Genetic analysis of global faba bean diversity, agronomic traits and selection signatures.

KEY MESSAGE: We identified marker-trait associations for key faba bean agronomic traits and genomic signatures of selection within a global germplasm collection. Faba bean (Vicia faba L.) is a high-protein grain legume crop with great potential for sustainable protein production. However, little is known about the genetics underlying trait diversity. In this study, we used 21,345 high-quality SNP markers to genetically characterize 2678 faba bean genotypes. We performed genome-wide association studies of key agronomic traits using a seven-parent-MAGIC population and detected 238 significant marker-trait associations linked to 12 traits of agronomic importance. Sixty-five of these were stable across multiple environments. Using a non-redundant diversity panel of 685 accessions from 52 countries, we identified three subpopulations differentiated by geographical origin and 33 genomic regions subjected to strong diversifying selection between subpopulations. We found that SNP markers associated with the differentiation of northern and southern accessions explained a significant proportion of agronomic trait variance in the seven-parent-MAGIC population, suggesting that some of these traits were targets of selection during breeding. Our findings point to genomic regions associated with important agronomic traits and selection, facilitating faba bean genomics-based breeding.

Trends of genetic changes uncovered by Env- and Eigen-GWAS in wheat and barley.

KEY MESSAGE: Variety age and population structure detect novel QTL for yield and adaptation in wheat and barley without the need to phenotype. The process of crop breeding over the last century has delivered new varieties with increased genetic gains, resulting in higher crop performance and yield. However, in many cases, the alleles and genomic regions underpinning this success remain unknown. This is partly due to the difficulty of generating sufficient phenotypic data on large numbers of historical varieties to enable such analyses. Here we demonstrate the ability to circumvent such bottlenecks by identifying genomic regions selected over 100 years of crop breeding using age of a variety as a surrogate for yield. Rather than collecting phenotype data, we deployed 'environmental genome-wide association scans' (EnvGWAS) based on variety age in two of the world's most important crops, wheat and barley, and detected strong signals of selection across both genomes. EnvGWAS identified 16 genomic regions in barley and 10 in wheat with contrasting patterns between spring and winter types of the two crops. To further examine changes in genome structure, we used the genomic relationship matrix of the genotypic data to derive eigenvectors for analysis in EigenGWAS. This detected seven major chromosomal introgressions that contributed to adaptation in wheat. EigenGWAS and EnvGWAS based on variety age avoid costly phenotyping and facilitate the identification of genomic tracts that have been under selection during breeding. Our results demonstrate the potential of using historical cultivar collections coupled with genomic data to identify chromosomal regions under selection and may help guide future plant breeding strategies to maximise the rate of genetic gain and adaptation.

Reprogramming of the wheat transcriptome in response to infection with Claviceps purpurea, the causal agent of ergot.

BACKGROUND: Ergot, caused by the fungal pathogen Claviceps purpurea, infects the female flowers of a range of cereal crops, including wheat. To understand the interaction between C. purpurea and hexaploid wheat we undertook an extensive examination of the reprogramming of the wheat transcriptome in response to C. purpurea infection through floral tissues (i.e. the stigma, transmitting and base ovule tissues of the ovary) and over time. RESULTS: C. purpurea hyphae were observed to have grown into and down the stigma at 24 h (H) after inoculation. By 48H hyphae had grown through the transmitting tissue into the base, while by 72H hyphae had surrounded the ovule. By 5 days (D) the ovule had been replaced by fungal tissue. Differential gene expression was first observed at 1H in the stigma tissue. Many of the wheat genes differentially transcribed in response to C. purpurea infection were associated with plant hormones and included the ethylene (ET), auxin, cytokinin, gibberellic acid (GA), salicylic acid and jasmonic acid (JA) biosynthetic and signaling pathways. Hormone-associated genes were first detected in the stigma and base tissues at 24H, but not in the transmitting tissue. Genes associated with GA and JA pathways were seen in the stigma at 24H, while JA and ET-associated genes were identified in the base at 24H. In addition, several defence-related genes were differential expressed in response to C. purpurea infection, including antifungal proteins, endocytosis/exocytosis-related proteins, NBS-LRR class proteins, genes involved in programmed cell death, receptor protein kinases and transcription factors. Of particular interest was the identification of differential expression of wheat genes in the base tissue well before the appearance of fungal hyphae, suggesting that a mobile signal, either pathogen or plant-derived, is delivered to the base prior to colonisation. CONCLUSIONS: Multiple host hormone biosynthesis and signalling pathways were significantly perturbed from an early stage in the wheat - C. purpurea interaction. Differential gene expression at the base of the ovary, ahead of arrival of the pathogen, indicated the potential presence of a long-distance signal modifying host gene expression.

Genetic and transcriptional dissection of resistance to Claviceps purpurea in the durum wheat cultivar Greenshank.

KEY MESSAGE: Four QTL for ergot resistance (causal pathogen Claviceps purpurea) have been identified in the durum wheat cultivar Greenshank. Claviceps purpurea is a pathogen of grasses that infects flowers, replacing the seed with an ergot sclerotium. Ergot presents a significant problem to rye, barley and wheat, in particular hybrid seed production systems. In addition, there is evidence that the highly toxic alkaloids that accumulate within sclerotia can cross-contaminate otherwise healthy grain. Host resistance to C. purpurea is rare, few resistance loci having been identified. In this study, four ergot resistance loci are located on chromosomes 1B, 2A, 5A and 5B in the durum wheat cv. Greenshank. Ergot resistance was assessed through analysis of phenotypes associated with C. purpurea infection, namely the number of inoculated flowers that produced sclerotia, or resulted in ovary death but no sclerotia, the levels of honeydew produced, total sclerotia weight and average sclerotia weight and size per spike. Ergot testing was undertaken in Canada and the UK. A major effect QTL, QCp.aafc.DH-2A, was detected in both the Canadian and UK experiments and had a significant effect on honeydew production levels. QCp.aafc.DH-5B had the biggest influence on total sclerotia weight per spike. QCp.aafc.DH-1B was only detected in the Canadian experiments and QCp.aafc.DH-5A in the UK experiment. An RNASeq analysis, undertaken to identify wheat differentially expressed genes associated with different combinations of the four ergot resistance QTL, revealed a disproportionate number of DEGs locating to the QCp.aafc.DH-1B, QCp.aafc.DH-2A and QCp.aafc.DH-5B QTL intervals.

Multi-parent populations in crops: a toolbox integrating genomics and genetic mapping with breeding.

Crop populations derived from experimental crosses enable the genetic dissection of complex traits and support modern plant breeding. Among these, multi-parent populations now play a central role. By mixing and recombining the genomes of multiple founders, multi-parent populations combine many commonly sought beneficial properties of genetic mapping populations. For example, they have high power and resolution for mapping quantitative trait loci, high genetic diversity and minimal population structure. Many multi-parent populations have been constructed in crop species, and their inbred germplasm and associated phenotypic and genotypic data serve as enduring resources. Their utility has grown from being a tool for mapping quantitative trait loci to a means of providing germplasm for breeding programmes. Genomics approaches, including de novo genome assemblies and gene annotations for the population founders, have allowed the imputation of rich sequence information into the descendent population, expanding the breadth of research and breeding applications of multi-parent populations. Here, we report recent successes from crop multi-parent populations in crops. We also propose an ideal genotypic, phenotypic and germplasm 'package' that multi-parent populations should feature to optimise their use as powerful community resources for crop research, development and breeding.

A Wristwatch-Based Wireless Sensor Platform for IoT Health Monitoring Applications.

A wristwatch-based wireless sensor platform for IoT wearable health monitoring applications is presented. The paper describes the platform in detail, with a particular focus given to the design of a novel and compact wireless sub-system for 868 MHz wristwatch applications. An example application using the developed platform is discussed for arterial oxygen saturation (SpO2) and heart rate measurement using optical photoplethysmography (PPG). A comparison of the wireless performance in the 868 MHz and the 2.45 GHz bands is performed. Another contribution of this work is the development of a highly integrated 868 MHz antenna. The antenna structure is printed on the surface of a wristwatch enclosure using laser direct structuring (LDS) technology. At 868 MHz, a low specific absorption rate (SAR) of less than 0.1% of the maximum permissible limit in the simulation is demonstrated. The measured on-body prototype antenna exhibits a -10 dB impedance bandwidth of 36 MHz, a peak realized gain of -4.86 dBi and a radiation efficiency of 14.53% at 868 MHz. To evaluate the performance of the developed 868 MHz sensor platform, the wireless communication range measurements are performed in an indoor environment and compared with a commercial Bluetooth wristwatch device.

Mapping-by-sequencing in complex polyploid genomes using genic sequence capture: a case study to map yellow rust resistance in hexaploid wheat.

Previously we extended the utility of mapping-by-sequencing by combining it with sequence capture and mapping sequence data to pseudo-chromosomes that were organized using wheat-Brachypodium synteny. This, with a bespoke haplotyping algorithm, enabled us to map the flowering time locus in the diploid wheat Triticum monococcum L. identifying a set of deleted genes (Gardiner et al., 2014). Here, we develop this combination of gene enrichment and sliding window mapping-by-synteny analysis to map the Yr6 locus for yellow stripe rust resistance in hexaploid wheat. A 110 MB NimbleGen capture probe set was used to enrich and sequence a doubled haploid mapping population of hexaploid wheat derived from an Avalon and Cadenza cross. The Yr6 locus was identified by mapping to the POPSEQ chromosomal pseudomolecules using a bespoke pipeline and algorithm (Chapman et al., 2015). Furthermore the same locus was identified using newly developed pseudo-chromosome sequences as a mapping reference that are based on the genic sequence used for sequence enrichment. The pseudo-chromosomes allow us to demonstrate the application of mapping-by-sequencing to even poorly defined polyploidy genomes where chromosomes are incomplete and sub-genome assemblies are collapsed. This analysis uniquely enabled us to: compare wheat genome annotations; identify the Yr6 locus - defining a smaller genic region than was previously possible; associate the interval with one wheat sub-genome and increase the density of SNP markers associated. Finally, we built the pipeline in iPlant, making it a user-friendly community resource for phenotype mapping.

Elevated temperature drives a shift from selfing to outcrossing in the insect-pollinated legume, faba bean (Vicia faba).

Climate change can threaten the reproductive success of plants, both directly, through physiological damage during increasingly extreme weather events, and indirectly, through disruption of plant-pollinator interactions. To explore how plant-pollinator interactions are modified by extreme weather, we exposed faba bean (Vicia faba) plants to elevated temperature for 5 d during flowering, simulating a heatwave. We then moved the plants to flight cages with either bumblebees or no pollinators, or to two field sites, where plants were enclosed in mesh bags or pollinated by wild insect communities. We used a morphological marker to quantify pollen movement between experimental plants. There was a substantial increase in the level of outcrossing by insect pollinators following heat stress. Proportion outcrossed seed increased from 17 % at control temperature, to 33 % following heat stress in the flight cages, and from 31 % to 80 % at one field site, but not at the other (33 % to 32 %). Abiotic stress can dramatically shift the relative contributions of cross- and self-pollination to reproduction in an insect pollinated plant. The resulting increases in gene flow have broad implications for genetic diversity and functioning of ecosystems, and may increase resilience by accelerating the selection of more stress-tolerant genotypes.

Enriching Mental Health Mobile Assessment and Intervention with Situation Awareness.

Current mobile devices allow the execution of sophisticated applications with the capacity for identifying the user situation, which can be helpful in treatments of mental disorders. In this paper, we present SituMan, a solution that provides situation awareness to MoodBuster, an ecological momentary assessment and intervention mobile application used to request self-assessments from patients in depression treatments. SituMan has a fuzzy inference engine to identify patient situations using context data gathered from the sensors embedded in mobile devices. Situations are specified jointly by the patient and mental health professional, and they can represent the patient's daily routine (e.g., "studying", "at work", "working out"). MoodBuster requests mental status self-assessments from patients at adequate moments using situation awareness. In addition, SituMan saves and displays patient situations in a summary, delivering them for consultation by mental health professionals. A first experimental evaluation was performed to assess the user satisfaction with the approaches to define and identify situations. This experiment showed that SituMan was well evaluated in both criteria. A second experiment was performed to assess the accuracy of the fuzzy engine to infer situations. Results from the second experiment showed that the fuzzy inference engine has a good accuracy to identify situations.

Plant-pathogen interactions: disease resistance in modern agriculture.

The growing human population will require a significant increase in agricultural production. This challenge is made more difficult by the fact that changes in the climatic and environmental conditions under which crops are grown have resulted in the appearance of new diseases, whereas genetic changes within the pathogen have resulted in the loss of previously effective sources of resistance. To help meet this challenge, advanced genetic and statistical methods of analysis have been used to identify new resistance genes through global screens, and studies of plant-pathogen interactions have been undertaken to uncover the mechanisms by which disease resistance is achieved. The informed deployment of major, race-specific and partial, race-nonspecific resistance, either by conventional breeding or transgenic approaches, will enable the production of crop varieties with effective resistance without impacting on other agronomically important crop traits. Here, we review these recent advances and progress towards the ultimate goal of developing disease-resistant crops.

A SNP-based consensus genetic map for synteny-based trait targeting in faba bean (Vicia faba L.).

Faba bean (Vicia faba L.) is a globally important nitrogen-fixing legume, which is widely grown in a diverse range of environments. In this work, we mine and validate a set of 845 SNPs from the aligned transcriptomes of two contrasting inbred lines. Each V. faba SNP is assigned by BLAST analysis to a single Medicago orthologue. This set of syntenically anchored polymorphisms were then validated as individual KASP assays, classified according to their informativeness and performance on a panel of 37 inbred lines, and the best performing 757 markers used to genotype six mapping populations. The six resulting linkage maps were merged into a single consensus map on which 687 SNPs were placed on six linkage groups, each presumed to correspond to one of the six V. faba chromosomes. This sequence-based consensus map was used to explore synteny with the most closely related crop species, lentil and the most closely related fully sequenced genome, Medicago. Large tracts of uninterrupted colinearity were found between faba bean and Medicago, making it relatively straightforward to predict gene content and order in mapped genetic interval. As a demonstration of this, we mapped a flower colour gene to a 2-cM interval of Vf chromosome 2 which was highly colinear with Mt3. The obvious candidate gene from 78 gene models in the collinear Medicago chromosome segment was the previously characterized MtWD40-1 gene controlling anthocyanin production in Medicago and resequencing of the Vf orthologue showed a putative causative deletion of the entire 5' end of the gene.

Plant-symbiotic fungi as chemical engineers: multi-genome analysis of the clavicipitaceae reveals dynamics of alkaloid loci.

The fungal family Clavicipitaceae includes plant symbionts and parasites that produce several psychoactive and bioprotective alkaloids. The family includes grass symbionts in the epichloae clade (Epichloë and Neotyphodium species), which are extraordinarily diverse both in their host interactions and in their alkaloid profiles. Epichloae produce alkaloids of four distinct classes, all of which deter insects, and some-including the infamous ergot alkaloids-have potent effects on mammals. The exceptional chemotypic diversity of the epichloae may relate to their broad range of host interactions, whereby some are pathogenic and contagious, others are mutualistic and vertically transmitted (seed-borne), and still others vary in pathogenic or mutualistic behavior. We profiled the alkaloids and sequenced the genomes of 10 epichloae, three ergot fungi (Claviceps species), a morning-glory symbiont (Periglandula ipomoeae), and a bamboo pathogen (Aciculosporium take), and compared the gene clusters for four classes of alkaloids. Results indicated a strong tendency for alkaloid loci to have conserved cores that specify the skeleton structures and peripheral genes that determine chemical variations that are known to affect their pharmacological specificities. Generally, gene locations in cluster peripheries positioned them near to transposon-derived, AT-rich repeat blocks, which were probably involved in gene losses, duplications, and neofunctionalizations. The alkaloid loci in the epichloae had unusual structures riddled with large, complex, and dynamic repeat blocks. This feature was not reflective of overall differences in repeat contents in the genomes, nor was it characteristic of most other specialized metabolism loci. The organization and dynamics of alkaloid loci and abundant repeat blocks in the epichloae suggested that these fungi are under selection for alkaloid diversification. We suggest that such selection is related to the variable life histories of the epichloae, their protective roles as symbionts, and their associations with the highly speciose and ecologically diverse cool-season grasses.

The identification of QTL controlling ergot sclerotia size in hexaploid wheat implicates a role for the Rht dwarfing alleles.

KEY MESSAGE: Four QTL conferring resistance to ergot were identified in the UK winter wheat varieties 'Robigus' and 'Solstice'. Two QTL co-located with semi-dwarfing alleles at the Rht loci Rht - 1B and Rht - 1D implicating a role of these DELLA proteins in infection success of Claviceps purpurea. The fungal pathogen Claviceps purpurea infects ovaries of a broad range of temperate grasses and cereals, including hexaploid wheat, causing a disease commonly known as ergot. Sclerotia produced in place of seed carry a cocktail of harmful alkaloid compounds that result in a range of symptoms in humans and animals, causing ergotism. Following a field assessment of C. purpurea infection in winter wheat, two varieties 'Robigus' and 'Solstice' were selected which consistently produced the largest differential effect on ergot sclerotia weights. They were crossed to produce a doubled haploid mapping population, and a marker map, consisting of 714 genetic loci and a total length of 2895 cM was produced. Four ergot reducing QTL were identified using both sclerotia weight and size as phenotypic parameters; QCp.niab.2A and QCp.niab.4B being detected in the wheat variety 'Robigus', and QCp.niab.6A and QCp.niab.4D in the variety 'Solstice'. The ergot resistance QTL QCp.niab.4B and QCp.niab.4D peaks mapped to the same markers as the known reduced height (Rht) loci on chromosomes 4B and 4D, Rht-B1 and Rht-D1, respectively. In both cases, the reduction in sclerotia weight and size was associated with the semi-dwarfing alleles, Rht-B1b from 'Robigus' and Rht-D1b from 'Solstice'. Two-dimensional, two-QTL scans identified significant additive interactions between QTL QCp.niab.4B and QCp.niab.4D, and between QCp.niab.2A and QCp.niab.4B when looking at sclerotia size, but not between QCp.niab.2A and QCp.niab.4D. The two plant height QTL, QPh.niab.4B and QPh.niab.4D, which mapped to the same locations as QCp.niab.4B and QCp.niab.4D, also displayed significant genetic interactions.

The pgip family in soybean and three other legume species: evidence for a birth-and-death model of evolution.

BACKGROUND: Polygalacturonase-inhibiting proteins (PGIPs) are leucine-rich repeat (LRR) plant cell wall glycoproteins involved in plant immunity. They are typically encoded by gene families with a small number of gene copies whose evolutionary origin has been poorly investigated. Here we report the complete characterization of the full complement of the pgip family in soybean (Glycine max [L.] Merr.) and the characterization of the genomic region surrounding the pgip family in four legume species. RESULTS: BAC clone and genome sequence analyses showed that the soybean genome contains two pgip loci. Each locus is composed of three clustered genes that are induced following infection with the fungal pathogen Sclerotinia sclerotiorum (Lib.) de Bary, and remnant sequences of pgip genes. The analyzed homeologous soybean genomic regions (about 126 Kb) that include the pgip loci are strongly conserved and this conservation extends also to the genomes of the legume species Phaseolus vulgaris L., Medicago truncatula Gaertn. and Cicer arietinum L., each containing a single pgip locus. Maximum likelihood-based gene trees suggest that the genes within the pgip clusters have independently undergone tandem duplication in each species. CONCLUSIONS: The paleopolyploid soybean genome contains two pgip loci comprised in large and highly conserved duplicated regions, which are also conserved in bean, M. truncatula and C. arietinum. The genomic features of these legume pgip families suggest that the forces driving the evolution of pgip genes follow the birth-and-death model, similar to that proposed for the evolution of resistance (R) genes of NBS-LRR-type.

Use of synteny to identify candidate genes underlying QTL controlling stomatal traits in faba bean (Vicia faba L.).

KEY MESSAGE: We have identified QTLs for stomatal characteristics on chromosome II of faba bean by applying SNPs derived from M. truncatula , and have identified candidate genes within these QTLs using synteny between the two species. Faba bean (Vicia faba L.) is a valuable food and feed crop worldwide, but drought often limits its production, and its genome is large and poorly mapped. No information is available on the effects of genomic regions and genes on drought adaptation characters such as stomatal characteristics in this species, but the synteny between the sequenced model legume, Medicago truncatula, and faba bean can be used to identify candidate genes. A mapping population of 211 F5 recombinant inbred lines (Mélodie/2 × ILB 938/2) were phenotyped to identify quantitative trait loci (QTL) affecting stomatal morphology and function, along with seed weight, under well-watered conditions in a climate-controlled glasshouse in 2013 and 2014. Canopy temperature (CT) was evaluated in 2013 under water-deficit (CTd). In total, 188 polymorphic single nucleotide polymorphisms (SNPs), developed from M. truncatula genome data, were assigned to nine linkage groups that covered ~928 cM of the faba bean genome with an average inter-marker distance of 5.8 cM. 15 putative QTLs were detected, of which eight (affecting stomatal density, length and conductance and CT) co-located on chromosome II, in the vicinity of a possible candidate gene-a receptor-like protein kinase found in the syntenic interval of M. truncatula chromosome IV. A ribose-phosphate pyrophosphokinase from M. truncatula chromosome V, postulated as a possible candidate gene for the QTL for CTd, was found some distance away in the same chromosome. These results demonstrate that genomic information from M. truncatula can successfully be translated to the faba bean genome.

Exploring the experiences of women living with metastatic breast cancer [MBC]: A systematic review of qualitative evidence.

PURPOSE: Metastatic breast cancer [MBC] is the leading cause of cancer death in women globally with no cure. Women diagnosed with MBC endure a catastrophic upheaval to multiple aspects of their life and a radically transformed future landscape. Evidence suggests that the provision of care for women living with metastatic breast cancer is inadequate, socially isolating and stigmatising. To date, this topic has received little research attention. To increase understanding of the experiences of women living with MBC, a synthesis of current evidence is required. This paper presents a review of qualitative evidence on women's experiences of MBC. METHODS: A qualitative evidence synthesis [QES] was conducted to synthesise primary qualitative research on the experiences of women living with MBC. Searches were performed of electronic databases Medline, Medline Ovid, PsycINFO, Psych articles, PubMED, CINAHL Complete, Scopus and grey literature databases. The methodological quality of the included studies was appraised using a modified version of the Critical Appraisal Skills Programme [CASP]. Title, abstract, and full-text screening were undertaken. A 'best fit' framework approach using the ARC [Adversity, Restoration, Compatibility] framework was used to guide data extraction and synthesis. Confidence in the findings was assessed using the Grading of Recommendations Assessment, Development and Evaluation, Confidence in the Evidence from Reviews of Qualitative research [GRADE-CERQual]. RESULTS: 28 papers from 21 research studies containing 478 women's experiences of living with MBC were deemed suitable for inclusion in this qualitative evidence synthesis. Findings are presented in a new conceptual framework RAAW [adapted from ARC] for women living with MBC under themes: Reality, Adversity, Adjustment and Wellbeing. Findings revealed that a diagnosis of MBC impacted every aspect of women's lives; this is different to a diagnosis of early breast cancer. An overarching theme of lack of support extended across various facets of their lives. A lack of psychological, emotional, and psychosocial support was evident, with a critical finding that models of care were not fit for purpose. Deficits included a lack of information, knowledge, inclusion in shared decision-making and MDT support, specifically the need for palliative care/oncology support access. Some women living with MBC wanted to be identified as having a chronic illness not a life-limiting illness. Culture and socioeconomic standing influenced the availability of various types of support. The impact of treatment and symptoms had an adverse effect on women's quality of life and affected their ability to adjust. CONCLUSION: This review synthesised the qualitative literature on the experiences of women living with MBC. The ARC framework used in the synthesis was adapted to develop a revised conceptual framework titled RAAW to represent the evidence from this review on experiences for women living with MBC; Reality & Adversity: A diagnosis of MBC; Adjustment: Living with MBC; Wellbeing: Awareness, meaning, engagement [RAAW; MBC].

Evaluation of the use of high-density SNP genotyping to implement UPOV Model 2 for DUS testing in barley.

Developments in high-throughput genotyping provide an opportunity to explore the application of marker technology in distinctness, uniformity and stability (DUS) testing of new varieties. We have used a large set of molecular markers to assess the feasibility of a UPOV Model 2 approach: "Calibration of threshold levels for molecular characteristics against the minimum distance in traditional characteristics". We have examined 431 winter and spring barley varieties, with data from UK DUS trials comprising 28 characteristics, together with genotype data from 3072 SNP markers. Inter varietal distances were calculated and we found higher correlations between molecular and morphological distances than have been previously reported. When varieties were grouped by kinship, phenotypic and genotypic distances of these groups correlated well. We estimated the minimum marker numbers required and showed there was a ceiling after which the correlations do not improve. To investigate the possibility of breaking through this ceiling, we attempted genomic prediction of phenotypes from genotypes and higher correlations were achieved. We tested distinctness decisions made using either morphological or genotypic distances and found poor correspondence between each method.

Genome-wide association mapping to candidate polymorphism resolution in the unsequenced barley genome.

Although commonplace in human disease genetics, genome-wide association (GWA) studies have only relatively recently been applied to plants. Using 32 phenotypes in the inbreeding crop barley, we report GWA mapping of 15 morphological traits across ∼500 cultivars genotyped with 1,536 SNPs. In contrast to the majority of human GWA studies, we observe high levels of linkage disequilibrium within and between chromosomes. Despite this, GWA analysis readily detected common alleles of high penetrance. To investigate the potential of combining GWA mapping with comparative analysis to resolve traits to candidate polymorphism level in unsequenced genomes, we fine-mapped a selected phenotype (anthocyanin pigmentation) within a 140-kb interval containing three genes. Of these, resequencing the putative anthocyanin pathway gene HvbHLH1 identified a deletion resulting in a premature stop codon upstream of the basic helix-loop-helix domain, which was diagnostic for lack of anthocyanin in our association and biparental mapping populations. The methodology described here is transferable to species with limited genomic resources, providing a paradigm for reducing the threshold of map-based cloning in unsequenced crops.

High Temperature Tolerance in a Novel, High-Quality Phaseolus vulgaris Breeding Line Is Due to Maintenance of Pollen Viability and Successful Germination on the Stigma.

The common bean (Phaseolus vulgaris L.) is an important nutritional source globally but is sensitive to high temperatures and thus particularly vulnerable to climate change. Derived from a breeding program at CIAT (Colombia), a heat-tolerant breeding line, named heat-tolerant Andean-type 4 (HTA4), was developed by a series of crosses of parents with a small-bean tepary genotype (Phaseolus acutifolius L.) in their pedigree, which might be the donor of heat stress (HS) tolerance. Importantly, in HTA4, the large, commercially desirable Andean-type beans was restored. To assess underlying tolerance mechanisms, HTA4, together with a heat-sensitive Colombian variety (Calima), was exposed to HS (31 °C/24 °C HS vs. 26 °C/19 °C day/night) under controlled environment conditions. Vegetative growth and photosynthetic performance were not negatively impacted by HS in either genotype, although senescence was delayed in Calima. HS during the reproductive stage caused an increase in pod number in Calima but with few fully developed seeds and many pods aborted and/or abscised. In contrast, HTA4 maintained a similar filled pod number under HS and a higher seed weight per plant. Pollen showed high sterility in Calima, with many non-viable pollen grains (24.9% viability compared to 98.4% in control) with a thicker exine and fewer starch granules under HS. Calima pollen failed to adhere to the stigma and germinate under HS. In HTA4, pollen viability was significantly higher than in Calima (71.1% viability compared to 95.4% under control), and pollen successfully germinated and formed pollen tubes in the style under HS. It is concluded that HTA4 is heat tolerant and maintains a high level of reproductive output due to its ability to produce healthy pollen that is able to adhere to the stigma.

'Raising the Pulse': The environmental, nutritional and health benefits of pulse-enhanced foods.

Diet is a key modulator of non-communicable diseases, and food production represents a major cause of environmental degradation and greenhouse gas emissions. Yet, 'nudging' people to make better food choices is challenging, as factors including affordability, convenience and taste often take priority over the achievement of health and environmental benefits. The overall 'Raising the Pulse' project aim is to bring about a step change in the nutritional value of the UK consumers' diet, and to do so in a way that leads to improved health and greater sustainability within the UK food system. To achieve our objectives, UK-specific faba bean production systems that optimise both end users' diets and environmental and economic sustainability of production will be implemented in collaboration with key stakeholders (including industry, the retail sector and government). Palatable faba bean flours will be produced and used to develop 'Raising the Pulse' food products with improved nutritional profile and environmental value. Consumer focus groups and workshops will establish attitudes, preferences, drivers of and barriers to increased consumption of such products. They will inform the co-creation of sensory testing and University-wide intervention studies to evaluate the effects of pulses and 'Raising the Pulse' foods on diet quality, self-reported satiety, nutritional knowledge, consumer acceptance and market potential. Nutrient bioavailability and satiety will be evaluated in a randomised-controlled postprandial human study. Finally, a system model will be developed that predicts changes to land use, environment, business viability, nutrition and human health after substitution of existing less nutritionally beneficial and environmentally sustainable ingredients with pulses. Government health and sustainability priorities will be addressed, helping to define policy-relevant solutions with significant beneficial supply chain economic impacts and transformed sustainable food systems to improve consumer diet quality, health and the environment.