Biology subjects

Khadari, B.

Publications and source records attributed to Khadari, B..

4 recordsLinked to original sources

bioRxiv2025

Diffuse and regionally structured domestication of the common fig (Ficus carica L.) in the Mediterranean Basin

Understanding domestication in perennial crops is crucial for unraveling the evolutionary trajectories that have shaped crop genetic diversity and for guiding future conservation and breeding efforts. The domestication of perennial Mediterranean fruit trees is less studied than that of annual crops. The common fig (Ficus carica L.) is thought to have been domesticated in the Levant before dispersion across the Mediterranean. However, pre-human fossils of F. carica in Europe suggest an ancient wild presence, challenging the assumption of a single eastern origin. We used microsatellite markers to genotype 949 fig accessions comprising cultivated and spontaneous individuals collected from 14 Mediterranean and Near Eastern countries representing F. carica sensu stricto and its two close relatives, F. carica subsp. rupestris, and, F. colchica. Principal component analysis revealed that F. carica sensu stricto forms a cohesive genetic group distinct from its two relatives, which are actually different species. Bayesian clustering revealed three major gene pools within F. carica sensu stricto -- Moroccan-Algerian, Northern Mediterranean, and Levantine--each containing both cultivated and spontaneous individuals. The Levantine group was the most differentiated, while the other two were closer genetically, together reflecting a longitudinal Mediterranean structure. Cultivated and spontaneous figs were genetically indistinguishable within each region, supporting a model of diffuse, regionally independent domestication rather than a single Levantine origin. These results highlight spontaneous populations and local landraces as key reservoirs of genetic variation, particularly in Morocco, Algeria, and the Levant. Our study provides a foundation for future genomic work to identify the genetic basis of key traits, emphasizing that practical breeding and conservation strategies should rely on regional biodiversity rather than a narrow set of elite cultivars to enhance fig resilience and productivity in the face of climate change and emerging disease pressures.

evolutionary biology↗

bioRxiv2025

Genomic insights into the local adaptation of spontaneously occurring populations of olive trees (Olea europaea ssp. europaea var. sylvestris) in the Mediterranean Basin

Living organisms are increasingly threatened by significant environmental changes, primarily driven by human-induced global alterations. Understanding and forecasting species adaptive responses to these environmental changes is therefore crucial for enhancing conservation efforts. In the Mediterranean Basin (MB), the average temperature is rising at a rate 20% faster than the global average, placing regional biodiversity at heightened risk. The study of local adaptation is thus particularly relevant. In the western MB, spontaneously occurring olive populations consist of both wild olives and admixed resulting of crop-to-wild gene flow. The wild is likely harbouring adaptive genetic variation shaped by local environmental pressures. In this study, we analysed target genomic sequencing data from spontaneously occurring populations (comprising both wild and admixed trees) as well as cultivated olive trees. We performed selective sweep and GEA analyses in wild olives to identify genomic regions associated with environmental variables. Our findings identified signatures of adaptation particularly associated with precipitation and temperature. Notably, admixed individuals retained many wild candidate SNPs in their genomes suggesting that they might retain a certain level of adaptation to their local environment. Those results are in line with recent studies suggesting hybrids could adapt more rapidly to novel environments than their parental populations. Key-words: Local adaptation, selective sweep detection, crop-to-wild gene flow, Olea europaea L., population genomics, genome-environment association

evolutionary biology↗

bioRxiv2023

Genomic evidence of genuine wild versus admixed olive populations evolving in the same natural environments in western Mediterranean Basin

Admixtures between wild animals and plants and their domesticated relatives are widely documented. This can have positive or negative impacts on the evolution of admixed populations in natural environments, yet the phenomenon is still misunderstood in long-lived woody species, contrary to short-lived crops. Wild olive Olea europaea L. occurs in the same eco-geographical range as domesticated olive, i.e. the Mediterranean Basin (MB). Moreover, it is an allogamous and anemophilous species whose seeds are disseminated by birds, i.e. factors that drive gene flow between crops and their wild relatives. Here we investigated the genetic structure of western MB wild olive populations in natural environments assuming a homogenous gene pool with limited impact of cultivated alleles, as previously suggested. We used a target sequencing method based on annotated genes from the Farga reference genome to analyze 27 western MB olive tree populations sampled in natural environments in France, Spain and Morocco. We also target sequenced cultivated olive tree accessions from the Worldwide Olive Germplasm Bank of Marrakech and Porquerolles and from an eastern MB wild olive tree population. We combined PCA, sNMF, pairwise Fst and TreeMix and clearly identified genuine wild olive trees throughout their natural distribution range along a north-south gradient including, for the first time, in southern France. However, contrary to our assumption, we highlighted more admixed than genuine wild olive trees. Our results raise questions regarding the admixed population evolution pattern in this environment, which might be facilitated by crop-to-wild gene flow.

evolutionary biology↗

bioRxiv2016

Evolutionary forces affecting synonymous variations in plant genomes

Base composition is highly variable among and within plant genomes, especially at third codon positions, ranging from GC-poor and homogeneous species to GC-rich and highly heterogeneous ones (particularly Monocots). Consequently, synonymous codon usage is biased in most species, even when base composition is relatively homogeneous. The causes of these variations are still under debate, with three main forces being possibly involved: mutational bias, selection and GC-biased gene conversion (gBGC). So far, both selection and gBGC have been detected in some species but how their relative strength varies among and within species remains unclear. Population genetics approaches allow to jointly estimating the intensity of selection, gBGC and mutational bias. We extended a recently developed method and applied it to a large population genomic datasets based on transcriptome sequencing of 11 angiosperm species spread across the phylogeny. We found that base composition is far from mutation-drift equilibrium in most genomes and that gBGC is a widespread and stronger process than selection. gBGC could strongly contribute to base composition variation among plant species, implying that it should be taken into account in plant genome analyses, especially for GC-rich ones.

evolutionary biology↗