GWAS reveals consistent QTL for drought and salt tolerance in a MAGIC population of 550 lines derived from intermating of 11 Upland cotton (Gossypium hirsutum) parents

Cotton is grown in arid and semi-arid regions where abiotic stresses such as drought and salt are prevalent. There is a lack of studies that simultaneously address the genetic and genomic basis of tolerance to drought and salt stress. In this study, a multi-parent advanced generation inter-cross (MAGIC) population of 550 recombinant inbred lines (RILs) together with their 11 Upland cotton parents with a total of 473,516 polymorphic SNP markers was used to identify quantitative trait loci (QTL) for drought tolerance (DT) and salt tolerance (ST) at the seedling stage based on two replicated greenhouse tests. Transgressive segregation occurred in the MAGIC-RILs, indicating that tolerant and sensitive alleles recombined for tolerance to the abiotic stress during the intermating process for the population development. A total of 20 QTL were detected for DT including 13 and 7 QTL based on plant height (PH) and dry shoot weight (DSW), respectively; and 23 QTL were detected for ST including 12 and 11 QTL for PH and DSW, respectively. There were several chromosomes with QTL clusters for abiotic stress tolerance including four QTL on chromosome A13 and three QTL on A01 for DT, and four QTL on D08 and three QTL on A11 for ST. Nine QTL (21% of the 43 QTL) detected were in common between DT and ST, indicating a common genetic basis for DT and ST. The narrow chromosomal regions for most of the QTL detected in this study allowed identification of 53 candidate genes associated with responses to salt and drought stress and abiotic stimulus. The QTL identified for both DT and ST have significantly augmented the repertoire of QTL for abiotic stress tolerance that can be used for marker-assisted selection to develop cultivars with resilience to drought and/or salt and further genomic studies towards the identification of drought and salt tolerance genes in cotton.

A, Chakraborty A, Thirunavukkarasu N. Multiple Genome Wide Association Mapping Models Identify Quantitative Trait Nucleotides for Brown Planthopper (Nilaparvata lugens) Resistance in MAGIC Indica Population of Rice

Brown planthopper (BPH), one of the most important pests of the rice (Oryza sativa) crop, becomes catastrophic under severe infestations and causes up to 60% yield loss. The highly disastrous BPH biotype in the Indian sub-continent is Biotype 4, which also known as the South Asian Biotype. Though many resistance genes were mapped until now, the utility of the resistance genes in the breeding programs is limited due to the breakdown of resistance and emergence of new biotypes. Hence, to identify the resistance genes for this economically important pest, we have used a multi-parent advanced generation intercross (MAGIC) panel consisting of 391 lines developed from eight indica founder parents. The panel was phenotyped at the controlled conditions for two consecutive years. A set of 27,041 cured polymorphic single nucleotide polymorphism (SNPs) and across-year phenotypic data were used for the identification of marker–trait associations. Genome-wide association analysis was performed to find out consistent associations by employing four single and two multi-locus models. Sixty-one SNPs were consistently detected by all six models. A set of 190 significant marker-associations identified by fixed and random model circulating probability unification (FarmCPU) were considered for searching resistance candidate genes. The highest number of annotated genes were found in chromosome 6 followed by 5 and 1. Ninety-two annotated genes identified across chromosomes of which 13 genes are associated BPH resistance including NB-ARC (nucleotide binding in APAF-1, R gene products, and CED-4) domain-containing protein, NHL repeat-containing protein, LRR containing protein, and WRKY70. The significant SNPs and resistant lines identified from our study could be used for an accelerated breeding program to develop new BPH resistant cultivars.

Effects of the MAGIC Guidelines on PICC Placement Volume: Advanced Practice Provider and Physician Trends Among Medicare Beneficiaries From 2010 to 2018

BACKGROUND. The Michigan Appropriateness Guide for Intravenous Catheters (MAGIC) was published in 2015, recommending more restricted indications for peripherally inserted central catheter (PICC) placement, particularly for those placed by physicians. Changes in PICC placement volume since the publication of MAGIC is largely unknown. OBJECTIVE. The purpose of this article was to study the trends in volume and reimbursement for PICC placement by physicians and advanced practice providers (APPs) for Medicare enrollees from 2010 to 2018 with specific attention to the changes in volume after the publication of MAGIC in 2015. METHODS. Claims from the Medicare Part B Physician/Supplier Procedure Summary Master File for the years 2010-2018 were extracted using the Current Procedural Terminology code for PICC placement. Total volume and payment amounts (for the professional component) were analyzed. Trendline slopes for volume per 100,000 Medicare beneficiaries before and after the 2015 publication of MAGIC were compared. RESULTS. Volume for PICC placement by physicians and APPs steadily declined from 243,837 in 2010 to 130,361 in 2018 (46.5%). The PICC placement volume decreased sharply after the 2015 publication of the MAGIC guidelines. The slope of the trendline for all providers from 2010 to 2015 was -3.4 compared with -7.3 from 2015 to 2018. The change in slope was more pronounced for radiologists (-3.1 to -5.6) than for APPs (0.0 to -1.1). Professional payment per procedure for radiologists decreased from $78.04 in 2010 to $70.17 in 2018, and reimbursement for APPs proportionally decreased from $65.76 to $60.66 during this time. The relative share of PICC placement by radiologists declined from 77.0% in 2010 to 70.6% in 2018, with a corresponding increase in relative share by APPs from 13.5% to 18.4%. The percentage placed in outpatient procedures increased from 15.1% to 18.2%. CONCLUSION. The volume of PICC placements has steadily decreased since 2010, with a sharper decline between 2015 and 2016 corresponding with the publication of the MAGIC evidence-based guidelines. The role of APPs in PICC placement has increased over this time period. CLINICAL IMPACT. The findings of this study suggest that evidence-based guidelines impact clinical practice on a national level.

Strong Recommendations Are Inappropriate in Person-Centred Care: The Case of Anti-Platelet Therapy

A 'Rapid Recommendation' has been produced by the GRADE group, in collaboration with MAGIC and BMJ, in response to an RCT showing Dual Anti-Platelet Therapy (DAPT) is superior to Aspirin alone for patients who had suffered acute high risk transient ischaemic attack or minor ischaemic stroke. The interactive MAGIC decision aid that accompanies each Rapid Recommendation is the main route to their clinical implementation. It can facilitate preference-sensitive person-centred care, but only if a Multi-Criteria Decision Analysis-based decision support tool is added. A demonstration version of such an add-on to the MAGIC aid, divested of recommendations, is available online. Exploring the results of different preference inputs into the tool raises questions about the strong recommendation for DAPT.

Determinants of QTL Mapping Power in the Realized Collaborative Cross

The Collaborative Cross (CC) is a mouse genetic reference population whose range of applications includes quantitative trait loci (QTL) mapping. The design of a CC QTL mapping study involves multiple decisions, including which and how many strains to use, and how many replicates per strain to phenotype, all viewed within the context of hypothesized QTL architecture. Until now, these decisions have been informed largely by early power analyses that were based on simulated, hypothetical CC genomes. Now that more than 50 CC strains are available and more than 70 CC genomes have been observed, it is possible to characterize power based on realized CC genomes. We report power analyses from extensive simulations and examine several key considerations: 1) the number of strains and biological replicates, 2) the QTL effect size, 3) the presence of population structure, and 4) the distribution of functionally distinct alleles among the founder strains at the QTL. We also provide general power estimates to aide in the design of future experiments. All analyses were conducted with our R package, SPARCC (Simulated Power Analysis in the Realized Collaborative Cross), developed for performing either large scale power analyses or those tailored to particular CC experiments.

Genetic Dissection of Resistance to the Three Fungal Plant Pathogens Blumeria graminis, Zymoseptoria tritici, and Pyrenophora tritici-repentis Using a Multiparental Winter Wheat Population

Bread wheat (Triticum aestivum L.) is one of the world’s most important crop species. The development of new varieties resistant to multiple pathogens is an ongoing task in wheat breeding, especially in times of increasing demand for sustainable agricultural practices. Despite this, little is known about the relations between various fungal disease resistances at the genetic level, and the possible consequences for wheat breeding strategies. As a first step to fill this gap, we analyzed the genetic relations of resistance to the three fungal diseases – powdery mildew (PM), septoria tritici blotch (STB), and tan spot (TS) – using a winter wheat multiparent advanced generation intercross population. Six, seven, and nine QTL for resistance to PM, STB, and TS, respectively, were genetically mapped. Additionally, 15 QTL were identified for the three agro-morphological traits plant height, ear emergence time, and leaf angle distribution. Our results suggest that resistance to STB and TS on chromosome 2B is conferred by the same genetic region. Furthermore, we identified two genetic regions on chromosome 1AS and 7AL, which are associated with all three diseases, but not always in a synchronal manner. Based on our results, we conclude that parallel marker-assisted breeding for resistance to the fungal diseases PM, STB, and TS appears feasible. Knowledge of the genetic co-localization of alleles with contrasting effects for different diseases, such as on chromosome 7AL, allows the trade-offs of selection of these regions to be better understood, and ultimately determined at the genic level.

R/qtl2: Software for Mapping Quantitative Trait Loci with High-Dimensional Data and Multiparent Populations

R/qtl2 is an interactive software environment for mapping quantitative trait loci (QTL) in experimental populations. The R/qtl2 software expands the scope of the widely-used R/qtl software package to include multiparental populations, better handles modern high-dimensional data....

R/qtl2 is an interactive software environment for mapping quantitative trait loci (QTL) in experimental populations. The R/qtl2 software expands the scope of the widely used R/qtl software package to include multiparent populations derived from more than two founder strains, such as the Collaborative Cross and Diversity Outbred mice, heterogeneous stocks, and MAGIC plant populations. R/qtl2 is designed to handle modern high-density genotyping data and high-dimensional molecular phenotypes, including gene expression and proteomics. R/qtl2 includes the ability to perform genome scans using a linear mixed model to account for population structure, and also includes features to impute SNPs based on founder strain genomes and to carry out association mapping. The R/qtl2 software provides all of the basic features needed for QTL mapping, including graphical displays and summary reports, and it can be extended through the creation of add-on packages. R/qtl2, which is free and open source software written in the R and C++ programming languages, comes with a test framework.

From Rapid Recommendation to Online Preference-Sensitive Decision Support: The Case of Severe Aortic Stenosis

The launch of ‘Rapid Recommendations’ by the Grading of Recommendations Assessment, Development and Evaluation (GRADE) group, in collaboration with Making GRADE the Irresistible Choice (MAGIC) and the British Medical Journal (BMJ), is a very interesting recent development in e-healthcare. Designed to respond quickly to developments that have created new decision situations, their first project resulted from the arrival of minimally invasive Transcatheter Aortic Valve Implantation (TAVI) as an alternative to Surgical Aortic Valve Replacement (SAVR), for patients with symptomatic severe aortic stenosis. The interactive MAGIC decision aid that accompanies a Rapid Recommendation and is the main route to its clinical implementation, represents a major advance in e-health, for a cardiovascular decision in this case. However, it needs to go further in order to facilitate fully person-centred care, where the weighted preferences of the individual person are elicited at the point of decision, and transparently integrated with the best (most personalised) estimates of option performances, to produce personalised, preference-sensitive option evaluations. This can be achieved by inputting the collated GRADE evidence on the criteria relevant in the TAVI/SAVR choice into a Multi-Criteria Decision Analysis-based decision support tool, generating a personalised, preference-sensitive opinion. A demonstration version of this add-on to the MAGIC aid, divested of recommendations, is available online as proof of method.

Genome-Wide Association Mapping in a Rice MAGIC Plus Population Detects QTLs and Genes Useful for Biofortification

The development of rice genotypes with micronutrient-dense grains and disease resistance is one of the major priorities in rice improvement programs. We conducted Genome-wide association studies (GWAS) using a Multi-parent Advanced Generation Inter-Cross (MAGIC) Plus population to identify QTLs and SNP markers that could potentially be integrated in biofortification and disease resistance breeding. We evaluated 144 MAGIC Plus lines for agronomic and biofortification traits over two locations for two seasons, while disease resistance was screened for one season in the screen house. X-ray fluorescence technology was used to measure grain Fe and Zn concentrations. Genotyping was carried out by genotype by sequencing and a total of 14,242 SNP markers were used in the association analysis. We used Mixed linear model (MLM) with kinship and detected 57 significant genomic regions with a -log10 (P-value) ≥ 3.0. The PH 1.1 and Zn 7.1 were consistently identified in all the four environments, ten QTLs qDF 3.1, qDF 6.2 qDF 9.1 qPH 5.1 qGL 3.1, qGW 3.1, qGW 11.1, and qZn 6.2 were detected in two environments, while two major loci qBLB 11.1 and qBLB 5.1 were identified for Bacterial Leaf Blight (BLB) resistance. The associated SNP markers were found to co-locate with known major genes and QTLs such as OsMADS50 for days to flowering, osGA20ox2 for plant height, and GS3 for grain length. Similarly, Xa4 and xa5 genes were identified for BLB resistance and Pi5(t), Pi28(t), and Pi30(t) genes were identified for Blast resistance. A number of metal homeostasis genes OsMTP6, OsNAS3, OsMT2D, OsVIT1, and OsNRAMP7 were co-located with QTLs for Fe and Zn. The marker-trait relationships from Bayesian network analysis showed consistency with the results of GWAS. A number of promising candidate genes reported in our study can be further validated. We identified several QTLs/genes pyramided lines with high grain Zn and acceptable yield potential, which are a good resource for further evaluation to release as varieties as well as for use in breeding programs.

Functional Mapping of Quantitative Trait Loci (QTLs) Associated With Plant Performance in a Wheat MAGIC Mapping Population

In crop genetic studies, the mapping of longitudinal data describing the spatio-temporal nature of agronomic traits can elucidate the factors influencing their formation and development. Here, we combine the mapping power and precision of a MAGIC wheat population with robust computational methods to track the spatio- temporal dynamics of traits associated with wheat performance. NIAB MAGIC lines were phenotyped throughout their lifecycle under smart house conditions. Growth models were fitted to the data describing growth trajectories of plant area, height, water use and senescence and fitted parameters were mapped as quantitative traits. Trait data from single time points were also mapped to determine when and how markers became and ceased to be significant. Assessment of temporal dynamics allowed the identification of marker-trait associations and tracking of trait development against the genetic contribution of key markers. We establish a data-driven approach for understanding complex agronomic traits and accelerate research in plant breeding.

The paradox of proteasome granules

Profound knowledge is available for the structure, function and regulation of proteasomes, the key proteases for ubiquitin-dependent protein degradation in dividing cells. Far less understood are proteasome structure and function in quiescence, the resting phase of our body's cells, as in yeast cells grown to stationary phase. In quiescent yeast proteasomes exit the nucleus and accumulate in cytoplasmic protein droplets, called proteasome storage granules (PSG). PSG-like structures also exist in non-dividing mammalian cells suggesting that the mechanism underlying PSG organization is conserved from yeast to human. The PSG has physiological significance as it protects yeast cells against stress and confers fitness during aging. The molecular architecture of PSG remains an enigma, since PSG freely move as spherical units without being surrounded by membranes through the cytoplasm. They rapidly resolve with the resumption of cell proliferation and proteasomes reenter the nucleus. Our systems biology and biochemical data revealed that PSG are mainly composed of proteasomes and free ubiquitin. Often intrinsically disordered proteins undergo liquid phase separations, allowing soluble proteins to condense into protein droplets in an aqueous solution. The question is which proteins and factors nucleate PSG formation, since proteasomes composed of folded subunits are able to degrade intrinsically disordered proteins.

Maximizing the potential of multi-parental crop populations

Most agriculturally significant crop traits are quantitatively inherited which limits the ease and efficiency of trait dissection. Multi-parent populations overcome the limitations of traditional trait mapping and offer new potential to accurately define the genetic basis of complex crop traits. The increasing popularity and use of nested association mapping (NAM) and multi-parent advanced generation intercross (MAGIC) populations raises questions about the optimal design and allocation of resources in their creation. In this paper we review strategies for the creation of multi-parent populations and describe two complementary in silico studies addressing the design and construction of NAM and MAGIC populations. The first simulates the selection of diverse founder parents and the second the influence of multi-parent crossing schemes (and number of founders) on haplotype creation and diversity. We present and apply two open software resources to simulate alternate strategies for the development of multi-parent populations.

Determining Phenological Patterns Associated with the Onset of Senescence in a Wheat MAGIC Mapping Population

The appropriate timing of developmental transitions is critical for adapting many crops to their local climatic conditions. Therefore, understanding the genetic basis of different aspects of phenology could be useful in highlighting mechanisms underpinning adaptation, with implications in breeding for climate change. For bread wheat (Triticum aestivum), the transition from vegetative to reproductive growth, the start and rate of leaf senescence and the relative timing of different stages of flowering and grain filling all contribute to plant performance. In this study we screened under Smart house conditions a large, multi-founder "NIAB elite MAGIC" wheat population, to evaluate the genetic elements that influence the timing of developmental stages in European elite varieties. This panel of recombinant inbred lines was derived from eight parents that are or recently have been grown commercially in the UK and Northern Europe. We undertook a detailed temporal phenotypic analysis under Smart house conditions of the population and its parents, to try to identify known or novel Quantitative Trait Loci associated with variation in the timing of key phenological stages in senescence. This analysis resulted in the detection of QTL interactions with novel traits such the time between "half of ear emergence above flag leaf ligule" and the onset of senescence at the flag leaf as well as traits associated with plant morphology such as stem height. In addition, strong correlations between several traits and the onset of senescence of the flag leaf were identified. This work establishes the value of systematically phenotyping genetically unstructured populations to reveal the genetic architecture underlying morphological variation in commercial wheat.

Allele mining and enhanced genetic recombination for rice breeding

Traditional rice varieties harbour a large store of genetic diversity with potential to accelerate rice improvement. For a long time, this diversity maintained in the International Rice Genebank has not been fully used because of a lack of genome information. The publication of the first reference genome of Nipponbare by the International Rice Genome Sequencing Project (IRGSP) marked the beginning of a systematic exploration and use of rice diversity for genetic research and breeding. Since then, the Nipponbare genome has served as the reference for the assembly of many additional genomes. The recently completed 3000 Rice Genomes Project together with the public database (SNP-Seek) provides a new genomic and data resource that enables the identification of useful accessions for breeding. Using disease resistance traits as case studies, we demonstrated the power of allele mining in the 3,000 genomes for extracting accessions from the GeneBank for targeted phenotyping. Although potentially useful landraces can now be identified, their use in breeding is often hindered by unfavourable linkages. Efficient breeding designs are much needed to transfer the useful diversity to breeding. Multi-parent Advanced Generation InterCross (MAGIC) is a breeding design to produce highly recombined populations. The MAGIC approach can be used to generate pre-breeding populations with increased genotypic diversity and reduced linkage drag. Allele mining combined with a multi-parent breeding design can help convert useful diversity into breeding-ready genetic resources.

Sensitivity analyses of MAGIC modelled predictions of future impacts of whole-tree harvest on soil calcium supply and stream acid neutralizing capacity

Forest biofuel is a main provider of energy in Sweden and the market is expected to grow even further in the future. Removal of logging residues via harvest can lead to short-term acidification but the long-term effects are largely unknown. The objectives of this study were to 1) model the long-term effect of whole-tree harvest (WTH) on soil and stream water acidity and 2) perform sensitivity analyses by varying the amounts of logging residues, calcium (Ca(2+)) concentrations in tree biomass and site productivity in nine alternate scenarios. Data from three Swedish forested catchments and the Model of Acidification of Groundwater in Catchments (MAGIC) were used to simulate changes in forest soil exchangeable Ca(2+) pools and stream water acid neutralizing capacity (ANC) at Gammtratten, Kindla and Aneboda. Large depletions in soil Ca(2+) supply and a reversal of the positive trend in stream ANC were predicted for all three sites after WTH. However, the magnitude of impact on stream ANC varied depending on site and the concentration of mobile strong acid anions. Contrary to common beliefs, the largest decrease in modelled ANC was observed at the well-buffered site Gammtratten. The effects at Kindla and Aneboda were much more limited and not large enough to offset the general recovery from acidification. Varying the tree biomass Ca(2+) concentrations exerted the largest impact on modelled outcome. Site productivity was the second most important variable whereas changing biomass amounts left on site only marginally affected the results. The outcome from the sensitivity analyses pointed in the same direction of change as in the base scenario, except for Kindla where soil Ca(2+) pools were predicted to be replenished under a given set of input data. The reliability of modelled outcome would increase by using site-specific Ca(2+) concentrations in tree biomass and field determined identification of site productivity.

Indirect detection of dark matter with γ rays

The details of what constitutes the majority of the mass that makes up dark matter in the Universe remains one of the prime puzzles of cosmology and particle physics today-80 y after the first observational indications. Today, it is widely accepted that dark matter exists and that it is very likely composed of elementary particles, which are weakly interacting and massive [weakly interacting massive particles (WIMPs)]. As important as dark matter is in our understanding of cosmology, the detection of these particles has thus far been elusive. Their primary properties such as mass and interaction cross sections are still unknown. Indirect detection searches for the products of WIMP annihilation or decay. This is generally done through observations of γ-ray photons or cosmic rays. Instruments such as the Fermi large-area telescope, high-energy stereoscopic system, major atmospheric gamma-ray imaging Cherenkov, and very energetic radiation imaging telescope array, combined with the future Cherenkov telescope array, will provide important complementarity to other search techniques. Given the expected sensitivities of all search techniques, we are at a stage where the WIMP scenario is facing stringent tests, and it can be expected that WIMPs will be either be detected or the scenario will be so severely constrained that it will have to be rethought. In this sense, we are on the threshold of discovery. In this article, I will give a general overview of the current status and future expectations for indirect searches of dark matter (WIMP) particles.

Efficient imputation of missing markers in low-coverage genotyping-by-sequencing data from multiparental crosses

We consider genomic imputation for low-coverage genotyping-by-sequencing data with high levels of missing data. We compensate for this loss of information by utilizing family relationships in multiparental experimental crosses. This nearly quadruples the number of usable markers when applied to a large rice Multiparent Advanced Generation InterCross (MAGIC) study.