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1.
Glob Health Sci Pract ; 12(1)2024 Feb 28.
Article in English | MEDLINE | ID: mdl-38242636

ABSTRACT

We document the development and institutionalization in Zambia of a health innovation for diarrhea treatment aimed at children aged younger than 5 years: a unique oral rehydration salts and zinc (ORSZ) co-pack. Seven recommendations from the World Health Organization/ExpandNet are used retrospectively to analyze and describe the successful scale-up of this innovation from its concept stage, including in-country expansion and policy, institutional, and regulatory changes. The 7 recommendations comprise using a participatory process, tailoring to the country context, designing research to test the innovation, testing the innovation, identifying success factors, and scaling up. The scale-up of co-packaged ORSZ in Zambia is shown to be sustainable. Five years after donor funding ended in 2018, an independent, local manufacturer continues to supply the private and public sectors on a commercially viable basis. Furthermore, national coverage of ORSZ increased from less than 1% in 2012 to 34% in 2018. A key success factor was the continuous facilitation over 8 years (spanning planning, trial, evaluation, and scale-up) by a learning and steering group chaired by the Ministry of Health, open to all and focused on learning transfer and ongoing alignment with other initiatives. Other success factors included a long lead-in of inclusive initial consultation, ideation, and planning with all key stakeholders to build on and mobilize existing resources, knowledge, structures, and systems; alignment with government policy; thorough testing and radical review of the product and its value chain before scale-up, including manufacture, distribution, policy, and regulatory matters; and adoption by the government of a co-packaging strategy to ensure cases of childhood diarrhea are treated with ORSZ. With appropriate local adaptations, this approach to scale-up could be replicated in other low- and middle-income countries as a strategy to increase coverage of ORSZ and potentially other health products.


Subject(s)
Salts , Zinc , Child , Humans , Zambia , Retrospective Studies , Diarrhea/therapy , Fluid Therapy
2.
Front Genet ; 14: 1164935, 2023.
Article in English | MEDLINE | ID: mdl-37229190

ABSTRACT

Genomic selection has recently become an established part of breeding strategies in cereals. However, a limitation of linear genomic prediction models for complex traits such as yield is that these are unable to accommodate Genotype by Environment effects, which are commonly observed over trials on multiple locations. In this study, we investigated how this environmental variation can be captured by the collection of a large number of phenomic markers using high-throughput field phenotyping and whether it can increase GS prediction accuracy. For this purpose, 44 winter wheat (Triticum aestivum L.) elite populations, comprising 2,994 lines, were grown on two sites over 2 years, to approximate the size of trials in a practical breeding programme. At various growth stages, remote sensing data from multi- and hyperspectral cameras, as well as traditional ground-based visual crop assessment scores, were collected with approximately 100 different data variables collected per plot. The predictive power for grain yield was tested for the various data types, with or without genome-wide marker data sets. Models using phenomic traits alone had a greater predictive value (R2 = 0.39-0.47) than genomic data (approximately R2 = 0.1). The average improvement in predictive power by combining trait and marker data was 6%-12% over the best phenomic-only model, and performed best when data from one full location was used to predict the yield on an entire second location. The results suggest that genetic gain in breeding programmes can be increased by utilisation of large numbers of phenotypic variables using remote sensing in field trials, although at what stage of the breeding cycle phenomic selection could be most profitably applied remains to be answered.

3.
Plant Genome ; 16(4): e20335, 2023 Dec.
Article in English | MEDLINE | ID: mdl-37138544

ABSTRACT

Wheat (Triticum aestivum L.) is a major source of nutrients for populations across the globe, but the amino acid composition of wheat grain does not provide optimal nutrition. The nutritional value of wheat grain is limited by low concentrations of lysine (the most limiting essential amino acid) and high concentrations of free asparagine (precursor to the processing contaminant acrylamide). There are currently few available solutions for asparagine reduction and lysine biofortification through breeding. In this study, we investigated the genetic architecture controlling grain free amino acid composition and its relationship to other traits in a Robigus × Claire doubled haploid population. Multivariate analysis of amino acids and other traits showed that the two groups are largely independent of one another, with the largest effect on amino acids being from the environment. Linkage analysis of the population allowed identification of quantitative trait loci (QTL) controlling free amino acids and other traits, and this was compared against genomic prediction methods. Following identification of a QTL controlling free lysine content, wheat pangenome resources facilitated analysis of candidate genes in this region of the genome. These findings can be used to select appropriate strategies for lysine biofortification and free asparagine reduction in wheat breeding programs.


Subject(s)
Amino Acids , Triticum , Amino Acids/genetics , Chromosome Mapping , Triticum/genetics , Triticum/chemistry , Asparagine/analysis , Asparagine/genetics , Lysine/genetics , Plant Breeding , Edible Grain/genetics , United Kingdom
4.
New Phytol ; 237(5): 1558-1573, 2023 03.
Article in English | MEDLINE | ID: mdl-36519272

ABSTRACT

The wheat flag leaf is the main contributor of photosynthetic assimilates to developing grains. Understanding how canopy architecture strategies affect source strength and yield will aid improved crop design. We used an eight-founder population to investigate the genetic architecture of flag leaf area, length, width and angle in European wheat. For the strongest genetic locus identified, we subsequently created a near-isogenic line (NIL) pair for more detailed investigation across seven test environments. Genetic control of traits investigated was highly polygenic, with colocalisation of replicated quantitative trait loci (QTL) for one or more traits identifying 24 loci. For QTL QFll.niab-5A.1 (FLL5A), development of a NIL pair found the FLL5A+ allele commonly conferred a c. 7% increase in flag and second leaf length and a more erect leaf angle, resulting in higher flag and/or second leaf area. Increased FLL5A-mediated flag leaf length was associated with: (1) longer pavement cells and (2) larger stomata at lower density, with a trend for decreased maximum stomatal conductance (Gsmax ) per unit leaf area. For FLL5A, cell size rather than number predominantly determined leaf length. The observed trade-offs between leaf size and stomatal morphology highlight the need for future studies to consider these traits at the whole-leaf level.


Subject(s)
Quantitative Trait Loci , Triticum , Chromosome Mapping , Triticum/anatomy & histology , Quantitative Trait Loci/genetics , Plant Leaves/anatomy & histology , Phenotype , Epidermal Cells
5.
Environ Entomol ; 51(4): 643-648, 2022 08 19.
Article in English | MEDLINE | ID: mdl-35762335

ABSTRACT

To work effectively, the eyes of nocturnal insects have a problem they must overcome. During the night, the light levels are low, so their eyes need to be very sensitive; but they also need a way of adapting to environmental light conditions, and protecting those sensitive organs, if a bright light is encountered. Human eyes have a pupil that changes size to regulate light input to the eye. Moths (Lepidoptera) use a light absorbing pigment that moves position to limit the light within the eye. This pigment migration is difficult to record because it is a dynamic process and will only occur in a live moth. This paper presents the first use of Ocular Coherence Tomography as a method of viewing anatomical detail in a compound eye. This is noninvasive and does not harm the insect. To demonstrate the effectiveness, this article documents the dynamic process of light adaptation within a moth's eye.


Subject(s)
Moths , Adaptation, Ocular , Animals , Humans , Insecta , Moths/physiology , Tomography, Optical Coherence , Vision, Ocular
6.
Theor Appl Genet ; 135(1): 301-319, 2022 Jan.
Article in English | MEDLINE | ID: mdl-34837509

ABSTRACT

KEY MESSAGE: Analysis of a wheat multi-founder population identified 14 yellow rust resistance QTL. For three of the four most significant QTL, haplotype analysis indicated resistance alleles were rare in European wheat. Stripe rust, or yellow rust (YR), is a major fungal disease of wheat (Triticum aestivum) caused by Puccinia striiformis Westend f. sp. tritici (Pst). Since 2011, the historically clonal European Pst races have been superseded by the rapid incursion of genetically diverse lineages, reducing the resistance of varieties previously showing durable resistance. Identification of sources of genetic resistance to such races is a high priority for wheat breeding. Here we use a wheat eight-founder multi-parent population genotyped with a 90,000 feature single nucleotide polymorphism array to genetically map YR resistance to such new Pst races. Genetic analysis of five field trials at three UK sites identified 14 quantitative trait loci (QTL) conferring resistance. Of these, four highly significant loci were consistently identified across all test environments, located on chromosomes 1A (QYr.niab-1A.1), 2A (QYr.niab-2A.1), 2B (QYr.niab-2B.1) and 2D (QYr.niab-2D.1), together explaining ~ 50% of the phenotypic variation. Analysis of these four QTL in two-way and three-way combinations showed combinations conferred greater resistance than single QTL, and genetic markers were developed that distinguished resistant and susceptible alleles. Haplotype analysis in a collection of wheat varieties found that the haplotypes associated with YR resistance at three of these four major loci were rare (≤ 7%) in European wheat, highlighting their potential utility for future targeted improvement of disease resistance. Notably, the physical interval for QTL QYr.niab-2B.1 contained five nucleotide-binding leucine-rich repeat candidate genes with integrated BED domains, of which two corresponded to the cloned resistance genes Yr7 and Yr5/YrSp.


Subject(s)
Disease Resistance/genetics , Plant Diseases/microbiology , Puccinia/physiology , Triticum/genetics , Genotype , Plant Diseases/genetics , Plant Diseases/immunology , Polymorphism, Single Nucleotide , Puccinia/immunology , Quantitative Trait Loci , Triticum/immunology , Triticum/microbiology
7.
J Exp Bot ; 72(8): 2965-2978, 2021 04 02.
Article in English | MEDLINE | ID: mdl-33578415

ABSTRACT

Crop height (Ht), heading date (Hd), and grain yield (GY) are inter-related in wheat. Independent manipulation of each is important for adaptation and performance. Validated quantitative trait loci (QTLs) for all three co-locate on chromosome 3A in the Avalon×Cadenza population, with increased Ht, Hd, and GY contributed by Cadenza. We asked if these are linked or pleiotropic effects using recombinant lines, and showed that Ht and Hd effects are independent. The Chinese Spring equivalent to the newly defined Ht interval contained a gene cluster involved in cell wall growth and displaying high levels of differential transcript expression. The Hd locus is larger and rearranged compared with the reference genome, but FT2 (Flowering Locus T2) is of particular interest. The Hd effect acted independently of photoperiod and vernalization, but did exhibit seasonal genotype×environment interaction. Recombinants were phenotyped for GY in replicated field experiments. GY was most associated with Cadenza alleles for later Hd, supporting physiological studies using the same lines proposing that 'late' alleles at this locus increase spike fertility and grain number (GN). The work has uncoupled height from heading and yield, and shown that one of very few validated GY QTLs in wheat is probably mediated by phenological variation.


Subject(s)
Quantitative Trait Loci , Triticum , Bread , Chromosome Mapping , Chromosomes , Phenotype , Quantitative Trait Loci/genetics , Triticum/genetics
8.
BMC Plant Biol ; 20(1): 407, 2020 Sep 03.
Article in English | MEDLINE | ID: mdl-32883202

ABSTRACT

BACKGROUND: Little is known about the initial, symptomless (latent) phase of the devastating wheat disease Septoria tritici blotch. However, speculations as to its impact on fungal success and disease severity in the field have suggested that a long latent phase is beneficial to the host and can reduce inoculum build up in the field over a growing season. The winter wheat cultivar Stigg is derived from a synthetic hexaploid wheat and contains introgressions from wild tetraploid wheat Triticum turgidum subsp. dicoccoides, which contribute to cv. Stigg's exceptional STB resistance, hallmarked by a long latent phase. We compared the early transcriptomic response to Zymoseptoria tritici of cv. Stigg to a susceptible wheat cultivar, to elucidate the mechanisms of and differences in pathogen recognition and disease response in these two hosts. RESULTS: The STB-susceptible cultivar Longbow responds to Z. tritici infection with a stress response, including activation of hormone-responsive transcription factors, post translational modifications, and response to oxidative stress. The activation of key genes associated with these pathways in cv. Longbow was independently observed in a second susceptible wheat cultivar based on an independent gene expression study. By comparison, cv. Stigg is apathetic in response to STB, and appears to fail to activate a range of defence pathways that cv. Longbow employs. Stigg also displays some evidence of sub-genome bias in its response to Z. tritici infection, whereas the susceptible cv. Longbow shows even distribution of Z. tritici responsive genes across the three wheat sub-genomes. CONCLUSIONS: We identify a suite of disease response genes that are involved in early pathogen response in susceptible wheat cultivars that may ultimately lead to susceptibility. In comparison, we hypothesise that rather than an active defence response to stave off disease progression, cv. Stigg's defence strategy is molecular lethargy, or a lower-amplitude of pathogen recognition that may stem from cv. Stigg's wild wheat-derived ancestry. Overall, we present insights into cv. Stigg's exceptional resistance to STB, and present key biological processes for further characterisation in this pathosystem.


Subject(s)
Ascomycota/physiology , Disease Resistance/genetics , Plant Diseases/genetics , Transcriptome , Triticum/genetics , Plant Diseases/microbiology , Triticum/microbiology
9.
Plant Biotechnol J ; 18(11): 2316-2327, 2020 11.
Article in English | MEDLINE | ID: mdl-32356579

ABSTRACT

Wheat contains abundant xylan in cell walls of all tissues, but in endosperm, there is an unusual form of xylan substituted only by arabinose (arabinoxylan; AX) that has long chains and low levels of feruloylation, a fraction of which is extractable in water (WE-AX). WE-AX acts as soluble dietary fibre but also gives rise to viscous extracts from grain, a detrimental trait for some non-food uses of wheat. Here, we show that a glycosyl transferase family 43 wheat gene abundantly expressed in endosperm complements the Arabidopsis irx9 mutant and so name the three homoeologous genes TaIRX9b. We generated wheat lines with a constitutive knockout of TaIRX9b by stacking loss-of-function alleles for these homeologues from a mutagenized hexaploid wheat population resulting in decreases in grain extract viscosity of 50%-80%. The amount and chain length of WE-AX molecules from grain of these triple-stack lines was decreased accounting for the changes in extract viscosity. Imaging of immature wheat grain sections of triple-stacks showed abolition of immunolabelling in endosperm with LM11 antibody that recognizes epitopes in AX, but also showed apparently normal cell size and shape in all cell types, including endosperm. We identified differentially expressed genes from endosperm of triple-stacks suggesting that compensatory changes occur to maintain this endosperm cell wall integrity. Consistent with this, we observed increased ferulate dimerization and increased cross-linking of WE-AX molecules in triple-stacks. These novel wheat lines lacking functional TaIRX9b therefore provide insight into control of wheat endosperm cell walls.


Subject(s)
Triticum , Xylans , Cell Wall , Edible Grain , Endosperm/genetics , Triticum/genetics
10.
Theor Appl Genet ; 133(3): 707-717, 2020 Mar.
Article in English | MEDLINE | ID: mdl-31834441

ABSTRACT

KEY MESSAGE: Yield penalty and increased grain protein content traits associated with Aegilops ventricosa 7D introgression have been mapped for the first time, and they are physically distinct from the eyespot resistance locus Pch1. Wheat wild relatives represent an important source of genetic variation, but introgression of agronomically relevant genes, such as for disease resistance, may lead to the simultaneous introduction of genetically linked deleterious traits. Pch1 is a dominant gene, conferring resistance to eyespot and was introgressed to wheat from Aegilops ventricosa as part of a large segment of the 7DV chromosome. This introgression has been associated with a significant yield reduction and a concomitant increase in grain protein content. In this study, we evaluated both traits and their relationship to the location of the Pch1 gene. We found that both QTLs were clearly distinct from the Pch1 gene, being located on a different linkage group to Pch1. In addition, we found that the QTL for increased grain protein content was strong and consistent across field trials, whereas the yield penalty QTL was unstable and environmentally dependent. The yield and grain protein content QTLs were genetically linked and located in the same linkage group. This finding is due in part to the small size of the population, and to the restricted recombination between wheat 7D and Ae. ventricosa 7Dv chromosomes. Although recombination in this interval is rare, it does occur. A recombinant line containing Pch1 and 7D_KASP6, the marker associated with increase in grain protein content, but not Xwmc221, the marker associated with the yield penalty effect, was identified.


Subject(s)
Aegilops/genetics , Disease Resistance/genetics , Edible Grain/growth & development , Grain Proteins/metabolism , Plant Diseases/genetics , Triticum/growth & development , Aegilops/metabolism , Chromosome Mapping , Chromosomes, Plant , Crosses, Genetic , Edible Grain/genetics , Edible Grain/metabolism , Genes, Plant , Genetic Introgression , Genetic Linkage , Genetic Markers , Phenotype , Quantitative Trait Loci , Triticum/genetics , Triticum/metabolism
11.
Theor Appl Genet ; 132(7): 1943-1952, 2019 Jul.
Article in English | MEDLINE | ID: mdl-30888431

ABSTRACT

Genomic selection offers several routes for increasing the genetic gain or efficiency of plant breeding programmes. In various species of livestock, there is empirical evidence of increased rates of genetic gain from the use of genomic selection to target different aspects of the breeder's equation. Accurate predictions of genomic breeding value are central to this, and the design of training sets is in turn central to achieving sufficient levels of accuracy. In summary, small numbers of close relatives and very large numbers of distant relatives are expected to enable predictions with higher accuracy. To quantify the effect of some of the properties of training sets on the accuracy of genomic selection in crops, we performed an extensive field-based winter wheat trial. In summary, this trial involved the construction of 44 F2:4 bi- and tri-parental populations, from which 2992 lines were grown on four field locations and yield was measured. For each line, genotype data were generated for 25 K segregating SNP markers. The overall heritability of yield was estimated to 0.65, and estimates within individual families ranged between 0.10 and 0.85. Genomic prediction accuracies of yield BLUEs were 0.125-0.127 using two different cross-validation approaches and generally increased with training set size. Using related crosses in training and validation sets generally resulted in higher prediction accuracies than using unrelated crosses. The results of this study emphasise the importance of the training panel design in relation to the genetic material to which the resulting prediction model is to be applied.


Subject(s)
Genomics/methods , Plant Breeding , Triticum/genetics , Crosses, Genetic , Genetic Markers , Genotype , Models, Genetic , Polymorphism, Single Nucleotide , Selection, Genetic
12.
Eye (Lond) ; 33(Suppl 1): 1-21, 2019 03.
Article in English | MEDLINE | ID: mdl-30926932

ABSTRACT

This report by a group of UK retina specialists and health professionals considers best practice recommendations for the management of sight-threatening neovascular age-related macular degeneration (nAMD), based on collective experience and expertise in routine clinical practice. The authors provide an update for ophthalmologists, allied healthcare professionals and commissioners on practice principles for optimal patient care and service provision standards. Refinement of care pathways for nAMD has improved access to intravitreal anti-vascular endothelial growth factor therapy but there are still variations in care and reported outcomes between clinic centres. Innovative organisational models of service provision allow providers to better match capacity with increasing demand. The authors review the recent NICE guideline for diagnosis and management of AMD, considerations for switching therapies and stopping treatment and need for regular monitoring of non-affected fellow eyes in patients with unilateral nAMD. Actions for delivery of high-quality care and to improve long-term patient outcomes are discussed. Local pathways need to detail nAMD target time to treat, maintenance of review intervals to ensure proactive treatment regimens are delivered on time and appropriate discharge for patients deemed low risk or no longer benefiting from treatment. Actual visual acuity outcomes achieved and maintenance of the level of vision when disease stability is achieved are considered good measures for judging the quality of care in the treatment of patients with nAMD. Robust community referral pathways must be in place for suspected reactivation of choroidal neovascularisation and rapid referral for second eye involvement. Practical considerations for intravitreal injection therapy are outlined.


Subject(s)
Angiogenesis Inhibitors/therapeutic use , Delivery of Health Care/methods , Macular Degeneration/drug therapy , Vascular Endothelial Growth Factor A/antagonists & inhibitors , Aftercare , Aged , Aged, 80 and over , Community Health Services/organization & administration , Community Health Services/standards , Delivery of Health Care/standards , Drug Substitution , Female , Hospitalization , Humans , Macular Degeneration/diagnosis , Macular Degeneration/nursing , Male , Middle Aged , Practice Guidelines as Topic , Practice Patterns, Physicians'/trends , Quality of Health Care/standards , Recurrence , Referral and Consultation/organization & administration , Remote Consultation/standards , Remote Consultation/statistics & numerical data , Risk Factors , Time-to-Treatment
13.
14.
Nat Plants ; 4(9): 662-668, 2018 09.
Article in English | MEDLINE | ID: mdl-30150615

ABSTRACT

Crop diseases reduce wheat yields by ~25% globally and thus pose a major threat to global food security1. Genetic resistance can reduce crop losses in the field and can be selected through the use of molecular markers. However, genetic resistance often breaks down following changes in pathogen virulence, as experienced with the wheat yellow (stripe) rust fungus Puccinia striiformis f. sp. tritici (Pst)2. This highlights the need to (1) identify genes that, alone or in combination, provide broad-spectrum resistance, and (2) increase our understanding of the underlying molecular modes of action. Here we report the isolation and characterization of three major yellow rust resistance genes (Yr7, Yr5 and YrSP) from hexaploid wheat (Triticum aestivum), each having a distinct recognition specificity. We show that Yr5, which remains effective to a broad range of Pst isolates worldwide, is closely related yet distinct from Yr7, whereas YrSP is a truncated version of Yr5 with 99.8% sequence identity. All three Yr genes belong to a complex resistance gene cluster on chromosome 2B encoding nucleotide-binding and leucine-rich repeat proteins (NLRs) with a non-canonical N-terminal zinc-finger BED domain3 that is distinct from those found in non-NLR wheat proteins. We developed diagnostic markers to accelerate haplotype analysis and for marker-assisted selection to expedite the stacking of the non-allelic Yr genes. Our results provide evidence that the BED-NLR gene architecture can provide effective field-based resistance to important fungal diseases such as wheat yellow rust.


Subject(s)
Basidiomycota , Disease Resistance/physiology , NLR Proteins/physiology , Plant Diseases/microbiology , Plant Immunity/genetics , Triticum/microbiology , Zinc Fingers/physiology , Disease Resistance/genetics , Genes, Plant/genetics , Genes, Plant/physiology , NLR Proteins/genetics , Plant Immunity/physiology , Triticum/genetics , Triticum/immunology , Zinc Fingers/genetics
15.
J Exp Bot ; 67(14): 4169-78, 2016 07.
Article in English | MEDLINE | ID: mdl-27217549

ABSTRACT

The precocious germination of cereal grains before harvest, also known as pre-harvest sprouting, is an important source of yield and quality loss in cereal production. Pre-harvest sprouting is a complex grain defect and is becoming an increasing challenge due to changing climate patterns. Resistance to sprouting is multi-genic, although a significant proportion of the sprouting variation in modern wheat cultivars is controlled by a few major quantitative trait loci, including Phs-A1 in chromosome arm 4AL. Despite its importance, little is known about the physiological basis and the gene(s) underlying this important locus. In this study, we characterized Phs-A1 and show that it confers resistance to sprouting damage by affecting the rate of dormancy loss during dry seed after-ripening. We show Phs-A1 to be effective even when seeds develop at low temperature (13 °C). Comparative analysis of syntenic Phs-A1 intervals in wheat and Brachypodium uncovered ten orthologous genes, including the Plasma Membrane 19 genes (PM19-A1 and PM19-A2) previously proposed as the main candidates for this locus. However, high-resolution fine-mapping in two bi-parental UK mapping populations delimited Phs-A1 to an interval 0.3 cM distal to the PM19 genes. This study suggests the possibility that more than one causal gene underlies this major pre-harvest sprouting locus. The information and resources reported in this study will help test this hypothesis across a wider set of germplasm and will be of importance for breeding more sprouting resilient wheat varieties.


Subject(s)
Germination/physiology , Plant Dormancy/physiology , Quantitative Trait Loci/genetics , Triticum/growth & development , Chromosome Mapping , Chromosomes, Plant/genetics , Chromosomes, Plant/physiology , Genes, Plant/genetics , Genes, Plant/physiology , Genotyping Techniques , Germination/genetics , Plant Dormancy/genetics , Polymorphism, Single Nucleotide/genetics , Quantitative Trait Loci/physiology , Triticum/genetics
16.
Theor Appl Genet ; 129(8): 1507-17, 2016 Aug.
Article in English | MEDLINE | ID: mdl-27160855

ABSTRACT

KEY MESSAGE: SNP markers were developed for the OWBM resistance gene Sm1 that will be useful for MAS. The wheat Sm1 region is collinear with an inverted syntenic interval in B. distachyon. Orange wheat blossom midge (OWBM, Sitodiplosis mosellana Géhin) is an important insect pest of wheat (Triticum aestivum) in many growing regions. Sm1 is the only described OWBM resistance gene and is the foundation of managing OWBM through host genetics. Sm1 was previously mapped to wheat chromosome arm 2BS relative to simple sequence repeat (SSR) markers and the dominant, sequence characterized amplified region (SCAR) marker WM1. The objectives of this research were to saturate the Sm1 region with markers, develop improved markers for marker-assisted selection (MAS), and examine the synteny between wheat, Brachypodium distachyon, and rice (Oryza sativa) in the Sm1 region. The present study mapped Sm1 in four populations relative to single nucleotide polymorphisms (SNPs), SSRs, Diversity Array Technology (DArT) markers, single strand conformation polymorphisms (SSCPs), and the SCAR WM1. Numerous high quality SNP assays were designed that mapped near Sm1. BLAST delineated the syntenic intervals in B. distachyon and rice using gene-based SNPs as query sequences. The Sm1 region in wheat was inverted relative to B. distachyon and rice, which suggests a chromosomal rearrangement within the Triticeae lineage. Seven SNPs were tested on a collection of wheat lines known to carry Sm1 and not to carry Sm1. Sm1-flanking SNPs were identified that were useful for predicting the presence or absence of Sm1 based upon haplotype. These SNPs will be a major improvement for MAS of Sm1 in wheat breeding programs.


Subject(s)
Chromosome Mapping , Genetic Linkage , Polymorphism, Single Nucleotide , Synteny , Triticum/genetics , Animals , Brachypodium/genetics , Chironomidae , DNA, Plant/genetics , Genes, Plant , Genetic Markers , Haplotypes , Oryza/genetics , Phenotype
18.
Plant Biotechnol J ; 13(5): 613-24, 2015 Jun.
Article in English | MEDLINE | ID: mdl-25382230

ABSTRACT

The identification of genetic markers linked to genes of agronomic importance is a major aim of crop research and breeding programmes. Here, we identify markers for Yr15, a major disease resistance gene for wheat yellow rust, using a segregating F2 population. After phenotyping, we implemented RNA sequencing (RNA-Seq) of bulked pools to identify single-nucleotide polymorphisms (SNP) associated with Yr15. Over 27 000 genes with SNPs were identified between the parents, and then classified based on the results from the sequenced bulks. We calculated the bulk frequency ratio (BFR) of SNPs between resistant and susceptible bulks, selecting those showing sixfold enrichment/depletion in the corresponding bulks (BFR > 6). Using additional filtering criteria, we reduced the number of genes with a putative SNP to 175. The 35 SNPs with the highest BFR values were converted into genome-specific KASP assays using an automated bioinformatics pipeline (PolyMarker) which circumvents the limitations associated with the polyploid wheat genome. Twenty-eight assays were polymorphic of which 22 (63%) mapped in the same linkage group as Yr15. Using these markers, we mapped Yr15 to a 0.77-cM interval. The three most closely linked SNPs were tested across varieties and breeding lines representing UK elite germplasm. Two flanking markers were diagnostic in over 99% of lines tested, thus providing a reliable haplotype for marker-assisted selection in these breeding programmes. Our results demonstrate that the proposed methodology can be applied in polyploid F2 populations to generate high-resolution genetic maps across target intervals.


Subject(s)
Basidiomycota/physiology , Plant Diseases/immunology , Polymorphism, Single Nucleotide/genetics , Triticum/genetics , Base Sequence , Breeding , Chromosome Mapping , Disease Resistance , Genetic Linkage , Genetic Markers/genetics , High-Throughput Nucleotide Sequencing , Polyploidy , RNA, Plant/chemistry , RNA, Plant/genetics , Sequence Analysis, RNA , Triticum/immunology
19.
J Strength Cond Res ; 28(12): 3557-66, 2014 Dec.
Article in English | MEDLINE | ID: mdl-24942166

ABSTRACT

Relationship between unilateral jumping ability and asymmetry on multidirectional speed in team-sport athletes. J Strength Cond Res 28(12): 3557-3566, 2014-The influence of unilateral jump performance, and between-leg asymmetries, on multidirectional speed has not been widely researched. This study analyzed how speed was related to unilateral jumping. Multidirectional speed was measured by 20-m sprint (0-5, 0-10, 0-20-m intervals), left- and right-leg turn 505, and modified T-test performance. Unilateral jump performance, and between-leg asymmetries, was measured by vertical (VJ), standing broad (SBJ), and lateral (LJ) jumping. Thirty male team-sport athletes (age = 22.60 ± 3.86 years; height = 1.80 ± 0.07 m; mass = 79.03 ± 12.26 kilograms) were recruited. Pearson's correlations (r) determined speed and jump performance relationships; stepwise regression ascertained jump predictors of speed (p ≤ 0.05). Subjects were divided into lesser and greater asymmetry groups from each jump condition. A 1-way analysis of variance found between-group differences (p ≤ 0.05). Left-leg VJ correlated with the 0-10 and 0-20-m intervals (r = -0.437 to -0.486). Right-leg VJ correlated with all sprint intervals and the T-test (r = -0.380 to -0.512). Left-leg SBJ and LJ correlated with all tests (r = -0.370 to -0.729). Right-leg SBJ and LJ related to all except the left-leg turn 505 (r = -0.415 to -0.650). Left-leg SBJ predicted the 20-m sprint. Left-leg LJ predicted the 505 and T-test. Regardless of the asymmetry used to form groups, no differences in speed were established. Horizontal and LJ performance related to multidirectional speed. Athletes with asymmetries similar to this study (VJ = ∼10%; SBJ = ∼3%; LJ = ∼5%) should not experience speed detriments.


Subject(s)
Acceleration , Athletes , Lower Extremity/physiology , Movement/physiology , Muscle Strength/physiology , Athletic Performance/physiology , Humans , Male , Young Adult
20.
J Pediatr Surg ; 49(2): 284-8; discussion 288, 2014 Feb.
Article in English | MEDLINE | ID: mdl-24528968

ABSTRACT

BACKGROUND/PURPOSE: The purpose of this study was to calculate the incidence of cholecystectomy among children aged ≤ 16 in England between 1997 and 2012 and to assess trends in risk factors. METHODS: A nationwide retrospective cohort study using the Hospital Episode Statistics Database for episodes of cholecystectomy in children aged ≤ 16 was performed. Age and sex-specific annual incidence rates were derived using Office of National Statistics mid-year population estimates. Trends in the observed case mix were tested using univariable linear regression. RESULTS: 2808 paediatric cholecystectomies were identified. The incidence of cholecystectomy increased from 0.78/100,000 to 2.7/100,000 (P<0.0001). Sex-specific incidences increased from 1.1 to 4.36/100,000 (P<0.0001) among girls and from 0.48 to 1.13/100,000 (P<0.0001) among boys. There were significant changes in case mix, with an increasing proportion of female cases (69% to 79%, P=0.02), an increase in cases of white ethnicity (48% to 77%, P<0.0001), but only a modest increase in those with a diagnosis of sickle cell anaemia (4% to 6%, P=0.02), and no significant increase in other haemolytic anaemias. CONCLUSIONS: There has been a three-fold increase in the incidence of paediatric cholecystectomy in England since 1997, with a particular rise among white females. Although data on BMI were not available, the observed effect may be a consequence of increasing levels of teenage obesity.


Subject(s)
Cholecystectomy/statistics & numerical data , Gallstones/surgery , Adolescent , Child , Child, Preschool , England/epidemiology , Female , Gallstones/epidemiology , Humans , Incidence , Infant , Male , Retrospective Studies , Risk Factors , Sex Factors
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