Using Association Mapping in Teosinte to Investigate the Function of Maize Selection-Candidate Genes

BACKGROUND:Large-scale screens of the maize genome identified 48 genes that show the putative signature of artificial selection during maize domestication or improvement. These selection-candidate genes may act as quantitative trait loci (QTL) that control the phenotypic differences between maize and its progenitor, teosinte. The selection-candidate genes appear to be located closer in the genome to domestication QTL than expected by chance. METHODS AND FINDINGS:As a step toward defining the traits controlled by these genes, we performed phenotype-genotype association mapping in teosinte for 32 of the 48 plus three other selection-candidate genes. Our analyses assayed 32 phenotypic traits, many of which were altered during maize domestication or improvement. We observed several significant associations between SNPs in the selection-candidate genes and trait variation in teosinte. These included two associations that surpassed the Bonferroni correction and five instances where a gene significantly associated with the same trait in both of our association mapping panels. Despite these significant associations, when compared as a group the selection-candidate genes performed no better than randomly chosen genes. CONCLUSIONS:Our results suggest association analyses can be helpful for identifying traits under the control of selection-candidate genes. Indeed, we present evidence for new functions for several selection-candidate genes. However, with the current set of selection-candidate genes and our association mapping strategy, we found very few significant associations overall and no more than we would have found with randomly chosen genes. We discuss possible reasons that a large number of significant genotype-phenotype associations were not discovered

The chemerin knockout rat reveals chemerin dependence in female, but not male, experimental hypertension

Measures of the adipokine chemerin are elevated in multiple cardiovascular diseases, including hypertension, but little mechanistic work has been done to implicate chemerin as being causative in such diseases. The chemerin knockout (KO) rat was created to test the hypothesis that removal of chemerin would reduce pressure in the normal and hypertensive state. Western analyses confirmed loss of chemerin in the plasma and tissues of the KO vs. wild‐type (WT) rats. Chemerin concentration in plasma and tissues was lower in WT females than in WT males, as determined by Western analysis. Conscious male and female KO rats had modest differences in baseline measures vs. the WT that included systolic, diastolic, mean arterial and pulse pressures, and heart rate, all measured telemetrically. The mineralocorticoid deoxycorticosterone acetate (DOCA) and salt water, combined with uninephrectomy as a hypertensive stimulus, elevated mean and systolic blood pressures of the male KO higher than the male WT. By contrast, all pressures in the female KO were lower than their WT throughout DOCA‐salt treatment. These results revealed an unexpected sex difference in chemerin expression and the ability of chemerin to modify blood pressure in response to a hypertensive challenge.—Watts, S. W., Darios, E. S., Mullick, A. E., Garver, H., Saunders, T. L., Hughes, E. D., Filipiak, W. E., Zeidler, M. G., McMullen, N., Sinal, C. J., Kumar, R. K., Ferland, D. J., Fink, G. D. The chemerin knockout rat reveals chemerin dependence in female, but not male, experimental hypertension. FASEB J. 32, 6596–6614 (2018). www.fasebj.orgPeer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/154357/1/fsb2fj201800479.pd

Multiomics modeling of the immunome, transcriptome, microbiome, proteome and metabolome adaptations during human pregnancy.

MotivationMultiple biological clocks govern a healthy pregnancy. These biological mechanisms produce immunologic, metabolomic, proteomic, genomic and microbiomic adaptations during the course of pregnancy. Modeling the chronology of these adaptations during full-term pregnancy provides the frameworks for future studies examining deviations implicated in pregnancy-related pathologies including preterm birth and preeclampsia.ResultsWe performed a multiomics analysis of 51 samples from 17 pregnant women, delivering at term. The datasets included measurements from the immunome, transcriptome, microbiome, proteome and metabolome of samples obtained simultaneously from the same patients. Multivariate predictive modeling using the Elastic Net (EN) algorithm was used to measure the ability of each dataset to predict gestational age. Using stacked generalization, these datasets were combined into a single model. This model not only significantly increased predictive power by combining all datasets, but also revealed novel interactions between different biological modalities. Future work includes expansion of the cohort to preterm-enriched populations and in vivo analysis of immune-modulating interventions based on the mechanisms identified.Availability and implementationDatasets and scripts for reproduction of results are available through: https://nalab.stanford.edu/multiomics-pregnancy/.Supplementary informationSupplementary data are available at Bioinformatics online

A BAC pooling strategy combined with PCR-based screenings in a large, highly repetitive genome enables integration of the maize genetic and physical maps

BACKGROUND: Molecular markers serve three important functions in physical map assembly. First, they provide anchor points to genetic maps facilitating functional genomic studies. Second, they reduce the overlap required for BAC contig assembly from 80 to 50 percent. Finally, they validate assemblies based solely on BAC fingerprints. We employed a six-dimensional BAC pooling strategy in combination with a high-throughput PCR-based screening method to anchor the maize genetic and physical maps. RESULTS: A total of 110,592 maize BAC clones (~ 6x haploid genome equivalents) were pooled into six different matrices, each containing 48 pools of BAC DNA. The quality of the BAC DNA pools and their utility for identifying BACs containing target genomic sequences was tested using 254 PCR-based STS markers. Five types of PCR-based STS markers were screened to assess potential uses for the BAC pools. An average of 4.68 BAC clones were identified per marker analyzed. These results were integrated with BAC fingerprint data generated by the Arizona Genomics Institute (AGI) and the Arizona Genomics Computational Laboratory (AGCoL) to assemble the BAC contigs using the FingerPrinted Contigs (FPC) software and contribute to the construction and anchoring of the physical map. A total of 234 markers (92.5%) anchored BAC contigs to their genetic map positions. The results can be viewed on the integrated map of maize [1,2]. CONCLUSION: This BAC pooling strategy is a rapid, cost effective method for genome assembly and anchoring. The requirement for six replicate positive amplifications makes this a robust method for use in large genomes with high amounts of repetitive DNA such as maize. This strategy can be used to physically map duplicate loci, provide order information for loci in a small genetic interval or with no genetic recombination, and loci with conflicting hybridization-based information

Generating a taxonomy for genetic conditions relevant to reproductive planning

As genome or exome sequencing (hereafter genome-scale sequencing) becomes more integrated into standard care, carrier testing is an important possible application. Carrier testing using genome-scale sequencing can identify a large number of conditions, but choosing which conditions/genes to evaluate as well as which results to disclose can be complicated. Carrier testing generally occurs in the context of reproductive decision-making and involves patient values in a way that other types of genetic testing may not. The Kaiser Permanente Clinical Sequencing Exploratory Research program is conducting a randomized clinical trial of preconception carrier testing that allows participants to select their preferences for results from among broad descriptive categories rather than selecting individual conditions. This paper describes 1) the criteria developed by the research team, the return of results committee (RORC), and stakeholders for defining the categories; 2) the process of refining the categories based on input from patient focus groups and validation through a patient survey; and, 3) how the RORC then assigned specific gene-condition pairs to taxonomy categories being piloted in the trial. The development of four categories (serious, moderate/mild, unpredictable, late onset) for sharing results allows patients to select results based on their values without separately deciding their interest in knowing their carrier status for hundreds of conditions. A fifth category, lifespan limiting, was always shared. The lessons learned may be applicable in other results disclosure situations, such as incidental findings

Genetic Analysis of Central Carbon Metabolism Unveils an Amino Acid Substitution That Alters Maize NAD-Dependent Isocitrate Dehydrogenase Activity

Background: Central carbon metabolism (CCM) is a fundamental component of life. The participating genes and enzymes are thought to be structurally and functionally conserved across and within species. Association mapping utilizes a rich history of mutation and recombination to achieve high resolution mapping. Therefore, applying association mapping in maize (Zea mays ssp. mays), the most diverse model crop species, to study the genetics of CCM is a particularly attractive system. Methodology/Principal Findings: We used a maize diversity panel to test the CCM functional conservation. We found heritable variation in enzyme activity for every enzyme tested. One of these enzymes was the NAD-dependent isocitrate dehydrogenase (IDH, E.C. 1.1.1.41), in which we identified a novel amino-acid substitution in a phylogenetically conserved site. Using candidate gene association mapping, we identified that this non-synonymous polymorphism was associated with IDH activity variation. The proposed mechanism for the IDH activity variation includes additional components regulating protein level. With the comparison of sequences from maize and teosinte (Zea mays ssp. Parviglumis), the maize wild ancestor, we found that some CCM genes had also been targeted for selection during maize domestication. Conclusions/Significance: Our results demonstrate the efficacy of association mapping for dissecting natural variation in primary metabolic pathways. The considerable genetic diversity observed in maize CCM genes underlies heritable phenotypic variation in enzyme activities and can be useful to identify putative functional sites

Physical and Genetic Structure of the Maize Genome Reflects Its Complex Evolutionary History

Maize (Zea mays L.) is one of the most important cereal crops and a model for the study of genetics, evolution, and domestication. To better understand maize genome organization and to build a framework for genome sequencing, we constructed a sequence-ready fingerprinted contig-based physical map that covers 93.5% of the genome, of which 86.1% is aligned to the genetic map. The fingerprinted contig map contains 25,908 genic markers that enabled us to align nearly 73% of the anchored maize genome to the rice genome. The distribution pattern of expressed sequence tags correlates to that of recombination. In collinear regions, 1 kb in rice corresponds to an average of 3.2 kb in maize, yet maize has a 6-fold genome size expansion. This can be explained by the fact that most rice regions correspond to two regions in maize as a result of its recent polyploid origin. Inversions account for the majority of chromosome structural variations during subsequent maize diploidization. We also find clear evidence of ancient genome duplication predating the divergence of the progenitors of maize and rice. Reconstructing the paleoethnobotany of the maize genome indicates that the progenitors of modern maize contained ten chromosomes

Ghosts of other stories: a synthesis of hauntology, crime and space

Criminology has long sought to illuminate the lived experience of those at the margins. More recently, there has been a turn toward the spatial in the discipline. This paper sets out an analytical framework that synthesizes spatial theory with hauntology. We demonstrate how a given space's violent histories can become embedded in the texts that constitute it and the language that describes it. The art installation ‘Die Familie Schneider’ is used as an example of how the incorporation of social trauma can lead to the formation of a spatial “crypt”. Cracking open this “crypt” allows us to draw out Derrida's notion of the specter within the context of a “haunted” city space

Whole number thinking, learning and development: neuro-cognitive, cognitive and developmental approaches

The participants of working group 2 presented a broad range of studies, 11 papers in total, related to whole number learning representing research groups from 11 countries as follows. Two large cross-sectional studies focused on developmental aspects of young children’s number learning provide a lens for re-examining ‘traditional’ features of number acquisition. van den Heuvel-Panhuizen (the Netherlands) presented a co-authored paper with Elia (Cyprus; Elia and van den Heuvel-Panhuizen 2015) on a cross-cultural study of kindergartners’ number competence focused on counting, additive and multiplicative thinking. Second, Milinković (2015) examined the development of young Serbian children’s initial understanding of representations of whole numbers and counting strategies in a large study of 3- to 7-year-olds. Children’s invented (formal) representations such as set representation and the number line were found to be limited in their recordings. In a South African study focused on early counting and addition, Roberts (2015) directs attention to the role of teachers by providing a framework to support teachers’ interpretation of young disadvantaged learners’ representations of number when engaging with whole number additive tasks. Some papers reflected the increasing role of neuroscientific concepts and methodologies utilised in research on WNA learning and development. Sinclair and Coles (2015) drew upon neuroscientific research to highlight the significant role of symbol-to-symbol connections and the use of fingers and touch counting exempli- fied by the TouchCounts iPad app. Gould (2015) reported aspects of a large Australian large study of children in the first years of schooling aimed at improving numeracy and literacy in disadvantaged communities. A case study exemplified how numerals were identified by relying on a mental number line by using location to retrieve number names. This raised the question addressed in the neuroscientific work of Dehaene and other papers focused on individual differences in how the brain processes numbers. The Italian PerContare1 project (Baccaglini-Frank 2015) built upon the collaboration between cognitive psychologists and mathematics educators, aimed at developing teaching strategies for preventing and addressing early low achievement in arithmetic. It takes an innovative approach to the development of number sense that is grounded upon a kinaesthetic and visual-spatial approach to part-whole relationships. Mulligan and Woolcott (2015) provided a discussion paper on the underlying nature of number. They presented a broader view of mathematics learning (including WNA) as linked to spatial interaction with the environment; the concept of connectivity across concepts and the development of underlying pattern and structural relationships are central to their approach