Biology subjects

Eizenberg, H.

Publications and source records attributed to Eizenberg, H..

7 recordsLinked to original sources

bioRxiv2025

Wild genes to the rescue: High-throughput genomics uncovers the wild source of broomrape resistance in sunflower

O_LIThe ongoing evolutionary arms race between crop plants and their parasites necessitates a constant exploration of new genetic resistance. Broomrape (Orobanche cumana), a devastating parasitic plant, presents a formidable challenge to sunflower production, yet the genetic mechanisms underlying host resistance are still largely unknown. C_LIO_LITo address this gap, we developed a high-throughput phenotyping platform to quantify root infestation in a highly diverse sunflower association mapping (SAM) population. Using a dual GWAS approach with both SNPs and k-mers, we were able to pinpoint the genetic basis of resistance. C_LIO_LIOur findings validate previously identified QTLs with greater resolution and reveal several novel candidate genes conferring resistance, including putative leucine-rich repeat receptor kinases. Critically, the k-mer mapping approach circumvented reference genome bias, highlighting key introgressions from wild Helianthus species that have contributed to broomrape resistance. C_LIO_LIThis research provides a powerful methodology for gene discovery and demonstrates that wild relatives remain a vital source of genetic material, offering breeders a significant advantage in the ongoing battle against rapidly evolving parasites. C_LI

plant biology↗

bioRxiv2023

A metabolic modeling-based framework for predicting trophic dependencies in native rhizobiomes of crop plants

The exchange of metabolites (i.e., metabolic interactions) between bacteria in the rhizosphere determines various plant-associated functions. Systematically understanding the metabolic interactions in the rhizosphere, as well as in other types of microbial communities, would open the door to the optimization of specific pre-defined functions of interest, and therefore to the harnessing of the functionality of various types of microbiomes. However, mechanistic knowledge regarding the gathering and interpretation of these interactions is limited. Here, we present a framework utilizing genomics and constraint based modeling approaches, aiming to interpret the hierarchical trophic interactions in the soil environment. 243 genome-scale metabolic models of bacteria associated with a specific disease suppressive vs disease conducive apple rhizospheres were drafted based on genome resolved metagenomes, comprising an in-silico native microbial community. Iteratively simulating microbial community members growth in a metabolomics-based apple root-like environment produced novel data on potential trophic successions, used to form a network of communal trophic dependencies. Network-based analyses have characterized interactions associated with beneficial vs non-beneficial microbiome functioning, pinpointing specific compounds and microbial species as potential disease supporting and suppressing agents. This framework provides a means for capturing trophic interactions and formulating a range of testable hypotheses regarding the metabolic capabilities of microbial communities within their natural environment. Essentially, it can be applied to different environments and biological landscapes, elucidating the conditions for the targeted manipulation of various microbiomes, and the execution of countless predefined functions.

microbiology↗

bioRxiv2023

Occurrence of Amaranthus palmeri in Israeli agriculture: status of spread and response to glyphosate and trifloxysulfuron

Amaranthus palmeri S. Watson is a dioecious annual weed species, originating from the Southern USA, spreading rapidly beyond its original range into Europe and the Mediterranean region. In Israel, A. palmeri distribution has expanded quickly in recent years, with farmers reporting on weed control failure using acetolactate synthase (ALS) inhibitors. Furthermore, recent studies have documented glyphosate-resistant cases from other countries in the region, such as Spain, Greece, and Turkey. We conducted a survey in order to understand A. palmeri distribution and study the occurrence of herbicide resistance to both glyphosate and trifloxysulfuron in different fields across the country. According to our data, A. palmeri population locations are aligned with the major agricultural areas for summer field crops, including the Hula Valley, Jezreel Valley, and the Southern Coastal Plain. Regarding herbicide responses, while several populations showed a reduced response to glyphosate, dose-response assays did not show resistance to the recommended labeled field rate. For the ALS inhibitor trifloxysulfuron, the proportion of resistant individuals was very high, especially in the southern coastline region, with an R-value of 0.77. Four populations used for dose-response studies were highly resistant, surviving at four times the recommended labeled field rate of trifloxysulfuron (30 g a.i. ha-1). Sequencing of the ALS gene, Trp574 to Leu alteration in resistant populations was recorded. The high level of resistance observed in this study, alongside the target-site mutation found in populations of A. palmeri, endangers the future use of ALS inhibitors in corn, cotton, and other summer crops grown in Israel.

plant biology↗

bioRxiv2022

An Orobanche cernua x Orobanche cumana segregating population provides insight into the regulation of germination specificity in a parasitic plant

Germination of seeds of Orobanche species requires specific chemicals exuded by host roots. A family of "divergent" KARRIKIN INSENSITIVE2 (KAI2d) genes encode proteins that recognize strigolactone (SL) class germination simulants. We explored specificity of germination stimulant detection by analyzing interspecific segregants of a cross between Orobanche cernua and O. cumana, closely related species that differ in stimulant response. O. cernua parasitizes tomato and germinates in response to the SL orobanchol, while O. cumana parasitizes sunflower and responds to dehydrocostus lactone (DCL). KAI2d genes were catalogued in parents and in segregants that showed stimulant specificity. KAI2d genes were also functionally assayed in the Arabidopsis kai2 mutant background. We identified five full-length KAI2d genes in O. cernua and eight in O. cumana. The O. cernua KAI2d2, as well as its ortholog in O. cumana, are associated with SL perception. A cluster of O. cumana KAI2d genes was genetically linked to DCL perception, although no specific receptor gene was identified by heterologous complementation. These findings support the KAI2d-mediated perception of SLs, but fall short of explaining how O. cumana perceives DCL. The ability of some O. cumana KAI2d genes to detect SLs points to the involvement of additional factors in regulating stimulant specificity.

plant biology↗

bioRxiv2019

Development of specific molecular markers to distinguish and quantify broomrape species in a soil sample from infected field

Broomrapes (Orobanche and Phelipanche) are obligate holoparasites that cause heavy damage to numerous crops, reducing the yield and its quality. The parasite develops in the soil and exerts the greatest damage prior to its emergence; therefore the majority of field loss may occur before diagnosis of infection. Because of the parasite tiny seed size (200 to 300 m) and dormancy for several decades in the field, it is very difficult to diagnose the parasite by conventional methods. Therefore, to restrict the parasite seeds spread and contamination to other commercial fields, development of DNA-based molecular markers to identify and quantify broomrape species in a soil sample is much needed. In this study, we developed a specific molecular marker (RbcL-M) based on rbcL (large subunit of the ribulose-bisphosphate carboxylase) gene from Orobanche crenata to differentiate between Orobanche crenata and Orobanche cumana. Likewise, a specific marker (ITS100) based upon unique sequences in the internal transcribed spacer (ITS) regions of the nuclear ribosomal DNA of Phelipanche aegyptiaca to quantify three species of the parasite (P. aegyptiaca, O. crenata and O. cumana) in a soil sample was developed. Genomic DNA was extracted from soil samples artificially infested with broomrape seeds or tissue of P. aegyptiaca, O. cumana and O. crenata and subjected to PCR analysis. RbcL-M marker successfully amplified a PCR product (1300bp) when O. crenata seeds or tissues (collected from several locations in Israel) were added to the soil samples. The same marker amplified a PCR product (1000bp) when O. cumana seeds or tissues were added to the soil samples. RbcL-M marker did not amplify soil samples with seeds or tissues of P. aegyptiaca or any soil-borne DNA. Furthermore, using ITS-100 marker and Real-Time PCR analysis, allowed quantitative diagnostic of the parasite in a soil sample from infected sunflower field. As expected the universal internal control primer (UCP-555) amplified a PCR product (555bp) when genomic DNA extracted from soil samples with or without broomrape tissues. The development of an efficient, simple and robust molecular marker to detect and distinguish between broomrape species, has a significant insights on assessment the level of infestation and planning eradication program to the parasite in a field crop.

molecular biology↗

bioRxiv2019

Genome-Scale reconstruction of Paenarthrobacter aurescens TC1 metabolic model towards the study of atrazine bioremediation

Atrazine is an herbicide and pollutant of great environmental concern that is naturally biodegraded by microbial communities. The efficiency of biodegradation can be improved through the stimulating addition of fertilizers, electron acceptors, etc. In recent years, metabolic modelling approaches have become widely used as an in silico tool for organism-level phenotyping and the subsequent development of metabolic engineering strategies including biodegradation improvement. Here, we constructed a genome scale metabolic model, iRZ960, for Paenarthrobacter aurescens TC1 - a widely studied atrazine degrader - aiming at simulating its degradation activity. A mathematical stoichiometric metabolic model was constructed based on a published genome sequence of P. aurescens TC1. An Initial draft model was automatically constructed using the RAST and KBase servers. The draft was developed into a predictive model through semi-automatic gap-filling procedures including manual curation. In addition to growth predictions under different conditions, model simulations were used to identify optimized media for enhancing the natural degradation of atrazine without a need in strain design via genetic modifications. Model predictions for growth and atrazine degradation efficiency were tested in myriad of media supplemented with different combinations of carbon and nitrogen sources that were verified in vitro. Experimental validations support the reliability of the models predictions for both bacterial growth (biomass accumulation) and atrazine degradation. Predictive tools, such as the presented model, can be applied for achieving optimal biodegradation efficiencies and for the development of ecologically friendly solutions for pollutant degradation in changing environments.

bioinformatics↗

bioRxiv2018

Use of a visible reporter marker- myb-related gene in crop plants to minimize herbicide usage against weeds

Weeds, a main threat to agricultural productivity worldwide, are mostly controlled by herbicides. To minimize herbicide usage by targeting it to weedy areas, we developed a new image-based methodology for robust weed detection that relies on manipulating the crop plants leaf hue, without affecting crop fitness. We generated transgenic tobacco (Nicotiana tabacum Xanthi) lines overexpressing anthocyanin pigment as a traceable marker that differentiates transgenes from the surrounding weeds at an early stage. Transformation with the anthocyanin VlmybA1-2 gene produced purple-colored leaves. Subsequent gene silencing with vector pTRV2:VlmybA1-2 significantly reduced anthocyanin pigments in tobacco leaves 40 days after agroinfiltration, with a concomitant reduction in VlmybA1-2 transcript levels. Purple hue faded gradually, and there were no fitness costs in terms of plant height or leaf number in the silenced vs. non-silenced tobacco transgenes. These results could lead to a new sustainable weed-control method that will alleviate weed-related ecological, agricultural and economic issues.

plant biology↗