The young ones

Dominant accounts of subcultural analysis have tended to read early British New Left writing on youth as a combination of high culturalist and neo-Marxist approaches. This article reassesses this position by showing the variety of methods and forms of analysis adopted by New Left writers in the 1950s, including autobiographical, ethnographic, sociological, cultural and fictional. In particular, it compares the writing on youth by Richard Hoggart, Stuart Hall and Colin MacInnes. It argues that their representations of youth were intricately bound up with general anxieties and concerns in 1950s culture, which created an ambiguous and dual interpretation of youth in ideological terms. It goes on to suggest that the way in which the subcultural subject was represented in textual and methodological terms affected the way in which it was interpreted ideologically. It also suggests that the traces of this representation are embedded in the way that youth is interpreted today

Narratives of Trauma and Loss in Caryl Phillips’s Crossing the River and A Distant Shore

This article argues that trauma is at the heart of Caryl Phillips’s fiction with particular reference to two novels, Crossing the River (1993) and A Distant Shore (2003). It assesses a number of writers associated with trauma theory and takes issue with the prevailing idea that trauma studies do not sit well with postcolonial literary practice. Close readings of the two novels reveal how their focus on trauma allows Phillips to articulate narratives that reveal post- and neo-colonial contexts

Re-annotation and re-analysis of the Campylobacter jejuni NCTC11168 genome sequence

BACKGROUND: Campylobacter jejuni is the leading bacterial cause of human gastroenteritis in the developed world. To improve our understanding of this important human pathogen, the C. jejuni NCTC11168 genome was sequenced and published in 2000. The original annotation was a milestone in Campylobacter research, but is outdated. We now describe the complete re-annotation and re-analysis of the C. jejuni NCTC11168 genome using current database information, novel tools and annotation techniques not used during the original annotation. RESULTS: Re-annotation was carried out using sequence database searches such as FASTA, along with programs such as TMHMM for additional support. The re-annotation also utilises sequence data from additional Campylobacter strains and species not available during the original annotation. Re-annotation was accompanied by a full literature search that was incorporated into the updated EMBL file [EMBL: AL111168]. The C. jejuni NCTC11168 re-annotation reduced the total number of coding sequences from 1654 to 1643, of which 90.0% have additional information regarding the identification of new motifs and/or relevant literature. Re-annotation has led to 18.2% of coding sequence product functions being revised. CONCLUSIONS: Major updates were made to genes involved in the biosynthesis of important surface structures such as lipooligosaccharide, capsule and both O- and N-linked glycosylation. This re-annotation will be a key resource for Campylobacter research and will also provide a prototype for the re-annotation and re-interpretation of other bacterial genomes

Multi-trait ensemble genomic prediction and simulations of recurrent selection highlight importance of complex trait genetic architecture for long-term genetic gains in wheat

Cereal crop breeders have achieved considerable genetic gain in genetically complex traits, such as grain yield, while maintaining genetic diversity. However, focus on selection for yield has negatively impacted other important traits. To better understand multi-trait selection within a breeding context, and how it might be optimized, we analysed genotypic and phenotypic data from a genetically diverse, 16-founder wheat multi-parent advanced generation inter-cross population. Compared to single-trait models, multi-trait ensemble genomic prediction models increased prediction accuracy for almost 90 % of traits, improving grain yield prediction accuracy by 3–52 %. For complex traits, non-parametric models (Random Forest) also outperformed simplified, additive models (LASSO), increasing grain yield prediction accuracy by 10–36 %. Simulations of recurrent genomic selection then showed that sustained greater forward prediction accuracy optimized long-term genetic gains. Simulations of selection on grain yield found indirect responses in related traits, involving optimized antagonistic trait relationships. We found multi-trait selection indices could effectively optimize undesirable relationships, such as the trade-off between grain yield and protein content, or combine traits of interest, such as yield and weed competitive ability. Simulations of phenotypic selection found that including Random Forest rather than LASSO genetic models, and multi-trait rather than single-trait models as the true genetic model accelerated and extended long-term genetic gain whilst maintaining genetic diversity. These results (i) suggest important roles of pleiotropy and epistasis in the wider context of wheat breeding programmes, and (ii) provide insights into mechanisms for continued genetic gain in a limited genepool and optimization of multiple traits for crop improvement

Maintenance of UK bread baking quality: Trends in wheat quality traits over 50 years of breeding and potential for future application of genomic-assisted selection

Improved selection of wheat varieties with high end-use quality contributes to sustainable food systems by ensuring productive crops are suitable for human consumption end-uses. Here, we investigated the genetic control and genomic prediction of milling and baking quality traits in a panel of 379 historic and elite, high-quality UK bread wheat (Triticum eastivum L.) varieties and breeding lines. Analysis of the panel showed that genetic diversity has not declined over recent decades of selective breeding while phenotypic analysis found a clear trend of increased loaf baking quality of modern milling wheats despite declining grain protein content. Genome-wide association analysis identified 24 quantitative trait loci (QTL) across all quality traits, many of which had pleiotropic effects. Changes in the frequency of positive alleles of QTL over recent decades reflected trends in trait variation and reveal where progress has historically been made for improved baking quality traits. It also demonstrates opportunities for marker-assisted selection for traits such as Hagberg falling number and specific weight that do not appear to have been improved by recent decades of phenotypic selection. We demonstrate that applying genomic prediction in a commercial wheat breeding program for expensive late-stage loaf baking quality traits outperforms phenotypic selection based on early-stage predictive quality traits. Finally, trait-assisted genomic prediction combining both phenotypic and genomic selection enabled slightly higher prediction accuracy, but genomic prediction alone was the most cost-effective selection strategy considering genotyping and phenotyping costs per sample

Limited haplotype diversity underlies polygenic trait architecture across 70 years of wheat breeding

Background Selection has dramatically shaped genetic and phenotypic variation in bread wheat. We can assess the genomic basis of historical phenotypic changes, and the potential for future improvement, using experimental populations that attempt to undo selection through the randomizing effects of recombination. Results We bred the NIAB Diverse MAGIC multi-parent population comprising over 500 recombinant inbred lines, descended from sixteen historical UK bread wheat varieties released between 1935 and 2004. We sequence the founders’ genes and promoters by capture, and the MAGIC population by low-coverage whole-genome sequencing. We impute 1.1 M high-quality SNPs that are over 99% concordant with array genotypes. Imputation accuracy only marginally improves when including the founders’ genomes as a haplotype reference panel. Despite capturing 73% of global wheat genetic polymorphism, 83% of genes cluster into no more than three haplotypes. We phenotype 47 agronomic traits over 2 years and map 136 genome-wide significant associations, concentrated at 42 genetic loci with large and often pleiotropic effects. Around half of these overlap known quantitative trait loci. Most traits exhibit extensive polygenicity, as revealed by multi-locus shrinkage modelling. Conclusions Our results are consistent with a gene pool of low haplotypic diversity, containing few novel loci of large effect. Most past, and projected future, phenotypic changes arising from existing variation involve fine-scale shuffling of a few haplotypes to recombine dozens of polygenic alleles of small effect. Moreover, extensive pleiotropy means selection on one trait will have unintended consequences, exemplified by the negative trade-off between yield and protein content, unless selection and recombination can break unfavorable trait-trait associations

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/

Aldehyde-mediated protein-to-surface tethering via controlled diazonium electrode functionalization using protected hydroxylamines

We report a diazonium electro-grafting method for the covalent modification of conducting surfaces with aldehyde-reactive hydroxylamine functionalities that facilitate the wiring of redox-active (bio)molecules to electrode surfaces. Hydroxylamine monolayer formation is achieved via a phthalimide-protection and hydrazine-deprotection strategy that overcomes the multilayer formation that typically complicates diazonium surface modification. This surface modification strategy is characterized using electrochemistry (electrochemical impedance spectroscopy and cyclic voltammetry), X-ray photoelectron spectroscopy and quartz crystal microbalance with dissipation monitoring. Thus-modified glassy carbon, boron-doped diamond and gold surfaces are all shown to ligate to small molecule aldehydes, yielding surface coverages of 150-170, 40 and 100 pmol cm-2, respectively. Bio-conjugation is demonstrated via the coupling of a dilute (50 µM) solution of periodate-oxidized horseradish peroxidase enzyme to a functionalized gold surface under bio-compatible conditions (H2O solvent, pH 4.5, 25 °C)

Multi-trait ensemble genomic prediction and simulations of recurrent selection highlight importance of complex trait genetic architecture for long-term genetic gains in wheat

Cereal crop breeders have achieved considerable genetic gain in genetically complex traits, such as grain yield, while maintaining genetic diversity. However, focus on selection for yield has negatively impacted other important traits. To better understand multi-trait selection within a breeding context, and how it might be optimized, we analysed genotypic and phenotypic data from a genetically diverse, 16-founder wheat multi-parent advanced generation inter-cross population. Compared to single-trait models, multi-trait ensemble genomic prediction models increased prediction accuracy for almost 90 % of traits, improving grain yield prediction accuracy by 3–52 %. For complex traits, non-parametric models (Random Forest) also outperformed simplified, additive models (LASSO), increasing grain yield prediction accuracy by 10–36 %. Simulations of recurrent genomic selection then showed that sustained greater forward prediction accuracy optimized long-term genetic gains. Simulations of selection on grain yield found indirect responses in related traits, involving optimized antagonistic trait relationships. We found multi-trait selection indices could effectively optimize undesirable relationships, such as the trade-off between grain yield and protein content, or combine traits of interest, such as yield and weed competitive ability. Simulations of phenotypic selection found that including Random Forest rather than LASSO genetic models, and multi-trait rather than single-trait models as the true genetic model accelerated and extended long-term genetic gain whilst maintaining genetic diversity. These results (i) suggest important roles of pleiotropy and epistasis in the wider context of wheat breeding programmes, and (ii) provide insights into mechanisms for continued genetic gain in a limited genepool and optimization of multiple traits for crop improvement