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268 results for “polyploid”

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dryad36/100

An efficient CRISPR-mediated genome editing system in diploid and polyploid Tragopogon (Asteraceae) enables functional studies of complex phenotypes and polyploid genome evolution

Polyploidy or whole-genome duplication (WGD) is a significant evolutionary force, especially in angiosperms. However, the underlying mechanisms governing polyploid genome evolution remain unclear, limited largely by a lack of functional analysis tools in organisms that best exemplify the earliest stages of WGD. Tragopogon (Asteraceae) includes an evolutionary model system for studying the immediate consequences of polyploidy. In this study, we significantly improved the genetic transformation of Tragopogon and obtained genome-edited T. porrifolius (2x) and T. mirus (4x) primary generation (T0) individuals. Using CRISPR/Cas9, we knocked out the dihydroflavonol 4-reductase (DFR) gene, which controls anthocyanin synthesis, in both T. porrifolius and T. mirus. All transgenic allotetraploid T. mirus individuals had at least one mutant DFR allele and 71.4% of the plants had all four DFR alleles (from both homeologs) edited, indicating a high efficiency of the CRISPR system in polyploid Tragopogon. The anticipated absence of the anthocyanin was observed in both leaf and floral tissues from T. porrifolius and T. mirus mutants. In addition, the mutations were inherited in the T1 generation. This study demonstrates a highly efficient CRISPR platform producing genome-edited Tragopogon individuals that have successfully completed their life cycle. The approaches used and challenges faced in building the CRISPR system in Tragopogon provide a framework for building similar systems in other nongenetic models. Genome editing in Tragopogon paves the way for novel functional biology studies of polyploid genome evolution and the consequences of WGD on complex traits, which holds enormous potential for both basic and applied research.

opencc-zeroJun 2024View details →

zenodo36/100

Genotyping measures and population genetic indices for assesing reproductive modes of polyploid Ludwigia grandiflora subsp. hexapetala in western Europe

Raw data used to assess reproductive modes in 53 sampled populations in western Europe (France and northern Spain). Ludwigia grandiflora subsp. hexapetala (Lgh) is a hermaphrodite, polyploid, partially clonal and heteromorphic plant that recently colonized multiple countries worldwide. Individuals in this species are either self-incompatible caused by a late-acting self-incompatible (LSI) system developing long-styled flowers, or self-compatible (SC) developing short-styled flowers. We used a SNP approach allowing confident allele dosage to genotype 53 LSI and SC populations of Lgh in France and northern Spain. We measured their genetic diversity and assessed their reproductive modes using methods adapted to autopolyploid species.

opencc-by-4.0Nov 2023View details →

zenodo36/100

Herbarium specimens reveal a cryptic invasion of polyploid Centaurea stoebe in Europe - ITS1 dataset

<h3>Description of the data and file structure</h3> We genotyped the ITS1 locus of 178 herbarium specimens using protocol described in Suchan et al. (2018; https://doi.org/10.1111/1755-0998.12948) and processed using custom script. The specimens were chosen after morphological determination of their cytotypes (morphological determination accuracy: 97.8%). We choose this subsample (3.5% of the total number of specimens) to represent comparable distributional ranges and collection dates across both cytotypes, including specimens from both the native and expanded ranges of tetraploid C. stoebe. Genotyping of the ITS1 locus unambiguously identifies the cytotype, as all tetraploid samples exhibit a unique ribotype B, which has never been found in diploid samples (Mráz et al., 2012; https://doi.org/10.1016/j.ympev.2011.11.006). <h4>Files and variables</h4> File: Centaurea_stoebe_ITS1_script.sh Description: This file contains the script used for processing raw sequence data to obtain a table with the numbers of reads in each sample mapping to the obtained ITS1 variants. The software used was: PEAR v0.9.6, cutadapt v.3.2, vsearch v2.28.1 File: Centaurea_stoebe_sample_list.xlsx Description: This file contains a list of analyzed herbarium specimens. Variables <ul> <li>ID - sample ID</li> <li>Lab working no. - Identifier of the samples in the ITS1 analyses, specifically in the Centaurea_stoebe_ITS1_sequence_numbers.xlsx file</li> <li>Morphology-based estimation - ploidy of the sample estimated with morphology (2 - diploid, 4 - tetraploid)</li> <li>ITS seq based estimation - ploidy of the sample estimated using ITS1 sequencing (2 - diploid, 4 - tetraploid)</li> <li>Congruence(1)/mismatch(0) - congruence (1) or mismatch (0) between morphological and genetic policy estimation</li> <li>Country of origin</li> <li>Herbarium</li> <li>Herbarium coll. number</li> <li>Collector</li> <li>Collection year</li> <li>Locality</li> <li>Latitude</li> <li>Longitude</li> </ul> File: Centaurea_stoebe_ITS1_sequences.fasta Description: This file contains sequences of the obtained ITS1 variants. File: Centaurea_stoebe_ITS1_sequence_numbers.xlsx Description: This file contains a table with the numbers of reads in each sample mapping to the obtained ITS1 variants. Variables <ul> <li>OTU - ITS1 variant number</li> <li>size - number of sequences from the total data clustered to the variant</li> <li>next columns contain numbers of reads mapped to each ITS1 variant for each sample</li> </ul> <h3>Code/software</h3> The code to process sequence data is included in Centaurea_stoebe_ITS1_script.sh file. The software used was: PEAR v0.9.6, cutadapt v.3.2, vsearch v2.28.

opencc-by-4.0Oct 2024View details →

dryad36/100

Does competitive asymmetry confer polyploid advantage under changing environments?

Competitive interactions drive critical ecological processes in plant communities. Yet how competitive interactions are influenced by polyploidy which has a widespread incidence in plants remains largely unknown. To evaluate the hypothesis of competitive asymmetry between polyploids and diploids, we set up competing tetraploid and diploid plants of perennial herbaceous Chrysanthemum indicum L. (Asteraceae) at different relative frequencies under contrasting soil water contents. We quantified the interaction intensity between competing plants of the same (intraploidy) and different (interploidy) ploidy levels, and measured functional traits related to gas exchange and plant water use to understand the underlying mechanisms. The stronger competitive effect of tetraploids on diploids than that of diploids on tetraploids provided evidence for the competitive asymmetry. As a stronger competitor, tetraploids were limited more by individuals of their own than by diploids. Such competitive asymmetry was not only maintained under reduced soil water content, but also translated into higher aboveground biomass of tetraploids. Tetraploids showed more resource-acquisitive traits than diploids under high soil water content and more resource-conservative traits under reduced soil water content. As such, the higher trait plasticity in tetraploids than diploids likely explained the competitive asymmetry. Synthesis. These results elucidate the nature and magnitude of species interactions between polyploid and diploid plants under changing environments and the underlying mechanisms, and provide important insights into the prevalence and persistence of polyploid plants under a changing climate.

opencc-zeroMar 2023View details →

dryad36/100

Differences in pathogen resistance between diploid and polyploid plants: a systematic review and meta-analysis

Polyploidy, the state of having more than two full sets of chromosomes, has been hypothesized to provide several evolutionary advantages to flowering plants, including increased ability to resist pathogens and parasites. However, studies comparing pathogen resistance in conspecific and congeneric diploids and polyploids have produced mixed results. While the supposed relationship between polyploidy and pathogen resistance has been commented on in several narrative reviews, it has never been subjected to a systematic meta-analysis. We examined the effect of polyploidy on pathogen resistance by synthesizing 214 effect sizes from 128 studies. We find that, overall, there is no consistent effect of polyploidy on pathogen resistance. Subgroup analyses suggest that polyploids perform significantly better than diploids only in resisting hemibiotrophic pathogens, and autopolyploids tend show greater resistance than allopolyploids. This is surprising given the fact that polyploids possess extra allele copies of R-gene alleles that provide resistance to biotrophic pathogens, and this pattern may indicate that signaling cascades needed to elicit hypersensitive responses are disrupted by polyploidy. Disruption is supported by the observation that, across all pathogens, autopolyploids show significantly greater resistance compared to diploids, whereas allopolyploids do not. This is corroborated by the observation that synthetic autopolyploids perform significantly better than their allopolyploid and established counterparts. Regarding pathogen type, diploids show greater resistance than polyploids to pathogens that are fungi or nematodes. Analyses of publication bias indicate little to no bias, and analyses of heterogeneity indicate that phylogeny explains almost none of the observed heterogeneity. These results underscore the importance of not only systematic review but also the strong degree to which the effects of polyploidy depend on ecological context.

opencc-zeroAug 2023View details →

dryad36/100

Comparative transmission genetics of introgressed chromatin in reciprocal advanced backcross populations in Gossypium (cotton) polyploids

Introgression is a potential source of valuable genetic variation and interspecific introgression lines are important resources for plant breeders to access novel alleles. Experimental advanced-generation backcross populations contain individuals with genomic compositions similar to those resulting from natural interspecific hybridization and provide opportunities to study the nature and transmission pattern of donor chromatin in recipient genomes. Here, we analyze transmission of donor chromatin in reciprocal backcrosses between G. hirsutum and G. barbadense. Across the genome, recurrent backcrossing in both backgrounds yielded donor chromatin at slightly higher frequencies than the Mendelian expectation in BC5F1 plants, while the average frequency of donor alleles in BC5F2 segregating families was less than expected. In the two subgenomes of polyploid cotton, the rate of donor chromatin introgression was similar. Although donor chromatin was tolerated over much of the recipient genomes, 21 regions recalcitrant to donor alleles were identified. Only limited correspondence is observed between the recalcitrant regions in the two backgrounds, suggesting the effect of species background on introgression of donor segments. Genetic breakdown was progressive, with floral abscission and seed inviability ongoing during backcrossing cycles. Regions of either high or low introgression tended to be in terminal chromosomal regions that are generally rich in both genes and crossover events, with long stretches around the centromere having limited crossover activity resulting in relatively constant low introgression frequencies. Constraints on fixation and selection of donor alleles highlights the challenges of utilizing introgression breeding in crop improvement.

opencc-zeroAug 2023View details →

dryad36/100

Sequencing data for: Chronosequence of invasion reveals minimal losses of population genomic diversity, niche expansion, and trait divergence in the polyploid, leafy spurge

Rapid evolution may play an important role in the range expansion of invasive species and modify forecasts of invasion, which are the backbone of land management strategies. However, losses of genetic variation associated with colonization bottlenecks may constrain trait and niche divergence at leading range edges, thereby impacting management decisions that anticipate future range expansion. The spatial and temporal scales over which adaptation contributes to invasion dynamics remain unresolved. We leveraged detailed records of the ~130-year invasion history of the invasive polyploid plant, leafy spurge (Euphorbia virgata), across ~500km in Minnesota, U.S.A. We examined the consequences of range expansion for population genomic diversity, niche breadth, and the evolution of germination behavior. Using genotyping-by-sequencing, we found some population structure in the range core, where introduction occurred, but panmixia among all other populations. Range expansion was accompanied by only modest losses in sequence diversity, with small, isolated populations at the leading edge harboring similar levels of diversity to those in the range core. The climatic niche expanded during most of the range expansion, and the niche of the range core was largely non-overlapping with the invasion front. Ecological niche models indicated that mean temperature of the warmest quarter was the strongest determinant of habitat suitability and that populations at the leading edge had the lowest habitat suitability. Guided by these findings, we tested for rapid evolution in germination behavior over the time course of range expansion using a common garden experiment and temperature manipulations. Germination behavior diverged from early to late phases of the invasion, with populations from later phases having higher dormancy at lower temperatures. Our results suggest that trait evolution may have contributed to niche expansion during invasion and that distribution models, which inform future management planning, may underestimate invasion potential without accounting for evolution.

opencc-zeroSep 2023View details →

dryad36/100