Embracing native diversity to enhance the maximum quantum efficiency of photosystem II in maize.

The sustainability of maize cultivation would benefit tremendously from early sowing, but is hampered by low temperatures during early development in temperate climates. We show that allelic variation within the gene encoding subunit M of the NADH-dehydrogenase-like (NDH) complex (ndhm1) in a European maize landrace affects several quantitative traits that are relevant during early development in cold climates through NDH-mediated cyclic electron transport (CET) around photosystem I, a process crucial for photosynthesis and photoprotection. Beginning with a genome-wide association study for maximum potential quantum yield of photosystem II in dark-adapted leaves (Fv/Fm), we capitalized on the large phenotypic effects of a hAT transposon insertion in ndhm1 on multiple quantitative traits (early plant height, Fv/Fm, chlorophyll content, and cold tolerance) caused by the reduced protein levels of NDHM and associated NDH components.

Seedling root system adaptation to water availability during maize domestication and global expansion.

The maize root system has been reshaped by indirect selection during global adaptation to new agricultural environments. In this study, we characterized the root systems of more than 9,000 global maize accessions and its wild relatives, defining the geographical signature and genomic basis of variation in seminal root number. We demonstrate that seminal root number has increased during maize domestication followed by a decrease in response to limited water availability in locally adapted varieties.

Genomic prediction using information across years with epistatic models and dimension reduction via haplotype blocks.

The importance of accurate genomic prediction of phenotypes in plant breeding is undeniable, as higher prediction accuracy can increase selection responses. In this regard, epistasis models have shown to be capable of increasing the prediction accuracy while their high computational load is challenging. In this study, we investigated the predictive ability obtained in additive and epistasis models when utilizing haplotype blocks versus pruned sets of SNPs by including phenotypic information from the last growing season.

Using phosphate amendments to reduce bioaccessible Pb in contaminated soils: A meta-analysis.

Measuring the reduction of bioaccessible (IVBA) Pb from the addition of phosphate amendments has been researched for more than 20 years. A range of effects have been observed from increases in IVBA Pb to almost 100% reduction. This study determined the mean change in IVBA Pb as a fraction of total Pb (AC) and relative to the IVBA Pb of the control soil (RC) with a random effects meta-analysis.

Genetic diversity of European maize landraces: Dataset on the molecular and phenotypic variation of derived doubled-haploid populations.

Genetic variation is the basis of selection, evolution and breeding. Maize landraces represent a rich source of allelic diversity, but their efficient utilization in breeding and research has been hampered by their heterogeneous and heterozygous nature and insufficient information about most accessions. While molecular inventories of germplasm repositories are growing steadily, linking these data to meaningful phenotypes for quantitative traits is challenging.

Theoretical and experimental assessment of genome-based prediction in landraces of allogamous crops.

Discovery and enrichment of favorable alleles in landraces are key to making them accessible for crop improvement. Here, we present two fundamentally different concepts for genome-based selection in landrace-derived maize populations, one based on doubled-haploid (DH) lines derived directly from individual landrace plants and the other based on crossing landrace plants to a capture line. For both types of populations, we show theoretically how allele frequencies of the ancestral landrace and the capture line translate into expectations for molecular and genetic variances.

[Project report on fostering scientific competencies in pain medicine in the context of student education].

Aim: The training of scientific skills and competencies is an essential part of academic medical studies. As part of the MaReCuM model study program at Heidelberg University's Mannheim Medical School, a fifth-year rotation on scientific skills in the field of pain medicine was implemented. This paper describes this competence-oriented rotation as well as the investigation of the educational effect.

Calibration and validation of predicted genomic breeding values in an advanced cycle maize population.

Model training on data from all selection cycles yielded the highest prediction accuracy by attenuating specific effects of individual cycles. Expected reliability was a robust predictor of accuracies obtained with different calibration sets. The transition from phenotypic to genome-based selection requires a profound understanding of factors that determine genomic prediction accuracy.

Accounting for epistasis improves genomic prediction of phenotypes with univariate and bivariate models across environments.

The accuracy of genomic prediction of phenotypes can be increased by including the top-ranked pairwise SNP interactions into the prediction model. We compared the predictive ability of various prediction models for a maize dataset derived from 910 doubled haploid lines from two European landraces (Kemater Landmais Gelb and Petkuser Ferdinand Rot), which were tested at six locations in Germany and Spain. The compared models were Genomic Best Linear Unbiased Prediction (GBLUP) as an additive model, Epistatic Random Regression BLUP (ERRBLUP) accounting for all pairwise SNP interactions, and selective Epistatic Random Regression BLUP (sERRBLUP) accounting for a selected subset of pairwise SNP interactions.

Generalized gametic relationships for flexible analyses of parent-of-origin effects.

A class of epigenetic inheritance patterns known as genomic imprinting allows alleles to influence the phenotype in a parent-of-origin-specific manner. Various pedigree-based parent-of-origin analyses of quantitative traits have attempted to determine the share of genetic variance that is attributable to imprinted loci. In general, these methods require four random gametic effects per pedigree member to account for all possible types of imprinting in a mixed model.

Exploiting genetic diversity in two European maize landraces for improving Gibberella ear rot resistance using genomic tools.

High genetic variation in two European maize landraces can be harnessed to improve Gibberella ear rot resistance by integrated genomic tools. Fusarium graminearum (Fg) causes Gibberella ear rot (GER) in maize leading to yield reduction and contamination of grains with several mycotoxins. This study aimed to elucidate the molecular basis of GER resistance among 500 doubled haploid lines derived from two European maize landraces, "Kemater Landmais Gelb" (KE) and "Petkuser Ferdinand Rot" (PE).

Discovery of beneficial haplotypes for complex traits in maize landraces.

Genetic variation is of crucial importance for crop improvement. Landraces are valuable sources of diversity, but for quantitative traits efficient strategies for their targeted utilization are lacking. Here, we map haplotype-trait associations at high resolution in ~1000 doubled-haploid lines derived from three maize landraces to make their native diversity for early development traits accessible for elite germplasm improvement.

Genomic imprinting analyses identify maternal effects as a cause of phenotypic variability in type 1 diabetes and rheumatoid arthritis.

Imprinted genes, giving rise to parent-of-origin effects (POEs), have been hypothesised to affect type 1 diabetes (T1D) and rheumatoid arthritis (RA). However, maternal effects may also play a role. By using a mixed model that is able to simultaneously consider all kinds of POEs, the importance of POEs for the development of T1D and RA was investigated in a variance components analysis.

Improving Imputation Quality in BEAGLE for Crop and Livestock Data.

Imputation is one of the key steps in the preprocessing and quality control protocol of any genetic study. Most imputation algorithms were originally developed for the use in human genetics and thus are optimized for a high level of genetic diversity. Different versions of BEAGLE were evaluated on genetic datasets of doubled haploids of two European maize landraces, a commercial breeding line and a diversity panel in chicken, respectively, with different levels of genetic diversity and structure which can be taken into account in BEAGLE by parameter tuning.

European maize landraces made accessible for plant breeding and genome-based studies.

Doubled-haploid libraries from landraces capture native genetic diversity for a multitude of quantitative traits and make it accessible for breeding and genome-based studies. Maize landraces comprise large allelic diversity. We created doubled-haploid (DH) libraries from three European flint maize landraces and characterized them with respect to their molecular diversity, population structure, trait means, variances, and trait correlations.

Correction: Care management intervention to strengthen self-care of multimorbid patients with type 2 diabetes in a German primary care network: A randomized controlled trial.

[This corrects the article DOI: 10.1371/journal.pone.

Care management intervention to strengthen self-care of multimorbid patients with type 2 diabetes in a German primary care network: A randomized controlled trial.

Purpose: This study aimed to assess the effectiveness of a care management intervention in improving self-management behavior in multimorbid patients with type 2 diabetes; care was delivered by medical assistants in the context of a primary care network (PCN) in Germany.

Methods: This study is an 18-month, multi-center, two-armed, open-label, patient-randomized parallel-group superiority trial (ISRCTN 83908315). The intervention group received the care management intervention in addition to the usual care.

HaploBlocker: Creation of Subgroup-Specific Haplotype Blocks and Libraries.

The concept of haplotype blocks has been shown to be useful in genetics. Fields of application range from the detection of regions under positive selection to statistical methods that make use of dimension reduction. We propose a novel approach ("HaploBlocker") for defining and inferring haplotype blocks that focuses on linkage instead of the commonly used population-wide measures of linkage disequilibrium.

Testcross performance of doubled haploid lines from European flint maize landraces is promising for broadening the genetic base of elite germplasm.

Selected doubled haploid lines averaged similar testcross performance as their original landraces, and the best of them approached the yields of elite inbreds, demonstrating their potential to broaden the narrow genetic diversity of the flint germplasm pool. Maize landraces represent a rich source of genetic diversity that remains largely idle because the high genetic load and performance gap to elite germplasm hamper their use in modern breeding programs. Production of doubled haploid (DH) lines can mitigate problems associated with the use of landraces in pre-breeding.

Meeting the needs of multimorbid patients with Type 2 diabetes mellitus - A randomized controlled trial to assess the impact of a care management intervention aiming to improve self-care.

Aims: This study explored the impact of a care management intervention aiming to improve self-care behavior in multimorbid individuals with Type 2 diabetes mellitus on health-related quality of life (HRQoL).

Methods: A patient-level randomized parallel-group superiority trial with 32 primary care practice teams, 11 care managers and 495 patients was conducted. The intervention was delivered as add-on to an already implemented disease management program and embedded in a network of primary care practices.

Turning Observed Founder Alleles into Expected Relationships in an Intercross Population.

Pedigree-derived relationships for individuals from an intercross of several lines cannot easily account for the segregation variance that is mainly caused by loci with alternative alleles fixed in different lines. However, when all founders are genotyped for a large number of markers, such relationships can be derived for descendants as expected genomic relationships conditional on the observed founder allele frequencies. A tabular method was derived in detail for autosomes and the X-chromosome.

Scanning the genomes of parents for imprinted loci acting in their un-genotyped progeny.

Depending on their parental origin, alleles at imprinted loci are fully or partially inactivated through epigenetic mechanisms. Their effects contribute to the broader class of parent-of-origin effects. Standard methodology for mapping imprinted quantitative trait loci in association studies requires phenotypes and parental origin of marker alleles (ordered genotypes) to be simultaneously known for each individual.

Is there an optimum level of diversity in utilization of genetic resources?

Capitalizing upon the genomic characteristics of long-term random mating populations, sampling from pre-selected landraces is a promising approach for broadening the genetic base of elite germplasm for quantitative traits. Genome-enabled strategies for harnessing untapped allelic variation of landraces are currently evolving. The success of such approaches depends on the choice of source material.

A comprehensive study of the genomic differentiation between temperate Dent and Flint maize.

Background: Dent and Flint represent two major germplasm pools exploited in maize breeding. Several traits differentiate the two pools, like cold tolerance, early vigor, and flowering time. A comparative investigation of their genomic architecture relevant for quantitative trait expression has not been reported so far.