β-Glucan content increase in Waxy-mutated barley is closely associated with positive stress responses and is regulated by ASR1

Mixed-linkage (1,3; 1,4)-β-D-glucan (MLG) impacts the food and industrial end-uses of barley, but the molecular mechanism of variations in MLG content remains unclear. MLG content usually increases in Waxy-mutated barley. This study applied transcriptomic, proteomic, and metabolomic analyses to Waxy-mutated recombinant inbred lines with higher MLG content and wild-type lines with lower MLG content, and identified candidate genes and pathways regulating MLG content through combining preliminary gene function analysis. MLG biosynthesis differed significantly during late grain development in the Waxy-mutated and wild-type barley lines. The MLG increase was closely associated with strongly active sugar and starch metabolism and stress-responsive plant hormones, particularly abscisic acid (ABA) signaling process. Stress-responsive transcript factors ILR3, BTF3, RGGA, and PR13 protein bind to CslF6, which is critical for barley MLG biosynthesis, and the stress-responsive gene ASR1 also had a positive effect on MLG increase. Waxy mutation enhances barley stress responses by activating ABA- or other stress-responsive plant hormones signaling processes, which facilitates MLG biosynthesis. This study provides a new approach for elucidating the variations in MLG content of barley grains.

Detection of consensus genomic regions and candidate genes for quality traits in barley using QTL meta-analysis

Improving barley grain quality is a major goal in barley breeding. In this study, a total of 35 papers focusing on quantitative trait loci (QTLs) mapping for barley quality traits published since 2000 were collected. Among the 454 QTLs identified in these studies, 349 of them were mapped onto high-density consensus maps, which were used for QTL meta-analysis. Through QTL meta-analysis, the initial QTLs were integrated into 41 meta-QTLs (MQTLs) with an average confidence interval (CI) of 1. 66 cM, which is 88.9% narrower than that of the initial QTLs. Among the 41 identified MQTLs, 25 were subsequently validated in publications using genome-wide association study (GWAS). From these 25 validated MQTLs, ten breeder's MQTLs were selected. Synteny analysis comparing barley and wheat MQTLs revealed orthologous relationships between eight breeder's MQTLs and 45 wheat MQTLs. Additionally, 17 barley homologs associated with rice quality traits were identified within the regions of the breeder's MQTLs through comparative analysis. The findings of this study provide valuable insights for molecular marker-assisted breeding and the identification of candidate genes related to quality traits in barley.

Barley grain (1,3;1,4)-β-glucan content: effects of transcript and sequence variation in genes encoding the corresponding synthase and endohydrolase enzymes

The composition of plant cell walls is important in determining cereal end uses. Unlike other widely consumed cereal grains barley is comparatively rich in (1,3;1,4)-β-glucan, a source of dietary fibre. Previous work showed Cellulose synthase-like genes synthesise (1,3;1,4)-β-glucan in several tissues. HvCslF6 encodes a grain (1,3;1,4)-β-glucan synthase, whereas the function of HvCslF9 is unknown. Here, the relationship between mRNA levels of HvCslF6, HvCslF9, HvGlbI (1,3;1,4)-β-glucan endohydrolase, and (1,3;1,4)-β-glucan content was studied in developing grains of four barley cultivars. HvCslF6 was differentially expressed during mid (8-15 DPA) and late (38 DPA) grain development stages while HvCslF9 transcript was only clearly detected at 8-10 DPA. A peak of HvGlbI expression was detected at 15 DPA. Differences in transcript abundance across the three genes could partially explain variation in grain (1,3;1,4)-β-glucan content in these genotypes. Remarkably narrow sequence variation was found within the HvCslF6 promoter and coding sequence and does not explain variation in (1,3;1,4)-β-glucan content. Our data emphasise the genotype-dependent accumulation of (1,3;1,4)-β-glucan during barley grain development and a role for the balance between hydrolysis and synthesis in determining (1,3;1,4)-β-glucan content, and suggests that other regulatory sequences or proteins are likely to be involved in this trait in developing grain.

Barley grain (1,3;1,4)-β-glucan content: effects of transcript and sequence variation in genes encoding the corresponding synthase and endohydrolase enzymes

The composition of plant cell walls is important in determining cereal end uses. Unlike other widely consumed cereal grains barley is comparatively rich in (1,3;1,4)-β-glucan, a source of dietary fibre. Previous work showed Cellulose synthase-like genes synthesise (1,3;1,4)-β-glucan in several tissues. HvCslF6 encodes a grain (1,3;1,4)-β-glucan synthase, whereas the function of HvCslF9 is unknown. Here, the relationship between mRNA levels of HvCslF6, HvCslF9, HvGlbI (1,3;1,4)-β-glucan endohydrolase, and (1,3;1,4)-β-glucan content was studied in developing grains of four barley cultivars. HvCslF6 was differentially expressed during mid (8-15 DPA) and late (38 DPA) grain development stages while HvCslF9 transcript was only clearly detected at 8-10 DPA. A peak of HvGlbI expression was detected at 15 DPA. Differences in transcript abundance across the three genes could partially explain variation in grain (1,3;1,4)-β-glucan content in these genotypes. Remarkably narrow sequence variation was found within the HvCslF6 promoter and coding sequence and does not explain variation in (1,3;1,4)-β-glucan content. Our data emphasise the genotype-dependent accumulation of (1,3;1,4)-β-glucan during barley grain development and a role for the balance between hydrolysis and synthesis in determining (1,3;1,4)-β-glucan content, and suggests that other regulatory sequences or proteins are likely to be involved in this trait in developing grain.

Association and genome analyses to propose putative candidate genes for malt quality traits

BACKGROUND

We studied the genetics of nine malt quality traits using association genetics in a panel of North Dakota, ICARDA, and Ethiopian barley lines. Grain samples harvested from Bekoji in 2011 and 2012 were used.

RESULTS

The mapping panel revealed strong population structure explained by inflorescence-type, geographic origin, and breeding history. North Dakota germplasm were superior in malt quality traits and they can be donors to improve malt quality properties. We identified 106 marker-trait associations (MTAs) for the nine traits, representing 81 genomic regions across all barley chromosomes. Chromosomes 3H, 5H, and 7H contained most of the MTAs (58.5%). Nearly 18.5% of these genomic regions contained two to three malt quality traits. Within ±250 kb of 81 genomic regions, we recovered 348 barley genes, with some potential impacting malt quality. These include invertase, β-fructofuranosidase, α-glucosidase, serine carboxypeptidase, and bidirectional sugar transporter SWEET14-like protein. Eighteen of these genes were also previously reported in the Hordeum Toolbox, and 17 of them highly expressed during the germination process.

CONCLUSION

The results from this study invite further follow-up functional characterization experiments to relate the genes with individual malt quality traits with higher confidence. It also provides germplasm resources for malt barley improvement. © 2018 Society of Chemical Industry.

Genome-wide association of yield traits in a nested association mapping population of barley reveals new gene diversity for future breeding

To explore wild barley as a source of useful alleles for yield improvement in breeding, we have carried out a genome-wide association scan using the nested association mapping population HEB-25, which contains 25 diverse exotic barley genomes superimposed on an ~70% genetic background of cultivated barley. A total of 1420 HEB-25 lines were trialled for nine yield-related grain traits for 2 years in Germany and Scotland, with varying N fertilizer application. The phenotypic data were related to genotype scores for 5398 gene-based single nucleotide polymorphism (SNP) markers. A total of 96 quantitative trait locus (QTL) regions were identified across all measured traits, the majority of which co-localize with known major genes controlling flowering time (Ppd-H2, HvCEN, HvGI, VRN-H1, and VRN-H3) and spike morphology (VRS3, VRS1, VRS4, and INT-C) in barley. Fourteen QTL hotspots, with at least three traits coinciding, were also identified, several of which co-localize with barley orthologues of genes controlling grain dimensions in rice. Most of the allele effects are specific to geographical location and/or exotic parental genotype. This study shows the existence of beneficial alleles for yield-related traits in exotic barley germplasm and provides candidate alleles for future improvement of these traits by the breeder.

Addition of Aegilops U and M Chromosomes Affects Protein and Dietary Fiber Content of Wholemeal Wheat Flour

Cereal grain fiber is an important health-promoting component in the human diet. One option to improve dietary fiber content and composition in wheat is to introduce genes from its wild relatives Aegilops biuncialis and Aegilops geniculata. This study showed that the addition of chromosomes 2Ug, 4Ug, 5Ug, 7Ug, 2Mg, 5Mg, and 7Mg of Ae. geniculata and 3Ub, 2Mb, 3Mb, and 7Mb of Ae. biuncialis into bread wheat increased the seed protein content. Chromosomes 1Ug and 1Mg increased the proportion of polymeric glutenin proteins, while the addition of chromosomes 1Ub and 6Ub led to its decrease. Both Aegilops species had higher proportions of β-glucan compared to arabinoxylan (AX) than wheat lines, and elevated β-glucan content was also observed in wheat chromosome addition lines 5U, 7U, and 7M. The AX content in wheat was increased by the addition of chromosomes 5Ug, 7Ug, and 1Ub while water-soluble AX was increased by the addition of chromosomes 5U, 5M, and 7M, and to a lesser extent by chromosomes 3, 4, 6Ug, and 2Mb. Chromosomes 5Ug and 7Mb also affected the structure of wheat AX, as shown by the pattern of oligosaccharides released by digestion with endoxylanase. These results will help to map genomic regions responsible for edible fiber content in Aegilops and will contribute to the efficient transfer of wild alleles in introgression breeding programs to obtain wheat varieties with improved health benefits. Key Message: Addition of Aegilops U- and M-genome chromosomes 5 and 7 improves seed protein and fiber content and composition in wheat.

Differential expression of the HvCslF6 gene late in grain development may explain quantitative differences in (1,3;1,4)-β-glucan concentration in barley

The cellulose synthase-like gene HvCslF6, which is essential for (1,3;1,4)-β-glucan biosynthesis in barley, collocates with quantitative trait loci (QTL) for grain (1,3;1,4)-β-glucan concentration in several populations, including CDC Bold × TR251. Here, an alanine-to-threonine substitution (caused by the only non-synonymous difference between the CDC Bold and TR251 HvCslF6 alleles) was mapped to a position within HvCSLF6 that seems unlikely to affect enzyme stability or function. Consistent with this, transient expression of full-length HvCslF6 cDNAs from CDC Bold and TR251 in Nicotianabenthamiana led to accumulation of similar amounts of (1,3;1,4)-β-glucan accumulation. Monitoring of HvCslF6 transcripts throughout grain development revealed a significant difference late in grain development (more than 30 days after pollination), with TR251 [the parent with higher grain (1,3;1,4)-β-glucan] exhibiting higher transcript levels than CDC Bold. A similar difference was observed between Beka and Logan, the parents of another population in which a QTL had been mapped in the HvCslF6 region. Sequencing of a putative promoter region of HvCslF6 revealed numerous polymorphisms between CDC Bold and TR251, but none between Beka and Logan. While the results of this work indicate that naturally occurring quantitative differences in (1,3;1,4)-β-glucan accumulation may be due to cis-regulated differences in HvCslF6 expression, these could not be attributed to any specific DNA sequence polymorphism. Nevertheless, information on HvCslF6 sequence polymorphism was used to develop molecular markers that could be used in barley breeding to select for the desired [low or high (1,3;1,4)-β-glucan] allele of the QTL.

A novel approach to monitor the hydrolysis of barley (Hordeum vulgare L) malt: a chemometrics approach

Malting barley is a process that has been profusely studied and is known to be influenced by several physical and biochemical properties of the grain. In particular, the amount of material that can be extracted from the malt (malt extract) is an important measure of brewing performance and end quality. The objectives of this study were (a) to compare the time course of hydrolysis of different malting barley (Hordeum vulgare L) varieties and (b) to evaluate the usefulness of mid-infrared (MIR) spectroscopy as high-throughput method to monitor malt hydrolysis. Differences in the pattern of hydrolysis were observed between the malt samples analyzed where samples from the same variety that have similar hot water extract (HWE) values tend to have the same pattern of hydrolysis. Principal component score plots based on the MIR spectra showed similar results. Partial least-squares discriminate analysis (PLS-DA) was used to classify malt samples according to their corresponding variety and time course of hydrolysis. The coefficient of determination (R(2)) and the standard error of cross validation (SECV) obtained for the prediction of variety and time course of hydrolysis were 0.67 (1.01) and 0.38 (19.90), respectively. These differences might be the result of the different composition in sugars between the barley varieties analyzed after malting, measured as wort density and not observed when only the HWE value at the end point is reported. This method offers the possibility to measure several parameters in malt simultaneously, reducing the time of analysis as well as requiring minimal sample preparation.

(1,3;1,4)-beta-D-glucans in cell walls of the poaceae, lower plants, and fungi: a tale of two linkages

(1,3;1,4)-beta-D-glucans consist of unbranched and unsubstituted chains of (1,3)- and (1,4)-beta-glucosyl residues, in which the ratio of (1,4)-beta-D-glucosyl residues to (1,3)-beta-D-glucosyl residues appears to influence not only the physicochemical properties of the polysaccharide and therefore its functional properties in cell walls, but also its adoption by different plant species during evolution. The (1,3;1,4)-beta-D-glucans are widely distributed as non-cellulosic matrix phase polysaccharides in cell walls of the Poaceae, which evolved relatively recently and consist of the grasses and commercially important cereal species, but they are less commonly found in lower vascular plants, such as the horsetails, in algae and in fungi. The (1,3;1,4)-beta-D-glucans have often been considered to be components mainly of primary cell walls, but recent observations indicate that they can also be located in secondary walls of certain tissues. Enzymes involved in the depolymerisation of (1,3;1,4)-beta-D-glucans have been well characterized. In contrast, initial difficulties in purifying the enzymes responsible for (1,3;1,4)-beta-D-glucan biosynthesis slowed progress in the identification of the genes that encode (1,3;1,4)-beta-D-glucan synthases, but emerging comparative genomics and associated techniques have allowed at least some of the genes that contribute to (1,3;1,4)-beta-D-glucan synthesis in the Poaceae to be identified. Whether similar genes and enzymes also mediate (1,3;1,4)-beta-D-glucan biosynthesis in lower plants and fungi is not yet known. Here, we compare the different fine structures of (1,3;1,4)-beta-D-glucans across the plant kingdom, present current information on the genes that have been implicated recently in their biosynthesis, and consider aspects of the cell biology of (1,3;1,4)-beta-D-glucan biosynthesis in the Poaceae.

Exploring the evolution of (1,3;1,4)-beta-D-glucans in plant cell walls: comparative genomics can help!

A key distinguishing feature of the grasses is that their cell walls contain (1,3;1,4)-beta-D-glucans, which are distributed almost exclusively within the Poaceae. The identification of genes that mediate in (1,3;1,4)-beta-D-glucan biosynthesis has been possible through relatively recent genome sequencing programmes and comparative genomics techniques. The evolution of a single new gene appears to have been sufficient for the first synthesis of (1,3;1,4)-beta-D-glucans and there is compelling evidence that existing hydrolytic enzymes were adapted for the specific hydrolysis of the polysaccharide during wall turnover or degradation. Manipulation of the expression levels of genes involved in (1,3;1,4)-beta-D-glucan synthesis is likely to provide opportunities to enhance the value of grasses and cereals in commercial applications such as human nutrition and biofuel production.