Search

Chickpea is a staple crop for many nations worldwide. Modeling genotype-by-environment interactions and assessing the genotype’s ability to contribute adaptive alleles are crucial for chickpea breeding. In this study, we evaluated 12 agronomically important traits of 159 accessions from the N.I. Vavilov All Russian Institute for Plant Genetic Resources collection. These included 145 landraces and 13 cultivars grown in different climatic conditions in Kuban (45°18′ N and 40°52′ E) in both 2016 and 2022, as well as in Astrakhan (46°06′ N and 48°04′ E) in 2022. Using the IIIVmrMLM model in multi-environmental mode, we identified 161 quantitative trait nucleotides (QTNs) with stable genetic effects across different environments. Furthermore, we have observed 254 QTN-by-environment interactions with distinct environment-specific effects. Notably, five of these interactions manifested large effects, with R2 values exceeding 10%, while the highest R2 value for stable QTNs was 4.7%. Within the protein-coding genes and their 1 Kb flanking regions, we have discerned 22 QTNs and 45 QTN-by-environment interactions, most likely tagging the candidate causal genes. The landraces obtained from the N.I Vavilov All Russian Institute for Plant Genetic Resources collection exhibit numerous favorable alleles at quantitative trait nucleotide loci, showing stable effects in the Kuban and Astrakhan regions. Additionally, they possessed a significantly higher number of Kuban-specific favorable alleles of the QTN-by-environment interaction loci compared to the Astrakhan-specific ones. The environment-specific alleles found at the QTN-by-environment interaction loci have the potential to enhance chickpea adaptation to specific climatic conditions.

At least 50% of factors predisposing to alcohol dependence (AD) are genetic and women affected with this disorder present with more psychiatric comorbidities, probably indicating different genetic factors involved. We aimed to run a genome-wide association study (GWAS) followed by a bioinformatic functional annotation of associated genomic regions in patients with AD and eight related clinical measures. A genome-wide significant association of rs220677 with AD (p-value = 1.33 × 10−8 calculated with the Yates-corrected χ2 test under the assumption of dominant inheritance) was discovered in female patients. Associations of AD and related clinical measures with seven other single nucleotide polymorphisms listed in previous GWASs of psychiatric and addiction traits were differently replicated in male and female patients. The bioinformatic analysis showed that regulatory elements in the eight associated linkage disequilibrium blocks define the expression of 80 protein-coding genes. Nearly 68% of these and of 120 previously published coding genes associated with alcohol phenotypes directly interact in a single network, where BDNF is the most significant hub gene. This study indicates that several genes behind the pathogenesis of AD are different in male and female patients, but implicated molecular mechanisms are functionally connected. The study also reveals a central role of BDNF in the pathogenesis of AD.

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) and nonautonomous (e.g., Alu), may lead to fluctuations in the number of these transposons in the genome over multiple cell generations. We developed and examined a simple model of retrotransposon dynamics under conditions where transposon replication machinery competed for cellular resources: namely, free ribosomes and available energy (i.e., ATP molecules). Such competition is likely to occur in stress conditions that a malfunctioning cell may experience as a result of a malignant transformation. The modeling revealed that the number of actively replicating LINE1 and Alu elements in a cell decreases with the increasing competition for resources; however, stochastic effects interfere with this simple trend. We stochastically simulated the transposon dynamics in a cell population and showed that the population splits into pools with drastically different transposon behaviors. The early extinction of active Alu elements resulted in a larger number of LINE1 copies occurring in the first pool, as there was no competition between the two types of transposons in this pool. In the other pool, the competition process remained and the number of L1 copies was kept small. As the level of available resources reached a critical value, both types of dynamics demonstrated an increase in noise levels, and both the period and the amplitude of predator–prey oscillations rose in one of the cell pools. We hypothesized that the presented dynamical effects associated with the impact of the competition for cellular resources inflicted on the dynamics of retrotransposable elements could be used as a characteristic feature to assess a cell state, or to control the transposon activity.