Fine mapping qGL2H, a major locus controlling grain length in barley (Hordeum vulgare L.)

Increasing yield is an important target for barley breeding programs. One approach to increase yield is by enhancing individual grain weights through the regulation of grain size. Fine mapping major grain size-related quantitative trait loci is necessary for future marker-assisted selection strategies, yet studies of this nature are limited in barley. In the present study, we utilised a doubled haploid population derived from two Australian malt barley varieties, Vlamingh and Buloke, coupled with extensive genotypic and phenotypic data from three independent environments. A major grain length locus identified on chromosome 2H designated qGL2H was fine mapped to a 140.9 Kb interval. qGL2H was able to account for 25.4% of the phenotypic variation for grain length and 10.2% for grain yield. Underlying qGL2H were three high-confidence predicted genes. One of these genes encodes a MYB transcription factor and represents a promising candidate for further genetic research

Multi-locus genome-wide association studies reveal novel alleles for flowering time under vernalisation and extended photoperiod in a barley MAGIC population

Optimal flowering time has a major impact on grain yield in crop species, including the globally important temperate cereal crop barley (Hordeum vulgare L.). Understanding the genetics of flowering is a key avenue to enhancing yield potential. Although bi-parental populations were used intensively to map genes controlling flowering, their lack of genetic diversity requires additional work to obtain desired gene combinations in the selected lines, especially when the two parental cultivars did not carry the genes. Multi-parent mapping populations, which use a combination of four or eight parental cultivars, have higher genetic and phenotypic diversity and can provide novel genetic combinations that cannot be achieved using bi-parental populations. This study uses a Multi-parent advanced generation intercross (MAGIC) population from four commercial barley cultivars to identify genes controlling flowering time in different environmental conditions. Genome-wide association studies (GWAS) were performed using 5,112 high-quality markers from Diversity Arrays Technology sequencing (DArT-seq), and Kompetitive allele-specific polymerase chain reaction (KASP) genetic markers were developed. Phenotypic data were collected from fifteen different field trials for three consecutive years. Planting was conducted at various sowing times, and plants were grown with/without additional vernalisation and extended photoperiod treatments. This study detected fourteen stable regions associated with flowering time across multiple environments. GWAS combined with pangenome data highlighted the role of CEN gene in flowering and enabled the prediction of different CEN alleles from parental lines. As the founder lines of the multi-parental population are elite germplasm, the favourable alleles identified in this study are directly relevant to breeding, increasing the efficiency of subsequent breeding strategies and offering better grain yield and adaptation to growing conditions

Hybridisation-based target enrichment of phenology genes to dissect the genetic basis of yield and adaptation in barley

Barley (Hordeum vulgare L.) is a major cereal grain widely used for livestock feed, brewing malts and human food. Grain yield is the most important breeding target for genetic improvement and largely depends on optimal timing of flowering. Little is known about the allelic diversity of genes that underlie flowering time in domesticated barley, the genetic changes that have occurred during breeding, and their impact on yield and adaptation. Here we report a comprehensive genomic assessment of a worldwide collection of 895 barley accessions based on the targeted resequencing of phenology genes. A versatile target‐capture method was used to detect genome‐wide polymorphisms in a panel of 174 flowering time‐related genes, chosen based on prior knowledge from barley, rice, and Arabidopsis thaliana. Association studies identified novel polymorphisms that accounted for observed phenotypic variation in phenology and grain yield, and explained improvements in adaptation as a result of historical breeding of Australian barley cultivars. We found that 50% of genetic variants associated with grain yield, and 67% of the plant height variation was also associated with phenology. The precise identification of favourable alleles provides a genomic basis to improve barley yield traits and to enhance adaptation for specific production areas

Comparison of airway measurements during influenza-induced tachypnea in infant and adult cotton rats

<p>Abstract</p> <p>Background</p> <p>Increased respiratory rate (tachypnea) is frequently observed as a clinical sign of influenza pneumonia in pediatric patients admitted to the hospital. We previously demonstrated that influenza infection of adult cotton rats (<it>Sigmodon hispidus</it>) also results in tachypnea and wanted to establish whether this clinical sign was observed in infected infant cotton rats. We hypothesized that age-dependent differences in lung mechanics result in differences in ventilatory characteristics following influenza infection.</p> <p>Methods</p> <p>Lung tidal volume, dynamic elastance, resistance, and pleural pressure were measured in a resistance and compliance system on mechanically-ventilated anesthestized young (14–28 day old) and adult (6–12 week old) cotton rats. Animals at the same age were infected with influenza virus, and breathing rates and other respiratory measurements were recorded using a whole body flow plethysmograph.</p> <p>Results</p> <p>Adult cotton rats had significantly greater tidal volume (TV), and lower resistance and elastance than young animals. To evaluate the impact of this increased lung capacity and stiffening on respiratory disease, young and adult animals were infected intra-nasally with influenza A/Wuhan/359/95. Both age groups had increased respiratory rate and enhanced pause (<it>Penh</it>) during infection, suggesting lower airway obstruction. However, in spite of significant tachypnea, the infant (unlike the adult) cotton rats maintained the same tidal volume, resulting in an increased minute volume. In addition, the parameters that contribute to <it>Penh </it>were different: while relaxation time between breaths and time of expiration was decreased in both age groups, a disproportionate increase in peak inspiratory and expiratory flow contributed to the increase in <it>Penh </it>in infant animals.</p> <p>Conclusion</p> <p>While respiratory rate is increased in both adult and infant influenza-infected cotton rats, the volume of air exchanged per minute (minute volume) is increased in the infant animals only. This is likely to be a consequence of greater lung elastance in the very young animals. This model replicates many respiratory features of humans and consequently may be a useful tool to investigate new strategies to treat respiratory disease in influenza-infected infants.</p

Fine mapping of qGL5H, a major grain length locus in barley (Hordeum vulgare L.)

Quantitative trait loci (QTLs) mapping has been used extensively in barley to detect QTLs that underlie complex traits such as grain size. In the present study, we utilised 312 double haploid lines derived from a cross between two Australian malting varieties, Vlamingh and Buloke, to dissect the genetic control of a number of grain size characteristics. Digital image analysis was used to measure grain size characteristics including length, width, thickness and plumpness which are important traits influencing barley yield and grain physical quality. Using data from four independent environments and molecular marker genotype data, we identified 23 significant QTLs for these four traits, ten of which were consensus QTLs and identified in two or more environments. A QTL region on chromosome 5H designated qGL5H that was associated with grain size was fine mapped to a 1.7 Mb interval. qGL5H was able to explain 21.6% of phenotypic variation for grain length within the population. This major QTL is an appropriate candidate for further genetic dissection

Genetic dissection of the interactions between semi-dwarfing genes sdw1 and ari-e and their effects on agronomic traits in a barley MAGIC population

The introduction of semi-dwarf cereal crop varieties in the 1960s enabled extensive increases in global food production. Semi-dwarf barley cultivars have shorter stature and improved stress resistance, grain yield and quality than tall varieties. The major semi-dwarf genes, sdw1 and ari-e, have been widely used in barley breeding programmes worldwide. In this study, we identified a novel sdw1 allele in cv. Lockyer and investigated the effect of sdw1 and ari-e and their interactions on plant height, flowering time and grain yield using a Multi-parent Advanced Generation Inter-cross (MAGIC) population generated from four elite barley cultivars. Allele-specific markers combined with Kompetitive Allele Specific Polymerase Chain Reaction (KASP) assays were used for fast and accurate screening of plants with different allele combinations. The results showed that the novel sdw1 allele from cv. Lockyer had similar effects on plant growth and phenology as the known sdw1.d allele. The two semi-dwarf genes sdw1 and ari-e had an additive effect for plant height with height reductions up to 27 cm. The ari-e gene triggered earlier flowering up to 6 days compared to WT and reduced the delay in flowering time caused by the sdw1 gene. The two semi-dwarf genes boosted grain yields by 20% in the sdw1 plants and up to 28% in plants with the two combined semi-dwarf genes. The results presented will benefit the development of higher-yielding and better-adapted barley cultivars

Airway narrowing assessed by anatomical optical coherence tomography in vitro: Dynamic airway wall morphology and function

Regulation of airway caliber by lung volume or bronchoconstrictor stimulation is dependent on physiological, structural, and mechanical events within the airway wall, including airway smooth muscle (ASM) contraction, deformation of the mucosa and cartilage, and tensioning of elastic matrices linking wall components. Despite close association between events in the airway wall and the resulting airway caliber, these have typically been studied separately: the former primarily using histological approaches, the latter with a range of imaging modalities. We describe a new optical technique, anatomical optical coherence tomography (aOCT), which allows changes at the luminal surface (airway caliber) to be temporally related to corresponding dynamic movements within the airway wall. A fiber-optic aOCT probe was inserted into the lumen of isolated, liquid-filled porcine airways. It was used to image the response to ASM contraction induced by neural stimulation and to airway inflation and deflation. Comparisons with histology indicated that aOCT provided highresolution images of the airway lumen including mucosal folds, the entire inner wall (mucosa and ASM), and partially the cartilaginous outer wall. Airway responses assessed by aOCT revealed several phenomena in "live" airways (i.e., not fixed) previously identified by histological investigations of fixed tissue, including a geometric relationship between ASM shortening and luminal narrowing, and sliding and bending of cartilage plates. It also provided direct evidence for distensibility of the epithelial membrane and anisotropic behavior of the airway wall. Findings suggest that aOCT can be used to relate changes in airway caliber to dynamic events in the wall of airways. Copyright © 2010 the American Physiological Society