Olivier C Martin

• PhD
• Research Director at French National Institute for Agriculture, Food, and Environment (INRAE)

The tight regulation of meiotic recombination between homologs is disrupted in Brassica AAC allotriploids, a genomic configuration that may have facilitated the formation of rapeseed (Brassica napus L.) ∼7,500 years ago. Indeed, the presence of the haploid C genome induces supernumerary crossovers between homologous A chromosomes with dramatically...

Random Boolean networks (RBNs) have been widely explored as models for understanding complex systems, in particular gene regulatory networks (GRNs). Stability (order) and instability (chaos), critical characteristics of any dynamic system, have naturally been a central focus in RBN research. Several measures have previously been introduced to asses...

The tight regulation of meiotic recombination between homologs is disrupted in Brassica AAC allotriploids, a genomic configuration that may have facilitated the formation of rapeseed (Brassica napus L.) ~7,500 years ago. Indeed, the presence of the haploid C genome induces supernumerary crossovers between homologous A chromosomes with dramatically...

Meiotic recombination is a key biological process in plant evolution and breeding, as it generates genetic diversity in each generation through the formation of crossovers (COs). However, due to their importance in genome stability, COs are highly regulated in frequency and distribution. We previously demonstrated that this strict regulation of COs...

During the founding of the field of quantitative genetics, Fisher formulated in 1918 his “infinitesimal model” that provided a novel mathematical framework to describe the Mendelian transmission of quantitative traits. If the infinitely many genes in that model are assumed to segregate independently during reproduction, corresponding to having no l...

Boolean models of gene regulatory networks (GRNs) have gained widespread traction as they can easily recapitulate cellular phenotypes via their attractor states. Their overall dynamics are embodied in a state transition graph (STG). Indeed, two Boolean networks (BNs) with the same network structure and attractors can have drastically different STGs...

Boolean networks (BNs) have been extensively used to model gene regulatory networks (GRNs). The dynamics of BNs depend on the network architecture and regulatory logic rules (Boolean functions (BFs)) associated with nodes. Nested canalyzing functions (NCFs) have been shown to be enriched among the BFs in the large-scale studies of reconstructed Boo...

Meiotic recombination is a key biological process in plant evolution and breeding, as it generates novel genetic diversity at each generation. However, due to its importance in chromosome segregation and genomic stability, crossovers are highly regulated in both frequency and distribution. We previously demonstrated that this strict regulation is n...

Boolean networks (BNs) have been extensively used to model the dynamics of gene regulatory networks (GRNs) that underlie cellular decisions. The dynamics of BNs depend on the network architecture and regulatory logic rules (or Boolean functions (BFs)) associated with nodes, both of which have been shown to be far from random in large-scale studies...

Boolean network (BN) models of gene regulatory networks (GRNs) have gained widespread traction as they can easily recapitulate cellular phenotypes via their attractor states. The overall dynamics of such models are embodied in the system's state transition graph (STG) which is highly informative. Indeed, even if two BN models have the same network...

Boolean models are a well-established framework to model developmental gene regulatory networks (DGRNs) for acquisition of cellular identities. During the reconstruction of Boolean DGRNs, even if the network structure is given, there is generally a large number of combinations of Boolean functions that will reproduce the different cell fates (biolo...

Boolean models are a well-established framework to model developmental gene regulatory networks (DGRN) for acquisition of cellular identity. During the reconstruction of Boolean DGRNs, even if the network structure is given, there is generally a very large number of combinations of Boolean functions (BFs) that will reproduce the different cell fate...

Background Genotyping and sequencing technologies produce increasingly large numbers of genetic markers with potentially high rates of missing or erroneous data. Therefore, the construction of linkage maps is more and more complex. Moreover, the size of segregating populations remains constrained by cost issues and is less and less commensurate wit...

Boolean networks have been widely used to model gene networks. However, such models are coarse-grained to an extent that they abstract away molecular specificities of gene regulation. Alternatively, bipartite Boolean network models of gene regulation explicitly distinguish genes from transcription factors (TFs). In such bipartite models, multiple T...

Boolean network models have widely been used to study the dynamics of gene regulatory networks. However, such models are coarse-grained to an extent that they abstract away molecular specificities of gene regulation. In contrast, bipartite Boolean network models of gene regulation explicitly distinguish genes from transcription factors (TFs). In su...

The properties of random Boolean networks have been investigated extensively as models of regulation in biological systems. However, the Boolean functions (BFs) specifying the associated logical update rules should not be expected to be random. In this contribution, we focus on biologically meaningful types of BFs, and perform a systematic study of...

Boolean modelling is a powerful framework to understand the operating principles of biological networks. The regulatory logic between biological entities in these networks is expressed as Boolean functions (BFs). There exist various types of BFs (and thus regulatory logic rules) which are meaningful in the biological context. In this contribution,...

In, essentially, all species where meiotic crossovers (COs) have been studied, they occur preferentially in open chromatin, typically near gene promoters and to a lesser extent, at the end of genes. Here, in the case of Arabidopsis thaliana , we unveil further trends arising when one considers contextual information, namely summarised epigenetic st...

Background Introgression of a quantitative trait locus (QTL) by successive backcrosses is used to improve elite lines (recurrent parent) by introducing alleles from exotic material (donor parent). In the absence of selection, the proportion of the donor genome decreases by half at each generation. However, since selection is for the donor allele at...

In essentially all species where meiotic crossovers have been studied, they occur preferentially in open chromatin, typically near gene promoters and to a lesser extent at the end of genes. Here, in the case of Arabidopsis thaliana, we unveil further trends arising when one considers contextual information, namely summarized epigenetic status, size...

Ethylene aplenty signals soil compaction It's tough to drive a spade through compacted soil, and plant roots seem to have the same problem when growing in compacted ground. Pandey et al. found that the problem is not, however, one of physical resistance but rather inhibition of growth through a signaling pathway. The volatile plant hormone ethylene...

Introgression of a QTL by successive backcrosses is a strategy that can be used to improve elite lines (recurrent parent) by bringing in alleles from exotic material (donor parent). In the absence of selection, the proportion of the donor genome decreases by half at each generation. However, since one selects for the donor allele at the QTL, the el...

Faba bean (Vicia faba L.) is a pulse crop of high nutritional value and high importance for sustainable agriculture and soil protection. With the objective of identifying gene-based SNPs, transcriptome sequencing was performed in order to reduce faba bean genome complexity. A set of 1,819 gene-based Snp markers polymorphic in three recombinant line...

Faba bean (Vicia faba L.) is a pulse crop of high nutritional value and high importance for sustainable agriculture and soil protection. With the objective of identifying gene-based SNPs, transcriptome sequencing was performed in order to reduce faba bean genome complexity. A set of 1,819 gene-based SNP markers polymorphic in three recombinant line...

Copy-number variants (CNVs) represent a large part of natural genetic diversity and contribute significantly to trait variation. As a complement to sequence-based approaches, Falque et al. propose an original method to both detect and map... Single nucleotide polymorphisms (SNPs) are used widely for detecting quantitative trait loci, or for searchi...

Meiotic recombination generates genetic diversity but in most species the number of crossovers per meiosis is limited. Previous modeling studies showed that increasing recombination can enhance response to selection. However, such studies did not assume a specific method of modifying recombination. Our objective was to test whether two methods used...

Recombinant Inbred Lines (RILs) are obtained through successive generations of inbreeding. In 1931 Haldane and Waddington published a landmark paper where they provided the probabilities of achieving any combination of alleles in 2-way RILs for 2 and 3 loci. In the case of sibling RILs where sisters and brothers are crossed at each generation, ther...

Single nucleotide polymorphisms (SNPs) are widely used for detecting quantitative trait loci or for searching for causal variants of diseases. Nevertheless, structural variations such as copy-number variants (CNVs) represent a large part of natural genetic diversity and contribute significantly to trait variation. Over the past decade, numerous met...

During meiosis, recombination ensures allelic exchanges through crossovers (COs) between the homologous chromosomes. Advances in comprehension of CO rules benefit from studies of mutations including structural chromosomal rearrangements that, when heterozygous, are known to impair COs in various organisms. In this work, we investigate the effect of...

Recombination generates genetic diversity but the number of crossovers per meiosis is limited in most species. Previous studies showed that increasing recombination can enhance response to selection. However, such studies did not assume a specific method of modifying recombination. Our objective was to test whether two methods used to increase reco...

Recombinant Inbred Lines (RILs) are obtained through generations of inbreeding until all alleles are fixed. In 1931 Haldane and Waddington published a landmark paper where they provided the probabilities of achieving any combination of alleles in 2-way RILs for 2 and 3 loci. In the case of SIB RILs where sisters and brothers are crossed at each gen...

Meiotic recombination is a major driver of genome evolution by creating new genetic combinations. To probe the factors driving variability of meiotic recombination, we used a high-throughput method to measure recombination rates in hybrids between SK1 and a total of 26 S. cerevisiae strains from different geographic origins and habitats. Fourteen i...

During meiosis, recombination ensures the allele exchange through crossovers (COs) between the homologous chromosomes and, additionally, their proper segregation. CO events are under a strict control but molecular mechanisms underlying CO regulation are still elusive. Some advances in this field were made by structural chromosomal rearrangements th...

Meiotic recombination is a major driver of genome evolution by creating new genetic combinations. To probe the factors driving variability of meiotic recombination, we used a high-throughput method to measure recombination rates in 26 S. cerevisiae strains from different geographic origins and habitats. Fourteen intervals were monitored for each st...

Meiotic recombination by crossovers is the main mechanism used by breeders to shuffle the genetic diversity. Nevertheless, loci separation is often hampered due to the strict regulation of meiotic recombination, which results in a few number of crossovers formed per pair of homologs (≤ 3) primarily located on chromosome extremities (Mercier et al.,...

Batch cultures are frequently used in experimental evolution to study the dynamics of adaptation. Although they are generally considered to simply drive a growth rate increase, other fitness components can also be selected for. Indeed, recurrent batches form a seasonal environment where different phases repeat periodically and different traits can...

Allelic recombination due to meiotic crossovers is a major driver of genome evolution, as well as a key player for the selection of high‐performing genotypes in economically important species. Therefore, we developed a high throughput and low cost method to measure recombination rates and crossover patterning (including interference) in large popul...

Plants depend on the signaling of the phytohormone auxin for their development and for responding to environmental perturbations. The associated biomolecular signaling network involves a negative feedback at the level of the Aux/IAA proteins which mediate the influence of auxin (the signal) on the ARF transcription factors (the drivers of the respo...

In the early 1930s, J. B. S. Haldane and C. H. Waddington collaborated on the consequences of genetic linkage and inbreeding. One elegant mathematical genetics problem solved by them concerns recombinant inbred lines (RILs) produced via repeated self or brother–sister mating. In this classic contribution, Haldane and Waddington derived an analytica...

Meiotic recombination by crossovers (COs) is tightly regulated, limiting its key role in producing genetic diversity. While one obligate CO occurs per pair of homologs, ensuring their proper segregation during meiosis, rarely more than three are formed and their distribution is not homogenous along chromosomes. In plants, Whole Genome Duplication (...

Meiotic recombination by crossovers (COs) is tightly regulated, limiting its key role in producing genetic diversity. However, while COs are usually restricted in number and not homogenously distributed along chromosomes, we show here how to disrupt these rules in Brassica species by using allotriploid hybrids (AAC, 2n = 3x = 29), resulting from th...

Meiotic observations of AA and AAC F1 hybrids at metaphase I. (a-d) Pollen Mother Cells showing ten bivalents for the diploids (a) ArAr’ and (b) AnAr’, or ten bivalents and nine univalents for the allotriploids (c) ArAr’Co and (d) AnAr’Cn. (e-j) FISH analyses for (e-g) ArAr’Co and (h-j) AnAr’Cn F1 hybrids. BAC FISH was carried out using Bob014O06 a...

Recombination rates in Centimorgan (cM) for each of the 10 homologous A chromosomes in AA and AAC F1 hybrids. Values obtained for the diploid hybrids are indicated from female ArAr’ in purple, female AnAr’ in red, and male AnAr’ in blue. Values obtained for the allotriploid hybrids are indicated from female ArAr’Co in light purple, female AnAr’Cn i...

Circos diagram comparing the recombination rates along the 10 A chromosomes in cM per Mbp between the AAC F1 hybrids. In the first outer circle are represented the 10 A chromosomes of the B. rapa cv. ‘Chiifu-401’ genome sequence version 1.5 [57]. Their sizes are indicated by the values in megabase pairs above each chromosome, and a ruler drawn unde...

Distributions of inter-crossover genetic distances in AA and AAC F1 hybrids for individual chromosomes. Comparison of the distribution of genetic distances between successive COs from populations deriving of females ArAr’ (in purple) vs ArAr’Co (in light purple), females AnAr’ (in red) vs AnAr’Cn (in pink) and males AnAr’ (in blue) vs AnAr’Cn (in l...

Distributions of inter-crossover genetic distances in the two genetic backgrounds of F1 hybrids when pooling all 10 chromosomes. Comparison of the distribution of genetic distances between successive COs from populations deriving of females ArAr’ (in purple) vs AnAr’ (in red), and females ArAr’Co (in light purple) vs AnAr’Cn (in pink). Data are poo...

Statistical comparisons of the shapes of recombination landscapes along the homologous A chromosomes in the two genetic backgrounds. The line "ALL" in the column "Chromosomes" correspond to the pooled analysis of the 10 chromosomes together. The "pvalue" column is the p-value for the H0 hypothesis that the shapes of the recombination landscapes alo...

Quantification of CO interference parameters using the Gamma-sprinkling and Beam-Film models for each of the AA and AAC F1 hybrids. The line "Average" in the column "Chromosome" corresponds to the average of the values obtained for the 10 chromosomes. The nu and Lambda parameters correspond to the strength of CO interference, and p to the proportio...

Genotyping data for the samples deriving from the female AnAr' F1 hybrid used for linkage analysis. (XLSX)

Frequency of crossovers per chromatid of the progenies deriving from the AA and AAC F1 hybrids. Values obtained for the diploid hybrids are indicated from female ArAr’ in purple, female AnAr’ in red, and male AnAr’ in blue. Values obtained for the allotriploid hybrids are indicated from female ArAr’Co in light purple, female AnAr’Cn in pink, and ma...

Illustration of the statistical test used to compare recombination landscapes between the two genetic backgrounds of F1 hybrids along the 10 homologous A chromosomes. The chromosome length is divided into 10 bins whose length is set to ensure that all bins contain the same total number of crossover when pooling data of both populations. Solid color...

Characteristics of SNP markers genetically mapped on the 10 homologous A chromosomes of each of the AA and AAC F1 hybrids combinations. (XLSX)

Chi-squared comparisons in the crossover rate heterogeneity per interval between adjacent linked SNP markers. (XLSX)

Relationship between the recombination rates between adjacent SNP markers and their physical locations along each of the homologous A chromosomes in AA and AAC F1 hybrids. For the line "ALL" in the column "Chromosomes", all the relative recombination rates between adjacent SNP markers were considered, and normalized per A chromosome, to test the re...

Genotyping data for the samples deriving from the female ArAr'Co F1 hybrid used for linkage analysis. (XLSX)

Genotyping data for the samples deriving from the male AnAr'Cn F1 hybrid used for linkage analysis. (XLSX)

Circos diagram comparing the recombination rates along the 10 A chromosomes in cM per Mbp between the AA F1 hybrids. In the first outer circle are represented the 10 A chromosomes of the B. rapa cv. ‘Chiifu-401’ genome sequence version 1.5 [57]. Their sizes are indicated by the values in megabase pairs above each chromosome, and a ruler drawn under...

Relationship between the relative recombination rates normalized per A chromosome (%) and their relative distance from the centromeres (%) for each AA and AAC F1 hybrid. Female ArAr’ (red circles): y = 0,135257x-1,195111; R2 = 0.53. Female ArAr’Co (pink squares): y = 0,027539x+3,861802; R2 = 0.09. Female AnAr’ (red circles): y = 0,117461x-0,360060;...

Meiotic behavior established from Pollen Mother Cells of each AA and AAC F1 hybrid produced. % Cells: percentage of cells with the expected behavior. I and II are respectively univalents and bivalents. (XLSX)

Statistical comparisons of the shapes of recombination landscapes along the homologous A chromosomes in male and female meiosis. The line "ALL" in the column "Chromosomes" correspond to the pooled analysis of the 10 chromosomes together. The "pvalue" column is the p-value for the H0 hypothesis that the shapes of the recombination landscapes along t...

Statistical comparisons of distributions of distances between successive COs in AA and AAC F1 hybrids. K-S test: Kolmogorov-Smirnov test for differences between the two experimental distributions. K-L Div. Kullback-Leibler divergence between the experimental distribution and the « no-interference » distribution. K-L Div. p-value: p-value for the H0...

Genotyping data for the samples deriving from the female ArAr' F1 hybrid used for linkage analysis. (XLSX)

Illustration of the statistical test used to compare recombination landscapes between the AA and AAC F1 hybrids along the 10 homologous A chromosomes. The chromosome length is divided into 10 bins whose length is set to ensure that all bins contain the same total number of crossover when pooling data of both populations. Solid colored lines represe...

Illustration of the statistical test used to compare recombination landscapes between male and female meiosis of F1 hybrids along the 10 homologous A chromosomes. The chromosome length is divided into 10 bins whose length is set to ensure that all bins contain the same total number of crossover when pooling data of both populations. Solid colored l...

Illustration of the relationships between the recombination rates per interval between linked SNP markers (in cM per Mbp) and their physical locations along each of the 10 A chromosomes (in Mbp) per AA and AAC F1 hybrid. The p-values and R2 are indicated in S7 Table. (PDF)

Distributions of inter-crossover genetic distances in male and female meiosis of F1 hybrids when pooling all 10 chromosomes. Comparison of the distribution of genetic distances between successive COs from populations deriving of female AnAr’ (in red) vs male AnAr’ (in blue), and female AnAr’Cn (in pink) vs male AnAr’Cn (in light blue). Data are poo...

Statistical comparisons of the shapes of recombination landscapes along the homologous A chromosomes in AA and AAC F1 hybrids. The line "ALL" in the column "Chromosomes" correspond to the pooled analysis of the 10 chromosomes together. The "pvalue" column is the p-value for the H0 hypothesis that the shapes of the recombination landscapes along the...

Genotyping data for the samples deriving from the female AnAr'Cn F1 hybrid used for linkage analysis. (XLSX)

Genotyping data for the samples deriving from the male AnAr' F1 hybrid used for linkage analysis. (XLSX)

Recombination is an important source of metabolic innovation, especially in prokaryotes, which have evolved the ability to survive on many different sources of chemical elements and energy. Metabolic systems have a well-understood genotype-phenotype relationship, which permits a quantitative and biochemically principled understanding of how recombi...

When relaxation towards an equilibrium or steady state is exponential at large times, one usually considers that the associated relaxation time τ, i.e., the inverse of that decay rate, is the longest characteristic time in the system. However that need not be true, and in particular other times such as the lifetime of an infinitesimal perturbation...

Supplementary informations: Short relaxation times but long transient times in both simple and complex reaction networks

New experimental results on bacterial growth inspire a novel top-down approach to study cell metabolism, combining mass balance and proteomic constraints to extend and complement Flux Balance Analysis. We introduce here Constrained Allocation Flux Balance Analysis, CAFBA, in which the biosynthetic costs associated to growth are accounted for in an...

New experimental results on bacterial growth inspire a novel top-down approach to study cell metabolism, combining mass balance and proteomic constraints to extend and complement Flux Balance Analysis. We introduce here Constrained Allocation Flux Balance Analysis, CAFBA, in which the biosynthetic costs associated to growth are accounted for in an...

Supplementary MatLab code. COBRA-compatible Matlab functions implementing CAFBA. (ZIP)

Supporting text. Supplementary notes, tables, figures and references. (PDF)

Living cells can maintain their internal states, react to changing environments, grow, differentiate, divide, etc. All these processes are tightly controlled by what can be called a regulatory program. The logic of the underlying control can sometimes be guessed at by examining the network of influences amongst genetic components. Some associated g...

Meiotic homologous recombination by crossovers (COs) is the main mechanism responsible for mixing genetic diversity in plant breeding. However, loci separations are limited due to the strict regulation of the rates and distribution of recombination events along the chromosomes. Indeed, rarely more than two COs occur between homologous chromosomes p...

This PDF file includes 10 supplementary texts (Texts S1-S10) and 18 supplementary figures (Figures S1-S18)

This PDF file includes 10 supplementary texts (Texts S1-S10) and 18 supplementary figures (Figures S1-S18)

Network architectures and operating principles reply to comments on "Drivers of structural features in gene regulatory networks: from biophysical constraints to biological function"

Significance During meiosis, chromosomes exchange segments in a process of crossing-over. The crossover number is tightly regulated so that at least one crossover (but not many more) is formed per chromosome. The process of crossover homeostasis is thought to play a major role in this regulation by ensuring a stable crossover number even if the num...

Analytic and computational methods developed within statistical physics have found applications in numerous disciplines. In this Letter, we use such methods to solve a long-standing problem in statistical genetics. The problem, posed by Haldane and Waddington [Genetics 16, 357 (1931)], concerns so-called recombinant inbred lines (RILs) produced by...

The hormone auxin is actively transported throughout plants via protein machineries including the dedicated transporter known as PIN. The associated transport is ordered with nearby cells driving auxin flux in similar directions. Here, we provide a model of both the auxin transport and of the dynamics of cellular polarization based on flux sensing....

Morphogenesis in plants is initiated in meristems, the cells there differentiating under the influence of signals from the hormone auxin. Auxin is actively transported throughout the meristem via dedicated transporters such as PIN. In the last decade it has been discovered that this transport is highly polarised, nearby cells driving auxin flux in...

Significance In many eukaryotes, two types of meiotic crossovers (COs) coexist: class I COs that show CO interference and class II COs that do not show interference. Little is known about the separate properties of these two CO pathways or their interaction in wild-type organisms because individual COs cannot be assigned by class using marker segre...

Crossovers (COs) are at the origin of genetic variability, occurring across successive generations, and they are also essential for the correct segregation of chromosomes during meiosis. Their number and position are precisely controlled, however the mechanisms underlying these controls are poorly understood. Neddylation/rubylation is a regulatory...

Recombinant inbred lines (RILs) provide a powerful way to localize chromosomal regions affecting traits of interest. RILs are produced by iterative inbreeding until all loci become fixed. In 1931 Haldane and Waddington derived the RIL genotype probabilities for 2 loci and then extended them to 3 loci. Interestingly, the cases of 4 or more loci have...

A metabolism can evolve through changes in its biochemical reactions that are caused by processes such as horizontal gene transfer and gene deletion. While such changes need to preserve an organism's viability in its environment, they can modify other important properties, such as a metabolism's maximal biomass synthesis rate and its robustness to...

Recombination is a major mechanism generating genetic diversity, but the control of the crossover rate remains a key question. In Brassica napus ( AACC , 2 n = 38), we can increase the homologous recombination between A genomes in AAC hybrids. Hypotheses for this effect include the number of C univalent chromosomes, the ratio between univalents and...

In sexually reproducing organisms, meiotic crossovers ensure the proper segregation of chromosomes and contribute to genetic diversity by shuffling allelic combinations. Such genetic reassortment is exploited in breeding to combine favorable alleles, and in genetic research to identify genetic factors underlying traits of interest via linkage or as...

In most organisms that have been studied, crossovers formed during meiosis exhibit interference: nearby crossovers are rare. Here we provide an in-depth study of crossover interference in Arabidopsis thaliana, examining crossovers genome-wide in over 1500 backcrosses for both male and female meiosis. This unique data set allows us to take a two-pat...

There are two types of photosynthesis, C3 and C4, and computational techniques have been used to explore how C4 plants evolved from their C3 ancestors.

The reconstruction of many biological networks has allowed detailed studies of their structural properties. Several features exhibited by these networks have been interpreted to be the result of evolutionary dynamics. For instance the degree distributions may follow from a preferential attachment of new genes to older ones during evolution. Here we...

The cell cycle is a tightly controlled process, yet it shows marked differences across species. Which of its structural features follow solely from the ability to control gene expression? We tackle this question in silico by examining the ensemble of all regulatory networks which satisfy the constraint of producing a given sequence of gene expressi...

Dendrogram of the investigated maize lines. Dendrogram for the 274 maize lines based on the marker data from the array for only the PZ (Panzea) markers. Method of analysis: NTSYS Similarity of qualitative data (DICE coefficient). (PDF)