Biology subjects

Fridman, E.

Publications and source records attributed to Fridman, E..

10 recordsLinked to original sources

bioRxiv2026

Beyond Averaging: Pleiotropic effects of Dry2.2 expose the evolution of growth bet-hedging in barley

RationaleDeveloping climate-resilient crops requires understanding the developmental and physiological mechanisms governing responses to unpredictable environmental stresses. While agricultural selection historically favored phenotypic uniformity, highly volatile conditions can favor risk-spreading "bet-hedging". However, because standard genetic mapping relies on shifting plot-level averages, loci controlling population-level variance remain cryptic. MethodsWe investigated the pleiotropic effects of the Dry2.2 quantitative trait locus (candidate gene HvCEN) using an allelic series of wild barley (Hordeum vulgare ssp. spontaneum) introgressions housed in distinct cultivated backgrounds, evaluated via high-resolution single-plant physiological phenotyping and mini-plot field trials. ResultsSpecific wild alleles confer robust developmental canalization under water limitation, maintain harvest traits, stabilize vascular lignification, and drive a uniform senescence escape strategy. Conversely, carriers of cultivated alleles deploy a bet-hedging strategy under stress, more than doubling inter-plant developmental variation (volume, maturity timing). This variance-driven strategy relies on epistatic interactions, rendering Dry2.2 invisible to traditional mean-centric GWAS plots. ConclusionImproving crop resilience in volatile climates requires expanding selection focus beyond static, plot-level averages to include the active genetic design of population-level variance strategies.

Plant Biology↗

bioRxiv2025

Prediction of harvest-related traits in barley using high-throughput phenotyping data and machine learning

Developing crop varieties that maintain productivity under drought is essential for future food security. Here, we investigated the potential of time-resolved high-throughput phenotyping to predict harvest-related traits and identify drought-stressed plants. Six barley lines (Hordeum vulgare) were grown in a greenhouse environment with well-watered and drought treatments, and phenotyped using RGB, thermal infrared, chlorophyll fluorescence and hyperspectral imaging sensors. Temporal phenomic classification model accurately distinguished between drought-treated and control plants, achieving high accuracy (R2 [≥] 0.97) even when exclusively using predictors only from the early phase after drought induction. Canopy temperature depression at the early stage and RGB-derived plant size estimates at the late stage were identified as key classification features. Temporal phenomic prediction model of harvest-related traits achieved particularly high mean R2 values for total biomass dry weight (0.97) and total spike weight (0.93), with RGB plant size estimators emerging as important predictors. Prediction accuracy for these traits remained high (R2 [≥] 0.84) when using only predictors from the first half of the experiment. Models trained on pooled drought and control data outperformed single-treatment models and retained high accuracy when applied across treatments. These findings support the integration of high-throughput phenotyping and temporal modelling to enable timely and more cost-effective selection of drought-resilient genotypes, and illustrate the broader potential of phenomics-driven approaches in accelerating crop improvement under stress-prone conditions.

plant biology↗

bioRxiv2025

Cytonuclear analysis of barley spike traits using a cytoplasm-aware population

The interplay between nuclear and cytoplasmic genomes--collectively known as cytonuclear interactions (CNIs)--is increasingly recognized as a key driver of phenotypic variation and adaptive potential across diverse organisms. Yet, leveraging cytoplasmic diversity and fully understanding CNIs contributions to agriculturally important traits remain major challenges in crop improvement, largely due to the scarcity of tailored genetic resources. In cultivated barley (Hordeum vulgare), limited genetic diversity relative to its wild relatives constrains adaptability to changing environments. While wild germplasm offers a reservoir of valuable alleles, the role of cytoplasmic variation and CNIs in shaping complex traits is still poorly understood. To address this gap, we present the Cytonuclear Multi-Parent Population (CMPP)--a novel interspecific resource comprising 951 BC2DH lines, generated from crosses between ten genetically diverse wild barley accessions (H. vulgare ssp. spontaneum) used as female founders and the elite cultivar Noga. This design facilitates the concurrent segregation and analysis of nuclear introgressions involving distinct wild versus cultivated cytoplasmic backgrounds from ten subfamilies. Phenotyping across multiple environments revealed that up to 5% of variation in key spike and grain trait BLUPs are explained by cytoplasm ({superscript 2} = 0.05), including Thousand Grain Weight (TGW), Grain Width (GW), and Fruiting Efficiency at Maturity (FEm). Notably, wild cytoplasms influenced trait stability, with the B1K-50-04 cytoplasm increasing TGW stability based on Shuklas measure. Genome-wide association studies (GWAS) employing Nested Association Mapping (NAM), FASTmrMLM, and MatrixEpistasis (ME) identified 76 marker-trait associations (MTAs). The ME approach specifically uncovered 16 cytonuclear QTL (cnQTL) exhibiting cytoplasm-dependent effects. Furthermore, we developed a genomic prediction (GP) strategy incorporating interactions between significant MTAs and population structure variables (subfamily and cytoplasm). This targeted interaction model ("Peaks + I") achieved cross-validation accuracies comparable to, or even exceeding, models using the full set of 6,679 SNPs, despite utilizing substantially fewer predictors, enabling quicker and more efficient validation runs. The CMPP provides a unique platform for dissecting cytoplasmic effects and CNIs, highlighting the importance of incorporating cytonuclear context in genetic mapping and prediction to effectively harness both nuclear and cytoplasmic diversity for crop improvement.

genetics↗

bioRxiv2025

Extensive photophysiological variation in wild barley is linked to environmental origin

O_LIIntraspecific variation between crop wild relatives (CWRs) represents a source of untapped genetic diversity for crop improvement. At the same time, improving photosynthesis in crops has the potential to enhance yield. Thus, exploring variation for photophysiology within CWRs is an important, yet underexplored, research area. C_LIO_LIWe describe a common garden experiment where 320 wild barley accessions were grown across two seasons. A photophysiology phenotyping pipeline was employed to quantify >30 traits within this diversity panel. Population genetics, genome-wide association analyses (GWAS) and deep phenotyping were performed to address local adaptation hypotheses. C_LIO_LIHeritable variation was detected across this photophysiological spectrum, with genotype-by-environment (GxE) interactions being prevalent. Evidence for local adaptation was observed in the form of subpopulation differences, signals of selection, and allele frequency variation associated to markers identified via GWAS. Phenotyping of representative accessions across distinct water availabilities highlighted a role for stomatal conductance (gs) in adaptation to dry environments. C_LIO_LIWe identified substantial variation in key photosynthesis-associated traits in a CWR closely related to barley, an economically important crop species. Our results demonstrate that this variation is partially due to local adaptation, where plasticity in gs appears important for maintaining photosynthesis and biomass accumulation in water restricted conditions. C_LI

plant biology↗

bioRxiv2021

Plasmotype condition nuclear pleiotropic effects on clock and fitness in barley

In plants, the role of chloroplasts and mitochondria (plasmotype) in controlling circadian clock plasticity and overall plant robustness has not been elucidated. In this study, we investigated the rhythmicity of chlorophyll fluorescence (Chl F) clock output, and fitness in the field at optimal and elevated temperatures, in three different barley populations. First, we examined a reciprocal DH population between two wild barley (Hordeum vulgare ssp. spontaneum), in which we identified two pleiotropic QTLs (frp2.1 and amp7.1) that modulate clock and fitness including conditioning of these effects by plasmotype diversity. In the second population, a complete diallel consisting of 11 genotypes (reciprocal hybrids differing in plasmotype), we observed a gradual reduction in plasmotype, ranging from 26% and 15% for Chl F and clock measurements to 5.3% and 3.7% for growth and reproductive traits, respectively. The third population studied was a collection of cytolines in which nine different wild plasmotypes replaced the cultivated Noga (H. vulgare) plasmotype. Here, the order and magnitude of the effects of the plasmotypes differed from what we observed in the diallel population, with the greatest effect of plasmotype diversity observed for clock period and amplitude. Comparison of the chloroplast sequences suggests several candidate genes in the plastid-encoded RNA polymerase (PEP) complex that may be responsible for the observed plasmotype effects. Overall, our results unravel previously unknown cytonuclear epistatic interactions that controls clock performance while also having pleiotropic effects on a plant field characteristics.

plant biology↗

bioRxiv2021

Physical geography, isolation by distance and environmental variables shape genomic variation of wild barley (Hordeum vulgare L. ssp. spontaneum in the Southern Levant

Determining the extent of genetic variation that reflects local adaptation in crop wild relatives is of interest to discovering useful genetic diversity for plant breeding. We investigated the association of genomic variation with geographical and environmental factors in wild barley (Hordeum vulgare L. ssp. spontaneum) populations of the Southern Levant using genotyping-by-sequencing (GBS) of 244 accessions of the Barley1K+ collection. Inference of population structure resulted in four genetic clusters that corresponded to eco-geographical habitats and a significant association of lower gene flow rates with geographical barriers, e.g. the Judaean Mountains and the Sea of Galilee. Redundancy analysis (RDA) revealed that spatial autocorrelation explained 45% and environmental variables explained 15% of total genomic variation. Only 4.5% of genomic variation was exclusively attributed to environmental variation if the component confounded with spatial autocorrelation was excluded. A synthetic environmental variable combining latitude, solar radiation, and accumulated precipitation explained the highest proportion of genomic variation (3.9%). After correcting for population structure, soil water capacity was the most important environmental variable explaining 1.18% of genomic variation. Genome scans with outlier analysis and genome-environment association studies were conducted to identify signatures of adaptation. RDA and outlier methods jointly detected selection signatures in the pericentromeric regions of chromosome 3H, 4H, and 5H, but they mostly disappeared after correction for population structure. In conclusion, adaptation to the highly diverse environments of the Southern Levant over short geographical ranges has a small effect on the genomic diversity of wild barley highlighting the importance of non-selective forces in genetic differentiation.

evolutionary biology↗

bioRxiv2020

Loss of Photosynthetic Rhythm Thermal Plasticity Under Domestication and RepurposingDrivers of Circadian Clock (DOC) Loci for Adaptive Breeding in Barley

Circadian clock rhythms are critical to control physiological and development traits, allowing, plants to adapt to changing environments. Here we show that the circadian rhythms of cultivated barley (Hordeum vulgare) have slowed and amplitude increased under domestication by comparing with its wild ancestor (H. spontaneum). Moreover, we show a significant loss of thermal plasticity during barley evolution for the period and more extensively for amplitude. Our genetic analysis indicates that wild allele at epistatic loci, which mutually condition clock variation and its thermal plasticity in interspecific crosses, are absent in a contemporary barley breeding panel. These epistatic interactions include conditioned effects of Drivers of Circadian (DOC) clock loci on chromosome 3 and 5, which mediate amplitude decrease and period lengthening, respectively, under domestication. Notably, two significant loci, DOC3.1 and DOC5.1, which are not associated with clock diversity in cultivated breeding material, do show pleiotropic effects on flowering time and grain yield at multiple experimental sites across the U.S. in a temperature-dependent manner. We suggest that transition from winter growth of wild barley (H. spontaneum) to spring growth of modern cultivars included the loss and repurposing of circadian clock regulators to yield adaptation by mechanisms yet to be clarified. Significance statementCircadian clock rhythms are crucial factors affecting crop adaptation to changing environments. If faced with increased temperature plants could respond with temperature compensation adaptation and maintain clock rhythms, or they can change period and/or amplitude to adapt. We used a combination of approaches: high-throughput clock analysis under optimal and elevated heat conditions, genome-wide association study (GWAS) with cultivated and wild diversity panels to identify changes under domestication and quantitative trait loci (QTL) that control the clock and its responses, and QTL-environment association for testing environmentally-conditioned effects of these QTLongrain yield and flowering timingacross US. Our findings provide insights into changes of circadian rhythms under domestication and genetic tools for plant breeders to develop better-adapted cultivars to changing environments.

genetics↗

bioRxiv2020

RECAS9: Recombining wild species introgression via mitotic gene editing in barley

Genetic loci underlying variation in traits with agronomic importance or genetic risk factors in human diseases have been identified by linkage analysis and genome-wide association studies. However, narrowing down the mapping to the individual causal genes and variations within these is much more challenging, and so is the ability to break linkage drag between beneficial and unfavourable loci in crop breeding. We developed RECAS9 as a transgene-free approach for precisely targeting recombination events by delivering CRISPR/Cas9 ribonucleotide protein (RNP) complex into heterozygous mitotic cells for the barley (Hordeum vulgare) Heat3.1 locus. A wild species (H. spontaneum) introgression in this region carries the agronomical unfavourable tough rachis phenotype (non-brittle) allele linked with a circadian clock accelerating QTL near GIGANTEA gene. We delivered RNP, which was targeted between two single nucleotide polymorphism (SNPs), to mitotic calli cells by particle bombardment. We estimated recombination events by next generation sequencing (NGS) and droplet digital PCR (ddPCR). While NGS analysis grieved from confounding effects of PCR recombination, ddPCR analysis allowed us to associate RNP treatment on heterozygous individuals with significant increase of homologous directed repair (HDR) between cultivated and wild alleles, with recombination rate ranging between zero to 57%. These results show for the first time in plants a directed and transgene free mitotic recombination driven by Cas9 RNP, and provide a starting point for precise breeding and fine scale mapping of beneficial alleles from crop wild relatives.

genetics↗

bioRxiv2018

Thermal plasticity of the circadian clock is under nuclear and cytoplasmic control in wild barley

Temperature compensation, expressed as the ability to maintain clock characteristics (mainly period) in face of temperature changes, is considered a key feature of circadian clock systems. In this study, we explore the genetic basis for circadian clock plasticity under high temperatures by utilizing a new doubled haploid (DH) population derived from two reciprocal Hordeum vulgare sps. spontaneum hybrids genotypes (crosses between B1K-50-04 and B1K-09-07). Genotyping by sequencing of DH lines indicated a rich recombination landscape, with minor fixation (less than 8%), for one of the parental alleles, yet with prevalent and varied segregation distortion across seven barley chromosomes. Phenotyping was conducted with a high-throughput platform under optimal and high temperature environments. Genetic analysis, which included QxE and binary-threshold models, identified a significant influence of the maternal organelle genome (the plasmotype), as well as several nuclear quantitative trait loci (QTL), on clock phenotypes (free-running period and amplitude). Moreover, it showed the differential contribution of cytoplasmic genome clock rhythm buffering against high temperature. Resequencing of the parental chloroplast indicated the presence of several candidate genes underlying these significant effects. This first reported plasmotype-driven clock plasticity paves the way for identifying an hitherto unknown impact of nuclear and plasmotype variations on clock robustness and on plant adaptation to changing environments.\n\nHighlightCircadian clock robustness to high temperature is controlled by nuclear and plasmotype quantitative trait loci in a wild barley (Hordeum vulgare ssp. spontaneum) reciprocal doubled haploid population.

genetics↗

bioRxiv2017

Genome scan identifies flowering-independent effects of barley HsDry2.2 locus on yield traits under water deficit

Increasing crop productivity under climate change requires the identification, selection and utilization of novel alleles for breeding. We analyzed the genotype and field phenotype of the barley HEB-25 multi-parent mapping population under well-watered and water-limited (WW and WL) environments for two years. A genome-wide association study (GWAS) for genotype by-environment interactions was performed for ten traits including flowering time (HEA), plant grain yield (PGY). Comparison of the GWAS for traits per-se to that for QTL-by-environment interactions (QxE), indicates the prevalence of QxE mostly for reproductive traits. One QxE locus on chromosome 2, Hordeum spontaneum Dry2.2 (HsDry2.2), showed a positive and conditional effect on PGY and grain number (GN). The wild allele significantly reduced HEA, however this earliness was not conditioned by water deficit. Furthermore, BC2F1 lines segregating for the HsDry2.2 showed the wild allele confers an advantage over the cultivated in PGY, GN and harvest index as well as modified shoot morphology, longer grain filling period and reduced senescence (only under drought), therefore suggesting adaptation mechanism against water deficit other than escape. This study highlights the value of evaluating wild relatives in search of novel alleles and clues to resilience mechanism underlying crop adaptation to abiotic stress.\n\nHighlightA flowering-time independent reproductive advantage of wild over cultivated allele under drought identified in a barley GWAS for genotype-by-environment interactions, with modified shoot morphology, reduced senescence and longer grain filling

genetics↗