Genetic dissection of photoperiod response based on GWAS of pre-anthesis phase duration in spring barley

Heading time is a complex trait, and natural variation in photoperiod responses is a major factor controlling time to heading, adaptation and grain yield. In barley, previous heading time studies have been mainly conducted under field conditions to measure total days to heading. We followed a novel approach and studied the natural variation of time to heading in a world-wide spring barley collection (218 accessions), comprising of 95 photoperiod-sensitive (Ppd-H1) and 123 accessions with reduced photoperiod sensitivity (ppd-H1) to long-day (LD) through dissecting pre-anthesis development into four major stages and sub-phases. The study was conducted under greenhouse (GH) conditions (LD; 16/8 h; ∼20/∼16°C day/night). Genotyping was performed using a genome-wide high density 9K single nucleotide polymorphisms (SNPs) chip which assayed 7842 SNPs. We used the barley physical map to identify candidate genes underlying genome-wide association scans (GWAS). GWAS for pre-anthesis stages/sub-phases in each photoperiod group provided great power for partitioning genetic effects on floral initiation and heading time. In addition to major genes known to regulate heading time under field conditions, several novel QTL with medium to high effects, including new QTL having major effects on developmental stages/sub-phases were found to be associated in this study. For example, highly associated SNPs tagged the physical regions around HvCO1 (barley CONSTANS1) and BFL (BARLEY FLORICAULA/LEAFY) genes. Based upon our GWAS analysis, we propose a new genetic network model for each photoperiod group, which includes several newly identified genes, such as several HvCO-like genes, belonging to different heading time pathways in barley

An eight-parent multiparent advanced generation inter-cross population for winter-sown wheat: creation, properties, and validation

MAGIC populations represent one of a new generation of crop genetic mapping resources combining high genetic recombination and diversity. We describe the creation and validation of an eight-parent MAGIC population consisting of 1091 F7 lines of winter-sown wheat (Triticum aestivum L.). Analyses based on genotypes from a 90,000-single nucleotide polymorphism (SNP) array find the population to be well-suited as a platform for fine-mapping quantitative trait loci (QTL) and gene isolation. Patterns of linkage disequilibrium (LD) show the population to be highly recombined; genetic marker diversity among the founders was 74% of that captured in a larger set of 64 wheat varieties, and 54% of SNPs segregating among the 64 lines also segregated among the eight founder lines. In contrast, a commonly used reference bi-parental population had only 54% of the diversity of the 64 varieties with 27% of SNPs segregating. We demonstrate the potential of this MAGIC resource by identifying a highly diagnostic marker for the morphological character "awn presence/absence" and independently validate it in an association-mapping panel. These analyses show this large, diverse, and highly recombined MAGIC population to be a powerful resource for the genetic dissection of target traits in wheat, and it is well-placed to efficiently exploit ongoing advances in phenomics and genomics. Genetic marker and trait data, together with instructions for access to seed, are available at http://www.niab.com/MAGIC/

A simple modification of the A. nidulans transformation protocol increases the transformation frequency

After transformation of Aspergillus nidulans with plasmid DNA the transformants are usually incubated at 37C until transformants appear. We have found that pre-incubation of the transformation plates at room temperature for 24h leads to increased transformation frequencies

Relationship between psychological and biological factors and physical activity and exercise behaviour in Filipino students

The aim of the present study was threefold. Firstly, it investigated whether a general measure or specific measure of motivational orientation was better in describing the relationship between motivation and exercise behaviour. Secondly, it examined the relationship between the four most popular indirect methods of body composition assessment and physical activity and exercise patterns. Thirdly, the interaction between motivation and body composition on physical activity and exercise behaviour was explored in a sample of 275 Filipino male and female students. Males were found to have higher levels of exercise whereas females had higher levels of physical activity. Furthermore, general self-motivation together with body weight and percentage body fat were found to be the best predictor of exercise behaviour whereas the tension/pressure subscale of the ‘Intrinsic Motivation Inventory’ (IMI) was the best predictor of levels of physical activity. However, significant gender differences were observed. That is, for the males only self-motivation and for the females only body weight and BMI predicted exercise behaviour. Also, tension/pressure predicted physical activity levels for the females but not the males. No inverse relationship was found between the four body composition measures and exercise and physical activity behaviour. The results support the notion that the psychobiological approach might be particularly relevant for high intensity exercise situations but also highlights some important gender differences. Finally, the results of this study emphasise the need for more cross-cultural research

Water's non-tetrahedral side

The case for liquid water having non-tetrahedral as well as tetrahedral coordination is put forward. Given the dependence of structure on the hydrogen bond definition, a recent conceptual breakthrough has been the topological hydrogen bond definition which overcomes the shortcomings of traditional cut-off-based hydrogen bond definitions. It identifies the hydrogen bonds in water's first coordination shell using assumed transition states as boundaries instead of fixed cut-offs. Here, the topological definition is applied to liquid water to characterise the distances, angles and energies of the hydrogen bonds for the different types of coordinations found. These coordinations include bent, trigonal, tetrahedral, trigonal bipyramidal, and octahedral structures, as well as bifurcated hydrogens, bifurcated oxygens and cyclic dimers, and larger polygons. All species are shown to have properties consistent with their classification, justifying their assignments, and supporting the structure of water as a continuous, single phase mixture. However, a detailed analysis to assess the existence of the assumed transition states reveals the remarkable finding that hydrogen bond switching via a bifurcated hydrogen under certain circumstances is a barrierless process. The likelihood of a switch depends on both the acceptor numbers and on the proximity of a donor to its acceptor. Specifically, a donor in an acceptor's outermost subshell switches uphill to an acceptor of the same or higher coordination to the starting acceptor, downhill to an acceptor of lower coordination by two or more, or sits bifurcated between two acceptors if the new acceptor has a coordination lower by only one. Which it is depends intimately on the donor molecule's oscillations and on other hydrogen bond switches that control the nearby acceptors' coordinations. Finally, a search is conducted for long-range structure in water in terms of asymmetry in the distribution of the donor-acceptor bias but none is found. This journal is © The Royal Society of Chemistry

Are block copolymer worms more effective Pickering emulsifiers than block copolymer spheres?

RAFT-mediated polymerisation-induced self-assembly (PISA) is used to prepare six types of amphiphilic block copolymer nanoparticles which were subsequently evaluated as putative Pickering emulsifiers for the stabilisation of n-dodecane-in-water emulsions. It was found that linear poly(glycerol monomethacrylate)–poly(2-hydroxypropyl methacrylate) (PGMA–PHPMA) diblock copolymer spheres and worms do not survive the high shear homogenisation conditions used for emulsification. Stable emulsions are obtained, but the copolymer acts as a polymeric surfactant; individual chains rather than particles are adsorbed at the oil–water interface. Particle dissociation during emulsification is attributed to the weakly hydrophobic character of the PHPMA block. Covalent stabilisation of these copolymer spheres or worms can be readily achieved by addition of ethylene glycol dimethacrylate (EGDMA) during the PISA synthesis. TEM studies confirm that the resulting cross-linked spherical or worm-like nanoparticles survive emulsification and produce genuine Pickering emulsions. Alternatively, stabilisation can be achieved by either replacing or supplementing the PHPMA block with the more hydrophobic poly(benzyl methacrylate) (PBzMA). The resulting linear spheres or worms also survive emulsification and produce stable n-dodecane-in-water Pickering emulsions. The intrinsic advantages of anisotropic worms over isotropic spheres for the preparation of Pickering emulsions are highlighted. The former particles are more strongly adsorbed at similar efficiencies compared to spheres and also enable smaller oil droplets to be produced for a given copolymer concentration. The scalable nature of PISA formulations augurs well for potential applications of anisotropic block copolymer nanoparticles as Pickering emulsifiers

Genome‐wide association mapping of Hagberg falling number, protein content, test weight and grain yield in UK wheat

Association mapping using crop cultivars allows identification of genetic loci of direct relevance to breeding. Here, 150 U.K. wheat (Triticum aestivum L.) cultivars genotyped with 23,288 single nucleotide polymorphisms (SNPs) were used for genome‐wide association studies (GWAS) using historical phenotypic data for grain protein content, Hagberg falling number (HFN), test weight, and grain yield. Power calculations indicated experimental design would enable detection of quantitative trait loci (QTL) explaining ≥20% of the variation (PVE) at a relatively high power of >80%, falling to 40% for detection of a SNP with an R(2) ≥ .5 with the same QTL. Genome‐wide association studies identified marker‐trait associations for all four traits. For HFN (h (2 )= .89), six QTL were identified, including a major locus on chromosome 7B explaining 49% PVE and reducing HFN by 44 s. For protein content (h (2 )= 0.86), 10 QTL were found on chromosomes 1A, 2A, 2B, 3A, 3B, and 6B, together explaining 48.9% PVE. For test weight, five QTL were identified (one on 1B and four on 3B; 26.3% PVE). Finally, 14 loci were identified for grain yield (h (2 )= 0.95) on eight chromosomes (1A, 2A, 2B, 2D, 3A, 5B, 6A, 6B; 68.1% PVE), of which five were located within 16 Mbp of genetic regions previously identified as under breeder selection in European wheat. Our study demonstrates the utility of exploiting historical crop datasets, identifying genomic targets for independent validation, and ultimately for wheat genetic improvement

Application of genomicsassisted breeding for generation of climate resilient crops: progress and prospects

CCAFS Climat

Evolutionary relationships among barley and <i>Arabidopsis</i> core circadian clock and clock-associated genes

The circadian clock regulates a multitude of plant developmental and metabolic processes. In crop species, it contributes significantly to plant performance and productivity and to the adaptation and geographical range over which crops can be grown. To understand the clock in barley and how it relates to the components in the Arabidopsis thaliana clock, we have performed a systematic analysis of core circadian clock and clock-associated genes in barley, Arabidopsis and another eight species including tomato, potato, a range of monocotyledonous species and the moss, Physcomitrella patens. We have identified orthologues and paralogues of Arabidopsis genes which are conserved in all species, monocot/dicot differences, species-specific differences and variation in gene copy number (e.g. gene duplications among the various species). We propose that the common ancestor of barley and Arabidopsis had two-thirds of the key clock components identified in Arabidopsis prior to the separation of the monocot/dicot groups. After this separation, multiple independent gene duplication events took place in both monocot and dicot ancestors. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s00239-015-9665-0) contains supplementary material, which is available to authorized users