Biology subjects

Nuzhdin, S.

Publications and source records attributed to Nuzhdin, S..

9 recordsLinked to original sources

bioRxiv2025

Insights from farming Macrocystis pyrifera offshore: phenotypic analysis, genome-wide association studies, genomic selection

Seaweed farming, as a part of aquaculture, offers a sustainable alternative to modern agricultural practices; however, genetic enhancement and breeding programs for most species are underdeveloped. We aimed to advance seaweed domestication by focusing on giant kelp (Macrocystis pyrifera), the fastest-growing haplodiplontic brown alga, which has significant ecological and commercial importance. We analyzed phenotypic data from two offshore experimental farms conducted in 2019 and 2020, which involved hundreds of outplanted genetically diverse sporophytes. We found that outplanting season and farm design had significant effects on giant kelp biomass. Broad-sense heritability estimates showed moderate (0.27-0.50) genetic contributions to two phenotypes, carbon content and total biomass. Genome-wide association studies for these phenotypes resulted in three statistically significant SNPs, located near or within genes involved in carbohydrate metabolism and cytoskeletal functions. In addition, we applied genomic selection models that integrated sporophyte phenotypes and parental gametophyte genotypes. These models utilized reduced sets of GWAS-ranked SNPs obtained by a procedure based on linkage disequilibrium estimations. Model testing yielded cross-validation accuracy values of up to 0.84 and predictive accuracy values of up to 0.40, demonstrating the potential of marker-assisted breeding for phenotype improvement. Our results provide foundational genomic resources and tools for domesticating and breeding M. pyrifera, offering a basis for developing giant kelp varieties with desirable traits.

genomics↗

bioRxiv2025

Phytohormones in Kappaphycus alvarezii: Genomic Insights, Activation Thresholds, and Implications for Seaweed-derived Biostimulants

The use of seaweed extracts in agriculture has gained significant attention in recent years, yet the genomic mechanisms underlying their activity remain poorly understood. Seaweeds such as Kappaphycus alvarezii synthesize diverse bioactive compounds, but their endogenous hormone pathways have been largely uncharacterized. Phytohormones, essential regulators of plant growth, reproduction, and stress responses, are central to the beneficial effects of these biostimulants. To uncover these mechanisms, we performed a genome-wide analysis of hormone biosynthesis and recognition pathways across thirteen algal species, focusing on nine classes of phytohormones. By integrating KEGG annotation, structural modeling, and eggNOG-based orthology, we assessed the completeness and conservation of hormone-associated pathways. Our results revealed consistent retention of key biosynthetic entry points, including IAM-related enzymes for auxin, TRIT1/CYP735A for cytokinins, GA oxidases for gibberellins, and pchA for salicylic acid, alongside divergent or absent canonical upstream enzymes. In parallel, partial but conserved signaling modules were identified for abscisic acid, ethylene, and other classes. This mosaic pattern, fragmented biosynthesis coupled with selectively retained signaling, suggests that algae employ noncanonical enzymatic routes or microbial complementation to sustain hormone activity. Expression profiling in K. alvarezii further revealed light-responsive regulation of auxin, cytokinin, GA, and ABA genes, highlighting their role in environmental adaptation. Together, these findings provide new genomic insights into algal hormone biology, establish the first structural and functional evidence for GA metabolism in red algae, and identify candidate phytohormones likely to contribute to the biostimulant activity of K. alvarezii extracts.

genomics↗

bioRxiv2022

Distinct selection signatures during domestication and improvement in crops: a tale of two genes in mungbean

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 compared the genetic footprints of domestication and improvement. The Asian wild population migrated to Australia at about 50 kya, and domestication happened in Asia about 9 kya selecting for non-shattering pods. The key candidate gene for this trait, VrMYB26a, has lower expression in cultivars, consistent with the reduced polymorphism in the promoter region reflecting hard selective sweep. The determinate stems were later selected as an improvement phenotype and associated with the gene VrDet1. Two ancient haplotypes reducing gene expression exhibit intermediate frequencies in cultivars, consistent with selection favoring independent haplotypes in soft selective sweep. Our results suggest domestication and improvement may leave different genomic signatures of selection, reflecting the fundamental differences in the two processes and highlighting the limitations of genome-scan methods relying on hard selective sweep.

plant biology↗

bioRxiv2022

The climatic constrains of the historical global spread of mungbean

While the domestication history has been investigated in many crops, the process 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 one thousand accessions to illustrate climatic adaptations role in dictating the unique routes of cultivation range expansion. Despite the geographical proximity between South and Central Asia, genetic evidence suggests mungbean cultivation first spread from South Asia to Southeast, East, and finally reached Central Asia. Combining evidence from demographic inference, climatic niche modeling, plant morphology, and records from ancient Chinese sources, we showed that the specific route was shaped by the unique combinations of climatic constraints and farmer practices across Asia, which imposed divergent selection favoring higher yield in the south but short-season and more drought-tolerant accessions in the north. Our results suggest that mungbean did not radiate from the domestication center as expected purely under human activity, but instead the spread of mungbean cultivation is highly constrained by climatic adaptation, echoing the idea that human commensals are more difficult to spread through the south-north axis of continents.

evolutionary biology↗

bioRxiv2021

Historical trade routes for diversification of domesticated chickpea inferred from landrace genomics

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 two market types: desi, which has a similar flower and seed coat color to chickpeas wild relatives; and kabuli, which has light-colored seed, and is linguistically tied to Central Asia but has an unknown geographic origin. Based on the genetic data from 421 chickpea landraces from six geographic regions, we tested complex historical hypotheses of chickpea migration and admixture on two levels: within and between major regions of cultivation. For the former, we developed popdisp, a Bayesian model of population dispersal from a regional center towards sample locations, and confirmed that chickpea spread within each region along trade routes rather than by simple diffusion. For the latter, migration between regions, we developed another model, migadmi, that evaluates multiple and nested admixture events. Applying this model to desi populations, we found both Indian and Middle Eastern traces in Ethiopian chickpea, suggesting presence of a seaway from South Asia to Ethiopia -- and the cultural legacy of the Queen of Sheba. As for the origin of kabuli chickpeas, we found significant evidence for an origin from Turkey rather than Central Asia.

plant biology↗

bioRxiv2018

Evolution of phenotypic plasticity in response to ethanol between sister species with different ecological histories (Drosophila melanogaster and D. simulans)

The contribution of phenotypic plasticity to adaptation is contentious, with contradictory empirical support for its role in evolution. Here I investigate the possibility that phenotype plasticity has contributed to adaptation to a novel resource. If phenotype plasticity contributes to adaptation, it is thought to evolve in a process termed genetic accommodation. Under this model, the initial response to the environment is widely variable due to cryptic genetic variation, which is then refined by selection to a single adaptive response. I examine the role of phenotypic plasticity in adaptation here by comparing two species of Drosophila that differ in their adaptation to ethanol (Drosophila melanogaster and D. simulans). Both species are human commensals with a recent cosmopolitan expansion, but only D. melanogaster is adapted to ethanol exposure. I measure phenotype plasticity in response to ethanol with gene expression and an approach that combines information about expression and alternative splicing. I find evidence for adaptation to ethanol through genetic accommodation, suggesting that the evolution of phenotype plasticity contributed to the ability of D. melanogaster to exploit a novel resource. I also find evidence that alternative splicing may be more important for the adaptive response to ethanol than overall changes in exon expression.

evolutionary biology↗

bioRxiv2017

Quantitative variation and evolution of spatially explicit morphogen expression in Drosophila

Robustness in development allows for the accumulation of neutral genetically based variation in expression, and here will be termed genetic stochasticity . This largely neutral variation is potentially important for both evolution and complex disease phenotypes. However, it has generally only been investigated as variation exhibited in the response to large genetic perturbations. In addition, work on variation in gene expression has similarly generally been limited to being spatial, or quantitative, but because of technical restrictions not both. Here we bridge these gaps by investigating replicated quantitative spatial gene expression using rigorous statistical models, in different genotypes, sexes, and species (Drosophila melanogaster and D. simulans). Using this type of quantitative approach with developmental data allows for effective comparison among conditions, including health versus disease. We apply this approach to the morphogenetic furrow, a wave of differentiation that sweeps across the developing eye disc. Within the morphogenetic furrow, we focus on four conserved morphogens, hairy, atonal, hedgehog, and Delta. Hybridization chain reaction quantitatively measures spatial gene expression, co-staining for all four genes simultaneously and with minimal effort. We find considerable variation in the spatial expression pattern of these genes in the eye between species, genotypes, and sexes. We also find that there has been evolution of the regulatory relationship between these genes. Lastly, we show that the spatial interrelationships of these genes evolved between species in the morphogenetic furrow. This is essentially the first population genetics of development as we are able to evaluate wild type differences in spatial and quantitative gene expression at the level of genotype, species and sex.

developmental biology↗

bioRxiv2017

Suppression of Transposable Elements in Leukemic Stem Cells

Genomic transposable elements (TEs) comprise nearly half of the human genome. The expression of TEs is considered potentially hazardous, as it can lead to insertional mutagenesis and genomic instability. However, recent studies have revealed that TEs are involved in immune-mediated cell clearance. Hypomethylating agents can increase the expression of TEs in cancer cells, inducing viral mimicry, causing interferon signalling and cancer cell killing. To investigate the role of TEs in the pathogenesis of acute myeloid leukaemia (AML), we studied TE expression in several cell fractions of AML while tracking its development (pre-leukemic haematopoietic stem cells, leukemic stem cells [LSCs], and leukemic blasts). LSCs, which are resistant to chemotherapy and serve as reservoirs for relapse, showed significant suppression of TEs and interferon pathways. Similarly, high-risk cases of myelodysplastic syndrome (MDS) showed far greater suppression of TEs than low-risk cases. We propose TE suppression as a mechanism for immune escape in AML and MDS. Repression of TEs co-occurred with the upregulation of several genes known to modulate TE expression, such as RNA helicases and autophagy genes. Thus, we have identified potential pathways that can be targeted to activate cancer immunogenicity via TEs in AML and MDS.

cancer biology↗

bioRxiv2017

Mapping Quantitative Trait Loci Underlying Circadian Light Sensitivity In Drosophila

Despite the significant advance in our understanding of the molecular basis of light entrainment of the circadian clock in Drosophila, the underlying genetic architecture is still largely unknown. The aim of this study was to identify loci associated with variation in circadian photosensitivity, which are important for the evolution of this trait. We have used complementary approaches that combined quantitative trait loci (QTL) mapping, complementation testing and transcriptome profiling to dissect this variation.\n\nWe identified a major QTL on chromosome 2, which was subsequently fine-mapped using deficiency complementation mapping into two smaller regions spanning 139 genes, some of which are known to be involved in functions which have been previously implicated in light entrainment. Two genes implicated with the clock and located within that interval, timeless and cycle, failed to complement the QTL, indicating that alleles of these genes contribute to the variation in light response. Specifically, we find that the timeless s/ls polymorphism that has been previously shown to constitute a latitudinal cline in Europe, is also segregating in our recombinant inbred lines, and is contributing to the phenotypic variation in light sensitivity.\n\nWe have also profiled gene expression in two recombinant inbred strains that differ significantly in their photosensitivity, and identified a total of 368 transcripts that showed differential expression (FDR < 0.1). Out of 131 transcripts that showed a significant RIL by treatment interaction (i.e. putative expression QTL), four are located within QTL2

genetics↗