Detecting epistatic selection with partially observed genotype data by using copula graphical models

Complementary approaches to dissect late leaf rust resistance in an interspecific raspberry population

Over the last 10 years, global raspberry production has increased by 47.89%, based mainly on the red raspberry species (Rubus idaeus). However, the black raspberry (Rubus occidentalis), although less consumed, is resistant to one of the most important diseases for the crop, the late leaf rust caused by Acculeastrum americanum fungus. In this context, genetic resistance is the most sustainable way to control the disease, mainly because there are no registered fungicides for late leaf rust in Brazil. Therefore, the aim was to understand the genetic architecture that controls resistance to late leaf rust in raspberries. For that, we used an interspecific multiparental population using the species mentioned above as parents, 2 different statistical approaches to associate the phenotypes with markers [GWAS (genome-wide association studies) and copula graphical models], and 2 phenotyping methodologies from the first to the 17th day after inoculation (high-throughput phenotyping with a multispectral camera and traditional phenotyping by disease severity scores). Our findings indicate that a locus of higher effect, at position 13.3 Mb on chromosome 5, possibly controls late leaf rust resistance, as both GWAS and the network suggested the same marker. Of the 12 genes flanking its region, 4 were possible receptors, 3 were likely defense executors, 1 gene was likely part of signaling cascades, and 4 were classified as nondefense related. Although the network and GWAS indicated the same higher effect genomic region, the network identified other different candidate regions, potentially complementing the genetic control comprehension.

Discovering the direct relations between nutrients and epigenetic ageing

BACKGROUND

Along with the ageing of society, the absolute prevalence of age-related diseases is expected to rise, leading to a substantial burden on healthcare systems and society. Thus, there is an urgent need to promote healthy ageing. As opposed to chronological age, biological age was introduced to accurately represent the ageing process, as it considers physiological deterioration that is linked to morbidity and mortality risk. Furthermore, biological age responds to various factors, including nutritional factors, which have the potential to mitigate the risk of age-related diseases. As a result, a promising biomarker of biological age known as the epigenetic clock has emerged as a suitable measure to investigate the direct relations between nutritional factors and ageing, thereby identifying potential intervention targets to improve healthy ageing.

METHODS

In this study, we analysed data from 3,969 postmenopausal women from the Women's Health Initiative to identify nutrients that are associated with the rate of ageing by using an accurate measure of biological age called the PhenoAge epigenetic clock. We used Copula Graphical Models, a data-driven exploratory analysis tool, to identify direct relationships between nutrient intake and age-acceleration, while correcting for every variable in the dataset.

RESULTS

We revealed that increased dietary intakes of coumestrol, beta-carotene and arachidic acid were associated with decelerated epigenetic ageing. In contrast, increased intakes of added sugar, gondoic acid, behenic acid, arachidonic acid, vitamin A and ash were associated with accelerated epigenetic ageing in postmenopausal women.

CONCLUSION

Our study discovered direct relations between nutrients and epigenetic ageing, revealing promising areas for follow-up studies to determine the magnitude and causality of our estimated diet-epigenetic relationships.

Natural variation in salt-induced root growth phases and their contribution to root architecture plasticity

The root system architecture of a plant changes during salt stress exposure. Different accessions of Arabidopsis thaliana have adopted different strategies in remodelling their root architecture during salt stress. Salt induces a multiphase growth response in roots, consisting of a stop phase, quiescent phase, recovery phase and eventually a new level of homoeostasis. We explored natural variation in the length of and growth rate during these phases in both main and lateral roots and find that some accessions lack the quiescent phase. Using mathematical models and correlation-based network, allowed us to correlate dynamic traits to overall root architecture and discover that both the main root growth rate during homoeostasis and lateral root appearance are the strongest determinants of overall root architecture. In addition, this approach revealed a trade-off between investing in main or lateral root length during salt stress. By studying natural variation in high-resolution temporal root growth using mathematical modelling, we gained new insights in the interactions between dynamic root growth traits and we identified key traits that modulate overall root architecture during salt stress.

Parent-offspring genotyped trios unravelling genomic regions with gametic and genotypic epistatic transmission bias on the cattle genome

Several biological mechanisms affecting the sperm and ova fertility and viability at developmental stages of the reproductive cycle resulted in observable transmission ratio distortion (i.e., deviation from Mendelian expectations). Gene-by-gene interactions (or epistasis) could also potentially cause specific transmission ratio distortion patterns at different loci as unfavorable allelic combinations are under-represented, exhibiting deviation from Mendelian proportions. Here, we aimed to detect pairs of loci with epistatic transmission ratio distortion using 283,817 parent-offspring genotyped trios (sire-dam-offspring) of Holstein cattle. Allelic and genotypic parameterization for epistatic transmission ratio distortion were developed and implemented to scan the whole genome. Different epistatic transmission ratio distortion patterns were observed. Using genotypic models, 7, 19 and 6 pairs of genomic regions were found with decisive evidence with additive-by-additive, additive-by-dominance/dominance-by-additive and dominance-by-dominance effects, respectively. Using the allelic transmission ratio distortion model, more insight was gained in understanding the penetrance of single-locus distortions, revealing 17 pairs of SNPs. Scanning for the depletion of individuals carrying pairs of homozygous genotypes for unlinked loci, revealed 56 pairs of SNPs with recessive epistatic transmission ratio distortion patterns. The maximum number of expected homozygous offspring, with none of them observed, was 23. Finally, in this study, we identified candidate genomic regions harboring epistatic interactions with potential biological implications in economically important traits, such as reproduction.

From Classical to Modern Computational Approaches to Identify Key Genetic Regulatory Components in Plant Biology

The selection of plant genotypes with improved productivity and tolerance to environmental constraints has always been a major concern in plant breeding. Classical approaches based on the generation of variability and selection of better phenotypes from large variant collections have improved their efficacy and processivity due to the implementation of molecular biology techniques, particularly genomics, Next Generation Sequencing and other omics such as proteomics and metabolomics. In this regard, the identification of interesting variants before they develop the phenotype trait of interest with molecular markers has advanced the breeding process of new varieties. Moreover, the correlation of phenotype or biochemical traits with gene expression or protein abundance has boosted the identification of potential new regulators of the traits of interest, using a relatively low number of variants. These important breakthrough technologies, built on top of classical approaches, will be improved in the future by including the spatial variable, allowing the identification of gene(s) involved in key processes at the tissue and cell levels.

Dietary Intakes of Vegetable Protein, Folate, and Vitamins B-6 and B-12 Are Partially Correlated with Physical Functioning of Dutch Older Adults Using Copula Graphical Models

BACKGROUND

In nutritional epidemiology, dealing with confounding and complex internutrient relations are major challenges. An often-used approach is dietary pattern analyses, such as principal component analysis, to deal with internutrient correlations, and to more closely resemble the true way nutrients are consumed. However, despite these improvements, these approaches still require subjective decisions in the preselection of food groups. Moreover, they do not make efficient use of multivariate dietary data, because they detect only marginal associations. We propose the use of copula graphical models (CGMs) to model and make statistical inferences regarding complex associations among variables in multivariate data, where associations between all variables can be learned simultaneously.

OBJECTIVE

We aimed to reconstruct nutritional intake and physical functioning networks in Dutch older adults by applying a CGM.

METHODS

We addressed this issue by uncovering the pairwise associations between variables while correcting for the effect of remaining variables. More specifically, we used a CGM to infer the precision matrix, which contains all the conditional independence relations between nodes in the graph. The nonzero elements of the precision matrix indicate the presence of a direct association. We applied this method to reconstruct nutrient-physical functioning networks from the combined data of 4 studies (Nu-Age, ProMuscle, ProMO, and V-Fit, total n = 662, mean ± SD age = 75 ± 7 y). The method was implemented in the R package nutriNetwork which is freely available at https://cran.r-project.org/web/packages/nutriNetwork.

RESULTS

Greater intakes of vegetable protein and vitamin B-6 were partially correlated with higher scores on the total Short Physical Performance Battery (SPPB) and the chair rise test. Greater intakes of vitamin B-12 and folate were partially correlated with higher scores on the chair rise test and the total SPPB, respectively.

CONCLUSIONS

We determined that vegetable protein, vitamin B-6, folate, and vitamin B-12 intakes are partially correlated with improved functional outcome measurements in Dutch older adults.

Standard Deviations: The Biological Bases of Transmission Ratio Distortion

The rule of Mendelian inheritance is remarkably robust, but deviations from the equal transmission of alternative alleles at a locus [a.k.a. transmission ratio distortion (TRD)] are also commonly observed in genetic mapping populations. Such TRD reveals locus-specific selection acting at some point between the diploid heterozygous parents and progeny genotyping and therefore can provide novel insight into otherwise-hidden genetic and evolutionary processes. Most of the classic selfish genetic elements were discovered through their biasing of transmission, but many unselfish evolutionary and developmental processes can also generate TRD. In this review, we describe methodologies for detecting TRD in mapping populations, detail the arenas and genetic interactions that shape TRD during plant and animal reproduction, and summarize patterns of TRD from across the genetic mapping literature. Finally, we point to new experimental approaches that can accelerate both detection of TRD and characterization of the underlying genetic mechanisms.

Screening for epistatic selection signatures: A simulation study

Detecting combinations of alleles that diverged between subpopulations via selection signature statistics can contribute to decipher the phenomenon of epistasis. This research focused on the simulation of genomic data from subpopulations under divergent epistatic selection (ES). We used D’_IS² and F_ST statistics in pairs of loci to scan the whole-genome. The results showed the ability to identify loci under additive-by-additive ES (ES_aa) by reporting large statistical departures between subpopulations with a high level of divergence, while it did not show the same advantage in the other types of ES. Despite this, limitations such as the difficulty to distinguish between the quasi-complete fixation of one locus by ES_aa from other events were observed. However, D’_IS² can detect loci under ES_aa by defining a minimum boundary for the minor allele frequency on a multiple subpopulation analysis where ES only takes place in one subset. Even so, the major limitation was distinguishing between ES and single-locus selection (SS); therefore, we can conclude that divergent locus can be also a result of ES. The test conditions with D-statistics of both Ohta (1982a, 1982b) and Black and Krafsur (1985) did not provide evidence to differentiate ES in our simulation framework of isolated subpopulations.