Search bioRxiv⌕ Search

Biology subjects

Samach, A.

Publications and source records attributed to Samach, A..

2 recordsLinked to original sources

Olive Flowering dependence on winter temperatures - linking empirical results to a dynamic model

Increasing winter temperatures jeopardize the yield of fruit trees requiring a prolonged and sufficiently cold winter to flower. Assessing the exact risk to different crop varieties is the first step in mitigating the harmful effect of climate change. Since empirically testing the impacts of many temperature scenarios is very time-consuming, quantitative predictive models could be extremely helpful in reducing the number of experiments needed. Here, we focus on olive (Olea europaea) - a traditional crop in the Mediterranean basin, a region expected to be severely affected by climatic change. Olive flowering and consequently yield depend on the sufficiency of cold periods and the lack of warm ones during the preceding winter. Yet, a satisfactory quantitative model forecasting its expected flowering under natural temperature conditions is still lacking. Previous models simply summed the number of cold hours during winter, as a proxy for flowering, but exhibited only mediocre agreement with empirical flowering values, possibly because they overlooked the order of occurrence of different temperatures. We empirically tested the effect of different temperature regimes on olive flowering intensity and flowering-gene expression. To predict flowering based on winter temperatures, we constructed a dynamic model, describing the response of a putative flowering factor to the temperature signal. The crucial ingredient in the model is an unstable intermediate, produced and degraded at temperature-dependent rates. Our model accounts not only for the number of cold and warm hours but also for their order. We used sets of empirical flowering and temperature data to fit the model parameters, applying numerical constrained optimization techniques, and successfully validated the model outcomes. Our model more accurately predicts flowering under winters with warm periods yielding low-to-moderate flowering and is more robust compared to previous models. This model is the first step toward a practical predictive tool, applicable under various temperature conditions.

plant biology↗

A CRISPR-induced DNA break can trigger crossover, chromosomal loss and chromothripsis-like rearrangements

The fate of DNA double-strand breaks (DSBs) generated by the Cas9 nuclease has been thoroughly studied. Repair via non-homologous end-joining (NHEJ) or homologous recombination (HR) is the common outcome. However, little is known about unrepaired DSBs and the type of damage they can trigger in plants. In this work, we designed a new assay that detects loss of heterozygosity (LOH) in somatic cells, enabling the study of a broad range of DSB-induced genomic events. The system relies on a mapped phenotypic marker which produces a light purple color (Betalain pigment) in all plant tissues. Plants with sectors lacking the Betalain marker upon DSB induction between the marker and the centromere were tested for LOH events. Using this assay we detected a flower with a twin yellow and dark purple sector, corresponding to a germinally transmitted somatic crossover event. We also identified instances of small deletions of genomic regions spanning the T-DNA and whole chromosome loss. In addition, we show that major chromosomal rearrangements including loss of large fragments, inversions, and translocations were clearly associated with the CRISPR-induced DSB. Detailed characterization of complex rearrangements by whole genome sequencing, molecular, and cytological analyses, supports a model in which breakage-fusion-bridge cycle followed by chromothripsis-like rearrangements had been induced. Our LOH assay provides a new tool for precise breeding via targeted crossover detection. It also uncovers CRISPR mediated chromothripsis-lke events that had not been previously identified in plants.

genetics↗