a faible cout reposant sur un nombre limite de marqueurs. [Traduit par la Redaction] Mots-cles: orge, genotypage par sequencage, polymorphisme mononucleotidique, population biparentale, evenement de recombinaison, carte de liaison genetique, carte consensus, position genetique., Introduction A genetic linkage map portrays the order and genetic positions of molecular markers and other loci on all chromosomes within an organism. It is most commonly inferred from marker [...]

Spot blotch, caused by Bipolaris sorokiniana, is a growing concern for barley (Hordeum vulgare) production in most humid, temperate growing regions of the world. Under epidemic conditions, this disease can reduce yields significantly. Reduction of kernel plumpness is associated with lower malt extract and consequently grain quality. Enhanced resistance to this disease is a major goal of western Canadian two‐row barley breeding programmes; however, two‐row barley is considered to be more susceptible than six‐row barley. Plant–pathogen interactions observed for Canadian germplasm are polygenic, where quantitative breeding methods could be beneficial for the development of resistant germplasm. A germplasm panel consisting of 200 two‐row, spring barley genotypes with differential reaction to spot blotch was evaluated at Brandon, Manitoba (MB), and Melfort, Saskatchewan (SK), over eight site years. Genome‐wide association study was conducted using a 50k single‐nucleotide polymorphism (SNP) Illumina iSelect genotyping array. The most‐resistant germplasm was found to carry Midwest Six‐rowed Durable Resistant Haplotype (MSDRH) alleles at the loci located on chromosomes 1H (Rcs‐qtl‐1H‐11_10764), 3H (Rcs‐qtl‐3H‐11_10565) and 7H (Rcs‐qtl‐7H‐11_20162, Rcs5 locus), where the 3H locus was found to be the most under‐represented in Canadian germplasm. Additional marker‐trait associations within nurseries were identified on chromosomes 1H, 2H and 4H. Several of the SNP markers identified were found to be polymorphic within the Canadian two‐row germplasm panel and thus could be useful for enhancing spot blotch resistance in two‐row barley for development of resistant cultivars. [ABSTRACT FROM AUTHOR]

Abstract Background Genetic markers are pivotal to modern genomics research; however, discovery and genotyping of molecular markers in oat has been hindered by the size and complexity of the genome, and by a scarcity of sequence data. The purpose of this study was to generate oat expressed sequence tag (EST) information, develop a bioinformatics pipeline for SNP discovery, and establish a method for rapid, cost-effective, and straightforward genotyping of SNP markers in complex polyploid genomes such as oat. Results Based on cDNA libraries of four cultivated oat genotypes, approximately 127,000 contigs were assembled from approximately one million Roche 454 sequence reads. Contigs were filtered through a novel bioinformatics pipeline to eliminate ambiguous polymorphism caused by subgenome homology, and 96 in silico SNPs were selected from 9,448 candidate loci for validation using high-resolution melting (HRM) analysis. Of these, 52 (54%) were polymorphic between parents of the Ogle1040 × TAM O-301 (OT) mapping population, with 48 segregating as single Mendelian loci, and 44 being placed on the existing OT linkage map. Ogle and TAM amplicons from 12 primers were sequenced for SNP validation, revealing complex polymorphism in seven amplicons but general sequence conservation within SNP loci. Whole-amplicon interrogation with HRM revealed insertions, deletions, and heterozygotes in secondary oat germplasm pools, generating multiple alleles at some primer targets. To validate marker utility, 36 SNP assays were used to evaluate the genetic diversity of 34 diverse oat genotypes. Dendrogram clusters corresponded generally to known genome composition and genetic ancestry. Conclusions The high-throughput SNP discovery pipeline presented here is a rapid and effective method for identification of polymorphic SNP alleles in the oat genome. The current-generation HRM system is a simple and highly-informative platform for SNP genotyping. These techniques provide a model for SNP discovery and genotyping in other species with complex and poorly-characterized genomes.

Background and Objectives: The effect of genotype × environment (G × E) on oat protein structural characteristics and functionality was studied using three oat genotypes grown in three different environments across the Canadian Prairies. Findings: The protein content of oat protein isolate (OPI) ranged from 76.9% to 90.2%. All structural characteristics except protein surface hydrophobicity were significantly impacted by G × E, whereas protein surface hydrophobicity strongly depended on the growing environment. SDS‐PAGE and FT‐IR analysis demonstrated that oat protein profile and secondary structure were significantly impacted by genotype rather than environment. Cultivar Summit grown in Alberta had the highest foaming capacity which was significantly higher than Summit grown in the other environments, indicating a strong influence of environment on OPI foaming capacity. Conclusion: The structure‐function properties of OPI extracted from the given cultivars were influenced by G × E however, further studies are needed to evaluate the stability of the tested cultivars over several years. Significance and Novelty: Understanding how OPI structure and functional properties are influenced by G × E will allow better utilization of OPI in the food industry by facilitating the development of OPI ingredients with predictable functional properties. [ABSTRACT FROM AUTHOR]

Low-temperature stress (LTS) is among the major abiotic stresses affecting the geographical distribution and productivity of the most important crops. Understanding the genetic basis of photosynthetic variation under cold stress is necessary for developing more climate-resilient barley cultivars. To that end, we investigated the ability of chlorophyll fluorescence parameters (FVFM, and FVF0) to respond to changes in the maximum quantum yield of Photosystem II photochemistry as an indicator of photosynthetic energy. A panel of 96 barley spring cultivars from different breeding zones of Canada was evaluated for chlorophyll fluorescence-related traits under cold acclimation and freeze shock stresses at different times. Genome-wide association studies (GWAS) were performed using a mixed linear model (MLM). We identified three major and putative genomic regions harboring 52 significant quantitative trait nucleotides (QTNs) on chromosomes 1H, 3H, and 6H for low-temperature tolerance. Functional annotation indicated several QTNs were either within the known or close to genes that play important roles in the photosynthetic metabolites such as abscisic acid (ABA) signaling, hydrolase activity, protein kinase, and transduction of environmental signal transduction at the posttranslational modification levels. These outcomes revealed that barley plants modified their gene expression profile in response to decreasing temperatures resulting in physiological and biochemical modifications. Cold tolerance could influence a long-term adaption of barley in many parts of the world. Since the degree and frequency of LTS vary considerably among production sites. Hence, these results could shed light on potential approaches for improving barley productivity under low-temperature stress. [ABSTRACT FROM AUTHOR]

Interest in malting hulless barley (HB) is driven by its potential to produce very high levels of malt extract, but elevated levels of wort ß-glucan and insufficient levels of enzymes in hulless malt have prevented its widespread use. The objective of this study was to highlight the recent advancements in quality improvement of Canadian HB for malting purposes. Five advanced HB lines were evaluated for various barley and malt quality characteristics. All hulless lines exhibited lower grain hardness and slightly lower kernel weight and diameter compared to AAC Synergy (a popular two-rowed covered Canadian variety). The average total starch content of the hulless barley lines (64.2%) was significantly higher than AAC Synergy (59.9%) but slightly lower than that of CDC Clear (65.1%). Despite the low friability values, HB malts had a crumbly texture with good solubility and enzyme accessibility resulting in ample production of fermentable sugars. The average chain length of starch hydrolysis products in wort of new HB lines was similar to that of AAC Synergy, indicating sufficient enzyme activities and a highly effective hydrolysis. The fine-grind extract levels from hulless malt were on average 8% higher than from AAC Synergy, and several new HB lines exceeded the level of CDC Clear extract by 0.7–1.0%. Compared to CDC Clear, the new HB lines showed a significant reduction in concentration of wort ß-glucans. The concentration and the average degree of polymerization of arabinoxylo-oligosaccharides in wort of HB lines were generally higher than in wort of AAC Synergy, partly explaining the higher viscosity of HB worts. In general, the recently developed HB lines exhibited excellent malting potential with significant improvements in the levels of malt enzymes, concentration of free amino nitrogen compounds, and β-glucans in wort. [ABSTRACT FROM AUTHOR]

The first doubled haploid oat linkage map constructed at MTT Agrifood Research Finland was supplemented with additional microsatellites and Diversity Array Technology (DArT) markers to produce a map containing 1058 DNA markers and 34 linkage groups. The map was used to locate quantitative trait loci (QTLs) for 11 important breeding traits analyzed from Finnish and Canadian field trials. The new markers enabled most of the linkage groups to be anchored to the 'Kanota' x 'Ogle' oat (Avena sativa L.) reference map and allowed comparison of the QTLs located in this study with those found previously. Two to 12 QTLs for each trait were discovered, of which several were expressed consistently across several environments. Key words: Avena sativa, DArT, DNA markers, doubled haploid, QTL. Resume : La premiere carte genetique de l'avoine produite avec des haploides doubles obtenus par MTT Agrifood Research Finland a ete bonifiee par l'ajout de marqueurs microsatellites additionnels et de marqueurs << Diversity Array Technology >> (DArT) pour produire une nouvelle carte comprenant 1058 marqueurs moleculaires et 34 groupes de liaison. Cette carte a ete employee pour localiser des QTL pour 11 caracteres d'importance agronomique mesures lors d'essais au champ en Finlande et au Canada. Les nouveaux marqueurs ont permis d'ancrer la plupart des groupes de liaison a la carte de reference 'Kanota x Ogle' et de comparer les QTL identifies au cours de ce travail avec ceux rapportes anterieurement. Entre 2 et 12 QTL pour chaque caractere ont ete identifies dont plusieurs etaient reproductibles au sein de plusieurs environnements. Mots-cles : Avena sativa, DArT, marqueurs moleculaires, haploide double, QTL. [Traduit par la Redaction], Introduction Several linkage maps of hexaploid oat (Avena sativa L.) exist (reviewed by Rines et al. 2006; Tanhuanpaa et al. 2008) with quantitative trait loci (QTLs) affecting important traits located [...]

Re-examining historical datasets is a proposed use for association mapping (AM) and is particularly valuable when the data describes time-consuming and/or expensive to measure traits. A collection of 91 elite two-row malting barley (Hordeum vulgare L.) lines entered in the western Canadian Cooperative Two-Row Barley Trials over a 13- yr period were analyzed by AM to identify markers associated with seven malting quality traits. A linear mixed-model incorporating population structure and familial relatedness identified 27 diversity array technology (DArT) markers associated with malting quality. These markers will assist selection of parents with complementary allele combinations for future crosses and help identify progeny with the desired alleles. Putative candidate expressed sequence tags (ESTs) responsible for marker-trait associations were identified for 19 of the 27 DArT markers and include genes important for seed storage protein accumulation, gibberellin-mediated gene expression, seed storage mobilization, and dormancy. Efforts to identify novel variability in these genes may present opportunities to improve malting quality. doi: 10.2135/cropsci2009.06.0334

Abstract Background Genetic markers are pivotal to modern genomics research; however, discovery and genotyping of molecular markers in oat has been hindered by the size and complexity of the genome, and by a scarcity of sequence data. The purpose of this study was to generate oat expressed sequence tag (EST) information, develop a bioinformatics pipeline for SNP discovery, and establish a method for rapid, cost-effective, and straightforward genotyping of SNP markers in complex polyploid genomes such as oat. Results Based on cDNA libraries of four cultivated oat genotypes, approximately 127,000 contigs were assembled from approximately one million Roche 454 sequence reads. Contigs were filtered through a novel bioinformatics pipeline to eliminate ambiguous polymorphism caused by subgenome homology, and 96 in silico SNPs were selected from 9,448 candidate loci for validation using high-resolution melting (HRM) analysis. Of these, 52 (54%) were polymorphic between parents of the Ogle1040 × TAM O-301 (OT) mapping population, with 48 segregating as single Mendelian loci, and 44 being placed on the existing OT linkage map. Ogle and TAM amplicons from 12 primers were sequenced for SNP validation, revealing complex polymorphism in seven amplicons but general sequence conservation within SNP loci. Whole-amplicon interrogation with HRM revealed insertions, deletions, and heterozygotes in secondary oat germplasm pools, generating multiple alleles at some primer targets. To validate marker utility, 36 SNP assays were used to evaluate the genetic diversity of 34 diverse oat genotypes. Dendrogram clusters corresponded generally to known genome composition and genetic ancestry. Conclusions The high-throughput SNP discovery pipeline presented here is a rapid and effective method for identification of polymorphic SNP alleles in the oat genome. The current-generation HRM system is a simple and highly-informative platform for SNP genotyping. These techniques provide a model for SNP discovery and genotyping in other species with complex and poorly-characterized genomes.