Jacques Léon David

L'institut Agro | Montpellier SupAgro | SUPAGRO · Biology and Ecology

[This corrects the article DOI: 10.1371/journal.pbio.3002287.].

The domestication of crops is associated with the genome-wide loss of nucleotide diversity caused by selection and genetic drift. Here we investigated 32 genotypes representing key stages in the domestication of tetraploid wheat, i.e. wild emmer, emmer and durum wheat. RNA-Seq analysis was combined with estimates of evolvability, heritability and Q...

How and why genetic diversity varies among species is a long-standing question in evolutionary biology. Life history traits (especially life-span and reproductive mode) have been shown to be main determinants, but the underlying causes are debated. Demographic history and linked selection have been proposed as main mechanisms, but their relative im...

In ecology, an increase in genetic diversity within a community in natural ecosystems increases its productivity, while in evolutionary biology, kinship selection predicts that relatedness on social traits improves fitness. Varietal mixtures, where different genotypes are grown together, show contrasting results, especially for grain yield where bo...

In the Saharan regions of Algeria wheat is cultivated by farmers in small areas of the oases. Saharan wheat landraces that are the result of natural and human selection in hostile environments for several centuries could represent an interesting material to improve abiotic stress tolerance in breeding programs. Indeed, a high level of drought, heat...

Plant domestication can be viewed as a form of co‐evolved interspecific mutualism between humans and crops for the benefit of the two partners. Here we ask how this plant‐human mutualism has, in turn, impacted beneficial interactions within crop species, between crop species, and between crops and their associated microbial partners. We focus on be...

A classic example of phenotypic plasticity in plants is the suit of phenotypic responses induced by a change in the ratio of red to far‐red light (R∶FR) as a result of shading, also known as the shade avoidance syndrome (SAS). While the adaptive consequences of this syndrome have been extensively discussed in natural ecosystems, how SAS varies with...

Agroecosystem diversification through increased crop genetic diversity could provide multiple services such as improved disease control or increased productivity. However, we still poorly understand how genetic diversity affects agronomic performance. We grew 179 inbred lines of durum wheat in pure stands and in 202 binary mixtures in field conditi...

Native African cereals (sorghum, millets) ensure food security to millions of low-income people from low fertility and drought-prone regions of Africa and Asia. In spite of their agronomic importance, the genetic bases of their phenotype and adaptations are still not well-understood. Here we focus on Sorghum bicolor , which is the fifth cereal worl...

Mounting evidence indicates the key role of nitrogen (N) on diverse processes in plant, including development and defense. Using a combined transcriptomics and metabolomics approach, we studied the response of seedlings to N starvation of two different tetraploid wheat genotypes from the two main domesticated subspecies: emmer and durum wheat. We f...

From the 17th century until the arrival of hybrids in 1960s, maize landraces were cultivated in the South-West of France (SWF), a traditional region for maize cultivation. A set of landraces were collected in this area between the 1950s and 1980s and were then conserved ex situ in a germplam collection. Previous studies using molecular markers on a...

Native African cereals (sorghum, millets) ensure food security to millions of low-income people from low fertility and drought-prone regions of Africa and Asia. In spite of their agronomic importance, the genetic bases of their phenotype and adaptations are still not well understood. Here we focus on Sorghum bicolor , which is the fifth cereal worl...

From the 17th century until the arrival of hybrids in 1960s, maize landraces were cultivated in the South-West of France, a traditional region for maize cultivation. A set of landraces were collected in this region between the 1950s and 1980s and were then conserved ex situ in a germplam collection. Previous studies using molecular markers on appro...

Few resistance genes providing defence against the major fungal diseases septoria tritici blotch (STB), septoria nodorum blotch, leaf rust (LR), and an emerging wheat blast disease have been identified in durum wheat. We identified sixteen fungal disease-associated QTL through genome-wide association mapping of 180 inbred lines sampled from a durum...

Mounting evidence indicates the key role of Nitrogen (N) on diverse processes in plant, including not only yield but also development and defense. Using a combined transcriptomics and metabolomics approach, we studied the response of seedlings to N starvation of two different tetraploid wheat genotypes from the two main domesticated subspecies, emm...

Wheat populations cultivated in the Saharan oases have been considered as potential parental germplasm for the improvement of drought, heat and salt tolerance. However, risks of genetic erosion have been reported, related to the degradation of the oases cropping systems and the introduction of modern wheat varieties. A better description and charac...

Variety mixtures, the cultivation of different genotypes within a field, have been proposed as a way to increase within‐crop diversity, allowing the development of more sustainable agricultural systems with reduced environmental costs. Although mixtures have often been shown to over‐yield the average of component varieties in pure stands, decreased...

PlantBreedGame : a serious game that puts students in the breeder’s seat

Cultivated wheats are derived from an intricate history of three genomes, A, B, and D, present in both diploid and polyploid species. It was recently proposed that the D genome originated from an ancient hybridization between the A and B lineages. However, this result has been questioned, and a robust phylogeny of wheat relatives is still lacking....

In South Italy durum wheat (Triticum durum Desf.) has a long-time tradition of growing and breeding. Accessions collected and now preserved ex situ are a valuable genetic resource, but their effective use in agriculture and breeding programs remains very low. In this study, a small number (44) of simple sequence repeats (SSR) molecular markers were...

Bread wheat and durum wheat derive from an intricate evolutionary history of three genomes, namely A, B and D, present in both extent diploid and polyploid species. Despite its importance for wheat research, no consensus on the phylogeny of the wheat clade has emerged so far, possibly because of hybridizations and gene flows that make phylogeny rec...

Key message: The resistance of durum wheat to the Wheat spindle streak mosaic virus (WSSMV) is controlled by two main QTLs on chromosomes 7A and 7B, with a huge epistatic effect. Wheat spindle streak mosaic virus (WSSMV) is a major disease of durum wheat in Europe and North America. Breeding WSSMV-resistant cultivars is currently the only way to c...

Author summary In protein coding genes, base composition strongly varies within and among plant genomes, especially at positions where changes do not alter the coded protein (synonymous variations). Some species, such as the model plant Arabidopsis thaliana, are relatively GC-poor and homogeneous while others, such as grasses, are highly heterogene...

Estimation of gBGC and selection intensities—Extension of Glémin et al. (2015). (PDF)

Data processing. (PDF)

Codon preferences for the eleven species. (XLSX)

Phylogenetic relationship between species used in this study. Top-left panel: phylogeny of the species used in the study. The phylogeny was computed with PhyML [75] on a set of 33 1–1 orthologous protein clusters obtained with SiLiX [76]. Top-right and bottom-left panels: dN and dS values between species used in this study. We used the branch model...

This contains: 1) the mathematica script used to jointly estimate gBGC and SCU from SFS and divergence data 2) the R script used to simulate SFS under various demographic scenarios 3) Processed site frequency spectra used in this analysis. (ZIP)

Data preparation. (PDF)

List of sampled species and individuals. (XLSX)

Summary of assemblies’ characteristics. (XLSX)

Results of all gBGC/SCU nested models. (XLSX)

Results of all models in the first part and rest of genes. (XLSX)

Distribution of GC3 content in the transcriptome of the 11 species. (PDF)

Neutrality and direction of selection indices under gBGC or SCU. (PDF)

RSCU (Relative synonymous codon usage) in the 11 species. Codons are grouped by amino acids. Codons ending with A or T are in blue, those ending with G or C in red. Blue colour corresponds to the most frequent codons and yellow to the least frequent. (PDF)

GC3 and gBGC gradients along genes starting with a start codon. In the first exon, B is significantly higher in Commelinid than in other species (Wilcoxon test p-value = 0.0043). B values and GC3 are significantly and positively correlated both on the first part of contigs (ρSpearman = 0.80, p-value = 0.0052) and in the rest of contigs (ρSpearman =...

Phylogeny with detailed branch lengths. Phylogeny of the species used in this study (see S5 Fig for Method) with detailed branch lengths for each individual branches. Only the branch between D. abyssinica and the other monocot species shows a bootstrap support lower than 0.98 (namely 0.71). (PDF)

Detailed results of gBGC and SCU estimates. (XLSX)

SFSs in the eleven species. Site-frequency spectra for synonymous gBGC SNPs, i.e. W→S, S→W or S→S and W→W SNPs grouped together as “neutral.” (PDF)

Plant domestication has led to considerable phenotypic modifications from wild species to modern varieties. However, although changes in key traits have been well documented, less is known about the underlying molecular mechanisms, such as the reduction of molecular diversity or global gene co-expression patterns. In this study, we used a combinati...

Motivation: Marker-assisted selection strongly relies on genetic maps to accelerate breeding programs. High-density maps are now available for numerous species. Dedicated tools are required to compare several high-density maps on the basis of their key characteristics, while pinpointing their differences and similarities. Results: We developed t...

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 th...

We produced a unique large dataset of reference transcriptomes to obtain new knowledge about the evolution of plant genomes and crop domestication. For this purpose we validated a RNA-Seq data assembly protocol to perform comparative population genomics. For the validation, we assessed and compared the quality of de novo Illumina short-read assembl...

Targeted sequence capture is a promising technology which helps reduce costs for sequencing and genotyping numerous genomic regions in large sets of individuals. Bait sequences are designed to capture specific alleles previously discovered in parents or reference populations. We studied a set of 135 RILs originating from a cross between an emmer cu...

Correlations between putative physical and genetic positions. The 14 durum wheat chromosomes are shown on the same plot, with the putative physical position of SNPs on the X-axis (bp) and the genetic position on the Y-axis (cM). It allows checking for markers having distinct genetic and putative attributions. (PDF)

Putative assignment of markers composing linkage groups. The characteristics of the 25 linkage groups (LG) are presented. For each LG, contigs containing markers are distributed on the 14 A+B chromosomes of the IWGSC reference according to their best blast score (physical putative assignment). For each LG, the percentage of markers with a consisten...

Fasta file containing the bait sequences. The set of baits used for this study is provided. Baits suspected to capture microsatellite-rich regions were removed. Bait names are as follows: A@pos|B|C|D|E with: A: contig name in the DWr (S1 File) pos: position of the polymorphism previously detected in the RNA-seq experiment between dic2 and silur i...

Analysis of 7A-4A and 5B-4A inconsistencies. Thirty markers showed inconsistency between the genetic and putative assignments to chromosomes. Their names, barley and IWGSC assignments (bp) and DS genetic positions (cM) are reported. Assignments were obtained by blast on barley [49] and IWGSC. The corresponding barley gene IDs are given when availab...

Durum Wheat reference transcriptome (DWr). The fasta file of the de novo assembly obtained from [38]. (GZ)

Detailed capture protocol. Description of the exact protocol used for the capture step. (DOC)

Method used to map low covered SNPs. This file explains how we estimated the genetic positions of SNPs that were genotyped for fewer than 100 individuals but more than 50. (DOCX)

Description of 10 durum wheat genetic maps. Among the populations used to build the consensus durum wheat map published by Maccaferri et al. [19], 10 have been genotyped on the 90K iSelect array [6]. The features of these maps are presented here and compared with the genotyping by capture approach. (XLSX)

Genetic map of the Dic2 x Silur population. The genetic map is provided here. Markers names follow the nomenclature A@pos, with A being the contig name in the DWr [38] and pos being the position of the SNP in this contig. The positions are given in cM. SNP type can be either “mapped” or “DL_mapped” if less than 100 individuals were genotyped (see S...

Gene flow from crop to wild relatives is a common phenomenon which can lead to reduced adaptation of the wild relatives to natural ecosystems and/or increased adaptation to agrosystems (weediness). With global warming, wild relative distributions will likely change, thus modifying the width and/or location of co-occurrence zones where crop-wild hyb...

Potential sympatry index between cultivated wheat and individual Aegilops species in the European zone: RCP4.5. (PDF)

Sample means and variable contribution. (PDF)

Potential predicted distributions: RCP4.5. (PDF)

Potential predicted distributions: RCP8.5. (PDF)

Potential species richness: RCP8.5. (PDF)

Global potential sympatry index between the six Aegilops species and cultivated wheat in the European zone: RCP8.5. (PDF)

Complete dataset. (XLSX)

Names of the climate models. (PDF)

Potential sympatry index between cultivated wheat and individual Aegilops species in the European zone: RCP8.5. (PDF)

Institutions contributing to the dataset. (PDF)

Detailed filling estimates and species ranking order. (PDF)

Background grids. (PDF)

Most frequent potential associations of at least three species: RCP8.5. (PDF)

Summary of changes in potential area of occupancy. (PDF)