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At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Is more better? Polyploidy in crops with diverse end uses and the potential for future applications

Increasing the number of chromosome sets can increase cell size and improve yields in some crops. Breeding polyploid crops introduces unique challenges compared to diploid species, which has deterred many from exploring the potential benefits. Despite this, recent technological advancements have alleviated some of the challenges related to complex genomes and enabled the improvement of many polyploid crops. Given these advancements, there is a need to review the use of higher ploidy crops and explore potential opportunities for increased chromosome number. Many of the leading bioenergy crops are polyploids and there may be additional opportunities to further diversify feedstocks for emerging bioenergy markets. Such diversification would help to meet the anticipated increase in renewable and sustainable energy demands. Here, in this perspective review, we review polyploid crops and the extent to which ploidy level impacts improvement and production. The advantages and disadvantages of each crop are discussed in the context of their ploidy level and end-use. Particular emphasis is given to the current role and potential of polyploidy in creating the next generation of bioenergy feedstocks. Polyploids present challenges to crop improvement due to their complex genomes, but many of these difficulties can and have been overcome with technological advancements. Approaches that facilitate the use of higher ploidy crops open a path to capturing the many benefits of polyploidy, such as increased fruit and seed size, vigour, diversity, biomass and yield quality. However, these benefits are not observed across all species. This further emphasizes the need to study higher ploidy in traditionally diploid crops.

bioenergy↗
DOE OSTI2024

Seagrass genomes reveal ancient polyploidy and adaptations to the marine environment

Here, we present chromosome-level genome assemblies from representative species of three independently evolved seagrass lineages: Posidonia oceanica, Cymodocea nodosa, Thalassia testudinum and Zostera marina. We also include a draft genome of Potamogeton acutifolius, belonging to a freshwater sister lineage to Zosteraceae. All seagrass species share an ancient whole-genome triplication, while additional whole-genome duplications were uncovered for C. nodosa, Z. marina and P. acutifolius. Comparative analysis of selected gene families suggests that the transition from submerged-freshwater to submerged-marine environments mainly involved fine-tuning of multiple processes (such as osmoregulation, salinity, light capture, carbon acquisition and temperature) that all had to happen in parallel, probably explaining why adaptation to a marine lifestyle has been exceedingly rare. Major gene losses related to stomata, volatiles, defence and lignification are probably a consequence of the return to the sea rather than the cause of it. These new genomes will accelerate functional studies and solutions, as continuing losses of the savannahs of the sea are of major concern in times of climate change and loss of biodiversity.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Transcriptome Dynamics of the Inflorescence in Reciprocally Formed Allopolyploid Tragopogon miscellus (Asteraceae)

Polyploidy is an important evolutionary mechanism and is prevalent among land plants. Most polyploid species examined have multiple origins, which provide genetic diversity and may enhance the success of polyploids. In some polyploids, recurrent origins can result from reciprocal crosses between the same diploid progenitors. Although great progress has been made in understanding the genetic consequences of polyploidy, the genetic implications of reciprocal polyploidization remain poorly understood, especially in natural polyploids. Tragopogon (Asteraceae) has become an evolutionary model system for studies of recent and recurrent polyploidy. Allotetraploid T. miscellus has formed reciprocally in nature with resultant distinctive floral and inflorescence morphologies (i.e., short- vs. long-liguled forms). In this study, we performed comparative inflorescence transcriptome analyses of reciprocally formed T. miscellus and its diploid parents, T. dubius and T. pratensis. In both forms of T. miscellus, homeolog expression of ~70% of the loci showed vertical transmission of the parental expression patterns (i.e., parental legacy), and ~20% of the loci showed biased homeolog expression, which was unbalanced toward T. pratensis. However, 17.9% of orthologous pairs showed different homeolog expression patterns between the two forms of T. miscellus. No clear effect of cytonuclear interaction on biased expression of the maternal homeolog was found. In terms of the total expression level of the homeologs studied, 22.6% and 16.2% of the loci displayed non-additive expression in short- and long-liguled T. miscellus, respectively. Unbalanced expression level dominance toward T. pratensis was observed in both forms of T. miscellus. Significantly, genes annotated as being involved in pectin catabolic processes were highly expressed in long-liguled T. miscellus relative to the short-liguled form, and the majority of these differentially expressed genes were transgressively down-regulated in short-liguled T. miscellus. Given the known role of these genes in cell expansion, they may play a role in the differing floral and inflorescence morphologies of the two forms. In summary, the overall inflorescence transcriptome profiles are highly similar between reciprocal origins of T. miscellus. However, the dynamic homeolog-specific expression and non-additive expression patterns observed in T. miscellus emphasize the importance of reciprocal origins in promoting the genetic diversity of polyploids.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Hijacking a rapid and scalable metagenomic method reveals subgenome dynamics and evolution in polyploid plants

Premise: The genomes of polyploid plants archive the evolutionary events leading to their present forms. However, plant polyploid genomes present numerous hurdles to the genome comparison algorithms for classification of polyploid types and exploring genome dynamics. Methods: Here, the problem of intra- and inter-genome comparison for examining polyploid genomes is reframed as a metagenomic problem, enabling the use of the rapid and scalable MinHashing approach. To determine how types of polyploidy are described by this metagenomic approach, plant genomes were examined from across the polyploid spectrum for both k-mer composition and frequency with a range of k-mer sizes. In this approach, no subgenome-specific k-mers are identified; rather, whole-chromosome k-mer subspaces were utilized. Results: Given chromosome-scale genome assemblies with sufficient subgenome-specific repetitive element content, literature-verified subgenomic and genomic evolutionary relationships were revealed, including distinguishing auto- from allopolyploidy and putative progenitor genome assignment. The sequences responsible were the rapidly evolving landscape of transposable elements. An investigation into the MinHashing parameters revealed that the downsampled k-mer space (genomic signatures) produced excellent approximations of sequence similarity. Furthermore, the clustering approach used for comparison of the genomic signatures is scrutinized to ensure applicability of the metagenomics-based method. Discussion: The easily implementable and highly computationally efficient MinHashing-based sequence comparison strategy enables comparative subgenomics and genomics for large and complex polyploid plant genomes. Such comparisons provide evidence for polyploidy-type subgenomic assignments. In cases where subgenome-specific repeat signal may not be adequate given a chromosomes' global k-mer profile, alternative methods that are more specific but more computationally complex outperform this approach.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Halophytes and heavy metals: A multi‐omics approach to understand the role of gene and genome duplication in the abiotic stress tolerance of Cakile maritima

Abstract Premise The origin of diversity is a fundamental biological question. Gene duplications are one mechanism that provides raw material for the emergence of novel traits, but evolutionary outcomes depend on which genes are retained and how they become functionalized. Yet, following different duplication types (polyploidy and tandem duplication), the events driving gene retention and functionalization remain poorly understood. Here we usedCakile maritima, a species that is tolerant to salt and heavy metals and shares an ancient whole‐genome triplication with closely related salt‐sensitive mustard crops (Brassica), as a model to explore the evolution of abiotic stress tolerance following polyploidy. Methods Using a combination of ionomics, free amino acid profiling, and comparative genomics, we characterize aspects of salt stress response inC. maritimaand identify retained duplicate genes that have likely enabled adaptation to salt and mild levels of cadmium. Results Cakile maritimais tolerant to both cadmium and salt treatments through uptake of cadmium in the roots. Proline constitutes greater than 30% of the free amino acid pool inC. maritimaand likely contributes to abiotic stress tolerance. We find duplicated gene families are enriched in metabolic and transport processes and identify key transport genes that may be involved inC. maritimaabiotic stress tolerance. Conclusions These findings identify pathways and genes that could be used to enhance plant resilience and provide a putative understanding of the roles of duplication types and retention on the evolution of abiotic stress response.

Plant Sciences↗
DOE OSTI2020

Genomic diversifications of five Gossypium allopolyploid species and their impact on cotton improvement

Abstract Polyploidy is an evolutionary innovation for many animals and all flowering plants, but its impact on selection and domestication remains elusive. Here we analyze genome evolution and diversification for all five allopolyploid cotton species, including economically important Upland and Pima cottons. Although these polyploid genomes are conserved in gene content and synteny, they have diversified by subgenomic transposon exchanges that equilibrate genome size, evolutionary rate heterogeneities and positive selection between homoeologs within and among lineages. These differential evolutionary trajectories are accompanied by gene-family diversification and homoeolog expression divergence among polyploid lineages. Selection and domestication drive parallel gene expression similarities in fibers of two cultivated cottons, involving coexpression networks and N 6 -methyladenosine RNA modifications. Furthermore, polyploidy induces recombination suppression, which correlates with altered epigenetic landscapes and can be overcome by wild introgression. These genomic insights will empower efforts to manipulate genetic recombination and modify epigenetic landscapes and target genes for crop improvement.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Patterns of genomic variation reveal a single evolutionary origin of the wild allotetraploid Mimulus sookensis

Abstract Polyploidy occurs across the tree of life and is especially common in plants. Because newly formed cytotypes are often incompatible with their progenitors, polyploidy is also said to trigger “instantaneous” speciation. If a polyploid can self-fertilize or reproduce asexually, it is even possible for one individual to produce an entirely new lineage, but how often this scenario occurs is unclear. Here, we investigate the evolutionary history of the wild allotetraploid Mimulus sookensis, which was formed through hybridization between self-compatible, diploid species in the Mimulus guttatus complex. We generate a chromosome-scale reference assembly for M. sookensis and define its distinct subgenomes. Despite previous reports suggesting multiple origins of this highly selfing polyploid, we discover patterns of population genomic variation that provide unambiguous support for a single origin. One M. sookensis subgenome is clearly derived from the selfer Mimulus nasutus, which organellar variation suggests is the maternal progenitor. The ancestor of the other subgenome is less certain, but it shares variation with both Mimulus decorus and M. guttatus, two outcrossing diploids with geographic ranges that overlap broadly with M. sookensis. This study establishes M. sookensis as an example of instantaneous speciation, likely facilitated by the polyploid’s predisposition to self-fertilize.

Environmental Sciences & Ecology↗
DOE OSTI2021

Three founding ancestral genomes involved in the origin of sugarcane

Modern sugarcane cultivars (Saccharum spp.) are high polyploids, aneuploids (2n = ~12 = ~120) derived from interspecific hybridizations between the domesticated sweet species Saccharum officinarum and the wild species S. spontaneum. To analyse the architecture and origin of such a complex genome, we analysed the sequences of all 12 hom(oe)ologous haplotypes (BAC clones) from two distinct genomic regions of a typical modern cultivar, as well as the corresponding sequence in Miscanthus sinense and Sorghum bicolor, and monitored their distribution among representatives of the Saccharum genus. The diversity observed among haplotypes suggested the existence of three founding genomes (A, B, C) in modern cultivars, which diverged between 0.8 and 1.3 Mya. Two genomes (A, B) were contributed by S. officinarum; these were also found in its wild presumed ancestor S. robustum, and one genome (C) was contributed by S. spontaneum. These results suggest that S. officinarum and S. robustum are derived from interspecific hybridization between two unknown ancestors (A and B genomes). The A genome contributed most haplotypes (nine or ten) while the B and C genomes contributed one or two haplotypes in the regions analysed of this typical modern cultivar. Interspecific hybridizations likely involved accessions or gametes with distinct ploidy levels and/or were followed by a series of backcrosses with the A genome. The three founding genomes were found in all S. barberi, S. sinense and modern cultivars analysed. None of the analysed accessions contained only the A genome or the B genome, suggesting that representatives of these founding genomes remain to be discovered. This evolutionary model, which combines interspecificity and high polyploidy, can explain the variable chromosome pairing affinity observed in Saccharum. It represents a major revision of the understanding of Saccharum diversity.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Is selfing a reproductive assurance promoting polyploid establishment? Reduced fitness, leaky self‐incompatibility and lower inbreeding depression in neotetraploids

Premise Newly formed polyploids face significant obstacles to persistence and population establishment because of fitness costs of intercytotype mating. Selfing provides the opportunity to escape mate limitation, enabling production of new individuals and increasing the likelihood of fixation of new polyploid lineages. Still, association between self‐compatibility and polyploidy is not always clear. We compared self‐incompatibility and inbreeding depression in neotetraploids and their diploid progenitor to explore the direct effects of whole genome duplications on self‐incompatibility and the implications of ploidy‐driven changes for polyploid establishment. Methods Outcross and self‐pollinations were performed in diploids and synthetic neotetraploids of Jasione maritima var. maritima , and reproductive success was measured through fruit and seed production and seed germination. Self‐ and outcross offspring were grown under controlled conditions, and plant performance was measured through several fitness parameters. Results Neotetraploids showed an overall lower performance than diploids. Reproductive success was negatively affected by selfing in both cytotypes. However, greater variation in the expression of self‐incompatibility was observed in neotetraploids; additionally, developmental and physiological parameters were not affected by selfing on neotetraploids, with an overall similar fitness of outcrossed and selfed individuals, resulting in lower inbreeding depression indexes. Conclusions Neotetraploids might have benefited from selfing at initial stages after their formation. Genome duplications resulted in leaky self‐incompatibility, enabling the production of offspring under minority cytotype disadvantage with similar fitness as outcrossed offspring. Our results support theoretical assumptions that selfing might be important for neopolyploid establishment, although changes in self‐incompatibility might not be abrupt.

Siopa, Catarina↗
DOE OSTI2021

Surveying Grassland Islands: the genetics and performance of Appalachian switchgrass (Panicum virgatum L.) collections

The interior Southeastern United States could contain novel germplasm for the bioenergy crop switchgrass due to its diverse habitats and geographic location between genetic subpopulations (Atlantic, Midwest, and Gulf). Collections from this region could accelerate breeding progress, contribute to conservation efforts, and improve understanding of isolated grasslands in the region. This study located 22 sites in the Midsouth region and obtained 1,521,210 single nucleotide polymorphism markers of 202 individuals through genotype-by-sequencing. Here, individuals were evaluated for flowering time, winter survival and tiller number. Comparison to a national diversity panel revealed that branches of two major subpopulations occur in the region with two levels of polyploidy: Atlantic tetraploids and Midwest octoploids. Two locations contained admixed octoploid individuals with Midwest and Gulf genetics. Field performance of the Midwest octoploids conformed with prior reported performance of the Midwest subpopulation, although three sites contained promising late flowering traits. The Atlantic tetraploids had moderate winter survival, short stature, and anomalously early flowering. Atlantic populations mostly occurred in marginal sites and their morphological and flowering time adaptations may be a resource conservation strategy. Demographic inference of historical effective population size variation in a subset of tetraploid locations indicated a widespread recent decline in effective population size. This pattern is consistent with isolation of these switchgrass communities from larger populations and is further supported by evidence of inbreeding within the populations (F I = 0.18). The populations documented in this study contain novel genetic diversity and adaptations to a range of marginal habitats. Therefore, this study provides a new source of germplasm for future breeding and conservation programs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Exceptional subgenome stability and functional divergence in the allotetraploid Ethiopian cereal teff

Teff (Eragrostis tef) is a cornerstone of food security in the Horn of Africa, where it is prized for stress resilience, grain nutrition, and market value. Here, we report a chromosome-scale assembly of allotetraploid teff (variety Dabbi) and patterns of subgenome dynamics. The teff genome contains two complete sets of homoeologous chromosomes, with most genes maintaining as syntenic gene pairs. TE analysis allows us to estimate that the teff polyploidy event occurred ~1.1 million years ago (mya) and that the two subgenomes diverged ~5.0 mya. Despite this divergence, we detect no large-scale structural rearrangements, homoeologous exchanges, or biased gene loss, in contrast to many other allopolyploids. The two teff subgenomes have partitioned their ancestral functions based on divergent expression across a diverse expression atlas. Together, these genomic resources will be useful for accelerating breeding of this underutilized grain crop and for fundamental insights into polyploid genome evolution.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Synthetic hybrids of six yeast species

Abstract Allopolyploidy generates diversity by increasing the number of copies and sources of chromosomes. Many of the best-known evolutionary radiations, crops, and industrial organisms are ancient or recent allopolyploids. Allopolyploidy promotes differentiation and facilitates adaptation to new environments, but the tools to test its limits are lacking. Here we develop an iterative method of Hybrid Production (iHyPr) to combine the genomes of multiple budding yeast species, generating Saccharomyces allopolyploids of at least six species. When making synthetic hybrids, chromosomal instability and cell size increase dramatically as additional copies of the genome are added. The six-species hybrids initially grow slowly, but they rapidly regain fitness and adapt, even as they retain traits from multiple species. These new synthetic yeast hybrids and the iHyPr method have potential applications for the study of polyploidy, genome stability, chromosome segregation, and bioenergy.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

A generalist–specialist trade-off between switchgrass cytotypes impacts climate adaptation and geographic range

Polyploidy results from whole-genome duplication and is a unique form of heritable variation with pronounced evolutionary implications. Different ploidy levels, or cytotypes, can exist within a single species, and such systems provide an opportunity to assess how ploidy variation alters phenotypic novelty, adaptability, and fitness, which can, in turn, drive the development of unique ecological niches that promote the coexistence of multiple cytotypes. Switchgrass, Panicum virgatum, is a widespread, perennial C4 grass in North America with multiple naturally occurring cytotypes, primarily tetraploids (4×) and octoploids (8×). Using a combination of genomic, quantitative genetic, landscape, and niche modeling approaches, we detect divergent levels of genetic admixture, evidence of niche differentiation, and differential environmental sensitivity between switchgrass cytotypes. Taken together, these findings support a generalist (8×)–specialist (4×) trade-off. Our results indicate that the 8× represent a unique combination of genetic variation that has allowed the expansion of switchgrass’ ecological niche and thus putatively represents a valuable breeding resource.

09 BIOMASS FUELS↗
DOE OSTI2023

The exceptional form and function of the giant bacterium Ca. Epulopiscium viviparus revolves around its sodium motive force

Epulopiscium spp. are the largest known heterotrophic bacteria; a large cigar-shaped individual is a million times the volume of Escherichia coli. To better understand the metabolic potential and relationship of Epulopiscium sp. type B with its host Naso tonganus, we generated a high-quality draft genome from a population of cells taken from a single fish. We propose the name Candidatus Epulopiscium viviparus to describe populations of this best-characterized Epulopiscium species. Metabolic reconstruction reveals more than 5% of the genome codes for carbohydrate active enzymes, which likely degrade recalcitrant host-diet algal polysaccharides into substrates that may be fermented to acetate, the most abundant short-chain fatty acid in the intestinal tract. Moreover, transcriptome analyses and the concentration of sodium ions in the host intestinal tract suggest that the use of a sodium motive force (SMF) to drive ATP synthesis and flagellar rotation is integral to symbiont metabolism and cellular biology. In natural populations, genes encoding both F-type and V-type ATPases and SMF generation via oxaloacetate decarboxylation are among the most highly expressed, suggesting that ATPases synthesize ATP and balance ion concentrations across the cell membrane. High expression of these and other integral membrane proteins may allow for the growth of its extensive intracellular membrane system. Further, complementary metabolism between microbe and host is implied with the potential provision of nitrogen and B vitamins to reinforce this nutritional symbiosis. The few features shared by all bacterial behemoths include extreme polyploidy, polyphosphate synthesis, and thus far, they have all resisted cultivation in the lab.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Comparative phylogenetics of repetitive elements in a diverse order of flowering plants (Brassicales)

Genome sizes of plants have long piqued the interest of researchers due to the vast differences among organisms. However, the mechanisms that drive size differences have yet to be fully understood. Two important contributing factors to genome size are expansions of repetitive elements, such as transposable elements (TEs), and whole-genome duplications (WGD). Although studies have found correlations between genome size and both TE abundance and polyploidy, these studies typically test for these patterns within a genus or species. The plant order Brassicales provides an excellent system to further test if genome size evolution patterns are consistent across larger time scales, as there are numerous WGDs. This order is also home to one of the smallest plant genomes, Arabidopsis thaliana—chosen as the model plant system for this reason—as well as to species with very large genomes. With new methods that allow for TE characterization from low-coverage genome shotgun data and 71 taxa across the Brassicales, we confirm the correlation between genome size and TE content, however, we are unable to reconstruct phylogenetic relationships and do not detect any shift in TE abundance associated with WGD.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Relics of interspecific hybridization retained in the genome of a drought-adapted peanut cultivar

Peanut (Arachis hypogaea L.) is a globally important oil and food crop frequently grown in arid, semi-arid, or dryland environments. Improving drought tolerance is a key goal for peanut crop improvement efforts. Here, we present the genome assembly and gene model annotation for “Line8,” a peanut genotype bred from drought-tolerant cultivars. Our assembly and annotation are the most contiguous and complete peanut genome resources currently available. The high contiguity of the Line8 assembly allowed us to explore structural variation both between peanut genotypes and subgenomes. We detect several large inversions between Line8 and other peanut genome assemblies, and there is a trend for the inversions between more genetically diverged genotypes to have higher gene content. We also relate patterns of subgenome exchange to structural variation between Line8 homeologous chromosomes. Unexpectedly, we discover that Line8 harbors an introgression from A.cardenasii, a diploid peanut relative and important donor of disease resistance alleles to peanut breeding populations. The fully resolved sequences of both haplotypes in this introgression provide the first in situ characterization of A.cardenasii candidate alleles that can be leveraged for future targeted improvement efforts. The completeness of our genome will support peanut biotechnology and broader research into the evolution of hybridization and polyploidy.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2026

Gene and genome duplications have contrasting impacts on biosynthetic and flower developmental pathways in California poppy

Benzylisoquinoline alkaloids (BIAs) represent a vast group of specialized plant metabolites with diverse pharmaceutical applications, synthesized by a variety of gene families. Among the multiple plant lineages that produce BIAs, the most notable is the poppy family (Papaveraceae), with California poppy (Eschscholzia californica) emerging as a model organism. Here, we report a haplotype-resolved genome assembly, in combination with a high-density expression atlas, for California poppy. Genome analyses reveal recent diversification of BIA biosynthesis genes in poppy through localized duplications. Furthermore, we demonstrate that the degree of phylogenetic relatedness among paralogs within BIA biosynthesis-associated gene families correlates with similarities in gene expression. In contrast, gene families involved in carotenoid biosynthesis, which contributes to the intense orange petal pigmentation, are not phylogenetically clustered, and floral developmental regulators exhibit a high degree of retention of gene duplicates associated with ancient polyploidy events. These findings illustrate alternative roles for gene and genome duplications as drivers of trait evolution. Given the position of California poppy in the angiosperm phylogeny, the high-quality genomic resources generated for this work constitute a valuable resource for comparative genomic and transcriptomic analyses for poppies and flowering plants more generally.

Rössner, Le-Han [Justus-Liebig University, Giessen↗