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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 the QTL, elimination of the donor genome around that QTL will be much slower than in the rest of the genome (i.e. linkage drag). Using markers to monitor the genome around the QTL and in the genetic background can accelerate the return to the recurrent parent genome. Successful introgression of a locus depends partly 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 recombination parameters. Results In this paper, we assess, by simulations in the context of Brassicaceae, the effect of increased recombination on the efficiency of introgression programs by studying the decrease in linkage drag and the recovery of the recurrent genome. The simulated selection schemes 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 initially lacked crossovers, an increase in recombination rate can decrease linkage drag by nearly ten-fold after the foreground selection and improves the return to the recurrent parent. However, if the QTL is in a region that is already rich in crossovers, an increase in recombination rate is detrimental. Conclusions Depending on the recombination rate in the region targeted for introgression, increasing it can be beneficial or detrimental. Thus, the simulations analysed in this paper help us understand how an increase in recombination rate can be beneficial. They also highlight the best methods that can be used to increase recombination rate, depending on the situation. Supplementary Information The online version contains supplementary material available at 10.1186/s12711-021-00619-0.

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.

With 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.

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 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. Numerous methods and softwares based on different technologies (amplicons, CGH, tiling, or SNP arrays, or sequencing) have already been developed to detect CNVs, 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 biparental mapping panels in two maize populations and one wheat population. 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.

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.

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 neoallopolyploids to form and adapt. Nevertheless, how neoallopolyploid genomes adapt to regulate their expression remains poorly understood. The hypothesis of a major role for small noncoding RNAs (sRNAs) in mediating the transcriptional response of neoallopolyploid genomes has progressively emerged. Generally, 21-nt sRNAs mediate posttranscriptional gene silencing by mRNA cleavage, whereas 24-nt sRNAs repress transcription (transcriptional gene silencing) through epigenetic modifications. Here, we characterize the global response of sRNAs to allopolyploidy in Brassica, using three independently resynthesized Brassica napus allotetraploids originating from crosses between diploid Brassica oleracea and Brassica rapa accessions, 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 noncoding 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 posttranscriptional gene silencing to transcriptional gene silencing shift at the first stages of the neoallopolyploid formation. We propose that reorganization of sRNA production is an early response to allopolyploidy in order to control the transcriptional reactivation of various noncoding elements and stress-related genes, thus ensuring genome stability during the first steps of neoallopolyploid formation.

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 26S. cerevisiaestrains 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 bycis-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.Author 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.Using 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.

Multiparental designs combined with dense genotyping of parents have been proposed as a way to increase the diversity and resolution of quantitative trait loci (QTL) mapping studies, using methods combining linkage disequilibrium information with linkage analysis (LDLA). Two new nested association mapping designs adapted to European conditions were derived from the complementary dent and flint heterotic groups of maize (Zea mays L.). Ten biparental dent families (N = 841) and 11 biparental flint families (N = 811) were genotyped with 56,110 single nucleotide polymorphism markers and evaluated as test crosses with the central line of the reciprocal design for biomass yield, plant height, and precocity. Alleles at candidate QTL were defined as (i) parental alleles, (ii) haplotypic identity by descent, and (iii) single-marker groupings. Between five and 16 QTL were detected depending on the model, trait, and genetic group considered. In the flint design, a major QTL (R2 = 27%) with pleiotropic effects was detected on chromosome 10, whereas other QTL displayed milder effects (R2 < 10%). On average, the LDLA models detected more QTL but generally explained lower percentages of variance, consistent with the fact that most QTL display complex allelic series. Only 15% of the QTL were common to the two designs. A joint analysis of the two designs detected between 15 and 21 QTL for the five traits. Of these, between 27 for silking date and 41% for tasseling date were significant in both groups. Favorable allelic effects detected in both groups open perspectives for improving biomass production.

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 >1500 backcrosses for both male and female meiosis. This unique data set allows us to take a two-pathway modeling approach based on superposing a fraction p of noninterfering crossovers and a fraction (1 − p) of interfering crossovers generated using the gamma model characterized by its interference strength nu. Within this framework, we fit the two-pathway model to the data and compare crossover interference strength between chromosomes and then along chromosomes. We find that the interfering pathway has markedly higher interference strength nu in female than in male meiosis and also that male meiosis has a higher proportion p of noninterfering crossovers. Furthermore, we test for possible intrachromosomal variations of nu and p. Our conclusion is that there are clear differences between left and right arms as well as between central and peripheral regions. Finally, statistical tests unveil a genome-wide picture of small-scale heterogeneities, pointing to the existence of hot regions in the genome where crossovers form preferentially without interference.

Genetic architecture of flowering time in maize was addressed by synthesizing a total of 313 quantitative trait loci (QTL) available for this trait. These were analyzed first with an overview statistic that highlighted regions of key importance and then with a meta-analysis method that yielded a synthetic genetic model with 62 consensus QTL. Six of these displayed a major effect. Meta-analysis led in this case to a twofold increase in the precision in QTL position estimation, when compared to the most precise initial QTL position within the corresponding region. The 62 consensus QTL were compared first to the positions of the few flowering-time candidate genes that have been mapped in maize. We then projected rice candidate genes onto the maize genome using a synteny conservation approach based on comparative mapping between the maize genetic map and japonica rice physical map. This yielded 19 associations between maize QTL and genes involved in flowering time in rice and in Arabidopsis. Results suggest that the combination of meta-analysis within a species of interest and synteny-based projections from a related model plant can be an efficient strategy for identifying new candidate genes for trait variation.

International audience; Crossovers (COs) shuffle genetic information and allow balanced segregation of homologous chromosomes during the first division of meiosis. In several organisms, mutants demonstrate that two molecularly distinct pathways produce COs. One pathway produces class I COs that exhibit interference (lowered probability of nearby COs), and the other pathway produces class II COs with little or no interference. However, the relative contributions, genomic distributions, and interactions of these two pathways are essentially unknown in nonmutant organisms because marker segregation only indicates that a CO has occurred, not its class type. Here, we combine the efficiency of light microscopy for revealing cellular functions using fluorescent probes with the high resolution of electron microscopy to localize and characterize COs in the same sample of meiotic pachytene chromosomes from wild-type tomato. To our knowledge, for the first time, every CO along each chromosome can be identified by class to unveil specific characteristics of each pathway. We find that class I and II COs have different recombination profiles along chromosomes. In particular, class II COs, which represent about 18% of all COs, exhibit no interference and are disproportionately represented in pericentric heterochromatin, a feature potentially exploitable in plant breeding. Finally, our results demonstrate that the two pathways are not independent because there is interference between class I and II COs.

The vast majority of meiotic recombination events (crossovers (COs) and non-crossovers (NCOs)) cluster in narrow hotspots surrounded by large regions devoid of recombinational activity. Here, using a new molecular approach in plants, called “pollen-typing”, we detected and characterized hundreds of CO and NCO molecules in two different hotspot regions in Arabidopsis thaliana. This analysis revealed that COs are concentrated in regions of a few kilobases where their rates reach up to 50 times the genome average. The hotspots themselves tend to cluster in regions less than 8 kilobases in size with overlapping CO distribution. Non-crossover (NCO) events also occurred in the two hotspots but at very different levels (local CO/NCO ratios of 1/1 and 30/1) and their track lengths were quite small (a few hundred base pairs). We also showed that the ZMM protein MSH4 plays a role in CO formation and somewhat unexpectedly we also found that it is involved in the generation of NCOs but with a different level of effect. Finally, factors acting in cis and in trans appear to shape the rate and distribution of COs at meiotic recombination hotspots., Author Summary During meiosis, genomes are reshuffled by recombination between homologous chromosomes. Reciprocal recombination events called crossovers are clustered in several kilobase-wide regions called hotspots, where their frequency is greatly enhanced compared to adjacent regions. Our understanding of hotspot organization is based on analyses performed in only a few species and rules differ between species. For the first time, hundreds of recombination events were analyzed in Arabidopsis thaliana revealing several new features: (i) crossovers are concentrated in hotspots where their rate reaches up to 50 times the genome average; (ii) non-crossovers events, (also called gene conversions not associated with crossovers) also occur in hotspots but at very different levels; and (iii) in the absence of the recombination protein MSH4, the crossover rate is dramatically reduced (70 times less than the wild-type level) and the crossover distribution within a hotspot is also largely modified; unexpectedly, the non-crossover rate was also altered (15% of the wild-type level at a hotspot). Finally we showed that factors acting in cis and in trans may influence the level and distribution of crossovers at and between hotspots.

International audience; The role played by whole-genome duplication (WGD) in evolution and adaptation is particularly well illustrated in allopolyploids, where WGD is concomitant with interspecific hybridization. This Genome Shock', usually accompanied by structural and functional modifications, has been associated with the activation of transposable elements (TEs). However, the impact of allopolyploidy on TEs has been studied in only a few polyploid species, and not in Brassica, which has been marked by recurrent polyploidy events. Here, we developed sequence-specific amplification polymorphism (SSAP) markers for three contrasting TEs, and compared profiles between resynthesized Brassica napus allotetraploids and their diploid Brassica progenitors. To evaluate restructuring at TE insertion sites, we scored changes in SSAP profiles and analysed a large set of differentially amplified SSAP bands. No massive structural changes associated with the three TEs surveyed were detected. However, several transposition events, specific to the youngest TE originating from the B.oleracea genome, were identified. Our study supports the hypothesis that TE responses to allopolyploidy are highly specific. The changes observed in SSAP profiles lead us to hypothesize that they may partly result from changes in DNA methylation, questioning the role of epigenetics during the formation of a new allopolyploid genome.

L'article original est publié par The American Society of Plant Biologists; International audience; Abscisic acid-, stress-, and ripening-induced (ASR) proteins were first described about 15 years ago as accumulating to high levels during plant developmental processes and in response to diverse stresses. Currently, the effects of ASRs on water deficit tolerance and the ways in which their physiological and biochemical functions lead to this stress tolerance remain poorly understood. Here, we characterized the ASR gene family from maize (Zea mays), which contains nine paralogous genes, and showed that maize ASR1 (ZmASR1) was encoded by one of the most highly expressed paralogs. Ectopic expression of ZmASR1 had a large overall impact on maize yield that was maintained under water-limited stress conditions in the field. Comparative transcriptomic and proteomic analyses of wild-type and ZmASR1-overexpressing leaves led to the identification of three transcripts and 16 proteins up-or down-regulated by ZmASR1. The majority of them were involved in primary and/or cellular metabolic processes, including branched-chain amino acid (BCAA) biosynthesis. Metabolomic and transcript analyses further indicated that ZmASR1-overexpressing plants showed a decrease in BCAA compounds and changes in BCAA-related gene expression in comparison with wild-type plants. Interestingly, within-group correlation matrix analysis revealed a close link between 13 decreased metabolites in ZmASR1-overexpressing leaves, including two BCAAs. Among these 13 metabolites, six were previously shown to be negatively correlated to biomass, suggesting that ZmASR1-dependent regulation of these 13 metabolites might contribute to regulate leaf growth, resulting in improvement in kernel yield.

Background During meiosis, homologous chromosomes exchange segments via the formation of crossovers. This phenomenon is highly regulated; in particular, crossovers are distributed heterogeneously along the physical map and rarely arise in close proximity, a property referred to as "interference". Crossover positions form patterns that give clues about how crossovers are formed. In several organisms including yeast, tomato, Arabidopsis, and mouse, it is believed that crossovers form via at least two pathways, one interfering, the other not. Results We have developed a software package - "CODA", for CrossOver Distribution Analyzer - which allows one to quantitatively characterize crossover patterns by fitting interference models to experimental data. Two families of interfering models are provided: the "gamma" model and the "beam-film" model. The user can specify single or two-pathways modeling, and the software package infers the model's parameters and their confidence intervals. CODA can handle data produced from measurements on bivalents or gametes, in the form of continuous crossover positions or marker genotyping. We illustrate the possibilities on data from Wheat, corn and mouse. Conclusions CODA extends the kind of crossover data that could be analyzed so far to include gametic data (rather than only bivalents/tetrads) when using two-pathways modeling. It will also enable users to perform analyses based on the beam-film model. CODA implements that model's complex physics and mathematics, and uses a summary statistic to overcomes the lack of a computable likelihood which has hampered its use till now.

In most species, crossovers (COs) are essential for the accurate segregation of homologous chromosomes at the first meiotic division. Their number and location are tightly regulated. Here, we report a detailed, genome-wide characterization of the rate and localization of COs in Arabidopsis thaliana, in male and female meiosis. We observed dramatic differences between male and female meiosis which included: (i) genetic map length; 575 cM versus 332 cM respectively; (ii) CO distribution patterns: male CO rates were very high at both ends of each chromosome, whereas female CO rates were very low; (iii) correlations between CO rates and various chromosome features: female CO rates correlated strongly and negatively with GC content and gene density but positively with transposable elements (TEs) density, whereas male CO rates correlated positively with the CpG ratio. However, except for CpG, the correlations could be explained by the unequal repartition of these sequences along the Arabidopsis chromosome. For both male and female meiosis, the number of COs per chromosome correlates with chromosome size expressed either in base pairs or as synaptonemal complex length. Finally, we show that interference modulates the CO distribution both in male and female meiosis., Author Summary Reciprocal exchanges of genetic material (crossovers) between homologous chromosomes ensure their proper segregation to generate gametes. Their number and location along chromosomes are tightly regulated. We localized precisely the position of 13,535 crossovers in more than 3,000 plants of Arabidopsis thaliana. While A. thaliana is a hermaphrodite plant with male and female meiosis occurring in the same flower and thus with the same genome, we observed dramatic differences in the distribution and the rate of crossovers along chromosomes in male and female meiosis. On average, chromosomes recombine 1.7 times more in male than in female meiosis. Moreover, male CO rates are very high at both ends of each chromosome, whereas female CO rates are very low. Finally, for the first time in a eukaryote, we show that the correlations between CO rates and various chromosome features differ in male and female meiosis. Female CO rates correlated strongly and negatively with GC content and gene density but positively with transposable elements density, whereas male CO rates correlated positively with the CpG ratio. However, most of the correlations could be explained by the structure of the Arabidopsis genome.

International audience; Earliness is very important for the adaptation of wheat to environmental conditions and the achievement of high grain yield. A detailed knowledge of key genetic components of the life cycle would enable an easier control by the breeders. The objective of the study was to investigate the effect of candidate genes on flowering time. Using a collection of hexaploid wheat composed of 235 lines from diverse geographical origins, we conducted an association study for six candidate genes for flowering time and its components (vernalization sensitivity and earliness per se). The effect on the variation of earliness components of polymorphisms within the copies of each gene was tested in ANOVA models accounting for the underlying genetic structure. The collection was structured in five groups that minimized the residual covariance. Vernalization requirement and lateness tend to increase according to the mean latitude of each group. Heading date for an autumnal sowing was mainly determined by the earliness per se. Except for the Constans (CO) gene orthologous of the barley HvCO3, all gene polymorphisms had a significant impact on earliness components. The three traits used to quantify vernalization requirement were primarily associated with polymorphisms at Vrn-1 and then at Vrn-3 and Luminidependens (LD) genes. We found a good correspondence between spring/winter types and genotypes at the three homeologous copies of Vrn-1. Earliness per se was mainly explained by polymorphisms at Vrn-3 and to a lesser extent at Vrn-1, Hd-1 and Gigantea (GI) genes. Vernalization requirement and earliness as a function of geographical origin, as well as the possible role of the breeding practices in the geographical distribution of the alleles and the hypothetical adaptive value of the candidate genes, are discussed.

International audience; Meiotic chromosome pairing involves not only recognition of homology but also juxtaposition of entire chromosomes in a topologically regular way. Analysis of filamentous fungus Sordaria macrospora reveals that recombination proteins Mer3, Msh4, and Mlh1 play direct roles in all of these aspects, in advance of their known roles in recombination. Absence of Mer3 helicase results in interwoven chromosomes, thereby revealing the existence of features that specifically ensure "entanglement avoidance." Entanglements that remain at zygotene, i.e., "interlockings," require Mlh1 for resolution, likely to eliminate constraining recombinational connections. Patterns of Mer3 and Msh4 foci along aligned chromosomes show that the double-strand breaks mediating homologous alignment have spatially separated ends, one localized to each partner axis, and that pairing involves interference among developing interhomolog interactions. We propose that Mer3, Msh4, and Mlh1 execute all of these roles during pairing by modulating the state of nascent double-strand break/partner DNA contacts within axis-associated recombination complexes.

Background Kernel moisture at harvest is an important trait since a low value is required to prevent unexpected early germination and ensure seed preservation. It is also well known that early germination occurs in viviparous mutants, which are impaired in abscisic acid (ABA) biosynthesis. To provide some insight into the genetic determinism of kernel desiccation in maize, quantitative trait loci (QTLs) were detected for traits related to kernel moisture and ABA content in both embryo and endosperm during kernel desiccation. In parallel, the expression and mapping of genes involved in kernel desiccation and ABA biosynthesis, were examined to detect candidate genes. Results The use of an intermated recombinant inbred line population allowed for precise QTL mapping. For 29 traits examined in an unreplicated time course trial of days after pollination, a total of 78 QTLs were detected, 43 being related to kernel desiccation, 15 to kernel weight and 20 to ABA content. Multi QTL models explained 35 to 50% of the phenotypic variation for traits related to water status, indicating a large genetic control amenable to breeding. Ten of the 20 loci controlling ABA content colocated with previously detected QTLs controlling water status and ABA content in water stressed leaves. Mapping of candidate genes associated with kernel desiccation and ABA biosynthesis revealed several colocations between genes with putative functions and QTLs. Parallel investigation via RT-PCR experiments showed that the expression patterns of the ABA-responsive Rab17 and Rab28 genes as well as the late embryogenesis abundant Emb5 and aquaporin genes were related to desiccation rate and parental allele effect. Database searches led to the identification and mapping of two zeaxanthin epoxidase (ZEP) and five novel 9-cis-epoxycarotenoid dioxygenase (NCED) related genes, both gene families being involved in ABA biosynthesis. The expression of these genes appeared independent in the embryo and endosperm and not correlated with ABA content in either tissue. Conclusions A high resolution QTL map for kernel desiccation and ABA content in embryo and endosperm showed several precise colocations between desiccation and ABA traits. Five new members of the maize NCED gene family and another maize ZEP gene were identified and mapped. Among all the identified candidates, aquaporins and members of the Responsive to ABA gene family appeared better candidates than NCEDs and ZEPs.

In wheat (Triticum aestivum L.), the crossover (CO) frequency increases gradually from the centromeres to the telomeres. However, little is known about the factors affecting both the distribution and the intensity of recombination along this gradient. To investigate this, we studied in detail the pattern of CO along chromosome 3B of bread wheat. A dense reference genetic map comprising 102 markers homogeneously distributed along the chromosome was compared to a physical deletion map. Most of the COs (90%) occurred in the distal subtelomeric regions that represent 40% of the chromosome. About 27% of the proximal regions surrounding the centromere showed a very weak CO frequency with only three COs found in the 752 gametes studied. Moreover, we observed a clear decrease of CO frequency on the distal region of the short arm. Finally, the intensity of interference was assessed for the first time in wheat using a Gamma model. The results showed m values of 1.2 for male recombination and 3.5 for female recombination, suggesting positive interference along wheat chromosome 3B.

In many species, sex-related differences in crossover (CO) rates have been described at chromosomal and regional levels. In this study, we determined the CO distribution along the entire Arabidopsis thaliana Chromosome 4 (18 Mb) in male and female meiosis, using high density genetic maps built on large backcross populations (44 markers, .1,300 plants). We observed dramatic differences between male and female map lengths that were calculated as 88 cM and 52 cM, respectively. This difference is remarkably parallel to that between the total synaptonemal complex lengths measured in male and female meiocytes by immunolabeling of ZYP1 (a component of the synaptonemal complex). Moreover, CO landscapes were clearly different: in particular, at both ends of the map, male CO rates were higher (up to 4-fold the mean value), whereas female CO rates were equal or even below the chromosomal average. This unique material gave us the opportunity to perform a detailed analysis of CO interference on Chromosome 4 in male and female meiosis. The number of COs per chromosome and the distances between them clearly departs from randomness. Strikingly, the interference level (measured by coincidence) varied significantly along the chromosome in male meiosis and was correlated to the physical distance between COs. The significance of this finding on the relevance of current CO interference models is discussed.

International audience; Cytokinin oxidases (CKOs) play a major role in the regulation of hormone levels in plants by irreversibly degrading cytokinins. Two new cDNAs from maize (CKO2 and CKO3) were cloned and CKO activity of a recombinant CKO3 enzyme was demonstrated. CKO2 and CKO3 encode flavoproteins with 93% identity among each other compared with 45% identity with CKO1. The respective genes were mapped to BIN 3.05/06 and BIN 8.06 which belong to duplicated regions of the maize genome. For a better understanding of the role of CKO2 and CKO3 in maize development, their expression profiles were analysed in different organs and during kernel development via semi-quantitative RT-PCR. Different spatial and temporal expression patterns were observed for the two genes, as well as for CKO1 and two additional genes CKO4 and CKO5. CKO2 to CKO5 genes were mainly expressed in vegetative tissues, with unique expression patterns. CKO1 was most strongly expressed in the kernel. All five genes were expressed at early stages of kernel development, a period when a peak in cytokinin levels and a high cell division rate in the endosperm have been described. However, each gene had its own expression profile with a major difference concerning the onset of expression.

Summary: Breeding programs face the challenge of integrating information from genomics and from quantitative trait loci (QTL) analysis in order to identify genomic sequences controlling the variation of important traits. Despite the development of integrative databases, building a consensus map of genes, QTL and other loci gathered from multiple maps remains a manual and tedious task. Nevertheless, this is a critical step to reveal co-locations between genes and QTL. Another important matter is to determine whether QTL linked to same traits or related ones is detected in independent experiments and located in the same region, and represents a single locus or not. Statistical tools such as meta-analysis can be used to answer this question. BioMercator has been developed to automate map compilation and QTL meta-analysis, and to visualize co-locations between genes and QTL through a graphical interface. Availability: Available upon request (http://moulon/~bioinfo/BioMercator/). Free of charge for academic use.

A CO2 assay circuit adapted to in vitro culture was designed to investigate CO2 exchanges in test tube-grown Vitis rupestris plantlets. The CO2 concentration of the air in culture tubes was measured by injection of samples in the open circuit. It was observed under the culture conditions used that the CO2 content stabilized during the light phase at 3 times the CO2 compensation point. Measurements of dark respiration under closed circuit conditions at every two-hour interval during the night did not reveal any limiting by lack of the substrate under mixotrophic culture conditions. A mathematical model of the influence of ambient CO2 concentration on net CO2 uptake rates under closed circuit conditions was devised and used to compare net photosynthesis at different lighting levels. Measurement of CO2 evolution into CO2-free air under open circuit conditions revealed a post-illumination burst characteristic of photorespiration which increased with the temperature.

In many species, sex-related differences in crossover (CO) rates have been described at chromosomal and regional levels. In this study, we determined the CO distribution along the entire Arabidopsis thaliana Chromosome 4 (18 Mb) in male and female meiosis, using high density genetic maps built on large backcross populations (44 markers, >1,300 plants). We observed dramatic differences between male and female map lengths that were calculated as 88 cM and 52 cM, respectively. This difference is remarkably parallel to that between the total synaptonemal complex lengths measured in male and female meiocytes by immunolabeling of ZYP1 (a component of the synaptonemal complex). Moreover, CO landscapes were clearly different: in particular, at both ends of the map, male CO rates were higher (up to 4-fold the mean value), whereas female CO rates were equal or even below the chromosomal average. This unique material gave us the opportunity to perform a detailed analysis of CO interference on Chromosome 4 in male and female meiosis. The number of COs per chromosome and the distances between them clearly departs from randomness. Strikingly, the interference level (measured by coincidence) varied significantly along the chromosome in male meiosis and was correlated to the physical distance between COs. The significance of this finding on the relevance of current CO interference models is discussed., Author Summary Meiotic crossovers between homologous chromosomes ensure their proper segregation to generate ultimately gametes. They also create new allelic combinations which contribute to the diversity of traits among individuals. In all eukaryotes, the number and the localization of crossovers along chromosomes are not random. In addition, crossovers are not independent of each other: the occurrence of a crossover lowers the probability that another crossover arises in its vicinity. The mechanism of this phenomenon, called “crossover interference,” is one of the most challenging puzzles that geneticists have been faced with in the last century. In this paper, we precisely described the distribution of crossovers along Chromosome 4 of the model plant species Arabidopsis thaliana, separately in male and female meiosis. Interestingly, we observed that crossovers are 1.7 more numerous in male than in female meiosis, and this increase is especially marked at the ends of the chromosome. Moreover, our results provide the first evidence that the level of interference along a chromosome is not a constant and is correlated with the physical distance between crossovers. These results shed new light on the determinism of crossover localization and could have important outcomes on the relevance of current models of crossover interference.