Biology subjects

Falque, M.

Publications and source records attributed to Falque, M..

14 recordsLinked to original sources

bioRxiv2026

Response to divergent selection on meiotic recombination in Saccharomyces cerevisiae

Meiotic recombination is a key driver of evolution in sexually reproducing species, reshaping genetic diversity by generating novel allelic combinations. The rate of recombination varies substantially across living organisms depending on cis- or trans-acting genetic elements, as seen in many species, including the yeast Saccharomyces cerevisiae. Here, we report on an experimental evolution-based study to better understand the factors shaping this natural variation. Starting with a genetically diverse population of S. cerevisiae, we have carried out recurrent divergent selection on recombination rate using a fluorescence-based sorting approach in four independent lineages. After ten generations, we observed an average response of recombination rate of +28% after positive selection and -24% after negative selection, within the interval used for selection. In the adjacent region, however, we observed a weaker response in the opposite direction, and no response in four other unlinked genomic regions. Whole-genome sequencing of individuals selected for high recombination revealed mixed outcomes in the four independently evolved lineages for high genome-wide recombination rates. However, all four lineages showed selection for high recombination locally, with particular haplotypes heavily favored and sequence- or structural variation-based heterozygosity selected against within the selection interval. Overall, this experimental evolution approach provides original and useful insights into the evolvability of the meiotic recombination rate and the associated genetic determinants.

genetics↗

bioRxiv2024

CAYSS: package for automatic Cytometry Analysis of Yeast Spore Segregation

Meiotic recombination is a powerful source of haplotypic diversity, and thus plays an important role in the dynamics of short-term adaptation. However, high-throughput quantitative measurement of recombination parameters is challenging because of the large size of offspring to be genotyped. One of the most efficient approaches for large-scale recombination measurement is to study the segregation of fluorescent markers in gametes. Applying this to yeast spores by flow cytometry has already been proved to be highly efficient, but manual analyses of density distributions of signal intensities is time-consuming and produces non-perfectly reproducible results. Such analyses are required to identify events corresponding to spores and to assign each of them to a genotypic class depending on their fluorescence intensity. The CAYSS package automatically reproduces the manual process that weve been developing to analyze yeast recombination for years, including Maximum-Likelihood estimation of fluorescence extinction (Raffoux et al. 2018a). When comparing the results of manual vs CAYSS automatic analyses of the same cytometry data, recombination rates and interference were on average very similar, with less than 3% differences on average and strong correlations (R2>0.9). In conclusion, as compared to manual analysis, CAYSS allows to save a lot of human time and produces totally reproducible results. The CAYSS software is freely available under GPL license from https://forgemia.inra.fr/gqe-base/cayss/-/releases. The package is also provided as Supplementary Material 1 and a tutorial may be found as Supplementary Material 2. TAKE AWAYThe CAYSS R package measures recombination rate and crossover interference from flow cytometry data of isolated yeast spores segregating for fluorescent markers. The analysis is fully automatic and reproducible. It includes spore identification from FSC and SSC data, genotype determination from fluorescence intensities, and Maximum Likelihood estimation of recombination parameters.

genetics↗

bioRxiv2024

Playing with the ploidy level enables to switch on and off the strict recombination control even in the vicinity of Brassica centromeres

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 not a fatality and that it can be naturally modified (3.6-fold increased frequency and altered distribution) in an allotriploid Brassica hybrid (2n=3x=29; AAC), resulting from a cross between B. napus (2n=4x=38; AACC) and B. rapa (2n=2x=20; AA). Taking advantage of the recently updated Brassica napus genome assembly, which now includes the pericentromeric regions, we unambiguously demonstrated that crossovers occur in these normally cold regions in allotriploids, with the presence of crossovers as close as 375 kb from the centromere. We deciphered that this modified recombination landscape (both frequency and distribution) can be maintained in successive generations of allotriploidy, with even a slight increase of crossover frequency. We also showed that this deregulated meiotic behavior may revert back to a strictly regulated one when recovering an allotetraploid progeny in the second generation. Overall, we provide here for the first time a practical and natural way to switch on and off the tight recombination control in a polyploid crop. We also discuss the potential role of this modified regulation of recombination in polyploid speciation success.

genetics↗

bioRxiv2023

MiniRead: a simple and inexpensive do-it-yourself device for multiple analyses of micro-organism growth kinetics

Fitness in micro-organisms can be proxied by growth parameters on different media and/or temperatures. This is achieved done by measuring optical density at 600 nm using a spectrophotometer, which measures the effect of absorbance and side scattering due to turbidity of cells suspensions. However, when growth kinetics must be monitored in many 96-well plates at the same time, buying several 96-channels spectrophotometers is often beyond budgets. The MiniRead device presented here is a simple and inexpensive do-it-yourself 96-well temperature-controlled turbidimeter designed to measure the interception of white light via absorption or side scattering through liquid culture medium. Turbidity is automatically recorded in each well at regular time intervals for up to several days or weeks. Output tabulated text files are recorded into a micro-SD memory card to be easily transferred to a computer. We propose also an R package which allows (1) to compute the non-linear calibration curves required to convert raw readings into cell concentration values, and (2) to analyze growth kinetics output files to automatically estimate growth parameters such as lag time, maximum growth rate, or cell concentration at the plateau. The MiniRead project is freely available under GPL license from https://forgemia.inra.fr/gqe-base/MiniRead. The project includes (1): user manual (Supplementary Material 1), firmware, list of electronic components and printed circuit board manufacturing files for the MiniRead device, and (2) a release containing the MiniRead R package for calibration and data analysis (Supplementary Material 2) with its tutorial (Supplementary Material 3). Detailed device building instructions are available at https://moulon.inrae.fr/materiel_labo/miniread/.

microbiology↗

bioRxiv2021

Quantitative modeling of fine-scale variations in the Arabidopsis thaliana crossover landscape

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 of underlying genomic regions and degree of divergence between homologs. For instance we find that intergenic recombination rate is reduced if those regions are less than 1.5 kb in size. Furthermore, we propose that the presence of single nucleotide polymorphisms is a factor driving enhanced crossover rate compared to when homologous sequences are identical, in agreement with previous works comparing rates in homozygous and heterozygous blocks. Lastly, by integrating these different factors, we produce a quantitative and predictive model of the recombination landscape that reproduces much of the experimental variation.

genetics↗

bioRxiv2021

An additional area of apple domestication with crop-wild gene flow, and also cultivation of the local wild apple, in the Caucasus

Anthropogenic and natural divergence processes remain poorly studied in crop-wild fruit tree complexes, especially in the Caucasus, a pivotal region for plant domestication. We investigated anthropogenic and natural divergence processes in apples in the Caucasus using 26 microsatellite markers amplified in 550 wild and cultivated samples. We found two genetically distinct cultivated populations in Iran that are differentiated from Malus domestica, the standard cultivated apple worldwide. Coalescent-based inferences showed that these two cultivated populations originated from specific domestication events of M. orientalis in Iran. One of the Iranian clusters comprised both cultivated and forest trees, suggesting that either farmers use local wild apple for cultivation or that some forest trees are feral cultivars. We found evidence of substantial wild-crop and crop-crop gene flow in the Caucasus, as has been described in apple in Europe. In the Caucasus, we identified seven genetically differentiated populations of wild apple (Malus orientalis). Niche modeling combined with genetic diversity estimates indicated that these populations likely resulted from range changes during past glaciations. This study identifies Iran as a key region in the domestication of apple and M. orientalis as an additional contributor to the cultivated apple gene pool. Domestication of the apple tree therefore involved multiple origins of domestication in different geographic locations and substantial crop-wild hybridization, as found in other fruit trees. This study also highlights the impact of climate change on the natural divergence of a wild fruit tree and provides a starting point for apple conservation and breeding programs in the Caucasus.

evolutionary biology↗

bioRxiv2020

Large-scale geographic survey provides insights into the colonization history of a major aphid pest on its cultivated apple host in Europe, North America and North Africa

AO_SCPLOWBSTRACTC_SCPLOWWith frequent host shifts involving the colonization of new hosts across large geographical ranges, crop pests are good models for examining the mechanisms of rapid colonization. The microbial partners of pest insects may also be involved in or affected by colonization processes, which has been little studied so far. We investigated the demographic history of the rosy apple aphid, Dysaphis plantaginea, a major pest of the cultivated apple (Malus domestica) in Europe, North Africa and North America, as well as the diversity of its microbiota. We genotyped a comprehensive sample of 714 colonies from Europe, Morocco and the US using mitochondrial (CytB and CO1), bacterial (16s rRNA and TrnpB), and 30 microsatellite markers. We detected five populations spread across the US, Morocco, Western and Eastern Europe and Spain. Populations showed weak genetic differentiation and high genetic diversity, except the ones from Morocco and North America that are likely the result of recent colonization events. Coalescent-based inferences revealed high levels of gene flow among populations during the colonization but did not allow determining the sequence of colonization of Europe, North America and Morroco by D. plantaginea, likely because of the weak genetic differentiation and the occurrence of gene flow among populations. We found that D. plantaginea rarely hosts other endosymbiotic bacteria than its obligate nutritional symbiont Buchnera aphidicola. This suggests that secondary endosymbionts did not play an important role in the rapid spread of the rosy apple aphid. These findings have fundamental importance for understanding pest colonization processes and implications for sustainable pest control programs.

evolutionary biology↗

bioRxiv2020

Enhancing backcross programs through increased recombination

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 elimination of the donor genome in the neighborhood of that QTL will be much slower (linkage drag). Using markers to monitor the genome around the QTL and in the background can accelerate the return to the recurrent parent genome. The success of an introgression will partly depend on the occurrence of crossovers at favorable positions. However, the number of crossovers per generation is limited and their distribution along the genome is heterogeneous. Recently, techniques have been developed to modify these two aspects of recombination. Here, we assess, by simulation, their effect on the efficiency of introgression programs by studying the reduction of the linkage drag and the recovery of the recurrent genome. The selection schemes we simulate begin by two generations of foreground selection and continue with one or more generations of background selection. Our results show that when the QTL is in a region that was initially lacking crossovers, increasing the recombination rate can decrease the linkage drag nearly ten-fold after the foreground selection and improves the return to the recurrent parent. However, if the QTL is in a region already rich in crossovers then increasing recombination proves to be detrimental. Key messageIn breeding programs, recombination is essential for introgression, but introducing more crossovers is beneficial only when the target is in a cold region, otherwise it is detrimental.

genetics↗

bioRxiv2019

CNVmap: a method and software to detect copy number variants from linkage mapping data

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 methods and softwares have been developed to detect CNVs. Such approaches are based on exploiting sequencing data or SNP arrays, but they bypass a wealth of information such as genotyping data from segregating populations, produced e.g. for QTL mapping. Here we propose an original method to both detect and genetically map CNVs using mapping panels. Specifically, we exploit the apparent heterozygous state of duplicated loci: peaks in appropriately defined genome-wide allelic profiles provide highly specific signatures that identify the nature and position of the CNVs. Our original method and software can detect and map automatically up to 33 different predefined types of CNVs based on segregation data only. We validate this approach on simulated and experimental bi-parental mapping panels in two maize and one wheat populations. Most of the events found correspond to having just one extra copy in one of the parental lines but the corresponding allelic value can be that of either parent. We also find cases with two or more additional copies, especially in wheat where these copies locate to homeologues. More generally, our computational tool can be used to give additional value, at no cost, to many datasets produced over the past decade from genetic mapping panels.

genetics↗

bioRxiv2019

Assessing by modeling the consequences of increased recombination in genomic selection of Oryza sativa and Brassica rapa.

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 recombination in plants could increase the genetic gain in a population undergoing genomic selection. The first method, in Oryza sativa, used a mutant of anti-crossover genes to increase global recombination without affecting the recombination landscape. The second one uses the ploidy level of a cross between Brassica rapa and Brassica napus to increase the recombination particularly in pericentromeric regions. These recombination landscapes were used to model recombination while quantitative trait loci positions were based on the actual gene distribution. We simulated selection programs with initially a cross between two inbred lines, for two species. Increased recombination enhanced the response to selection. The amount of enhancement in the cumulative gain largely depended on the species and the number of quantitative trait loci (2, 10, 20, 50, 200 or 1000 per chromosome). Genetic gains were increased up to 30% after 20 generations. Furthermore, modifying the recombination landscape was the most effective: the gain was larger by 25% with the first method and 33% with the second one in B. rapa, and 15% compared to 11% in O. sativa. Thus, increased recombination enhances the genetic gain in genomic selection for long-term selection programs, with visible effects after four to five generations.

genetics↗

bioRxiv2019

Genomic footprints of local adaptation along elevation gradients associate with present phenotypic variation in teosintes

Local adaptation across species range is widespread. Yet, much has to be discovered on its environmental drivers, the underlying functional traits and their molecular determinants. Because elevation gradients display continuous environmental changes at a short geographical scale, they provide an exceptional opportunity to investigate these questions. Here, we used two common gardens to phenotype 1664 plants from 11 populations of annual teosintes. These populations were sampled across two elevation gradients in Mexico. Our results point to a syndrome of adaptation to altitude with the production of offspring that flowered earlier, produced less tillers, and larger, longer and heavier grains with increasing elevation. We genotyped these plants for 178 outlier single nucleotide polymorphisms (SNPs), which had been chosen because they displayed excess of allele differentiation and/or correlation with environmental variables in six populations with contrasted altitudes. A high proportion of outlier SNPs associated with the phenotypic variation of at least one trait. We tested phenotypic pairwise correlations between traits, and found that the higher the correlation, the greater the number of common associated SNPs. In addition, allele frequencies at 87 of the outlier SNPs correlated with an environmental component best summarized by altitudinal variation on a broad sample of 28 populations. Chromosomal inversions were enriched for both phenotypically-associated and environmentally-correlated SNPs. Altogether, our results are consistent with the set-up of an altitudinal syndrome promoted by local adaptation of teosinte populations in the face of gene flow. We showed that pleiotropy is pervasive and potentially has constrained the evolution of traits. Finally, we recovered variants underlying phenotypic variation at adaptive traits. Because elevation mimics climate change through space, these variants may be relevant for future maize breeding. Author summaryAcross their native range, species encounter a diversity of habitats promoting local adaptation of geographically distributed populations. While local adaptation is widespread, much has yet to be discovered about the conditions of its emergence, the targeted traits, their molecular determinants and the underlying ecological drivers. Here we employed a reverse ecology approach, combining phenotypes and genotypes, to mine the determinants of local adaptation of teosinte populations distributed along two steep altitudinal gradients in Mexico. Evaluation of 11 populations in two common gardens located at mid-elevation pointed to the set-up of an altitudinal syndrome, in spite of gene flow. We scanned genomes to identify loci with allele frequencies shifts along elevation. Interestingly, variation at these loci was commonly associated to variation of phenotypes. Because elevation mimics climate change through space, these variants may be relevant for future maize breeding.

evolutionary biology↗

bioRxiv2018

Assessing the response of small RNA populations to allopolyploidy using resynthesized Brassica napus allotetraploids

Allopolyploidy, combining interspecific hybridization with whole genome duplication, has had significant impact on plant evolution. Its evolutionary success is related to the rapid and profound genome reorganizations that allow neo-allopolyploids to form and adapt. Nevertheless, how neo-allopolyploid genomes adapt to regulate their expression remains poorly understood. The hypothesis of a major role for small non-coding RNAs (sRNAs) in mediating the transcriptional response of neo-allopolyploid genomes has progressively emerged. Generally, 21-nt sRNAs mediate post-transcriptional gene silencing (PTGS) by mRNA cleavage whereas 24-nt sRNAs repress transcription (transcriptional gene silencing, TGS) through epigenetic modifications. Here, we characterize the global response of sRNAs to allopolyploidy in Brassica, using three independently resynthesized B. napus allotetraploids surveyed at two different generations in comparison with their diploid progenitors. Our results suggest an immediate but transient response of specific sRNA populations to allopolyploidy. These sRNA populations mainly target non-coding components of the genome but also target the transcriptional regulation of genes involved in response to stresses and in metabolism; this suggests a broad role in adapting to allopolyploidy. We finally identify the early accumulation of both 21- and 24-nt sRNAs involved in regulating the same targets, supporting a PTGS-to-TGS shift at the first stages of the neo-allopolyploid formation. We propose that reorganization of sRNA production is an early response to allopolyploidy in order to control the transcriptional reactivation of various non-coding elements and stress-related genes, thus ensuring genome stability during the first steps of neo-allopolyploid formation.

evolutionary biology↗

bioRxiv2018

Recombination suppression in heterozygotes for a pericentric inversion induces interchromosomal effect on crossovers in Arabidopsis

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 that are known at heterozygous state to impair COs in various organisms. In this paper, we have investigated the effect that a large pericentric inversion involving chromosome 3 of Arabidopsis thaliana has on male and female recombination. The inversion associated to a T-DNA dependent mutation likely resulted from a side effect of the T-DNA integration. Reciprocal backcross populations, each consisting of over 400 individuals, obtained from the T-DNA mutant and the wild type, both crossed with Landsberg, have been analyzed at genome-wide level by 143 SNPs. We found a strong suppression of COs in the rearranged region in both male and female meiosis. As expected, we did not detect single COs in the inverted region consistently with the post-meiotic selection operating against unbalanced gametes. Cytological analysis of chiasmata in F1 plants confirmed that COs are effectively dropping in chromosome 3 pair. Indeed, CO failure within the inversion is not altogether counterbalanced by CO increase in the regions outside the inversion on chromosome 3. Strikingly, this CO suppression induces a significant increase of COs in chromosome pairs 1, 2 and 5 in male meiosis. We conclude that these chromosomes acquire additional COs thereby compensating the recombination suppression occurring in chromosome 3, similarly to what has been described as interchromosomal (IC) effect in other organisms. In female meiosis, IC effect is not evident. This may be related to the fact that CO number in female is close to the minimum value imposed by the obligatory CO rule.\n\nAuthor SummaryIt is well known that chromosome structure changes in heterozygous condition influence the pattern of meiotic recombination at broad scale. In natural populations, inversions are recognized as the most effective force to reduce COs. In this way, adaptive allele combinations which otherwise would be broken by recombination are maintained. In the present work, we studied the effect on recombination of a large pericentric inversion involving Arabidopsis chromosome 3. The analysis on heterozygous populations provided evidence of strong recombination suppression in chromosome 3. However, the most striking aspect of this study is the finding that the failure of chromosome 3 to recombine is coupled to increased CO frequencies on the other chromosome pairs in male meiosis. These CO compensatory increases are strictly an interchromosomal (IC) effect as was first described in Drosophila. As far as we know, it is the first time IC effect has been reported in plants. Unfortunately, the molecular mechanisms underlying IC effect in the other organisms are still elusive. To understand how a CO change on just one chromosome triggers the global response of the meiocyte to obtain the adequate CO number/cell remains a fascinating question in sexually reproducing species.

genetics↗

bioRxiv2018

Role of cis, trans, and inbreeding effects on meiotic recombination in Saccharomyces cerevisiae

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 strain, covering chromosomes VI and XI entirely, and part of chromosome I. We found an average number of crossovers per chromosome ranging between 1.0 and 9.5 across strains (\"domesticated\" or not), which is higher than the average between 0.5 and 1.5 found in most organisms. In the different intervals analyzed, recombination showed up to 9-fold variation across strains but global recombination landscapes along chromosomes varied less. We also built an incomplete diallel experiment to measure recombination rates in one region of chromosome XI in 10 different crosses involving five parental strains. Our overall results indicate that recombination rate is increasingly positively correlated with sequence similarity between homologs (i) in DSB rich regions within intervals, (ii) in entire intervals, and (iii) at the whole genome scale. Therefore, these correlations cannot be explained by cis-effects only. In addition, by using a quantitative genetics analysis, we identified an inbreeding effect that reduces recombination rate in homozygous genotypes while other interaction effects (specific combining ability) or additive effects (general combining ability) are found to be weak. Finally, we measured significant crossover interference in some strains, and interference intensity was positively correlated with crossover number.\n\nAuthor SummaryMeiosis is a key process for sexually reproducing organisms by producing gametes with a halved set of genetic material. An essential step of meiosis is the formation of crossovers which are reciprocal exchanges of genetic material between chromosomes inherited from both parents. Crossovers ensure proper chromosome segregation and thus viable gametes. They also create novel genetic diversity which contributes to evolution and permits genetic improvement of agriculturally important species. Most living organisms produce between one and three crossovers per chromosome, and tight regulatory mechanisms control the number of crossovers and their distribution along chromosomes. In spite of their potential importance for biotechnological applications, such mechanisms are still poorly understood.\n\nUsing a high throughput method based on fluorescent markers, we investigated the diversity of recombination in the budding yeast Saccharomyces cerevisiae. We observed up to 9-fold differences in numbers of crossovers across hybrids obtained by crossing different strains with a common tester, and this variation was correlated with the degree of DNA sequence similarity between homologous chromosomes. By also investigating homozygotes, we conclude that on the one hand too much sequence divergence impairs recombination in distantly-related hybrids, and on the other hand complete homozygosity is also associated with lower numbers of crossovers.

genetics↗