Biology subjects

Dirlewanger, E.

Publications and source records attributed to Dirlewanger, E..

6 recordsLinked to original sources

bioRxiv2026

A Bayesian multidimensional approach to decipher the genetic basis of dynamic phenotypes in multiple species

Deciphering the genetic architecture of complex quantitative phenotypes remains challenging in quantitative genetics. These traits not only depend of multiple genetic factors but are also established over time and environments. Although quantitative genetics has investigated the genetic determinism of phenotypic plasticity in contrasted environmental conditions, the time related phenotypic plasticity has received less attention. Here we proposed a multivariate Bayesian framework, the Bayesian Varying Coefficient Model, designed for analysing the genetic architecture of the time related phenotypic plasticity by a multilocus approach. We applied the BVCM to time series phenotypes measured at various time scales (daily, monthly, yearly) across a diverse set of biological species. We included in this study: yeast (Saccharomyces cerevisiae), fungi (Fusarium graminearum), eucalyptus (Eucalyptus urophylla x E. grandis), and sweet cherry tree (Prunus avium). The BVCM results were compared with those obtained with a known genome-wide association method carried out time by time. For all species and traits, the BVCM was able to detect the major QTL identified by marker-trait association methods and revealed additional genetic regions of weak effect. It also increased the phenotypic variance explained for most of the phenotypes considered. It revealed dynamic QTLs with transitory, increasing or decreasing effects over time. By considering both the temporal and genetic multivariate structures in a single statistical model, we increased our understanding of the genetic architecture of complex traits notably by reducing the issue of missing heritability. More broadly, this work raises the foundation for extended applications in functional genomics, evolutionary ecology, and crop breeding programs, in which time-related phenotypic plasticity remains crucial for predicting and selecting key quantitative complex traits. Key messageBy capturing the genetic factors influencing the time related phenotypic plasticity, our approach contributes to a deeper understanding of the dynamic nature of genotype-phenotype relationships.

genetics↗

bioRxiv2019

Management of a Walnut Germplasm Collection: Which of SSR or SNP Markers Are Most Suitable to Preserve Biodiversity?

The preservation of the maximum of diversity within the smallest number of accessions is one of the challenges of germplasm management. To construct core-collections, the assessment of the population structure and the relationships between the accessions represents a key step and the choice of suitable molecular markers is the starting point. Since the expansion of available SNP-based genomics tools, a debate has emerged regarding the usefulness of the widely used microsatellites (SSRs) markers. In this study, we analysed a part of the INRAE walnut germplasm collection of 150 accessions, unique in Europe for walnut biodiversity conservation, by comparing the power of both types of marker. We found that the first level of structure is equally detected using 13 SSRs or the Axiom J. regia 700K SNP array, and is in relation with the geographical origin of the accessions. For K=2, there was no exchange of accession between the two groups when both markers were compared. We also highlighted empirically that approximately 100 SNPs are needed to obtain similar clustering to SSRs in Principal Coordinate Analysis (PCoA). The neighbor-joining trees constructed were also consistent between both types of marker. The main differences lied in the upper levels of structure from K=3 to K=6, more powerful using the SNPs, and in the percentage of the explained variation in PCoA for K=2, higher using SSRs. We then constructed core-collections of 50 accessions, a crucial step in genetic resources management to reduce the costs and preserve the allelic diversity. Using two different construction methods, both SSR and SNP markers were suitable and able to keep at least 88.57% of the alleles. 32/50 accessions were in common between the two markers, for both methods. We concluded that the use of either marker is dependent on the researchers goal.

genetics↗

bioRxiv2019

From bud formation to flowering: transcriptomic state defines the cherry developmental phases of sweet cherry bud dormancy

BackgroundBud dormancy is a crucial stage in perennial trees and allows survival over winter to ensure optimal flowering and fruit production. Recent work highlighted physiological and molecular events occurring during bud dormancy in trees. However, they usually examined bud development or bud dormancy in isolation. In this work, we aimed to further explore the global transcriptional changes happening throughout bud development and dormancy onset, progression and release.\n\nResultsUsing next-generation sequencing and modelling, we conducted an in-depth transcriptomic analysis for all stages of flower buds in several sweet cherry (Prunus avium L.) cultivars that are characterized for their contrasted dates of dormancy release. We find that buds in organogenesis, paradormancy, endodormancy and ecodormancy stages are defined by the expression of genes involved in specific pathways, and these are conserved between different sweet cherry cultivars. In particular, we found that DORMANCY ASSOCIATED MADS-box (DAM), floral identity and organogenesis genes are up-regulated during the pre-dormancy stages while endodormancy is characterized by a complex array of signalling pathways, including cold response genes, ABA and oxidation-reduction processes. After dormancy release, genes associated with global cell activity, division and differentiation are activated during ecodormancy and growth resumption. We then went a step beyond the global transcriptomic analysis and we developed a model based on the transcriptional profiles of just seven genes to accurately predict the main bud dormancy stages.\n\nConclusionsOverall, this study has allowed us to better understand the transcriptional changes occurring throughout the different phases of flower bud development, from bud formation in the summer to flowering in the following spring. Our work sets the stage for the development of fast and cost effective diagnostic tools to molecularly define the dormancy stages. Such integrative approaches will therefore be extremely useful for a better comprehension of complex phenological processes in many species.

plant biology↗

bioRxiv2018

Hormonal balance finely tunes dormancy status in sweet cherry flower buds

In temperate trees, optimal timing and quality of flowering directly depend on adequate winter dormancy progression, regulated by a combination of chilling and warm temperatures. Physiological, genetic and functional genomic studies have shown that hormones play a key role in bud dormancy establishment, maintenance and release. We combined physiological, transcriptional analyses, quantification of abscisic acid (ABA) and gibberellins (GAs), and modelling to further investigate how these signaling pathways are associated with dormancy progression in the flower buds of two sweet cherry cultivars. Our results demonstrated that GA-associated pathways have distinct functions and may be differentially related with dormancy. In addition, ABA levels rise at the onset of dormancy, associated with enhanced expression of ABA biosynthesis PavNCED genes, and decreased prior to dormancy release. Following the observations that ABA levels are correlated with dormancy depth, we identified PavUG71B6, a sweet cherry UDP-GLYCOSYLTRANSFERASE gene that up-regulates active catabolism of ABA to ABA-GE and may be associated with low ABA content in the early cultivar. Subsequently, we modelled ABA content and dormancy behavior in three cultivars based on the expression of a small set of genes regulating ABA levels. These results strongly suggest the central role of ABA pathway in the control of dormancy progression and open up new perspectives for the development of molecular-based phenological modelling.

plant biology↗

bioRxiv2018

Chromatin immunoprecipitation-sequencing and RNA-sequencing for complex and low-abundance tree buds

Chromatin immunoprecipitation-sequencing (ChIP-seq) is a robust technique to study interactions between proteins, such as histones or transcription factors, and DNA. This technique in combination with RNA-sequencing (RNA-seq) is a powerful tool to better understand biological processes in eukaryotes. We developed a combined ChIP-seq and RNA-seq protocol for tree buds (Prunus avium L., Prunus persica L Batch, Malus x domestica Borkh.) that has also been successfully tested on Arabidopsis thaliana and Saccharomyces cerevisiae. Tree buds contain phenolic compounds that negatively interfere with ChIP and RNA extraction. In addition to solving this problem, our protocol is optimised to work on small amounts of material. Furthermore, one of the advantages of this protocol is that samples for ChIP-seq are cross-linked after flash freezing, making it possible to work on trees growing in the field and to perform ChIP-seq and RNA-seq on the same starting material. Focusing on dormant buds in sweet cherry, we explored the link between expression level and H3K4me3 enrichment for all genes, including a strong correlation between H3K4me3 enrichment at the DORMANCY-ASSOCIATED MADS-box 5 (PavDAM5) loci and its expression pattern. This protocol will allow analysis of chromatin and transcriptomic dynamics in tree buds, notably during its development and response to the environment.

plant biology↗

bioRxiv2018

Productivity definition of the chilling requirement reveals underestimation of the impact of climate change on winter chill accumulation

Evaluation of chilling requirements (CR) of cultivars of temperate fruit trees provides key information to assess regional suitability, according to winter chill, for both industry expansion and ongoing profitability as climate change continues. Traditional methods for calculating CR use climate controlled chambers and define CR using a fixed budburst percentage, usually close to 50% (CR-50%), without considering the productivity level associated to this percentage. This CR-50% definition may underestimate the real CR of tree crops for optimal productivity. This underestimation is particularly important to consider as winter chill accumulation is declining in many regions due to climate change. In this work we used sweet cherry to analyse the traditional method for calculating CR in many Rosaceae species (CR-50%) and compared the results with more a restrictive, productivity focused method, with CR defined with a 90% bud break level (90%, CRm-90%) close to the optimal budburst which assures productivity. Climate projections of winter chill suitability across Europe using CR-50% and CRm-90% were calculated. Regional suitability landscape was highly dependent on the method used to define CR and differences were found for a wide area of the European geography, both cold and mild winter areas. Our results suggest a need to use an optimal budburst level for the assessment of CR for sweet cherry. The use of traditional methods to determine CR can result in an underestimation of productivity CR with negative consequences for the fruit industry, particularly as climate change advances.

plant biology↗