Biology subjects

Mandel, T.

Publications and source records attributed to Mandel, T..

7 recordsLinked to original sources

bioRxiv2025

Genome size variation is attributed to adaptive purging of transposable elements

A substantial variation in genome size has been observed among individuals of the same species. Theory predicts that increased genome size may confer an advantage in populations with small effective size. However, contradictory evidence for the correlation with environmental variation, and limited understanding of the underlying genetic mechanisms, has cast doubts on the adaptive role of genome size variation. To address this, we studied two Hordeum species which were collected at the same sites along a wide range of environments but different in life habit (annual/perrenial) and mating strategy (self/out-crossing). We observed significant variation in genome size, with differences of up to 10% consistently detected in both species. Mating system influenced only the proportion of variation maintained within populations but not the overall range of genome size. In both species, drought emerged as the primary environmental factor associated with genome expansion, with transposable elements (TE) accumulation identified as the main driver of this expansion. Genome-wide association studies revealed that TE silencing is the key mechanism regulating genome size, and that selection favors smaller genomes among individuals growing at suitable habitats. Under increasingly stressful conditions, the regulation of TE activity fades, leading to TE accumulation and genome expansion, thereby increasing genetic variation available for selection. This integrative study provides a comprehensive view of how genome size is regulated in natural populations and highlights its exaptive role in inducing genetic variation under environmental stress.

evolutionary biology↗

bioRxiv2024

Transposable elements are entangled in rapid adaptation to climate change

Biodiversity conservation is urged at biodiversity hotspots that are under constant threat from anthropogenic development, yet a careful examination of the adaptive potential is a prerequisite for action. The Levant is considered a biodiversity hotspot and the distribution edge for many species, including important crop wild relatives. This region is under accelerated desertification and constantly disturbed by human activities, thus urging intervenient action. We collected and sequenced 300 wild barley plants along an eco-geographic gradient following a unique ecological-genetic sampling design. This scheme enabled to overcome the tight correlation between environmental and geographic distances. Phenotypic data was collected from 3600 progeny plants over three years and enabled to identify adaptive haplotype blocks comprised of phenological regulating genes tightly linked to drought and heat responsive genes. These haplotype blocks were highly enriched for transposable elements insertions, likely regulating genetic variation around adaptive genes, especially in stressed populations. Ecological and evolutionary models using over 2600 observations were combined to predict maladaptive risk, indicating that populations will be funneled into higher water availability refugia habitats while increasing isolation. Our findings highlight the main factors affecting rapid local adaptation and provide important recommendations for biodiversity management and conservation.

plant biology↗

bioRxiv2023

Rectus Femoris Muscle Elasticity and Stiffness Correlates with Maximal Oxygen Consumption in Triathletes

VO2max is considered single best indicator of cardiovascular fitness and aerobic endurance. We analyzed retrospectively, are there any relationships between muscle parameters and oxygen consumption in a study where the myoton equipment was used to establish muscle biomechanical properties, such as elasticity, stiffness, and tension (measured as oscillation frequency) in triathletes. Eight muscles were studied in 14 male triathletes over three years. Relaxed and contracted states of muscles were measured. VO2max was recorded in these athletes up to four times during this period. Average values were calculated for each athlete and High (max 71.8-min 62.3 ml/kg/min) and Low (59.1-51.3) oxygen consumption groups were formed. Higher oxygen consumption correlated significantly (r=-0.58; p=0.029) with improved elasticity (represented by smaller decrement values) of the rectus femoris muscle in a contracted state. Also, in the High VO2max group, this muscle (in a relaxed state) was significantly more elastic and stiffer at the same time compared to the Low group. An ultrasound registration was also conducted to observe the depth of the devices impact in the posterior crural muscles. It was confirmed that deep and substantial tissue disturbances were caused by this impact. According to our findings, myotonometry is an adequate method to establish muscle parameters. Elasticity and stiffness of the rectus femoris muscle may determine success in triathlon.

physiology↗

bioRxiv2022

The genomics of linkage drag in sunflower

Crop wild relatives represent valuable sources of alleles for crop improvement, including adaptation to climate change and emerging diseases. However, introgressions from wild relatives might have deleterious effects on desirable traits, including yield, due to linkage drag. Here we comprehensively analyzed the genomic and phenotypic impacts of wild introgressions into cultivated sunflower to estimate the impacts of linkage drag. First, we generated new reference sequences for seven cultivated and one wild sunflower genotype, as well as improved assemblies for two additional cultivars. Next, relying on previously generated sequences from wild donor species, we identified introgressions in the cultivated reference sequences, as well as the sequence and structural variants they contain. We then used a ridge regression model to test the effects of the introgressions on phenotypic traits in the cultivated sunflower association mapping population. We found that introgression has introduced substantial sequence and structural variation into the cultivated sunflower gene pool, including > 3,000 new genes. While introgressions reduced genetic load at protein-coding sequences and positively affected traits associated with abiotic stress resistance, they mostly had negative impacts on yield and quality traits. Introgressions found at high frequency in the cultivated gene pool had larger effects than low frequency introgressions, suggesting that the former likely were targeted by artificial selection. Also, introgressions from more distantly related species were more likely to be maladaptive than those from the wild progenitor of cultivated sunflower. Thus, pre-breeding efforts should focus, as far as possible, on closely related and fully compatible wild relatives.

genomics↗

bioRxiv2022

The H3K27me3 epigenetic mark is crucial for callus cell identity and for the acquisition of new fate during root and shoot regeneration

We combined molecular, genomic and genetic approaches to study the molecular mechanisms underlying cell totipotency and competency to regenerate in Arabidopsis. By performing comparative analysis of mRNA-seq and chromatin landscapes between leaf differentiated cells and callus totipotent cells and between WT callus and calli derived from the emf2 mutant, exhibiting impaired regenerative capacity we revealed the following: 1. That callus cells express numerous genes of many developmental pathways such as root, leaf, embryo, shoot, meristem and seed. This suggests a mechanism to allow rapid response to a signal by maintaining genes of all potential developmental pathways active, without the needs to release transcriptional silencing and to go through the intricate multistep process of transcription. 2. That key transcription factors that are sufficient to derive differentiation or organogenesis are silenced and marked by the H3K27me3. 3. That callus derived from the emf2 mutant which is impaired in setting the H3K27methylation, lost the capacity to regenerate and that 78 transcription factors from which 18 regulate flower development, where up-regulated compared with WT callus. Altogether our results suggest that competency to regenerate is achieved by keeping the chromatin of developmental genes active, and that upon a signal for cell fate switch, a mechanism to repress those genes is required to allow the one desired developmental pathway to dominate. When this mechanism is impaired the capacity to regenerate is decline.

developmental biology↗

bioRxiv2021

Decoupling the molecular regulation of perenniality and flowering in bulbous barley (Hordeum bulbosum)

Global crop production is being challenged by rapid population growth, declining natural resources, and dramatic climatic turnovers. These challenges have prompted plant breeders to explore new ventures to enhance adaptation and sustainability in crops. One intriguing approach to make agriculture more sustainable is by turning annual systems into perennial which offers many economic and biodiversity-friendly benefits. Previous attempts to develop a perennial cereal crop employed a classical breeding approach and extended over a long period with limited success. Thus, elucidating the genetic basis of perenniality at the molecular level can accelerate the breeding process. Here, we investigated the genetic basis of bulb formation in the barley congener species Hordeum bulbosum by elucidating the transcripts presence/absence variation compared with other annual species in the Poaceae, and a differential expression analysis of meristem tissues. The PAV analysis recaptured the expected phylogeny and indicated that H. bulbosum is enriched with developmental and disease responsive genes that are absent among annual species. Next, the abundance of transcripts was quantified and allowed to identify differentially expressed genes that are associated with bulb formation pathways in addition to major circadian clock genes that regulate flowering. A first model for the bulb formation pathway is suggested and include developmental and starch biosynthesis genes. To the best of our knowledge this is the first transcriptome developed for H. bulbosum and the first attempt to describe the regulation of bulb initiation in cereals at the molecular level.

plant biology↗

bioRxiv2021

Image processing and genome-wide association studies in sunflower identify loci associated with seed-coat characteristics

Sunflower seeds (technically achenes) are characterized by a wide spectrum of sizes, shapes, and colors. These traits are genetically correlated with the branching plant architecture loci, which were introgressed into restorer lines to facilitate efficient hybrid production. To break this genetic correlation between branching and seed traits, high resolution mapping of the genes that regulate seed traits is necessary. Recent progress in genomics permits acquisition of comprehensive genotyping data for a large diversity panel, yet a major constraint for exploring the genetic basis of important phenotypes across large diversity panels is the ability to screen and characterize them efficiently. Here, we implement a cost-effective image analysis pipeline to phenotype seed characteristics in a large sunflower diversity panel comprised of 287 individuals that represents most of the genetic variation in cultivated sunflower. A genome-wide association analysis was performed for seed-coat size and shape traits and significant signals were identified around genes regulating phytohormone activity. In addition, significant seed-coat color QTLs were identified and candidate genes that effect pigmentation were detected including a phytomelanin regulating gene on chromosome 17. Finally, QTLs associated with the seed-coat striped pattern were identified and phytohormone regulating candidate genes were detected. The implementation of image analysis phenotyping for GWAS allowed efficient screening of a large diversity panel and identification of valuable genetic factors effecting seed characteristics at the finest resolution to date.

genetics↗