
kwa-kwa ra-raRussian Academy of Sciences | RAS
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Publications (200)
Flowering is initiated in response to environmental cues, with the photoperiod and ambient temperature being the main ones. The regulatory pathways underlying floral transition are well studied in Arabidopsis thaliana but remain largely unknown in legumes. Here, we first applied an in silico approach to infer the regulatory inputs of four FT-like g...
Bulk segregant analysis was applied to the evaluation of F2 population developed by crossing two flax cultivars which differ in the resistance genes to Fusarium wilt. The causative agent of this disease, the fungus Fusarium oxysporum f. sp. lini, is one of the main flax pathogens causing enormous economic damage to the linen industry worldwide. DNA...
Chickpea (Cicer arientinum) is an important crop grown in the Middle East, Central Asia, Turkey, India and southern Russia and used in a wide variety of traditional dishes. The decrease in genetic diversity during domestication, as well as the crop's greater sensitivity to abiotic and biotic stresses, provides the idea of using landraces in breedin...
An important direction in cancer prevention is the development of novel strategies that can be used in the treatment by affecting the mechanisms of the regulatory pathways and genomic elements involved in malignant transformation. Strategy proposed in this study is to initiate cell death mechanisms in response to the depletion of the energy resourc...
A bulk segregant analysis (BSA) was used to analyze the F2 population from crossing two flax varieties that differ in fusarium wilt resistance genes. The causative agent of this disease, the fungus Fusarium oxysporum f. sp. lini is one of the main pathogens of flax, causing huge economic damage to its global production. Sequencing of DNA pools of h...
In many plant species, flowering is promoted by the cold treatment or vernalization. The mechanism of vernalization-induced flowering has been extensively studied in Arabidopsis but remains largely unknown in legumes. The orthologs of the FLC gene, a major regulator of vernalization response in Arabidopsis, are absent or non-functional in the verna...
Chickpea (Cicer arientinum) is an important leguminous crop, which is widely grown especially in the Near East. In wet weather conditions, the susceptibility of chickpeas to fungal diseases such as Ascochyta blight and Fusarium blight increases. Thus, selection of disease-resistant and early-ripening varieties is critically needed. The present stud...
Citation: Vedeneeva, E.; Gursky, V.; Samsonova, M.; Neganova, I.
Domestication is the long and complex process underlying the evolution of crops, in which artificial directional selection transformed wild progenitors into the desired form, affecting genomic variation and leaving traces of selection at targeted loci. However, whether genes controlling important domestication traits follow the same evolutionary pa...
Automatic feature extraction methods have gained increasing attention in modern image processing. The confocal images of the single-layered epithelium of the developing Drosophila eye may form an excellent model system to develop methods for complex feature extraction. The aim of this work was to explore Cartesian genetic programming for determinat...
While the domestication process has been investigated in many crops, the detailed route of cultivation range expansion and factors governing this process received relatively little attention. Here, using mungbean (Vigna radiata var. radiata) as a test case, we investigated the genomes of more than 1000 accessions to illustrate climatic adaptation’s...
While the domestication process has been investigated in many crops, the detailed route of cultivation range expansion and factors governing this process received relatively little attention. Here, using mungbean (Vigna radiata var. radiata) as a test case, we investigated the genomes of more than 1000 accessions to illustrate climatic adaptation’s...
While the domestication process has been investigated in many crops, the detailed route of cultivation range expansion and factors governing this process received relatively little attention. Here, using mungbean (Vigna radiata var. radiata) as a test case, we investigated the genomes of more than 1000 accessions to illustrate climatic adaptation’s...
According to archaeological records, chickpea (Cicer arietinum) was first domesticated in the Fertile Crescent about 10k years BP. Its subsequent diversification in Middle East, South Asia, Ethiopia, and the Western Mediterranean, however, remains obscure and cannot be resolved using only archeological and historical evidence. Moreover, chickpea ha...
Chickpea (Cicer arietinum L.) is a major grain legume and a good source of plant-based protein. However, comprehensive knowledge of flowering time control in Cicer is lacking. In this study, we acquire high-throughput transcriptome sequencing data and analyze changes in gene expression during floral transition in the early flowering cultivar ICCV 9...
Human pluripotent stem cells are promising for a wide range of research and therapeutic purposes. Their maintenance in culture requires the deep control of their pluripotent and clonal status. A non-invasive method for such control involves day-to-day observation of the morphological changes, along with imaging colonies, with the subsequent automat...
Flowering time is an important target for breeders in developing new varieties adapted to changing conditions. In this work, a new approach is proposed in which the SNP markers influencing time to flowering in mung bean are selected as important features in a random forest model. The genotypic and weather data are encoded in artificial image object...
In this paper, we explore potential genetic factors in control of flax phenotypes associated with fiber by mining a collection of 306 flax accessions from the Federal Research Centre of the Bast Fiber Crops, Torzhok, Russia. In total, 11 traits were assessed in the course of 3 successive years. A genome-wide association study was performed for each...
Domestication and improvement are two crucial processes underlying the evolution of crops. Domestication transformed wild plants into a utilizable form for humans; improvement refined cultivars adapting to distinct environments and local preferences. Using whole-genome re-sequencing of Vigna radiata, we investigated the demographic history and comp...
Vernalization is the requirement for exposure to low temperatures to trigger flowering. The best knowledge about the mechanisms of vernalization response has been accumulated for Arabidopsis and cereals. In Arabidopsis thaliana, vernalization involves an epigenetic silencing of the MADS-box gene FLOWERING LOCUS C (FLC), which is a flowering repress...
While the domestication process has been investigated in many crops, the detailed route of cultivar range expansion and factors governing this process received relatively little attention. Here using mungbean ( Vigna radiata var. radiata ) as a test case, we investigated the genomes of more than one thousand accessions to illustrate climatic adapta...
A collection of flax accessions maintained by the Russian Federal Research Center for Bast Fiber Crops was characterized to evaluate its resistance to Fusarium wilt. 297 samples representing different morphotypes and selection status were infected with highly virulent MI39 strain of Fusarium oxysporum f. sp. lini. Evaluation of disease symptoms was...
C4 photosynthesis increases the efficiency of carbon fixation by spatially separating high concentrations of molecular oxygen from rubisco. The specialized leaf anatomy required for this separation evolved independently many times. The morphology of C4 root systems is also distinctive and adapted to support high rates of photosynthesis; however, li...
The solution of the so-called mixed-integer optimization problem is an important challenge for modern life sciences. A wide range of methods has been developed for its solution, including metaheuristics approaches. Here, a modification is proposed of the differential evolution entirely parallel (DEEP) method introduced recently that was successfull...
Genetic diversity in a breeding program is essential to overcome modern-day environmental challenges faced by humanity and produce robust, resilient crop cultivars with improved agronomic characteristics, as well as to trace crop domestication history. Flax (Linum usitatissimum), one of the first crops domesticated by mankind, has been traditionall...
Modern flax cultivars are susceptible to many diseases; arguably, the most economically damaging of these is the Fusarium wilt fungal disease. Over the past decades international flax breeding initiatives resulted in the development of resistant cultivars. However, much remains to be learned about the mechanisms of resistance to Fusarium infection...
Flowering time is an important target for breeders in developing new varieties adapted to changing conditions. A new approach is proposed that uses Approximate Bayesian Computation with Differential Evolution to construct a pool of models for flowering time. The functions for daily progression of the plant from planting to flowering are obtained in...
Unlike transcriptional regulation, the post-transcriptional mechanisms underlying zygotic segmentation gene expression in early Drosophila embryo have been insufficiently investigated. Condition-specific post-transcriptional regulation plays an important role in the development of many organisms. Our recent study revealed the domain- and genotype-s...
Transposons are genomic elements that can relocate within a host genome using a ‘cut’- or ‘copy-and-paste’ mechanism. They make up a significant part of many genomes, serve as a driving force for genome evolution, and are linked with Mendelian diseases and cancers. Interactions between two specific retrotransposon types, autonomous (e.g., LINE1/L1)...
Accurate prediction of flowering time helps breeders to develop new varieties that can achieve maximal efficiency in a changing climate. A methodology was developed for the construction of a simulation model for flowering time in which a function for daily progression of the plant from one to the next phenological phase is obtained in analytic form...
An updated model of wild chickpea flowering time.
Structural Equation Modeling (SEM) is an umbrella term that includes numerous multivariate statistical techniques that are employed throughout a plethora of research areas, ranging from social to natural sciences. Until recently, SEM software was either commercial or restricted to niche languages, and the lack of SEM packages compatible with more m...
C4 photosynthesis increases the efficiency of carbon fixation by spatially separating high concentrations of molecular oxygen from rubisco. The specialized leaf anatomy required for this separation evolved independently many times. C4 root systems are highly branched, an adaptation thought to support high rates of photosynthesis; however, little is...
Transition to flowering is an important stage of plant development. Many regulatory modules that control floral transition are conservative across plants. This process is best studied for the model plant Arabidopsis thaliana. The homologues of Arabidopsis genes responsible for the flowering initiation in legumes have been identified, and available...
Understanding molecular mechanisms of sexually dimorphic organ growth is a fundamental problem of developmental biology. Recent quantitative studies showed that the Drosophila compound eye is a convenient model to study the determination of the final organ size. In Drosophila, females have larger eyes than males and this is evident even after corre...
According to archaeological records, chickpea ( Cicer arietinum ) was first domesticated in the Fertile Crescent 10 thousand years ago. Its subsequent diversification in South Asia, Ethiopia, and the Western Mediterranean, however, remains obscure and cannot be resolved using only archeological and historical evidence. In particular, chickpea has t...
Background
Mungbean ( Vigna radiata (L.) R. Wilczek, or green gram) is important tropical and sub-tropical legume and a rich source of dietary protein and micronutrients. In this study we employ GWAS to examine the genetic basis of variation in several important traits in mungbean, using the mini-core collection established by the World Vegetable C...
Background
Phenology data collected recently for about 300 accessions of Vigna radiata (mungbean) is an invaluable resource for investigation of impacts of climatic factors on plant development.
Results
We developed a new mathematical model that describes the dynamic control of time to flowering by daily values of maximal and minimal temperature,...
Background:
There is a plethora of methods for genome-wide association studies. However, only a few of them may be classified as multi-trait and multi-locus, i.e. consider the influence of multiple genetic variants to several correlated phenotypes.
Results:
We propose a multi-trait multi-locus model which employs structural equation modeling (SE...
A defining challenge of the 21st century is meeting the nutritional demands of the growing human population, under a scenario of limited land and water resources and under the specter of climate change. The Vavilov seed bank contains numerous landraces collected nearly a hundred years ago, and thus may contain ‘genetic gems’ with the potential to e...
In many biological systems gene expression at mRNA and protein levels is not identical. Rigorous comparison of such differences on a spatio-temporal scale is still not feasible by high-throughput transcriptomic and proteomic analyses of early embryo development. Here, we characterize differences between mRNA and protein expression of Drosophila seg...
Mungbean (Vigna radiata) (L.) R.Wilczek and urdbean (V. mungo) (L.) Hepper are two warm-season legumes that are nutritionally dense and contribute to food security. Despite their value, they have historically been underutilized. The N. I. Vavilov’s All-Russian Institute of Plant Genetic Resources Vigna germplasm collection is particularly critical...
Domestication and subsequent breeding have eroded genetic diversity in the modern chickpea crop by ˜100-fold. Corresponding reductions to trait variation create the need, and an opportunity, to identify and harness the genetic capacity of wild species for crop improvement. Here we analyze trait segregation in a series of wild x cultivated hybrid po...
Background
Accurate prediction of crop flowering time is required for reaching maximal farm efficiency. Several models developed to accomplish this goal are based on deep knowledge of plant phenology, requiring large investment for every individual crop or new variety. Mathematical modeling can be used to make better use of more shallow data and to...
The impact of deleterious variation on both plant fitness and crop productivity is not completely understood and is a hot topic of debates. The deleterious mutations in plants have been solely predicted using sequence conservation methods rather than function-based classifiers due to lack of well-annotated mutational datasets in these organisms. He...
Initiation of flowering moves plants from vegetative to reproductive development. The time when this transition happens (flowering time), an important indicator of productivity, depends on both endogenous and environmental factors. The core genetic regulatory network canalizing the flowering signals to the decision to flower has been studied extens...
Here, we review the latest publications on dynamics and interpretation of morphogen gradients in Drosophila early embryo. The instructive cues provided by these gradients are further interpreted by target genes to enable correct cell fate specification. Moreover, recent studies point on the dynamic and active input from gradients themselves. Latest...
Schizophrenia (SCZ) is a psychiatric disorder of unknown etiology. There is evidence suggesting that aberrations in neurodevelopment are a significant attribute of schizophrenia pathogenesis and progression. To identify biologically relevant molecular abnormalities affecting neurodevelopment in SCZ we used cultured neural progenitor cells derived f...
The genomes of mammals contain thousands of deleterious mutations. It is important to be able to recognize them with high precision. In conservation biology, the small size of fragmented populations results in accumulation of damaging variants. Preserving animals with less damaged genomes could optimize conservation efforts. In breeding of farm ani...
Structural equation modeling (SEM) is a second-generation multivariate method to estimate the causal interactions in a set of variables and includes, as special cases, several statistical methods (regression analysis, path analysis, and confirmatory factor analysis). This review focuses on all of the main SEM models and various methods used to opti...
Annotating the genotype-phenotype relationship, and developing a proper quantitative description of the relationship, requires understanding the impact of natural genomic variation on gene expression. We apply a sequence-level model of gap gene expression in the early development of Drosophila to analyze single nucleotide polymorphisms (SNPs) in a...
The Vavilov Institute of Plant Genetic Resources (VIR), in St. Petersburg, Russia, houses a unique genebank, with historical collections of landraces. When they were collected, the geographical distribution and genetic diversity of most crops closely reflected their historical patterns of cultivation established over the preceding millennia. We emp...
The quantitative characterization of endocytic vesicles in images acquired with microscope is critically important for deciphering of endocytosis mechanisms. Image segmentation is the most important step of quantitative image analysis. In spite of availability of many segmentation methods, the accurate segmentation is challenging when the images ar...
Background
Cis-regulatory sequences are often composed of many low-affinity transcription factor binding sites (TFBSs). Determining the evolutionary and functional importance of regulatory sequence composition is impeded without a detailed knowledge of the genotype-phenotype map. ResultsWe simulate the evolution of regulatory sequences involved in...
We present a novel tool for processing and analysis of images of gene expression patterns stored in a relational database. This tool, known as ImageServer, is portable across different software/hardware platforms and supports both basic and subject domain oriented operations on images. The tool is used to process and analyze images stored in FlyEx...
Differential Evolution Entirely Parallel (DEEP) package is a software for finding unknown real and integer parameters in dynamical models of biological processes by minimizing one or even several objective functions that measure the deviation of model solution from data. Numerical solutions provided by the most efficient global optimization methods...
This review deals with the recent studies expanding the idea of positional information in the early
embryogenesis of Drosophila melanogaster. Previous studies showed that, in the course of segment determination
in Drosophila, information created by gradients of products of maternal coordinate genes is not “read”
statically, being interpreted by the...
The statistical thermodynamics based approach provides a promising framework for construction of the genotype-phenotype map in many biological systems. Among important aspects of a good model connecting the DNA sequence information with that of a molecular phenotype (gene expression) is the selection of regulatory interactions and relevant transcri...
Supporting Information. Comparison figures.