Intraspecific variation of recombination rate in maize

An ultra-high-density genetic map provides insights into genome synteny, recombination landscape and taproot skin colour in radish (Raphanus sativus L.)

High-density genetic map is a valuable tool for exploring novel genomic information, quantitative trait locus (QTL) mapping and gene discovery of economically agronomic traits in plant species. However, high-resolution genetic map applied to tag QTLs associated with important traits and to investigate genomic features underlying recombination landscape in radish (Raphanus sativus) remains largely unexplored. In this study, an ultra-high-density genetic map with 378 738 SNPs covering 1306.8 cM in nine radish linkage groups (LGs) was developed by a whole-genome sequencing-based approach. A total of 18 QTLs for 11 horticulture traits were detected. The map-based cloning data indicated that the R2R3-MYB transcription factor RsMYB90 was a crucial candidate gene determining the taproot skin colour. Comparative genomics analysis among radish, Brassica rapa and B. oleracea genome revealed several genomic rearrangements existed in the radish genome. The highly uneven distribution of recombination was observed across the nine radish chromosomes. Totally, 504 recombination hot regions (RHRs) were enriched near gene promoters and terminators. The recombination rate in RHRs was positively correlated with the density of SNPs and gene, and GC content, respectively. Functional annotation indicated that genes within RHRs were mainly involved in metabolic process and binding. Three QTLs for three traits were found in the RHRs. The results provide novel insights into the radish genome evolution and recombination landscape, and facilitate the development of effective strategies for molecular breeding by targeting and dissecting important traits in radish.

Crossover Interference: Shedding Light on the Evolution of Recombination

Through recombination, genes are freed to evolve more independently of one another, unleashing genetic variance hidden in the linkage disequilibrium that accumulates through selection combined with drift. Yet crossover numbers are evolutionarily constrained, with at least one and not many more than one crossover per bivalent in most taxa. Crossover interference, whereby a crossover reduces the probability of a neighboring crossover, contributes to this homogeneity. The mechanisms by which interference is achieved and crossovers are regulated are a major current subject of inquiry, facilitated by novel methods to visualize crossovers and to pinpoint recombination events. Here, we review patterns of crossover interference and the models built to describe this process. We then discuss the selective forces that have likely shaped interference and the regulation of crossover numbers.

Assessing by Modeling the Consequences of Increased Recombination in Recurrent Selection of Oryza sativa and Brassica rapa

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 to increase recombination in plants could increase genetic gain in a population undergoing recurrent selection such as in genomic selection programs. The first method, in Oryza sativa, used a mutant of anti-crossover genes, increasing global recombination without affecting the recombination landscape shape. The second one used the ploidy level of a cross between Brassica rapa and Brassica napus, increasing recombination especially in pericentromeric regions. Our modeling framework used these recombination landscapes and sampled quantitative trait loci positions from the actual gene distributions. 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, increasing recombination in cold regions was the most effective: the gain was larger by 25% with the first method and 34% with the second one in B. rapa, and 12% compared to 16% in O. sativa In summary, increased recombination enhances the genetic gain in long-term selection programs, with visible effects after four to five generations.

Progressive heterosis in genetically defined tetraploid maize

Progressive heterosis, i.e., the additional hybrid vigor in double-cross tetraploid hybrids not found in their single-cross tetraploid parents, has been documented in a number of species including alfalfa, potato, and maize. In this study, four artificially induced maize tetraploids, directly derived from standard inbred lines, were crossed in pairs to create two single-cross hybrids. These hybrids were then crossed to create double-cross hybrids containing genetic material from all four original lines. Replicated field-based phenotyping of the materials over four years indicated a strong progressive heterosis phenotype in tetraploids but not in their diploid counterparts. In particular, the above ground dry weight phenotype of double-cross tetraploid hybrids was on average 34% and 56% heavier than that of the single-cross tetraploid hybrids and the double-cross diploid counterparts, respectively. Additionally, whole-genome resequencing of the original inbred lines and further analysis of these data did not show the expected spectrum of alleles to explain tetraploid progressive heterosis under the complementation of complete recessive model. These results underscore the reality of the progressive heterosis phenotype, its potential utility for increasing crop biomass production, and the need for exploring alternative hypothesis to explain it at a molecular level.

Population genomics reveals a fine-scale recombination landscape for genetic improvement of cotton

Recombination breaks up ancestral linkage disequilibrium, creates combinations of alleles, affects the efficiency of natural selection, and plays a major role in crop domestication and improvement. However, there is little knowledge regarding the variation in the population-scaled recombination rate in cotton. We constructed recombination maps and characterized the difference in the genomic landscape of the population-scaled recombination rate between Gossypium hirsutum and G. arboreum and sub-genomes based on the 381 sequenced G. hirsutum and 215 G. arboreum accessions. Comparative genomics identified large structural variations and syntenic genes in the recombination regions, suggesting that recombination was related to structural variation and occurred preferentially in the distal chromosomal regions. Correlation analysis indicated that recombination was only slightly affected by geographical distribution and breeding period. A genome-wide association study (GWAS) was performed with 15 agronomic traits using 267 cotton accessions and identified 163 quantitative trait loci (QTL) and an important candidate gene (Ghir_COL2) for early maturity traits. Comparative analysis of recombination and a GWAS revealed that the QTL of fibre quality traits tended to be more common in high-recombination regions than were those of yield and early maturity traits. These results provide insights into the population-scaled recombination landscape, suggesting that recombination contributed to the domestication and improvement of cotton, which provides a useful reference for studying recombination in other species.

Construction of Genetic Linkage Maps in Multiparental Populations

Construction of genetic linkage maps has become a routine step for mapping quantitative trait loci (QTL), particularly in animal and plant breeding populations. Many multiparental populations have recently been produced to increase genetic diversity and QTL mapping resolution. However, few software packages are available for map construction in these populations. In this paper, we build a general framework for the construction of genetic linkage maps from genotypic data in diploid populations, including bi- and multiparental populations, cross-pollinated (CP) populations, and breeding pedigrees. The framework is implemented as an automatic pipeline called magicMap, where the maximum multilocus likelihood approach utilizes genotypic information efficiently. We evaluate magicMap by extensive simulations and eight real datasets: one biparental, one CP, four multiparent advanced generation intercross (MAGIC), and two nested association mapping (NAM) populations, the number of markers ranging from a few hundred to tens of thousands. Not only is magicMap the only software capable of accommodating all of these designs, it is more accurate and robust to missing genotypes and genotyping errors than commonly used packages.

Genotyping-by-sequencing and SNP-arrays are complementary for detecting quantitative trait loci by tagging different haplotypes in association studies

BACKGROUND

Single Nucleotide Polymorphism (SNP) array and re-sequencing technologies have different properties (e.g. calling rate, minor allele frequency profile) and drawbacks (e.g. ascertainment bias). This lead us to study their complementarity and the consequences of using them separately or combined in diversity analyses and Genome-Wide Association Studies (GWAS). We performed GWAS on three traits (grain yield, plant height and male flowering time) measured in 22 environments on a panel of 247 F1 hybrids obtained by crossing 247 diverse dent maize inbred lines with a same flint line. The 247 lines were genotyped using three genotyping technologies (Genotyping-By-Sequencing, Illumina Infinium 50 K and Affymetrix Axiom 600 K arrays).

RESULTS

The effects of ascertainment bias of the 50 K and 600 K arrays were negligible for deciphering global genetic trends of diversity and for estimating relatedness in this panel. We developed an original approach based on linkage disequilibrium (LD) extent in order to determine whether SNPs significantly associated with a trait and that are physically linked should be considered as a single Quantitative Trait Locus (QTL) or several independent QTLs. Using this approach, we showed that the combination of the three technologies, which have different SNP distributions and densities, allowed us to detect more QTLs (gain in power) and potentially refine the localization of the causal polymorphisms (gain in resolution).

CONCLUSIONS

Conceptually different technologies are complementary for detecting QTLs by tagging different haplotypes in association studies. Considering LD, marker density and the combination of different technologies (SNP-arrays and re-sequencing), the genotypic data available were most likely enough to well represent polymorphisms in the centromeric regions, whereas using more markers would be beneficial for telomeric regions.

A large nested association mapping population for breeding and quantitative trait locus mapping in Ethiopian durum wheat

The Ethiopian plateau hosts thousands of durum wheat (Triticum turgidum subsp. durum) farmer varieties (FV) with high adaptability and breeding potential. To harness their unique allelic diversity, we produced a large nested association mapping (NAM) population intercrossing fifty Ethiopian FVs with an international elite durum wheat variety (Asassa). The Ethiopian NAM population (EtNAM) is composed of fifty interconnected bi-parental families, totalling 6280 recombinant inbred lines (RILs) that represent both a powerful quantitative trait loci (QTL) mapping tool, and a large pre-breeding panel. Here, we discuss the molecular and phenotypic diversity of the EtNAM founder lines, then we use an array featuring 13 000 single nucleotide polymorphisms (SNPs) to characterize a subset of 1200 EtNAM RILs from 12 families. Finally, we test the usefulness of the population by mapping phenology traits and plant height using a genome wide association (GWA) approach. EtNAM RILs showed high allelic variation and a genetic makeup combining genetic diversity from Ethiopian FVs with the international durum wheat allele pool. EtNAM SNP data were projected on the fully sequenced AB genome of wild emmer wheat, and were used to estimate pairwise linkage disequilibrium (LD) measures that reported an LD decay distance of 7.4 Mb on average, and balanced founder contributions across EtNAM families. GWA analyses identified 11 genomic loci individually affecting up to 3 days in flowering time and more than 1.6 cm in height. We argue that the EtNAM is a powerful tool to support the production of new durum wheat varieties targeting local and global agriculture.

Discovery of genomic regions and candidate genes controlling shelling percentage using QTL-seq approach in cultivated peanut (Arachis hypogaea L.)

Cultivated peanut (Arachis hypogaea L.) is an important grain legume providing high-quality cooking oil, rich proteins and other nutrients. Shelling percentage (SP) is the 2nd most important agronomic trait after pod yield and this trait significantly affects the economic value of peanut in the market. Deployment of diagnostic markers through genomics-assisted breeding (GAB) can accelerate the process of developing improved varieties with enhanced SP. In this context, we deployed the QTL-seq approach to identify genomic regions and candidate genes controlling SP in a recombinant inbred line population (Yuanza 9102 × Xuzhou 68-4). Four libraries (two parents and two extreme bulks) were constructed and sequenced, generating 456.89-790.32 million reads and achieving 91.85%-93.18% genome coverage and 14.04-21.37 mean read depth. Comprehensive analysis of two sets of data (Yuanza 9102/two bulks and Xuzhou 68-4/two bulks) using the QTL-seq pipeline resulted in discovery of two overlapped genomic regions (2.75 Mb on A09 and 1.1 Mb on B02). Nine candidate genes affected by 10 SNPs with non-synonymous effects or in UTRs were identified in these regions for SP. Cost-effective KASP (Kompetitive Allele-Specific PCR) markers were developed for one SNP from A09 and three SNPs from B02 chromosome. Genotyping of the mapping population with these newly developed KASP markers confirmed the major control and stable expressions of these genomic regions across five environments. The identified candidate genomic regions and genes for SP further provide opportunity for gene cloning and deployment of diagnostic markers in molecular breeding for achieving high SP in improved varieties.

Usefulness Criterion and Post-selection Parental Contributions in Multi-parental Crosses: Application to Polygenic Trait Introgression

Predicting the usefulness of crosses in terms of expected genetic gain and genetic diversity is of interest to secure performance in the progeny and to maintain long-term genetic gain in plant breeding. A wide range of crossing schemes are possible including large biparental crosses, backcrosses, four-way crosses, and synthetic populations. In silico progeny simulations together with genome-based prediction of quantitative traits can be used to guide mating decisions. However, the large number of multi-parental combinations can hinder the use of simulations in practice. Analytical solutions have been proposed recently to predict the distribution of a quantitative trait in the progeny of biparental crosses using information of recombination frequency and linkage disequilibrium between loci. Here, we extend this approach to obtain the progeny distribution of more complex crosses including two to four parents. Considering agronomic traits and parental genome contribution as jointly multivariate normally distributed traits, the usefulness criterion parental contribution (UCPC) enables to (i) evaluate the expected genetic gain for agronomic traits, and at the same time (ii) evaluate parental genome contributions to the selected fraction of progeny. We validate and illustrate UCPC in the context of multiple allele introgression from a donor into one or several elite recipients in maize (Zea mays L.). Recommendations regarding the interest of two-way, three-way, and backcrosses were derived depending on the donor performance. We believe that the computationally efficient UCPC approach can be useful for mate selection and allocation in many plant and animal breeding contexts.

Linkage-based genome assembly improvement of oil palm (Elaeis guineensis)

Meiotic crossovers in outbred species, such as oil palm (Elaeis guineensis Jacq., 2n = 32) contribute to allelic re-assortment in the genome. Such genetic variation is usually exploited in breeding to combine positive alleles for trait superiority. A good quality reference genome is essential for identifying the genetic factors underlying traits of interest through linkage or association studies. At the moment, an AVROS pisifera genome is publicly available for oil palm. Distribution and frequency of crossovers throughout chromosomes in different origins of oil palm are still unclear. Hence, an ultrahigh-density genomic linkage map of a commercial Deli dura x AVROS pisifera family was constructed using the OP200K SNP array, to evaluate the genetic alignment with the genome assembly. A total of 27,890 linked SNP markers generated a total map length of 1,151.7 cM and an average mapping interval of 0.04 cM. Nineteen linkage groups represented 16 pseudo-chromosomes of oil palm, with 61.7% of the mapped SNPs present in the published genome. Meanwhile, the physical map was also successfully extended from 658 Mb to 969 Mb by assigning unplaced scaffolds to the pseudo-chromosomes. A genic linkage map with major representation of sugar and lipid biosynthesis pathways was subsequently built for future studies on oil related quantitative trait loci (QTL). This study improves the current physical genome of the commercial oil palm, and provides important insights into its recombination landscape, eventually unlocking the full potential genome sequence-enabled biology for oil palm.

Manipulation of crossover frequency and distribution for plant breeding

The crossovers (COs) that occur during meiotic recombination lead to genetic diversity upon which natural and artificial selection can act. The potential of tinkering with the mechanisms of meiotic recombination to increase the amount of genetic diversity accessible for breeders has been under the research spotlight for years. A wide variety of approaches have been proposed to increase CO frequency, alter CO distribution and induce COs between non-homologous chromosomal regions. For most of these approaches, translational biology will be crucial for demonstrating how these strategies can be of practical use in plant breeding. In this review, we describe how tinkering with meiotic recombination could benefit plant breeding and give concrete examples of how these strategies could be implemented into breeding programs.

Technological advances in maize breeding: past, present and future

Maize has for many decades been both one of the most important crops worldwide and one of the primary genetic model organisms. More recently, maize breeding has been impacted by rapid technological advances in sequencing and genotyping technology, transformation including genome editing, doubled haploid technology, parallelled by progress in data sciences and the development of novel breeding approaches utilizing genomic information. Herein, we report on past, current and future developments relevant for maize breeding with regard to (1) genome analysis, (2) germplasm diversity characterization and utilization, (3) manipulation of genetic diversity by transformation and genome editing, (4) inbred line development and hybrid seed production, (5) understanding and prediction of hybrid performance, (6) breeding methodology and (7) synthesis of opportunities and challenges for future maize breeding.

Single gametophyte sequencing reveals that crossover events differ between sexes in maize

Meiotic crossover (CO) plays a key role in producing gametophytes and generating genetic variation. The patterns of CO production differ inter- and intra-species, as well as between sexes. However, sex-specific patterns of CO production have not been accurately profiled independently of genetic backgrounds in maize. Here, we develop a method to isolate single female gametophyte for genomes sequencing in maize. We show that more COs are observed in male (19.3 per microspore) than in female (12.4 per embryo sac). Based on Beam-Film model, the more designated class I and II COs are identified in male than in female. In addition, CO maturation inefficiency (CMI) is detected in some genetic backgrounds, suggesting that maize may be an ideal model for dissecting CMI. This research provides insights toward understanding the molecular mechanism of CO production between sexes and may help to improve maize breeding efficiency through paternal selection.

Where to Cross Over? Defining Crossover Sites in Plants

It is believed that recombination in meiosis serves to reshuffle genetic material from both parents to increase genetic variation in the progeny. At the same time, the number of crossovers is usually kept at a very low level. As a consequence, many organisms need to make the best possible use from the one or two crossovers that occur per chromosome in meiosis. From this perspective, the decision of where to allocate rare crossover events becomes an important issue, especially in self-pollinating plant species, which experience limited variation due to inbreeding. However, the freedom in crossover allocation is significantly limited by other, genetic and non-genetic factors, including chromatin structure. Here we summarize recent progress in our understanding of those processes with a special emphasis on plant genomes. First, we focus on factors which influence the distribution of recombination initiation sites and discuss their effects at both, the single hotspot level and at the chromosome scale. We also briefly explain the aspects of hotspot evolution and their regulation. Next, we analyze how recombination initiation sites translate into the development of crossovers and their location. Moreover, we provide an overview of the sequence polymorphism impact on crossover formation and chromosomal distribution.

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 hybrids between SK1 and a total of 26 Saccharomyces 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 ninefold 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 DNA double-strand-break-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. We also estimated that cis and trans effects explained 38 and 17%, respectively, of the variance of recombination rate. 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.

The genetic architecture of genome-wide recombination rate variation in allopolyploid wheat revealed by nested association mapping

Recombination affects the fate of alleles in populations by imposing constraints on the reshuffling of genetic information. Understanding the genetic basis of these constraints is critical for manipulating the recombination process to improve the resolution of genetic mapping, and reducing the negative effects of linkage drag and deleterious genetic load in breeding. Using sequence-based genotyping of a wheat nested association mapping (NAM) population of 2,100 recombinant inbred lines created by crossing 29 diverse lines, we mapped QTL affecting the distribution and frequency of 102 000 crossovers (CO). Genome-wide recombination rate variation was mostly defined by rare alleles with small effects together explaining up to 48.6% of variation. Most QTL were additive and showed predominantly trans-acting effects. The QTL affecting the proximal COs also acted additively without increasing the frequency of distal COs. We showed that the regions with decreased recombination carry more single nucleotide polymorphisms (SNPs) with possible deleterious effects than the regions with a high recombination rate. Therefore, our study offers insights into the genetic basis of recombination rate variation in wheat and its effect on the distribution of deleterious SNPs across the genome. The identified trans-acting additive QTL can be utilized to manipulate CO frequency and distribution in the large polyploid wheat genome opening the possibility to improve the efficiency of gene pyramiding and reducing the deleterious genetic load in the low-recombining pericentromeric regions of chromosomes.

Low-coverage resequencing detects meiotic recombination pattern and features in tomato RILs

Traditional plant breeding relies on meiotic recombination for mixing of parental alleles to create novel allele combinations. Detailed analysis of recombination patterns in model organisms shows that recombination is tightly regulated within the genome, but frequencies vary extensively along chromosomes. Despite being a model organism for fruit developmental studies, high-resolution recombination patterns are lacking in tomato. In this study, we developed a novel methodology to use low-coverage resequencing to identify genome-wide recombination patterns and applied this methodology on 60 tomato Recombinant Inbred Lines (RILs). Our methodology identifies polymorphic markers from the low-coverage resequencing population data and utilizes the same data to locate the recombination breakpoints in individuals by using a variable sliding window. We identified 1,445 recombination sites comprising 112 recombination prone regions enriched for AT-rich DNA motifs. Furthermore, the recombination prone regions in tomato preferably occurred in gene promoters over intergenic regions, an observation consistent with Arabidopsis thaliana, Zea mays and Mimulus guttatus. Overall, our cost effective method and findings enhance the understanding of meiotic recombination in tomato and suggest evolutionarily conserved recombination associated genomic features.

High-resolution crossover mapping reveals similarities and differences of male and female recombination in maize

Meiotic crossovers (COs) are not uniformly distributed across the genome. Factors affecting this phenomenon are not well understood. Although many species exhibit large differences in CO numbers between sexes, sex-specific aspects of CO landscape are particularly poorly elucidated. Here, we conduct high-resolution CO mapping in maize. Our results show that CO numbers as well as their overall distribution are similar in male and female meioses. There are, nevertheless, dissimilarities at local scale. Male and female COs differ in their locations relative to transcription start sites in gene promoters and chromatin marks, including nucleosome occupancy and tri-methylation of lysine 4 of histone H3 (H3K4me3). Our data suggest that sex-specific factors not only affect male–female CO number disparities but also cause fine differences in CO positions. Differences between male and female CO landscapes indicate that recombination has distinct implications for population structure and gene evolution in male and in female meioses.

Sex-specific meiotic crossover (CO) landscapes have been identified in multiple species. Here, the authors show that male and female meioses in maize have similar CO landscapes, and differences between COs in the two sexes only exists in their location relative to transcription start sites and some chromatin marks.

Variation in recombination frequency and distribution across eukaryotes: patterns and processes

Recombination, the exchange of DNA between maternal and paternal chromosomes during meiosis, is an essential feature of sexual reproduction in nearly all multicellular organisms. While the role of recombination in the evolution of sex has received theoretical and empirical attention, less is known about how recombination rate itself evolves and what influence this has on evolutionary processes within sexually reproducing organisms. Here, we explore the patterns of, and processes governing recombination in eukaryotes. We summarize patterns of variation, integrating current knowledge with an analysis of linkage map data in 353 organisms. We then discuss proximate and ultimate processes governing recombination rate variation and consider how these influence evolutionary processes. Genome-wide recombination rates (cM/Mb) can vary more than tenfold across eukaryotes, and there is large variation in the distribution of recombination events across closely related taxa, populations and individuals. We discuss how variation in rate and distribution relates to genome architecture, genetic and epigenetic mechanisms, sex, environmental perturbations and variable selective pressures. There has been great progress in determining the molecular mechanisms governing recombination, and with the continued development of new modelling and empirical approaches, there is now also great opportunity to further our understanding of how and why recombination rate varies.This article is part of the themed issue 'Evolutionary causes and consequences of recombination rate variation in sexual organisms'.

Meta-analysis of chromosome-scale crossover rate variation in eukaryotes and its significance to evolutionary genomics

Understanding the distribution of crossovers along chromosomes is crucial to evolutionary genomics because the crossover rate determines how strongly a genome region is influenced by natural selection on linked sites. Nevertheless, generalities in the chromosome-scale distribution of crossovers have not been investigated formally. We fill this gap by synthesizing joint information on genetic and physical maps across 62 animal, plant and fungal species. Our quantitative analysis reveals a strong and taxonomically widespread reduction of the crossover rate in the centre of chromosomes relative to their peripheries. We demonstrate that this pattern is poorly explained by the position of the centromere, but find that the magnitude of the relative reduction in the crossover rate in chromosome centres increases with chromosome length. That is, long chromosomes often display a dramatically low crossover rate in their centre, whereas short chromosomes exhibit a relatively homogeneous crossover rate. This observation is compatible with a model in which crossover is initiated from the chromosome tips, an idea with preliminary support from mechanistic investigations of meiotic recombination. Consequently, we show that organisms achieve a higher genome-wide crossover rate by evolving smaller chromosomes. Summarizing theory and providing empirical examples, we finally highlight that taxonomically widespread and systematic heterogeneity in crossover rate along chromosomes generates predictable broad-scale trends in genetic diversity and population differentiation by modifying the impact of natural selection among regions within a genome. We conclude by emphasizing that chromosome-scale heterogeneity in crossover rate should urgently be incorporated into analytical tools in evolutionary genomics, and in the interpretation of resulting patterns.

Haplotype-Based Genome-Wide Prediction Models Exploit Local Epistatic Interactions Among Markers

Genome-wide prediction approaches represent versatile tools for the analysis and prediction of complex traits. Mostly they rely on marker-based information, but scenarios have been reported in which models capitalizing on closely-linked markers that were combined into haplotypes outperformed marker-based models. Detailed comparisons were undertaken to reveal under which circumstances haplotype-based genome-wide prediction models are superior to marker-based models. Specifically, it was of interest to analyze whether and how haplotype-based models may take local epistatic effects between markers into account. Assuming that populations consisted of fully homozygous individuals, a marker-based model in which local epistatic effects inside haplotype blocks were exploited (LEGBLUP) was linearly transformable into a haplotype-based model (HGBLUP). This theoretical derivation formally revealed that haplotype-based genome-wide prediction models capitalize on local epistatic effects among markers. Simulation studies corroborated this finding. Due to its computational efficiency the HGBLUP model promises to be an interesting tool for studies in which ultra-high-density SNP data sets are studied. Applying the HGBLUP model to empirical data sets revealed higher prediction accuracies than for marker-based models for both traits studied using a mouse panel. In contrast, only a small subset of the traits analyzed in crop populations showed such a benefit. Cases in which higher prediction accuracies are observed for HGBLUP than for marker-based models are expected to be of immediate relevance for breeders, due to the tight linkage a beneficial haplotype will be preserved for many generations. In this respect the inheritance of local epistatic effects very much resembles the one of additive effects.

FANCM Limits Meiotic Crossovers in Brassica Crops

Meiotic crossovers (COs) are essential for proper chromosome segregation and the reshuffling of alleles during meiosis. In WT plants, the number of COs is usually small, which limits the genetic variation that can be captured by plant breeding programs. Part of this limitation is imposed by proteins like FANCM, the inactivation of which results in a 3-fold increase in COs in Arabidopsis thaliana. Whether the same holds true in crops needed to be established. In this study, we identified EMS induced mutations in FANCM in two species of economic relevance within the genus Brassica. We showed that CO frequencies were increased in fancm mutants in both diploid and tetraploid Brassicas, Brassica rapa and Brassica napus respectively. In B. rapa, we observed a 3-fold increase in the number of COs, equal to the increase observed previously in Arabidopsis. In B. napus we observed a lesser but consistent increase (1.3-fold) in both euploid (AACC) and allohaploid (AC) plants. Complementation tests in A. thaliana suggest that the smaller increase in crossover frequency observed in B. napus reflects residual activity of the mutant C copy of FANCM. Altogether our results indicate that the anti-CO activity of FANCM is conserved across the Brassica, opening new avenues to make a wider range of genetic diversity accessible to crop improvement.

Uncovering the dispersion history, adaptive evolution and selection of wheat in China

Wheat was introduced to China approximately 4500 years ago, where it adapted over a span of time to various environments in agro-ecological growing zones. We investigated 717 Chinese and 14 Iranian/Turkish geographically diverse, locally adapted wheat landraces with 27 933 DArTseq (for 717 landraces) and 312 831 Wheat660K (for a subset of 285 landraces) markers. This study highlights the adaptive evolutionary history of wheat cultivation in China. Environmental stresses and independent selection efforts have resulted in considerable genome-wide divergence at the population level in Chinese wheat landraces. In total, 148 regions of the wheat genome show signs of selection in at least one geographic area. Our data show adaptive events across geographic areas, from the xeric northwest to the mesic south, along and among homoeologous chromosomes, with fewer variations in the D genome than in the A and B genomes. Multiple variations in interdependent functional genes such as regulatory and metabolic genes controlling germination and flowering time were characterized, showing clear allelic frequency changes corresponding to the dispersion of wheat in China. Population structure and selection data reveal that Chinese wheat spread from the northwestern Caspian Sea region to South China, adapting during its agricultural trajectory to increasingly mesic and warm climatic areas.

The evolution of recombination rates in finite populations during ecological speciation

Recombination can impede ecological speciation with gene flow by mixing locally adapted genotypes with maladapted migrant genotypes from a divergent population. In such a scenario, suppression of recombination can be selectively favoured. However, in finite populations evolving under the influence of random genetic drift, recombination can also facilitate adaptation by reducing Hill-Robertson interference between loci under selection. In this case, increased recombination rates can be favoured. Although these two major effects on recombination have been studied individually, their joint effect on ecological speciation with gene flow remains unexplored. Using a mathematical model, we investigated the evolution of recombination rates in two finite populations that exchange migrants while adapting to contrasting environments. Our results indicate a two-step dynamic where increased recombination is first favoured (in response to the Hill-Robertson effect), and then disfavoured, as the cost of recombining locally with maladapted migrant genotypes increases over time (the maladaptive gene flow effect). In larger populations, a stronger initial benefit for recombination was observed, whereas high migration rates intensify the long-term cost of recombination. These dynamics may have important implications for our understanding of the conditions that facilitate incipient speciation with gene flow and the evolution of recombination in finite populations.

Modification of meiotic recombination by natural variation in plants

Meiosis is a specialized cell division that produces haploid gametes required for sexual reproduction. During the first meiotic division, homologous chromosomes pair and undergo reciprocal crossing over, which recombines linked sequence variation. Meiotic recombination frequency varies extensively both within and between species. In this review, we will examine the molecular basis of meiotic recombination rate variation, with an emphasis on plant genomes. We first consider cis modification caused by polymorphisms at the site of recombination, or elsewhere on the same chromosome. We review cis effects caused by mismatches within recombining joint molecules, the effect of structural hemizygosity, and the role of specific DNA sequence motifs. In contrast, trans modification of recombination is exerted by polymorphic loci encoding diffusible molecules, which are able to modulate recombination on the same and/or other chromosomes. We consider trans modifiers that act to change total recombination levels, hotspot locations, or interactions between homologous and homeologous chromosomes in polyploid species. Finally, we consider the significance of genetic variation that modifies meiotic recombination for adaptation and evolution of plant species.

Detection of genomic loci associated with chromosomal recombination using high-density linkage mapping in Setaria

Meiotic recombination is essential to sexual reproduction and the generation of genetic diversity. Variation in recombination rates is presently of particular interest due to efforts being made to increase the rate of genetic gain in agricultural crops by breaking up large linkage disequilibrium blocks containing both beneficial and detrimental alleles. Here, a high-density genetic linkage map of Setaria was constructed using tunable genotyping by sequencing (tGBS) analysis of a population of recombinant inbred lines (RILs). Several regions of the Setaria genome exhibited significant levels of segregation distortion (SD), and recombination crossovers (COs) were also detected. The regions with high SD generally tended to have fewer COs, particularly for pericentromeric chromosomal areas. Recombination crossovers detected in Setaria were unevenly distributed across the genome and occurred more often in intergenic regions. Quantitative trait loci (QTLs) contributing towards the recombination frequency (Type I) and occurrence of COs in designated loci (Type II) were identified, and Type II QTLs garnered higher statistical power. The result of this study suggest that QTLs analysis of Type II traits using RILs might provide an opportunity to further understand meiotic recombination using high throughput genome sequencing and genotyping technologies.

Predicting genomic selection efficiency to optimize calibration set and to assess prediction accuracy in highly structured populations

KEY MESSAGE

We propose a criterion to predict genomic selection efficiency for structured populations. This criterion is useful to define optimal calibration set and to estimate prediction reliability for multiparental populations. Genomic selection refers to the use of genotypic information for predicting the performance of selection candidates. It has been shown that prediction accuracy depends on various parameters including the composition of the calibration set (CS). Assessing the level of accuracy of a given prediction scenario is of highest importance because it can be used to optimize CS sampling before collecting phenotypes, and once the breeding values are predicted it informs the breeders about the reliability of these predictions. Different criteria were proposed to optimize CS sampling in highly diverse panels, which can be useful to screen collections of genotypes. But plant breeders often work on structured material such as biparental or multiparental populations, for which these criteria are less adapted. We derived from the generalized coefficient of determination (CD) theory different criteria to optimize CS sampling and to assess the reliability associated to predictions in structured populations. These criteria were evaluated on two nested association mapping (NAM) populations and two highly diverse panels of maize. They were efficient to sample optimized CS in most situations. They could also estimate at least partly the reliability associated to predictions between NAM families, but they could not estimate differences in the reliability associated to the predictions of NAM families using the highly diverse panels as calibration sets. We illustrated that the CD criteria could be adapted to various prediction scenarios including inter and intra-family predictions, resulting in higher prediction accuracies.

Genetic Gain Increases by Applying the Usefulness Criterion with Improved Variance Prediction in Selection of Crosses

A crucial step in plant breeding is the selection and combination of parents to form new crosses. Genome-based prediction guides the selection of high-performing parental lines in many crop breeding programs which ensures a high mean performance of progeny. To warrant maximum selection progress, a new cross should also provide a large progeny variance. The usefulness concept as measure of the gain that can be obtained from a specific cross accounts for variation in progeny variance. Here, it is shown that genetic gain can be considerably increased when crosses are selected based on their genomic usefulness criterion compared to selection based on mean genomic estimated breeding values. An efficient and improved method to predict the genetic variance of a cross based on Markov chain Monte Carlo samples of marker effects from a whole-genome regression model is suggested. In simulations representing selection procedures in crop breeding programs, the performance of this novel approach is compared with existing methods, like selection based on mean genomic estimated breeding values and optimal haploid values. In all cases, higher genetic gain was obtained compared with previously suggested methods. When 1% of progenies per cross were selected, the genetic gain based on the estimated usefulness criterion increased by 0.14 genetic standard deviation compared to a selection based on mean genomic estimated breeding values. Analytical derivations of the progeny genotypic variance-covariance matrix based on parental genotypes and genetic map information make simulations of progeny dispensable, and allow fast implementation in large-scale breeding programs.

Bayesian Networks Illustrate Genomic and Residual Trait Connections in Maize (Zea mays L.)

Relationships among traits were investigated on the genomic and residual levels using novel methodology. This included inference on these relationships via Bayesian networks and an assessment of the networks with structural equation models. The methodology employed three steps. First, a Bayesian multiple-trait Gaussian model was fitted to the data to decompose phenotypic values into their genomic and residual components. Second, genomic and residual network structures among traits were learned from estimates of these two components. Network learning was performed using six different algorithmic settings for comparison, of which two were score-based and four were constraint-based approaches. Third, structural equation model analyses ranked the networks in terms of goodness of fit and predictive ability, and compared them with the standard multiple-trait fully recursive network. The methodology was applied to experimental data representing the European heterotic maize pools Dent and Flint (Zea mays L.). Inferences on genomic and residual trait connections were depicted separately as directed acyclic graphs. These graphs provide information beyond mere pairwise genetic or residual associations between traits, illustrating for example conditional independencies and hinting at potential causal links among traits. Network analysis suggested some genetic correlations as potentially spurious. Genomic and residual networks were compared between Dent and Flint.

How do the type of QTL effect and the form of the residual term influence QTL detection in multi-parent populations? A case study in the maize EU-NAM population

In the QTL analysis of multi-parent populations, the inclusion of QTLs with various types of effects can lead to a better description of the phenotypic variation and increased power. For the type of QTL effect in QTL models for multi-parent populations (MPPs), various options exist to define them with respect to their origin. They can be modelled as referring to close parental lines or to further away ancestral founder lines. QTL models for MPPs can also be characterized by the homo- or heterogeneity of variance for polygenic effects. The most suitable model for the origin of the QTL effect and the homo- or heterogeneity of polygenic effects may be a function of the genetic distance distribution between the parents of MPPs. We investigated the statistical properties of various QTL detection models for MPPs taking into account the genetic distances between the parents of the MPP. We evaluated models with different assumptions about the QTL effect and the form of the residual term using cross validation. For the EU-NAM data, we showed that it can be useful to mix in the same model QTLs with different types of effects (parental, ancestral, or bi-allelic). The benefit of using cross-specific residual terms to handle the heterogeneity of variance was less obvious for this particular data set.

Increased Power To Dissect Adaptive Traits in Global Sorghum Diversity Using a Nested Association Mapping Population

Adaptation of domesticated species to diverse agroclimatic regions has led to abundant trait diversity. However, the resulting population structure and genetic heterogeneity confounds association mapping of adaptive traits. To address this challenge in sorghum [Sorghum bicolor (L.) Moench]-a widely adapted cereal crop-we developed a nested association mapping (NAM) population using 10 diverse global lines crossed with an elite reference line RTx430. We characterized the population of 2214 recombinant inbred lines at 90,000 SNPs using genotyping-by-sequencing. The population captures ∼70% of known global SNP variation in sorghum, and 57,411 recombination events. Notably, recombination events were four- to fivefold enriched in coding sequences and 5' untranslated regions of genes. To test the power of the NAM population for trait dissection, we conducted joint linkage mapping for two major adaptive traits, flowering time and plant height. We precisely mapped several known genes for these two traits, and identified several additional QTL. Considering all SNPs simultaneously, genetic variation accounted for 65% of flowering time variance and 75% of plant height variance. Further, we directly compared NAM to genome-wide association mapping (using panels of the same size) and found that flowering time and plant height QTL were more consistently identified with the NAM population. Finally, for simulated QTL under strong selection in diversity panels, the power of QTL detection was up to three times greater for NAM vs. association mapping with a diverse panel. These findings validate the NAM resource for trait mapping in sorghum, and demonstrate the value of NAM for dissection of adaptive traits.

Safeguarding Our Genetic Resources with Libraries of Doubled-Haploid Lines

Thousands of landraces are stored in seed banks as "gold reserves" for future use in plant breeding. In many crops, their utilization is hampered because they represent heterogeneous populations of heterozygous genotypes, which harbor a high genetic load. We show, with high-density genotyping in five landraces of maize, that libraries of doubled-haploid (DH) lines capture the allelic diversity of genetic resources in an unbiased way. By comparing allelic differentiation between heterozygous plants from the original landraces and 266 derived DH lines, we find conclusive evidence that, in the DH production process, sampling of alleles is random across the entire allele frequency spectrum, and purging of landraces from their genetic load does not act on specific genomic regions. Based on overall process efficiency, we show that generating DH lines is feasible for genetic material that has never been selected for inbreeding tolerance. We conclude that libraries of DH lines will make genetic resources accessible to crop improvement by linking molecular inventories of seed banks with meaningful phenotypes.

Genetic Determinants of Crop Timing and Quality Traits in Two Interspecific Petunia Recombinant Inbred Line Populations

The rate at which plants develop new nodes (development rate) is a major determinant of crop production time, yet the genetic control of this process, including genetic interactions with crop quality parameters, is poorly understood. We employed a modified genotyping-by-sequencing approach and generated genetic linkage maps with 6,291 and 3,297 single nucleotide polymorphisms (SNPs) for the interspecific Petunia recombinant inbred line (RIL) population - P. axillaris × P. exserta (AE) and P. integrifolia × P. axillaris (IA), respectively. Comparative mapping between the populations revealed perfect collinearity of marker order but different recombination frequency at the corresponding linkage groups (LGs). Quantitative trait loci (QTL) mapping conducted for development traits and other important quality traits indicated QTL clustered on chromosome 1, 2, 4 and 6 for the AE population and chromosome 1, 2, 5 and 6 for the IA population. Additionally, 209 differentially expressed unique transcripts were identified in shoot apex tissue between fast- and slow-developing RILs, 13 of which mapped to within 1 cM of a development rate QTL. These results will facilitate the identification of novel genes controlling crop timing and quality traits in Petunia and highlight the power of using multiple interspecific populations to elucidate genetic determinants of natural variation.

Fast diffusion of domesticated maize to temperate zones

Adaptation to a temperate climate was a prerequisite for the spread of maize across a broad geographical range. To explicitly explore the demographic process underlying maize adaptation, we used a diffusion-based method to model the differentiation between temperate and tropical populations using the Non-Stiff Stalk group as a proxy for temperate maize. Based on multiple sequential Markovian coalescent approaches, we estimate that tropical and temperate maize diverged approximately 3'000 to 5'000 years ago and the population size shrank after the split. Using composite likelihood approaches, we identified a distinct tropical-temperate divergence event initiated 4'958 years ago (95% confidence interval (CI): 4'877-5'039) from an ancestral population whose effective size was 24,162 (95% CI: 23,914-24,409). We found that continuous gene flow between tropical and temperate maize accompanied the differentiation of temperate maize. Long identical-by-descent tracts shared by tropical and temperate inbred lines have been identified, which might be the result of gene flow between tropical and temperate maize or artificial selection during domestication and crop improvement. Understanding the demographic history of maize diffusion not only provides evidence for population dynamics of maize, but will also assist the identification of regions under selection and the genetic basis of complex traits of agronomic importance.

Building Ultra-High-Density Linkage Maps Based on Efficient Filtering of Trustable Markers

The study is focused on addressing the problem of building genetic maps in the presence of ∼10³-10⁴ of markers per chromosome. We consider a spectrum of situations with intrachromosomal heterogeneity of recombination rate, different level of genotyping errors, and missing data. In the ideal scenario of the absence of errors and missing data, the majority of markers should appear as groups of cosegregating markers ("twins") representing no challenge for map construction. The central aspect of the proposed approach is to take into account the structure of the marker space, where each twin group (TG) and singleton markers are represented as points of this space. The confounding effect of genotyping errors and missing data leads to reduction of TG size, but upon a low level of these effects surviving TGs can still be used as a source of reliable skeletal markers. Increase in the level of confounding effects results in a considerable decrease in the number or even disappearance of usable TGs and, correspondingly, of skeletal markers. Here, we show that the paucity of informative markers can be compensated by detecting kernels of markers in the marker space using a clustering procedure, and demonstrate the utility of this approach for high-density genetic map construction on simulated and experimentally obtained genotyping datasets.

Amplifying recombination genome-wide and reshaping crossover landscapes in Brassicas

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 the cross between the allotetraploid rapeseed (B. napus, AACC, 2n = 4x = 38) and one of its diploid progenitors (B. rapa, AA, 2n = 2x = 20). We produced mapping populations from different genotypes of both diploid AA and triploid AAC hybrids, used as female and/or as male. Each population revealed nearly 3,000 COs that we studied with SNP markers well distributed along the A genome (on average 1 SNP per 1.25 Mbp). Compared to the case of diploids, allotriploid hybrids showed 1.7 to 3.4 times more overall COs depending on the sex of meiosis and the genetic background. Most surprisingly, we found that such a rise was always associated with (i) dramatic changes in the shape of recombination landscapes and (ii) a strong decrease of CO interference. Hybrids carrying an additional C genome exhibited COs all along the A chromosomes, even in the vicinity of centromeres that are deprived of COs in diploids as well as in most studied species. Moreover, in male allotriploid hybrids we found that Class I COs are mostly responsible for the changes of CO rates, landscapes and interference. These results offer the opportunity for geneticists and plant breeders to dramatically enhance the generation of diversity in Brassica species by disrupting the linkage drag coming from limits on number and distribution of COs.

Complexity of genetic mechanisms conferring nonuniformity of recombination in maize

Recombinations occur nonuniformly across the maize genome. To dissect the genetic mechanisms underlying the nonuniformity of recombination, we performed quantitative trait locus (QTL) mapping using recombinant inbred line populations. Genome-wide QTL scan identified hundreds of QTLs with both cis-prone and trans- effects for recombination number variation. To provide detailed insights into cis- factors associated with recombination variation, we examined the genomic features around recombination hot regions, including density of genes, DNA transposons, retrotransposons, and some specific motifs. Compared to recombination variation in whole genome, more QTLs were mapped for variations in recombination hot regions. The majority QTLs for recombination hot regions are trans-QTLs and co-localized with genes from the recombination pathway. We also found that recombination variation was positively associated with the presence of genes and DNA transposons, but negatively related to the presence of long terminal repeat retrotransposons. Additionally, 41 recombination hot regions were fine-mapped. The high-resolution genotyping of five randomly selected regions in two F₂ populations verified that they indeed have ultra-high recombination frequency, which is even higher than that of the well-known recombination hot regions sh1-bz and a1-sh2. Taken together, our results further our understanding of recombination variation in plants.

A high-resolution reference genetic map positioning 8.8 K genes for the conifer white spruce: structural genomics implications and correspondence with physical distance

Over the last decade, extensive genetic and genomic resources have been developed for the conifer white spruce (Picea glauca, Pinaceae), which has one of the largest plant genomes (20 Gbp). Draft genome sequences of white spruce and other conifers have recently been produced, but dense genetic maps are needed to comprehend genome macrostructure, delineate regions involved in quantitative traits, complement functional genomic investigations, and assist the assembly of fragmented genomic sequences. A greatly expanded P. glauca composite linkage map was generated from a set of 1976 full-sib progeny, with the positioning of 8793 expressed genes. Regions with significant low or high gene density were identified. Gene family members tended to be mapped on the same chromosomes, with tandemly arrayed genes significantly biased towards specific functional classes. The map was integrated with transcriptome data surveyed across eight tissues. In total, 69 clusters of co-expressed and co-localising genes were identified. A high level of synteny was found with pine genetic maps, which should facilitate the transfer of structural information in the Pinaceae. Although the current white spruce genome sequence remains highly fragmented, dozens of scaffolds encompassing more than one mapped gene were identified. From these, the relationship between genetic and physical distances was examined and the genome-wide recombination rate was found to be much smaller than most estimates reported for angiosperm genomes. This gene linkage map shall assist the large-scale assembly of the next-generation white spruce genome sequence and provide a reference resource for the conifer genomics community.

Meiotic recombination gets stressed out: CO frequency is plastic under pressure

Meiotic recombination ensures the fertility of gametes and creates novel genetic combinations. Although meiotic crossover (CO) frequency is under homeostatic control, CO frequency is also plastic in nature and can respond to environmental conditions. Most investigations have focused on temperature and recombination, but other external and internal stimuli also have important roles in modulating CO frequency. Even less is understood about the molecular mechanisms that underly these phenomenon, but recent work has begun to advance our knowledge in this field. In this review, we identify and explore potential mechanisms including changes in: the synaptonemal complex, chromatin state, DNA methylation, and RNA splicing.

Wheat Landrace Genome Diversity

Understanding the genomic complexity of bread wheat is important for unraveling domestication processes, environmental adaptation, and for future of...

Understanding the genomic complexity of bread wheat (Triticum aestivum L.) is a cornerstone in the quest to unravel the processes of domestication and the following adaptation of domesticated wheat to a wide variety of environments across the globe. Additionally, it is of importance for future improvement of the crop, particularly in the light of climate change. Focusing on the adaptation after domestication, a nested association mapping (NAM) panel of 60 segregating biparental populations was developed, mainly involving landrace accessions from the core set of the Watkins hexaploid wheat collection optimized for genetic diversity. A modern spring elite variety, “Paragon,” was used as common reference parent. Genetic maps were constructed following identical rules to make them comparable. In total, 1611 linkage groups were identified, based on recombination from an estimated 126,300 crossover events over the whole NAM panel. A consensus map, named landrace consensus map (LRC), was constructed and contained 2498 genetic loci. These newly developed genetics tools were used to investigate the rules underlying genome fluidity or rigidity, e.g., by comparing marker distances and marker orders. In general, marker order was highly correlated, which provides support for strong synteny between bread wheat accessions. However, many exceptional cases of incongruent linkage groups and increased marker distances were also found. Segregation distortion was detected for many markers, sometimes as hot spots present in different populations. Furthermore, evidence for translocations in at least 36 of the maps was found. These translocations fell, in general, into many different translocation classes, but a few translocation classes were found in several accessions, the most frequent one being the well-known T5B:7B translocation. Loci involved in recombination rate, which is an interesting trait for plant breeding, were identified by QTL analyses using the crossover counts as a trait. In total, 114 significant QTL were detected, nearly half of them with increasing effect from the nonreference parents.

Dynamics of male meiotic recombination frequency during plant development using Fluorescent Tagged Lines in Arabidopsis thaliana

Meiotic homologous recombination plays a central role in creating genetic variability, making it an essential biological process relevant to evolution and crop breeding. In this study, we used pollen-specific fluorescent tagged lines (FTLs) to measure male meiotic recombination frequency during the development of Arabidopsis thaliana. Interestingly, a subset of pollen grains consistently shows loss of fluorescence expression in tested lines. Using nine independent FTL intervals, the spatio-temporal dynamics of male recombination frequency was assessed during plant development, considering both shoot type and plant age as independent parameters. In most genomic intervals assayed, male meiotic recombination frequency is highly consistent during plant development, showing no significant change between different shoot types and during plant aging. However, in some genomic regions, such as I1a and I5a, a small but significant effect of either developmental position or plant age were observed, indicating that the meiotic CO frequency in those intervals varies during plant development. Furthermore, from an overall view of all nine genomic intervals assayed, both primary and tertiary shoots show a similar dynamics of increasing recombination frequency during development, while secondary and lateral shoots remain highly stable. Our results provide new insights in the dynamics of male meiotic recombination frequency during plant development.

Unbiased K-mer Analysis Reveals Changes in Copy Number of Highly Repetitive Sequences During Maize Domestication and Improvement

The major component of complex genomes is repetitive elements, which remain recalcitrant to characterization. Using maize as a model system, we analyzed whole genome shotgun (WGS) sequences for the two maize inbred lines B73 and Mo17 using k-mer analysis to quantify the differences between the two genomes. Significant differences were identified in highly repetitive sequences, including centromere, 45S ribosomal DNA (rDNA), knob, and telomere repeats. Genotype specific 45S rDNA sequences were discovered. The B73 and Mo17 polymorphic k-mers were used to examine allele-specific expression of 45S rDNA in the hybrids. Although Mo17 contains higher copy number than B73, equivalent levels of overall 45S rDNA expression indicates that transcriptional or post-transcriptional regulation mechanisms operate for the 45S rDNA in the hybrids. Using WGS sequences of B73xMo17 doubled haploids, genomic locations showing differential repetitive contents were genetically mapped, which displayed different organization of highly repetitive sequences in the two genomes. In an analysis of WGS sequences of HapMap2 lines, including maize wild progenitor, landraces, and improved lines, decreases and increases in abundance of additional sets of k-mers associated with centromere, 45S rDNA, knob, and retrotransposons were found among groups, revealing global evolutionary trends of genomic repeats during maize domestication and improvement.

Distribution, position and genomic characteristics of crossovers in tomato recombinant inbred lines derived from an interspecific cross between Solanum lycopersicum and Solanum pimpinellifolium

We determined the crossover (CO) distribution, frequency and genomic sequences involved in interspecies meiotic recombination by using parent-assigned variants of 52 F₆ recombinant inbred lines obtained from a cross between tomato, Solanum lycopersicum, and its wild relative, Solanum pimpinellifolium. The interspecific CO frequency was 80% lower than reported for intraspecific tomato crosses. We detected regions showing a relatively high and low CO frequency, so-called hot and cold regions. Cold regions coincide to a large extent with the heterochromatin, although we found a limited number of smaller cold regions in the euchromatin. The CO frequency was higher at the distal ends of chromosomes than in pericentromeric regions and higher in short arm euchromatin. Hot regions of CO were detected in euchromatin, and COs were more often located in non-coding regions near the 5' untranslated region of genes than expected by chance. Besides overrepresented CCN repeats, we detected poly-A/T and AT-rich motifs enriched in 1-kb promoter regions flanking the CO sites. The most abundant sequence motifs at CO sites share weak similarity to transcription factor-binding sites, such as for the C2H2 zinc finger factors class and MADS box factors, while InterPro scans detected enrichment for genes possibly involved in the repair of DNA breaks.

Natural variation and dosage of the HEI10 meiotic E3 ligase control Arabidopsis crossover recombination

During meiosis, homologous chromosomes undergo crossover recombination, which creates genetic diversity and balances homolog segregation. Despite these critical functions, crossover frequency varies extensively within and between species. Although natural crossover recombination modifier loci have been detected in plants, causal genes have remained elusive. Using natural Arabidopsis thaliana accessions, we identified two major recombination quantitative trait loci (rQTLs) that explain 56.9% of crossover variation in Col×Ler F2 populations. We mapped rQTL1 to semidominant polymorphisms in HEI10, which encodes a conserved ubiquitin E3 ligase that regulates crossovers. Null hei10 mutants are haploinsufficient, and, using genome-wide mapping and immunocytology, we show that transformation of additional HEI10 copies is sufficient to more than double euchromatic crossovers. However, heterochromatic centromeres remained recombination-suppressed. The strongest HEI10-mediated crossover increases occur in subtelomeric euchromatin, which is reminiscent of sex differences in Arabidopsis recombination. Our work reveals that HEI10 naturally limits Arabidopsis crossovers and has the potential to influence the response to selection.

Interconnections between meiotic recombination and sequence polymorphism in plant genomes

1022 I. 1022 II. 1023 III. 1023 IV. 1025 V. 1026 1027 References 1027 SUMMARY: Meiosis is fundamental to sexual reproduction and creates genetic variation in progeny. During meiosis paired homologous chromosomes undergo recombination, which can result in reciprocal crossovers. This process can recombine independently arising mutations onto the same chromosome. Recombination locations are highly variable between meioses, although total crossover numbers are tightly regulated. In addition to the effect of meiosis on genetic variation, sequence polymorphisms between homologous chromosomes can feedback onto the recombination pathways. Here we review the major crossover pathways in plants and some of the known homeostatic mechanisms that act during meiotic recombination. We then examine how sequence polymorphisms between homologous chromosomes, that is, heterozygosity, can influence meiotic recombination pathways in cis and trans. Finally, we provide a brief perspective on the relevance of these interconnections for natural selection and adaptation in plants.

Evolution of meiotic recombination genes in maize and teosinte

Background

Meiotic recombination is a major source of genetic variation in eukaryotes. The role of recombination in evolution is recognized but little is known about how evolutionary forces affect the recombination pathway itself. Although the recombination pathway is fundamentally conserved across different species, genetic variation in recombination components and outcomes has been observed. Theoretical predictions and empirical studies suggest that changes in the recombination pathway are likely to provide adaptive abilities to populations experiencing directional or strong selection pressures, such as those occurring during species domestication. We hypothesized that adaptive changes in recombination may be associated with adaptive evolution patterns of genes involved in meiotic recombination.

Results

To examine how maize evolution and domestication affected meiotic recombination genes, we studied patterns of sequence polymorphism and divergence in eleven genes controlling key steps in the meiotic recombination pathway in a diverse set of maize inbred lines and several accessions of teosinte, the wild ancestor of maize. We discovered that, even though the recombination genes generally exhibited high sequence conservation expected in a pathway controlling a key cellular process, they showed substantial levels and diverse patterns of sequence polymorphism. Among others, we found differences in sequence polymorphism patterns between tropical and temperate maize germplasms. Several recombination genes displayed patterns of polymorphism indicative of adaptive evolution.

Conclusions

Despite their ancient origin and overall sequence conservation, meiotic recombination genes can exhibit extensive and complex patterns of molecular evolution. Changes in these genes could affect the functioning of the recombination pathway, and may have contributed to the successful domestication of maize and its expansion to new cultivation areas.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-017-3486-z) contains supplementary material, which is available to authorized users.

Sequencing of Single Pollen Nuclei Reveals Meiotic Recombination Events at Megabase Resolution and Circumvents Segregation Distortion Caused by Postmeiotic Processes

Meiotic recombination is a fundamental mechanism to generate novel allelic combinations which can be harnessed by breeders to achieve crop improvement. The recombination landscape of many crop species, including the major crop barley, is characterized by a dearth of recombination in 65% of the genome. In addition, segregation distortion caused by selection on genetically linked loci is a frequent and undesirable phenomenon in double haploid populations which hampers genetic mapping and breeding. Here, we present an approach to directly investigate recombination at the DNA sequence level by combining flow-sorting of haploid pollen nuclei of barley with single-cell genome sequencing. We confirm the skewed distribution of recombination events toward distal chromosomal regions at megabase resolution and show that segregation distortion is almost absent if directly measured in pollen. Furthermore, we show a bimodal distribution of inter-crossover distances, which supports the existence of two classes of crossovers which are sensitive or less sensitive to physical interference. We conclude that single pollen nuclei sequencing is an approach capable of revealing recombination patterns in the absence of segregation distortion.