Search NASA⌕ Search

SEARCH · Search NASA

Results for “polyploid”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 55 records · Page 3
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Effects of Desiccation and Freezing on Microbial Ionizing Radiation Survivability: Considerations for Mars Sample Return

Increasingly, national space agencies are expanding their goals to include Mars exploration with sample return. To better protect Earth and its biosphere from potential extraterrestrial sources of contamination, as set forth in the Outer Space Treaty of 1967, international efforts to develop planetary protection measures strive to understand the danger of cross-contamination processes in Mars sample return missions. We aim to better understand the impact of the martian surface on microbial dormancy and survivability. Radiation resistance of microbes is a key parameter in considering survivability of microbes over geologic times on the frigid, arid surface of Mars that is bombarded by solar and galactic cosmic radiation. We tested the influence of desiccation and freezing on the ionizing radiation survival of six model microorganisms: vegetative cells of two bacteria (Deinococcus radiodurans, Escherichia coli) and a strain of budding yeast (Saccharomyces cerevisiae); and vegetative cells and endospores of three Bacillus bacteria (B. subtilis, B. megaterium, B. thuringiensis). Desiccation and freezing greatly increased radiation survival of vegetative polyploid microorganisms when applied separately, and when combined, desiccation and freezing increased radiation survival even more so. Thus, the radiation survival threshold of polyploid D. radiodurans cells can be extended from the already high value of 25 kGy in liquid culture to an astonishing 140 kGy when the cells are both desiccated and frozen. However, such synergistic radioprotective effects of desiccation and freezing were not observed in monogenomic or digenomic Bacillus cells and endospores, which are generally sterilized by 12 kGy. This difference is associated with a critical requirement for survivability under radiation, that is, repair of genome damage caused by radiation. Deinococcus radiodurans and S. cerevisiae accumulate similarly high levels of the Mn antioxidants that are required for extreme radiation resistance, as do endospores, though they greatly exceed spores in radioresistance because they contain multiple identical genome copies, which in D. radiodurans are joined by persistent Holliday junctions. We estimate ionizing radiation survival limits of polyploid DNA-based life-forms to be hundreds of millions of years of background radiation while buried in the martian subsurface. Our findings imply that forward contamination of Mars will essentially be permanent, and backward contamination is a possibility if life ever existed on Mars.

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 OSTI2022

Multiple origins, one evolutionary trajectory: gradual evolution characterizes distinct lineages of allotetraploid Brachypodium

The “genomic shock” hypothesis posits that unusual challenges to genome integrity such as whole genome duplication may induce chaotic genome restructuring. Decades of research on polyploid genomes have revealed that this is often, but not always the case. While some polyploids show major chromosomal rearrangements and derepression of transposable elements in the immediate aftermath of whole genome duplication, others do not. Nonetheless, all polyploids show gradual diploidization over evolutionary time. To evaluate these hypotheses, we produced a chromosome-scale reference genome for the natural allotetraploid grass Brachypodium hybridum, accession “Bhyb26.” We compared 2 independently derived accessions of B. hybridum and their deeply diverged diploid progenitor species Brachypodium stacei and Brachypodium distachyon. The 2 B. hybridum lineages provide a natural timecourse in genome evolution because one formed 1.4 million years ago, and the other formed 140 thousand years ago. The genome of the older lineage reveals signs of gradual post-whole genome duplication genome evolution including minor gene loss and genome rearrangement that are missing from the younger lineage. In neither B. hybridum lineage do we find signs of homeologous recombination or pronounced transposable element activation, though we find evidence supporting steady post-whole genome duplication transposable element activity in the older lineage. Gene loss in the older lineage was slightly biased toward 1 subgenome, but genome dominance was not observed at the transcriptomic level. We propose that relaxed selection, rather than an abrupt genomic shock, drives evolutionary novelty in B. hybridum, and that the progenitor species’ similarity in transposable element load may account for the subtlety of the observed genome dominance.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Discovering the desirable alleles contributing to the lignocellulosic biomass traits in Saccharum germplasm collections for energy cane improvement

1) The success in crop improvement programs depends largely on the extent of genetic variability available. Germplasm collections assembles all the available genetic resources and are critical for long-term crop improvement. This world sugarcane germplasm collection contains enormous genetic variability for various morphological traits, biomass yield components, adaptation and many quality traits, prospectively imbeds a large number of valuable alleles for biofuel traits such as high biomass yield, quantity and quality of lignocelluloses, stress tolerance, and nutrient use efficiency. The germplasm collection is of little value unless it is characterized and utilized for crop improvement. In this project, we phenotypically and genotypically characterized the sugarcane world germplasm collection (The results were published in two papers already and another two papers are to be published). This data will be made available for public to refer to for germplasm unitization specifically in the sugarcane and energy cane breeding programs. In addition, we are identifying the alleles contributing to the biomass traits in sugarcane germplasm. This part of project is very challenging due to the large genome and highly polyploid level of this crop. We firstly established a high throughput sugarcane genotyping pipeline in the genome and bioinformatics era (a paper is published in 2016). We identified and modified a software for genome-wide association analysis of polyploid species. The results of the alleles associated to the biomass traits will be published soon, which will help the scientific community understand the genetic makeup of the biomass components of sugarcane. Molecular breeders can develop markers for marker assisted selection of biomass traits improvement. Further, the development and release of new energy cane cultivars through this project not only improved genetic diversity but also improved dry biomass yields and resistance to diseases. These new cultivars were tested on marginal soils in Florida and showed very promising yield potential that is important for the successful use of energy cane as a dedicated feedstock for lignocellulosic ethanol production. 2) Multiple techniques at different project progress stages were utilized. For example, for the whole world germplasm accession genotyping, a cheap widely used SSR marker genotyping platform was utilized due to the large number of samples (over thousand). But the throughput of this technique is low in generating data points. However, the purpose the genotyping is to form a core collection for further high throughput genotyping. Thus the results from the SSR genotyping was quite good enough to generated the core collection. To genotype the few hundred core collection accessions, an target enrichment sequencing technology was used, which is not only high throughput in generating large number of genotyping data, but also has the candidate genes targeted to genotyping. The data generated would be sufficient in identifying the alleles contributing to the traits of interests. All the techniques used in this project are effective though extensive time was invested specifically for establish the pipeline in the experimental design, data analysis, and different approach comparison. 3) the research can benefit to the public in polyploid genotyping and new and cost efficient genotyping platform development

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

A mosaic monoploid reference sequence for the highly complex genome of sugarcane

Sugarcane ( Saccharum spp.) is a major crop for sugar and bioenergy production. Its highly polyploid, aneuploid, heterozygous, and interspecific genome poses major challenges for producing a reference sequence. We exploited colinearity with sorghum to produce a BAC-based monoploid genome sequence of sugarcane. A minimum tiling path of 4660 sugarcane BAC that best covers the gene-rich part of the sorghum genome was selected based on whole-genome profiling, sequenced, and assembled in a 382-Mb single tiling path of a high-quality sequence. A total of 25,316 protein-coding gene models are predicted, 17% of which display no colinearity with their sorghum orthologs. We show that the two species, S. officinarum and S. spontaneum , involved in modern cultivars differ by their transposable elements and by a few large chromosomal rearrangements, explaining their distinct genome size and distinct basic chromosome numbers while also suggesting that polyploidization arose in both lineages after their divergence.

59 BASIC BIOLOGICAL 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 OSTI2025

Apomixis in Farmers’ Fields: Overview, Case Studies from Forage Grasses and Considerations for Future Apomictic Crops

Apomixis occurs naturally in several commercially important species from diverse plant families. While in some of these species apomixis is yet to be exploited in breeding schemes aimed at fixing heterosis, genetic progress and cultivar development, in other species apomixis has been integrated at different stages of breeding. Some of the most relevant examples come from the subfamily Panicoideae, the second largest subfamily of the Poaceae, and are the main focus of this review. The subfamily encompasses many tropical and sub-tropical grasses and grains of worldwide economic importance. Apomictic tropical forages are prime examples of how apomixis can be used and exploited in the development of marketable cultivars, which are essential to the meat and milk production industries globally. The main commercial forages used as grass pastures covering millions of hectares in tropical and sub-tropical regions are polyploids exhibiting gametophytic apomixis that belong to the genus Urochloa spp. (brachiariagrasses) and to the species Megathyrsus maximus (guineagrass). Buffel grass (Cenchrus ciliaris) and Paspalum spp. are other important apomictic forages bred and used in these regions. Breeding involves large germplasm collections from the centers of origin of the species, and for most of them, sexually reproducing diploid plants have been found. Chromosomically duplicated plants that maintain sexual reproduction are used in crosses with apomictic genotypes for the development and selection of cultivars to be marketed or used as progenitors in subsequent breeding cycles. The peculiarities of each genus/species breeding programs, the cultivars obtained from these programs, and the impact of use of marker assisted selection in cultivar development are presented. In addition, the test or implementation of new technologies such as high throughput phenotyping, and the use of machine learning methods for trait prediction and genomic selection are positively impacting the selection and speed of development of new polyploid apomictic cultivars. Furthermore, genetic transformation techniques, including genome editing, provide an additional layer for design of tailor-made, customer-oriented cultivars.

Cenchrus↗
DOE OSTI2026

Data for Protoplast Fusion as a Strategy to Increase Ploidy in Rhodotorula toruloides for Strain Development

Rhodotorula toruloides is a red oleaginous yeast with growing commercial interest because of its hardiness and exceptional lipid production capacity. Because it is a basidiomycete yeast with a complex life cycle, many of the classical breeding methods used with ascomycetes are unavailable for strain improvement. However, we have been able to construct polyploid yeast by fusing protoplasts of parents with the same mating type. Fusing of Y-6985 (A2) and Y-48190 (A2), which had been transformed with complementary antibiotic markers, led to the recovery of two diploids and one triploid. The stability of the fusion yeasts was tested by plating them on non-selective medium after several growth cycles under antibiotics and then testing five colonies per strain for nuclear DNA contents using flow cytometry and standard cell cycle analysis: the triploid and one diploid were stable. Fusants inherited their mitochondria from a single parent, which was demonstrated using restriction fragment length polymorphism (RFLP) of mitochondrial DNA. The phenotypic properties of the parents and fusants were compared in glucose fed-batch bioreactor studies and cellulosic sugar batch cultures. The final lipid titers for the fed-batch cultures were 24.9–39.7 g/L with Y-6985 and the diploid and triploid performing the best and worst, respectively. The fusants demonstrated intermediate hardiness for growth on hydrolysate prepared with dilute-acid pretreated switchgrass and were outperformed by Y-48190. Unlike one of the haploid parents, the fusants grew in 70% v/v concentrated hydrolysate. However, they did not grow as fast as the other haploid. In this study, a modernized protoplast fusion method is resurrected a useful tool for strain development in this yeast, which is complementary with other available methods.

FOS: Biological sciences↗
DOE OSTI2022

High-throughput detection of T-DNA insertion sites for multiple transgenes in complex genomes

Abstract Background Genetic engineering of crop plants has been successful in transferring traits into elite lines beyond what can be achieved with breeding techniques. Introduction of transgenes originating from other species has conferred resistance to biotic and abiotic stresses, increased efficiency, and modified developmental programs. The next challenge is now to combine multiple transgenes into elite varieties via gene stacking to combine traits. Generating stable homozygous lines with multiple transgenes requires selection of segregating generations which is time consuming and labor intensive, especially if the crop is polyploid. Insertion site effects and transgene copy number are important metrics for commercialization and trait efficiency. Results We have developed a simple method to identify the sites of transgene insertions using T-DNA-specific primers and high-throughput sequencing that enables identification of multiple insertion sites in the T 1 generation of any crop transformed via Agrobacterium . We present an example using the allohexaploid oil-seed plant Camelina sativa to determine insertion site location of two transgenes. Conclusion This new methodology enables the early selection of desirable transgene location and copy number to generate homozygous lines within two generations.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Identifying biomass yield potential of tetra, hexa, and octoploid prairie cordgrass populations grown on marginal lands

As the demand for renewable energy sources with reduced carbon emissions to the atmosphere increases, bioenergy crops remain an attractive alternative to fossil fuels. Another appeal of bioenergy crops is the potential utilization of marginal lands not suitable for food crops. Prairie cordgrass is a perennial warm season polyploid grass species being considered as a bioenergy crop that also exhibits a high tolerance for salinity and flooding. The ploidy level of prairie cordgrass has previously been suggested to correlate with agronomic traits. However, little is known about the agricultural performance of prairie cordgrass on marginal lands and if a correlation of ploidy level to stress tolerance exists. In this experiment, the productivity of tetraploids, hexaploids, and octoploids was investigated when grown on three different marginal sites including waterlogged, saline, and low-nutrient gravelly soils. Here we found that prairie cordgrass populations annually produced dry biomass on a wet marginal site comparable to normal cropland. However, the productivity was remarkedly decreased at both a salt-affected site and a limestone mine reclamation site. We were unable to conclude that different ploidy levels affected the biomass yield of prairie cordgrass grown under abiotic stress. However, there was a differential response of populations to various types of marginal sites. Finally, these results indicate potential genetic resources for developing breeding targets and identifying mechanisms of abiotic stress tolerance. Moreover, we highlight the need to generate diverse ploidy levels of prairie cordgrass in the same genetic backgrounds for future testing.

09 BIOMASS FUELS↗
DOE OSTI2025

Synthetic feed-forward loop circuit boosts transgene expression in sugarcane

Bio-based products derived from natural plant-derived materials offer a promising alternative to petroleum-based products, which are essential for achieving global sustainability (Gupta et al. 2022). Sugarcane provides 40% of the world’s biofuel (Brant et al. 2025). Recently, metabolic engineering of sugarcane for hyperaccumulation of biomass oil is emerging as a strategy to elevate the crop’s energy content (Cao et al. 2023; Maitra et al. 2024). Synthetic transcription factors offer a powerful tool for modulating entire metabolic pathways by enabling fine-tuned activation or repression of specific genes (Liu and Stewart 2016; Hooghvorst and Altpeter 2023). However, the application of these technologies faces challenges, including the availability of well-characterized genetic building blocks for precise manipulation of gene expression, and the inherently challenging properties of gene expression in highly polyploid crops like sugarcane (Liu and Stewart 2016).

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

The genomic footprints of wild Saccharum species trace domestication, diversification, and modern breeding of sugarcane

Sugarcane is a major crop of unclear origins due to its complex polyploid interspecific genome. We analyzed genome ancestries using whole-genome sequence data from 390 representative accessions based on repeated k-mers and chloroplast phylogeny. The results provided evidence that Saccharum officinarum was domesticated in the New Guinea region from the S. robustum wild species and revealed that its genome is a mosaic involving different S. robustum subgroups. We discovered a wild Saccharum contributor to most modern cultivars, likely originating from East Melanesia. We highlighted two early centers of sugarcane diversification associated with human transport, one in continental Asia through hybridization with different S. spontaneum subgroups and one in the Melanesian and Polynesian islands via hybridization with the discovered ancestor and Miscanthus. Finally, we revealed the genome ancestry of modern cultivars, highlighting untapped wild Saccharum diversity as a source of alleles for breeding programs.

Garsmeur, Olivier [CIRAD, Montpellier (France). Ag↗
DOE OSTI2017

Draft Genome Sequence of Mentha longifolia and Development of Resources for Mint Cultivar Improvement

The genus Mentha encompasses species cultivated for their essential oils, which are formulated into a vast array of consumer products. Desirable oil characteristics and resistance to the fungal disease Verticillium wilt are top priorities for the mint industry. However, cultivated mints have complex polyploid genomes and are sterile. Breeding efforts, therefore, require the development of genomic resources for fertile mint species. Here, we present draft de novo genome and plastome assemblies for a wilt-resistant South African accession of Mentha longifolia (L.) Huds., a diploid species ancestral to cultivated peppermint and spearmint. The 353 Mb contained 35,597 predicted protein-coding genes, including 292 disease resistance gene homologs, and nine genes determining essential oil characteristics. A genetic linkage map ordered 1,397 genome scaffolds on 12 pseudochromosomes. Over two million simple sequence repeats were identified, which will aid molecular marker development. The M. longifolia genome is a valuable resource for both metabolic engineering and molecular breeding. This is exemplified by employing the genome sequence to clone and functionally characterize promoters in a peppermint cultivar, and demonstrating the utility of a glandular trichome-specific promoter to increase expression of a biosynthetic gene, thereby modulating essential oil composition.

Aromatic Plant, Essential Oil, Genome, Mint, Verti↗
DOE OSTI2018

Multi-tasking Sulf1/Sulf2 enzymes do not only facilitate extracellular cell signalling but also participate in cell cycle related nuclear events

Highlights: • Dynamic SULF1/2 mobilisation to nucleus during cell cycle. • SULF1/2 co-ordinate extracellular cell signalling with nuclear role in cell cycle. • SULF1/2 overexpression increases cell proliferation while inhibition reduces growth. This study demonstrates highly dynamic spatial and temporal pattern of SULF1/SULF2 expression in a number of neuronal cell types growing in normal culture medium that included their transient nuclear mobilisation. Their nuclear translocation became particularly apparent during cell proliferation as both SULF1/SULF2 demonstrated not only cell membrane associated expression, their known site of function but also transient nuclear mobilisation during nuclear cell division. Nuclear localisation was apparent not only by immunocytochemical staining but also confirmed by immunoblotting staining of isolated nuclear fractions of C6, U87 and N2A cells. Immunocytochemical analysis demonstrated rapid nuclear exit of both SULF1/SULF2 following cell division that was slightly delayed but not blocked in a fraction of the polyploid cells observed in C6 cells. The overexpression of both Sulf1 and Sulf2 genes in C6 and U87 cells markedly promoted in vitro growth of these cells accompanied by nuclear mobilisation while inhibition of both these genes inhibited cell proliferation with little or no nuclear SULF1/SULF2 mobilisation. SULF1/SULF2 activity in these cells thus demonstrated a clear co-ordination of extracellular cell signalling with nuclear events related to cell proliferation.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

Systems biology approach to study the role of miRNA in promoter targeting during megakaryopoiesis

Highlights: • miRNAs could regulate Cyclins and CDKs by targeting their promoters. • Perl programming was used to identify putative targets of miRNA in promoters. • miR-1273g-3p and miR-619-5p showed significance with longest seed sequence matches. • Through CDK10, CDK11 and Cyclin, these two miRNAs could regulate cell cycle during megakaryopoiesis. The distinct process of megakaryopoiesis requires occurrence of endomitosis for polyploidization of the megakaryocytes. Although, Cyclins, CDKs and have been described to regulate endomitosis, the exact mechanism still remains an enigma. miRNA which were otherwise known as post transcriptional gene silencers are now emerging with various non-canonical functions including gene regulation at pre-transcriptional level by miRNA binding at promoter region. Out of the many processes they regulate, miRNA have been manifested to play a role in megakaryocyte differentiation. In this study an attempt has been made to identify miRNA that could regulate cell cycle genes (Cyclins and CDKs) by targeting their promoters, during megakaryopoiesis. A new computational algorithm was implemented using Perl programming to identify putative targets of miRNA in CDK and Cyclin promoters. Perl script was also used to check nuclear localizing miRNA based on the presence of a consensus sequence. Real-time PCR was performed to analyze the expression of miRNA and their predicted targets in Dami vs. PMA treated Dami cells. Putative targets of miRNAs with longest, high complementarity matches in CDK/Cyclin promoters were obtained. We identified two significant miRNA, miR-1273g-3p and miR-619-5p with longest seed sequence matches. We further identified three main targets (CDK10, CDK11, Cyclin F) through which these two miRNA could regulate cell cycle during megakaryopoiesis. Our results reinforce the role of promoting targeting miRNA in regulation of cell cycle through certain CDK/Cyclins to support the process of endomitosis during megakaryopoiesis.

60 APPLIED LIFE 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↗