We present Ancestral Genome Reconstruction (AGR), an exploratory framework for the automated inference of "paleogenomes" from large-scale comparative datasets. By analyzing 84 extant angiosperm species, we reconstructed 10 key ancestral angiosperm genomes millions of years old. These reconstructed ancestors were instrumental in (1) estimating when angiosperms emerged, when major botanical families originated, and when shared ancestral whole-genome duplication events occurred; and (2) tracing the evolutionary trajectories of ancestral chromosomes and genes, especially those that may have driven the emergence of key life-history traits (e.g., woody vs. herbaceous, aquatic vs. terrestrial, C3 vs. C4, and symbiotic root-nodulating vs. non-nodulating species). We demonstrated that these paleogenomes serve as tractable backbones for inter-crop translational research. Through an open-access web tool, OrthoViewer, we identified orthologs that have retained the same ancestral genomic context, favoring the identification of genes associated with "phenologs"- orthologous genes across species driving analogous phenotypes, traits, or processes-exemplified by FUWA for yield components, FLC for flowering time, and DDM1 for DNA methylation. Taken together, this study provides a testable paleogenomic workflow, opening novel avenues for integrating evolutionary genomics data into modern climate-smart crop breeding and supporting the agroecological transition.

Abstract AGR, for Ancestral Genome Reconstruction, is an automatic publicly available and open-source pipeline to infer paleogenomes from modern species genome comparisons exploiting the concept of inter-species chromosomal synteny relationships’ hierarchical clustering that can be used to unveil how ancestral genomes, genes, sequences and functions have been shaped during million years of present-day plant evolution.

BACKGROUND: Epigenetic mechanisms including DNA methylation are assumed to play crucial roles in the maintenance of genome integrity, regulation of gene expression and development, and their increasing exploitation in breeding applications is anticipated. However, the relationship between DNA methylation and gene expression remains ambiguous and difficult to generalize. Here we explored the hypothesized causality between the level of transcription and cytosine methylation at the 5’ end of genes (around transcription start sites and start codons) in relation to whole-genome duplication in natural and synthetic allohexaploid wheat (Triticum/Aegilops complex). RESULTS: Using transcriptomes and a sequence capture protocol coupled with bisulfite sequencing, we observed sometimes significant, but overall very weak associations between gene expression and 5’ end methylation on a genome-wide scale. In synthetic wheat allohexaploids, global methylation differences between subgenomes are not triggered by the polyploidization, as the subgenome patterns are rather faithfully inherited from parents. A small number of genes differentially methylated between the parents and synthetics was consistently recovered in reciprocal synthetics and subsequent generations. Differences in transcription between homeologs are not clearly associated with 5’ end methylation in either natural or synthetic wheat. Overall, allopolyploidization triggers only minor methylation changes around transcription start sites and start codons of nascent wheat allopolyploids, and these are not statistically associated with differential expression. Although there is a measurable methylation difference between silent and expressed genes in the developing grain, our results do not support the hypothesis that 5’ end DNA methylation is engaged in the regulation of gene expression in natural and synthetic wheat. CONCLUSIONS: While a ‘genome shock’ hypothesis predicts extensive transcriptomic and epigenetic reorganization after polyploidization, DNA methylation patterns around transcription start sites are generally undisturbed in nascent wheat allohexaploids. Although this stability might indicate importance for gene regulation, a clear relationship between DNA methylation and transcription was not observed either on a genome-wide scale, or among triads of homeologous genes.

"Cytosine methylation plays an important role in the regulation of gene expression in plants." Some iteration of this statement can be found in most papers centered on plant epigenetics and has become a widely accepted textbook claim. However, our generalized understanding of how DNA methylation exerts control over transcription is now challenged by observations demonstrating that transcriptional levels of most genes are unresponsive to DNA methylation changes. On a genome-wide scale, associations between DNA methylation and transcription are usually statistically weak. Even when correlations are found, the cause and effect can be difficult to identify, as methylation changes sometimes follow rather than precede transcriptional changes. While a growing number of studies explore a possible connection between differentially expressed genes (DEGs) and differentially methylated genes (DMGs), we demonstrate here that DEG-DMG overlaps are often significantly smaller than what could be expected by chance. This indicates that, contrary to expectations, changes in DNA methylation and changes in transcription sometimes avoid one another. Here, we discuss such observations and their implications for the hypothesis of a widespread control of gene expression directly by DNA methylation. While there are well-documented examples where DNA methylation regulates transcription, we argue that such cases represent a minority of genes, and we opine that approaches of reverse epigenetics are therefore unlikely to find broad application in breeding.

Over the past 10,000 years, the development of civilization has been enabled by the domestication of plants and animals tailored to human needs. The Triticeae tribe, including barley and wheat, has emerged as one of the most important sources of staple foods worldwide. Here, comparing genomes of wheat and barley genotypes from around the world, we unveiled genomic footprints of convergent selection affecting genes involved in crop adaptation and productivity, as well as a lack of parallel selection for diverse genes delivering genetic diversity specific to particular geographic and associated environmental conditions. We demonstrate that studying convergent selection between crops can help to identify genes crucial for adaptation and sources of diversity for improving cultivated species—forming the basis of the proposed concept of inter-crop translational research for breeding. Convergent selection between crops can help to identify genetic variants with important roles in adaptation as a source of diversity for the improvement of cultivated species through the concept of inter-crop translational research for breeding.

To breed for climate resilient crops, an understanding of the genetic and environmental factors influencing adaptation is critical. Barley provides a model species to study adaptation to climate change. Here we present a detailed analysis of genetic variation at a major photoperiod response locus and relate this to the domestication history and dispersal of barley. The PPD-H1 locus (a PSEUDO-RESPONSE REGULATOR 7) promotes flowering under long-day conditions, and a natural mutation at this locus resulted in a recessive, late-flowering ppd-H1 allele. This mutation proved beneficial in high-latitude environments such as Northern Europe, where it allows extended vegetative growth during long spring days. We infer the origin of the mutated late-flowering ppd-H1 allele by re-sequencing a large geo-referenced collection of 942 Hordeum spontaneum, 5 Hordeum agriocrithon and 1110 domesticated (Hordeum vulgare) barleys. We demonstrate that the late-flowering phenotype originated from Desert-type wild barley in the Southern Levant and present evidence suggesting a post-domestication origin of the mutated ppd-H1 allele.

Barley is one of the founder crops of the Neolithic transition in West Asia. While recent advances in genomics have provided a rather detailed picture of barley domestication, there are contradictory views on how the domestication process affected genetic diversity. We set out to revisit this question by integrating public DNA sequencing data from ancient barley and wide collections of extant wild and domesticated accessions. Using two previously overlooked approaches - analyses of chloroplast genomes and genome-wide proportions of private variants - we found that the barley cultivated six millennia ago was genetically unique and more diverse when compared to extant landraces and cultivars. Moreover, the chloroplast genomes revealed a link between the ancient barley, an obscure wild genotype from north-eastern Libya, and a distinct population of barley cultivated in Ethiopia/Eritrea. Based on these results, we hypothesize past existence of a wider North African population that included both wild and cultivated types and suffered from genetic erosion in the past six millennia, likely due to a rapid desertification that ended the Holocene African humid period. Besides providing clues about the origin of Ethiopian landraces, the hypothesis explains the post-domestication loss of diversity observed in barley. Analyses of additional samples will be necessary to resolve the history of African barley and its contribution to the extant cultivated gene pool.

In the last 20 years, several techniques have been developed for quantifying DNA methylation, the most studied epigenetic marks in eukaryotes, including the gold standard method, whole-genome bisulfite sequencing (WGBS). WGBS quantifies genome-wide DNA methylation but has several inconveniences rendering it less suitable for population-scale epigenetic studies. The high cost of deep sequencing and the large amounts of data generated prompted us to seek an alternative approach. Restricting studies to parts of the genome would be a satisfactory alternative had there not been a major limitation: the need to select upstream targets corresponding to differentially methylated regions as targets. Given the need to study large numbers of samples, we propose a strategy for investigating DNA methylation variation in natural populations, taking into account the structural complexity of genomes, their size, and their content in unique coding regions versus repeated regions as transposable elements. We first identified regions of highly variable DNA methylation in a subset of genotypes representative of the biological diversity in the population by WGBS. We then analysed the variations of DNA methylation in these targeted regions at the population level by sequencing capture bisulfite (SeqCapBis). The entire strategy was then validated by applying it to another species. Our strategy was developed as a proof of concept on natural populations of two forest species: Populus nigra and Quercus petraea. We developed a strategy and a workflow for quantifying epigenetic diversity in natural populations combining whole-genome and targeted capture sequencing for DNA methylation.

We developed a strategy and a workflow for quantifying epigenetic diversity in natural populations combining whole genome and targeted capture sequencing for DNA methylation. We first identified regions of highly variable DNA methylation in a representative subset of genotypes representative of the biological diversity in the population by WGBS. We then analysed the variations of DNA methylation in these targeted regions at the population level by Sequencing Capture Bisulphite (SeqCapBis).

BACKGROUND:Bread wheat is a recent allohexaploid (genomic constitution AABBDD) that emerged through a hybridization between tetraploid Triticum turgidum (AABB) and diploid Aegilops tauschii (DD) less than 10,000 years ago. The hexaploidization can be re-created artificially, producing synthetic wheat that has been used to study immediate genomic responses to polyploidization. The scale of the consequences of polyploidization, and their mechanism of establishment, remain uncertain.RESULTS:Here we sampled several synthetic wheats from alternative parental genotypes and reciprocal crosses, and examined transcriptomes from two different tissues and successive generations. We did not detect any massive reprogramming in gene expression, with only around 1% of expressed genes showing significant differences compared to their lower-ploidy parents. Most of this differential expression is located on the D subgenome, without consistency in the direction of the expression change. Homoeolog expression bias in synthetic wheat is similar to the pattern observed in the parents. Both differential expression and homoeolog bias are tissue-specific. While up to three families of transposable elements became upregulated in wheat synthetics, their position and distance are not significantly associated with expression changes in proximal genes.DISCUSSION:While only a few genes change their expression pattern after polyploidization, they can be involved in agronomically important pathways. Alternative parental combinations can lead to opposite changes on the same subset of D-located genes, which is relevant for harnessing new diversity in wheat breeding. Tissue specificity of the polyploidization-triggered expression changes indicates the remodelling of transcriptomes in synthetic wheat is plastic and likely caused by regulome interactions rather than permanent changes. We discuss the pitfalls of transcriptomic comparisons across ploidy levels that can inflate the de-regulation signal.CONCLUSIONS:Transcriptomic response to polyploidization in synthetic AABBDD wheat is modest and much lower than some previous estimates. Homoeolog expression bias in wheat allohexaploids is mostly attributed to parental legacy, with polyploidy having a mild balancing effect.

Grasses derive from a family of monocotyledonous plants that includes crops of major economic importance such as wheat, rice, sorghum and barley, sharing a common ancestor some 100 million years ago. The genomic attributes of plant adaptation remain obscure and the consequences of recurrent whole genome duplications (WGD) or polyploidization events, a major force in plant evolution, remain largely speculative. We conducted a comparative analysis of omics data from ten grass species to unveil structural (inversions, fusions, fissions, duplications, substitutions) and regulatory (expression and methylation) basis of genome plasticity, as possible attributes of plant long lasting evolution and adaptation. The present study demonstrates that diverged polyploid lineages sharing a common WGD event often present the same patterns of structural changes and evolutionary dynamics, but these patterns are difficult to generalize across independent WGD events as a result of non-WGD factors such as selection and domestication of crops. Polyploidy is unequivocally linked to the evolutionary success of grasses during the past 100 million years, although it remains difficult to attribute this success to particular genomic consequences of polyploidization, suggesting that polyploids harness the potential of genome duplication, at least partially, in lineage-specific ways. Overall, the present study clearly demonstrates that post-polyploidization reprogramming is more complex than traditionally reported in investigating single species and calls for a critical and comprehensive comparison across independently polyploidized lineages.

SUMMARY How perennial organisms adapt to environments is a key question in biology. To address this question, we investigated ten natural black poplar ( Populus nigra ) populations from Western Europe, a keystone forest tree of riparian ecosystems. We assessed the role of (epi)genetic regulation in driving tree species evolution and adaptation over several millions of years (macro-evolution) up to a few generations (micro-evolution). At the macro-evolution scale, polar experienced differential structural (gene loss) and regulation (expression and methylation) reprogramming between sister genomic compartments inherited from polyploidization events. More interestingly, at the micro-evolution scale, both genetic and epigenetic variations differentiate populations from different geographic origins, targeting specifically genes involved in disease resistance, immune response, hormonal and stress response that can be considered as key functions of local adaptation of long lifespan species. Moreover, genes involved in cambium formation, an important functional trait for forest trees, as well as basal functions for cell survival are constitutively expressed though methylation control. These results highlight DNA methylation as a marker of population differentiation, evolutionary adaptation to diverse ecological environments and ultimately opening the need to take epigenetic marks into account in breeding strategies, especially for woody plants.

Recently, entire genebank collections of wheat have been extensively characterized with sequencing data. We have identified introgressions using these genotyping-by-sequencing and whole-genome sequencing data. On the basis of our results, we provide information about predicted introgressions at 1-Mb resolution for 9,172 wheat samples as a resource for breeders and scientists. We recommend that all plant genetic resources, including genebank collections, be characterized using a combination of variant calling and introgression prediction. This is necessary to identify potential duplicates in collections efficiently and reliably, and to select promising germplasms with potentially beneficial introgressions for further characterization and prospective breeding application.

Bread wheat is a recent allohexaploid (genomic constitution AABBDD) that emerged through a hybridization between tetraploid Triticum turgidum (AABB) and diploid Aegilops tauschii (DD) <10,000 years ago. The hexaploidization can be re-created artificially, producing synthetic wheat that has been used to study immediate genomic responses to polyploidization. Here we produced several synthetic wheats from alternative parental genotypes and reciprocal crosses, and examined transcriptomes from two different tissues and successive generations. We did not detect a massive reprogramming in gene expression, with only ∼1% of expressed genes showing significant differences compared to their lower-ploidy parents. Most of the differential expression is located on the D subgenome, without consistency in the direction of the expression change. Leaves and developing endosperm show distinct patterns of homoeologous expression bias, and almost non-overlapping sets of differentially expressed genes, implying that the polyploidization-triggered reprogramming is not effectuated through permanent (epi)genetic changes. While 0-3 families of transposable elements (TEs) became upregulated in wheat synthetics, we did not detect any significant association between TEs and the expression of nearby genes. We conclude that the modest tissue-specific and partially genotype-specific transcriptomic response to polyploidization is likely caused by rare incompatibilities of parental regulomes, and we discuss the pitfalls of transcriptomic comparisons across ploidy levels that can inflate the de-regulation signal.

Asian cultivated rice shows allelic variation in sodium transporter, OsHKT1;5, correlating with shoot sodium exclusion (salinity tolerance). These changes map to intra/extracellularly-oriented loops that occur between four transmembrane-P loop-transmembrane (MPM) motifs in OsHKT1;5. HKT1;5 sequences from more recently evolved Oryza species (O. sativa/O. officinalis complex species) contain two expansions that involve two intracellularly oriented loops/helical regions between MPM domains, potentially governing transport characteristics, while more ancestral HKT1;5 sequences have shorter intracellular loops. We compared homology models for homoeologous OcHKT1;5-K and OcHKT1;5-L from halophytic O. coarctata to identify complementary amino acid residues in OcHKT1;5-L that potentially enhance affinity for Na+. Using haplotyping, we showed that Asian cultivated rice accessions only have a fraction of HKT1;5 diversity available in progenitor wild rice species (O. nivara and O. rufipogon). Progenitor HKT1;5 haplotypes can thus be used as novel potential donors for enhancing cultivated rice salinity tolerance. Within Asian rice accessions, 10 non-synonymous HKT1;5 haplotypic groups occur. More HKT1;5 haplotypic diversities occur in cultivated indica gene pool compared to japonica. Predominant Haplotypes 2 and 10 occur in mutually exclusive japonica and indica groups, corresponding to haplotypes in O. sativa salt-sensitive and salt-tolerant landraces, respectively. This distinct haplotype partitioning may have originated in separate ancestral gene pools of indica and japonica, or from different haplotypes selected during domestication. Predominance of specific HKT1;5 haplotypes within the 3000 rice dataset may relate to eco-physiological fitness in specific geo-climatic and/or edaphic contexts.

Wheat occupies a special role in global food security since, in addition to providing 20% of our carbohydrates and protein, almost 25% of the global production is traded internationally. The importance of wheat for food security was recognised by the Chief Agricultural Scientists of the G20 group of countries when they endorsed the establishment of the Wheat Initiative in 2011. The Wheat Initiative was tasked with supporting the wheat research community by facilitating collaboration, information and resource sharing and helping to build the capacity to address challenges facing production in an increasingly variable environment. Many countries invest in wheat research. Innovations in wheat breeding and agronomy have delivered enormous gains over the past few decades, with the average global yield increasing from just over 1 tonne per hectare in the early 1960s to around 3.5 tonnes in the past decade. These gains are threatened by climate change, the rapidly rising financial and environmental costs of fertilizer, and pesticides, combined with declines in water availability for irrigation in many regions. The international wheat research community has worked to identify major opportunities to help ensure that global wheat production can meet demand. The outcomes of these discussions are presented in this paper.

We used genotyping-by-sequencing to investigate the evolutionary history of bere, the oldest barley variety still cultivated in Britain and possibly in all of Europe. With a panel of 203 wild and 401 cultivated barley accessions, including 35 samples identified as bere, we obtained filtered datasets comprising up to 1,946,469 single nucleotide polymorphisms (SNPs). The beres formed two genetically-distinct groups, the larger of which included beres from Orkney and the Scottish Western Isles, as well as varieties not identified as bere from the Faroe Islands. This group of beres was distinct from other British barleys, but had a close genetic affiliation with Scandinavian accessions. Although the data were partly compatible with the traditional view that bere was introduced to Scotland by the Vikings during the eighth century AD, the evidence as whole suggested that the bere and Scandinavian barleys are sister groups descended from a more distant common progenitor, possibly dating to the Bronze Age when hulled barleys first become common in northern Europe. More recently, there has been gene flow from these beres into Polish barleys, possibly following export of grain to the Baltic region during periods when Orkney was under Norwegian or Danish rule. A second, smaller group of beres, which included a traditional Welsh variety, was genetically distinct from the main group and probably represents a more recent introduction of barley from central Europe. Our results emphasize the uniqueness of bere barley and its importance as a heritage crop and a potential source of germplasm for breeding programmes.

Additional file 9: Table S3. Protein-changing variants identified as possible selection targets for each sweep and each group.

AbstractThe breeding efforts of the twentieth century contributed to large increases in yield but selection may have increased vulnerability to environmental perturbations. In that context, there is a growing demand for methodology to re-introduce useful variation into cultivated germplasm. Such efforts can focus on the introduction of specific traits monitored through diagnostic molecular markers identified by QTL/association mapping or selection signature screening. A combined approach is to increase the global diversity of a crop without targeting any particular trait.A considerable portion of the genetic diversity is conserved in genebanks. However, benefits of genetic resources (GRs) in terms of favorable alleles have to be weighed against unfavorable traits being introduced along. In order to facilitate utilization of GR, core collections are being identified and progressively characterized at the phenotypic and genomic levels. High-throughput genotyping and sequencing technologies allow to build prediction models that can estimate the genetic value of an entire genotyped collection. In a pre-breeding program, predictions can accelerate recurrent selection using rapid cycles in greenhouses by skipping some phenotyping steps. In a breeding program, reduced phenotyping characterization allows to increase the number of tested parents and crosses (and global genetic variance) for a fixed budget. Finally, the whole cross design can be optimized using progeny variance predictions to maximize short-term genetic gain or long-term genetic gain by constraining a minimum level of diversity in the germplasm. There is also a potential to further increase the accuracy of genomic predictions by taking into account genotype by environment interactions, integrating additional layers of omics and environmental information.Here, we aim to review some relevant concepts in population genomics together with recent advances in quantitative genetics in order to discuss how the combination of both disciplines can facilitate the use of genetic diversity in plant (pre) breeding programs.

The colonization of land by descendants of charophyte green algae marked a turning point in Earth history that enabled the development of the diverse terrestrial ecosystems we see today. Early land plants diversified into three gametophyte-dominant lineages, namely the hornworts, liverworts, and mosses, collectively known as bryophytes, and a sporophyte-dominant lineage, the vascular plants, or tracheophytes. In recent decades, the prevailing view of evolutionary relationships among these four lineages has been that the tracheophytes were derived from a bryophyte ancestor. However, recent phylogenetic evidence has suggested that bryophytes are monophyletic, and thus that the first split among land plants gave rise to the lineages that today we recognize as the bryophytes and tracheophytes. We present a phylogenetic analysis of chloroplast protein-coding data that also supports the monophyly of bryophytes. This newly compiled data set consists of 83 chloroplast genes sampled across 30 taxa that include chlorophytes and charophytes, including four members of the Zygnematophyceae, and land plants, that were sampled following a balanced representation of the main bryophyte and tracheophyte lineages. Analyses of non-synonymous site nucleotide data and amino acid translation data result in congruent phylogenetic trees showing the monophyly of bryophytes, with the Zygnematophyceae as the charophyte group most closely related to land plants. Analyses showing that bryophytes and tracheophytes evolved separately from a common terrestrial ancestor have profound implications for the way we understand the evolution of plant life cycles on land and how we interpret the early land plant fossil record.