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The Plant Genome Jun 2023Many of the world's most important crops are polyploid. The presence of more than two sets of chromosomes within their nuclei and frequently aberrant reproductive... (Review)
Review
Many of the world's most important crops are polyploid. The presence of more than two sets of chromosomes within their nuclei and frequently aberrant reproductive biology in polyploids present obstacles to conventional breeding. The presence of a larger number of homoeologous copies of each gene makes random mutation breeding a daunting task for polyploids. Genome editing has revolutionized improvement of polyploid crops as multiple gene copies and/or alleles can be edited simultaneously while preserving the key attributes of elite cultivars. Most genome-editing platforms employ sequence-specific nucleases (SSNs) to generate DNA double-stranded breaks at their target gene. Such DNA breaks are typically repaired via the error-prone nonhomologous end-joining process, which often leads to frame shift mutations, causing loss of gene function. Genome editing has enhanced the disease resistance, yield components, and end-use quality of polyploid crops. However, identification of candidate targets, genotyping, and requirement of high mutagenesis efficiency remain bottlenecks for targeted mutagenesis in polyploids. In this review, we will survey the tremendous progress of SSN-mediated targeted mutagenesis in polyploid crop improvement, discuss its challenges, and identify optimizations needed to sustain further progress.
Topics: Plant Breeding; Mutagenesis; Gene Editing; Mutation; Crops, Agricultural; Polyploidy
PubMed: 36692095
DOI: 10.1002/tpg2.20298 -
Trends in Ecology & Evolution May 2024Cold temperatures have been posited as a key driver of polyploidy (possession of multiple chromosome sets). However, high temperatures associated with fire, and the...
Cold temperatures have been posited as a key driver of polyploidy (possession of multiple chromosome sets). However, high temperatures associated with fire, and the indirect impact of post-fire environments in polypoid formation and establishment deserve more attention for a comprehensive understanding of polyploid ecology, evolution, and current distributions.
Topics: Biological Evolution; Cold Temperature; Fires; Polyploidy
PubMed: 38521739
DOI: 10.1016/j.tree.2024.02.007 -
Nature Ecology & Evolution Jan 2019Deciphering the global distribution of polyploid plants is fundamental for understanding plant evolution and ecology. Many factors have been hypothesized to affect the...
Deciphering the global distribution of polyploid plants is fundamental for understanding plant evolution and ecology. Many factors have been hypothesized to affect the uneven distribution of polyploid plants across the globe. Nevertheless, the lack of large comparative datasets has restricted such studies to local floras and to narrow taxonomical scopes, limiting our understanding of the underlying drivers of polyploid plant distribution. We present a map portraying the worldwide polyploid frequencies, based on extensive spatial data coupled with phylogeny-based polyploidy inference for tens of thousands of species. This allowed us to assess the potential global drivers affecting polyploid distribution. Our data reveal a clear latitudinal trend, with polyploid frequency increasing away from the equator. Climate, especially temperature, appears to be the most influential predictor of polyploid distribution. However, we find this effect to be mostly indirect, mediated predominantly by variation in plant lifeforms and, to a lesser extent, by taxonomical composition and species richness. Thus, our study presents an emerging view of polyploid distribution that highlights attributes that facilitate the establishment of new polyploid lineages by providing polyploids with sufficient time (that is, perenniality) and space (low species richness) to compete with pre-adapted diploid relatives.
Topics: Biological Evolution; Forests; Phylogeography; Plants; Polyploidy
PubMed: 30697006
DOI: 10.1038/s41559-018-0787-9 -
Nature Reviews. Genetics Nov 2005Polyploids - organisms that have multiple sets of chromosomes - are common in certain plant and animal taxa, and can be surprisingly stable. The evidence that has... (Review)
Review
Polyploids - organisms that have multiple sets of chromosomes - are common in certain plant and animal taxa, and can be surprisingly stable. The evidence that has emerged from genome analyses also indicates that many other eukaryotic genomes have a polyploid ancestry, suggesting that both humans and most other eukaryotes have either benefited from or endured polyploidy. Studies of polyploids soon after their formation have revealed genetic and epigenetic interactions between redundant genes. These interactions can be related to the phenotypes and evolutionary fates of polyploids. Here, I consider the advantages and challenges of polyploidy, and its evolutionary potential.
Topics: Evolution, Molecular; Gene Expression Regulation, Plant; Genome, Plant; Models, Genetic; Plant Physiological Phenomena; Plants; Polyploidy
PubMed: 16304599
DOI: 10.1038/nrg1711 -
Methods in Molecular Biology (Clifton,... 2015Most plant species are known to be either ancient or recent polyploids, containing more than one genome as a result of past interspecific hybridization events... (Review)
Review
Most plant species are known to be either ancient or recent polyploids, containing more than one genome as a result of past interspecific hybridization events (allopolyploidy) and/or genome doubling (autopolyploidy). Genotyping in polyploid species offers a set of unique challenges. Most molecular marker methodologies are made more complex by polyploidy, as multilocus alleles are generally produced when a single locus is targeted. Genotyping by sequencing is also more challenging in polyploids, with problematic assemblies of duplicated regions and difficulties in distinguishing between inter- and intragenomic polymorphisms. Strategies for identifying and overcoming the challenges of polyploidy in plant genotyping are proposed.
Topics: Alleles; Genetic Markers; Genotype; Genotyping Techniques; Plants; Polyploidy
PubMed: 25373756
DOI: 10.1007/978-1-4939-1966-6_12 -
The American Journal of Pathology Jun 2019The liver contains diploid and polyploid hepatocytes (tetraploid, octaploid, etc.), with polyploids comprising ≥90% of the hepatocyte population in adult mice....
The liver contains diploid and polyploid hepatocytes (tetraploid, octaploid, etc.), with polyploids comprising ≥90% of the hepatocyte population in adult mice. Polyploid hepatocytes form multipolar spindles in mitosis, which lead to chromosome gains/losses and random aneuploidy. The effect of aneuploidy on liver function is unclear, and the degree of liver aneuploidy is debated, with reports showing aneuploidy affects 5% to 60% of hepatocytes. To study relationships among liver polyploidy, aneuploidy, and adaptation, mice lacking E2f7 and E2f8 in the liver (LKO), which have a polyploidization defect, were used. Polyploids were reduced fourfold in LKO livers, and LKO hepatocytes remained predominantly diploid after extensive proliferation. Moreover, nearly all LKO hepatocytes were euploid compared with control hepatocytes, suggesting polyploid hepatocytes are required for production of aneuploid progeny. To determine whether reduced polyploidy impairs adaptation, LKO mice were bred onto a tyrosinemia background, a disease model whereby the liver can develop disease-resistant, regenerative nodules. Although tyrosinemic LKO mice were more susceptible to morbidities and death associated with tyrosinemia-induced liver failure, they developed regenerating nodules similar to control mice. Analyses revealed that nodules in the tyrosinemic livers were generated by aneuploidy and inactivating mutations. In summary, we identified new roles for polyploid hepatocytes and demonstrated that they are required for the formation of aneuploid progeny and can facilitate adaptation to chronic liver disease.
Topics: Adaptation, Physiological; Animals; E2F7 Transcription Factor; Gene Knockdown Techniques; Hepatocytes; Liver Regeneration; Lung Injury; Mice; Mice, Inbred NOD; Mice, Knockout; Polyploidy; Repressor Proteins
PubMed: 30928253
DOI: 10.1016/j.ajpath.2019.02.008 -
International Journal of Molecular... 2012Polyploidy is a very common phenomenon in the plant kingdom, where even diploid species are often described as paleopolyploids. The polyploid condition may bring about... (Review)
Review
Polyploidy is a very common phenomenon in the plant kingdom, where even diploid species are often described as paleopolyploids. The polyploid condition may bring about several advantages compared to the diploid state. Polyploids often show phenotypes that are not present in their diploid progenitors or exceed the range of the contributing species. Some of these traits may play a role in heterosis or could favor adaptation to new ecological niches. Advances in genomics and sequencing technology may create unprecedented opportunities for discovering and monitoring the molecular effects of polyploidization. Through this review, we provide an overview of technologies and strategies that may allow an in-depth analysis of polyploid genomes. After introducing some basic aspects on the origin and genetics of polyploids, we highlight the main tools available for genome and gene expression analysis and summarize major findings. In the last part of this review, the implications of next generation sequencing are briefly discussed. The accumulation of knowledge on polyploid formation, maintenance, and divergence at whole-genome and subgenome levels will not only help plant biologists to understand how plants have evolved and diversified, but also assist plant breeders in designing new strategies for crop improvement.
Topics: Genome, Plant; Genomics; High-Throughput Nucleotide Sequencing; Phenotype; Plants; Polyploidy
PubMed: 22949863
DOI: 10.3390/ijms130810316 -
Genetics Aug 2023Polyploidy is an important generator of evolutionary novelty across diverse groups in the Tree of Life, including many crops. However, the impact of whole-genome...
Polyploidy is an important generator of evolutionary novelty across diverse groups in the Tree of Life, including many crops. However, the impact of whole-genome duplication depends on the mode of formation: doubling within a single lineage (autopolyploidy) versus doubling after hybridization between two different lineages (allopolyploidy). Researchers have historically treated these two scenarios as completely separate cases based on patterns of chromosome pairing, but these cases represent ideals on a continuum of chromosomal interactions among duplicated genomes. Understanding the history of polyploid species thus demands quantitative inferences of demographic history and rates of exchange between subgenomes. To meet this need, we developed diffusion models for genetic variation in polyploids with subgenomes that cannot be bioinformatically separated and with potentially variable inheritance patterns, implementing them in the dadi software. We validated our models using forward SLiM simulations and found that our inference approach is able to accurately infer evolutionary parameters (timing, bottleneck size) involved with the formation of auto- and allotetraploids, as well as exchange rates in segmental allotetraploids. We then applied our models to empirical data for allotetraploid shepherd's purse (Capsella bursa-pastoris), finding evidence for allelic exchange between the subgenomes. Taken together, our model provides a foundation for demographic modeling in polyploids using diffusion equations, which will help increase our understanding of the impact of demography and selection in polyploid lineages.
Topics: Polyploidy; Biological Evolution; Hybridization, Genetic; Capsella; Demography
PubMed: 37279657
DOI: 10.1093/genetics/iyad107 -
Plant Reproduction Mar 2023Polyploidy, which arises from genome duplication, has occurred throughout the history of eukaryotes, though it is especially common in plants. The resulting increased... (Review)
Review
Polyploidy, which arises from genome duplication, has occurred throughout the history of eukaryotes, though it is especially common in plants. The resulting increased size, heterozygosity, and complexity of the genome can be an evolutionary opportunity, facilitating diversification, adaptation and the evolution of functional novelty. On the other hand, when they first arise, polyploids face a number of challenges, one of the biggest being the meiotic pairing, recombination and segregation of the suddenly more than two copies of each chromosome, which can limit their fertility. Both for developing polyploidy as a crop improvement tool (which holds great promise due to the high and lasting multi-stress resilience of polyploids), as well as for our basic understanding of meiosis and plant evolution, we need to know both the specific nature of the challenges polyploids face, as well as how they can be overcome in evolution. In recent years there has been a dramatic uptick in our understanding of the molecular basis of polyploid adaptations to meiotic challenges, and that is the focus of this review.
Topics: Evolution, Molecular; Polyploidy; Plants; Meiosis; Genome, Plant
PubMed: 36149479
DOI: 10.1007/s00497-022-00448-1 -
The New Phytologist Apr 2010Polyploidization and recombination are two important processes driving evolution through the building and reshaping of genomes. Allopolyploids arise from hybridization... (Review)
Review
Polyploidization and recombination are two important processes driving evolution through the building and reshaping of genomes. Allopolyploids arise from hybridization and chromosome doubling among distinct, yet related species. Polyploids may display novel variation relative to their progenitors, and the sources of this variation lie not only in the acquisition of extra gene dosages, but also in the genomic changes that occur after divergent genomes unite. Genomic changes (deletions, duplications, and translocations) have been detected in both recently formed natural polyploids and resynthesized polyploids. In resynthesized Brassica napus allopolyploids, there is evidence that many genetic changes are the consequence of homoeologous recombination. Homoeologous recombination can generate novel gene combinations and phenotypes, but may also destabilize the karyotype and lead to aberrant meiotic behavior and reduced fertility. Thus, natural selection plays a role in the establishment and maintenance of fertile natural allopolyploids that have stabilized chromosome inheritance and a few advantageous chromosomal rearrangements. We discuss the evidence for genome rearrangements that result from homoeologous recombination in resynthesized B. napus and how these observations may inform phenomena such as chromosome replacement, aneuploidy, non-reciprocal translocations and gene conversion seen in other polyploids.
Topics: Brassica napus; Chromosome Pairing; Chromosome Segregation; Models, Genetic; Polyploidy; Recombination, Genetic
PubMed: 20002315
DOI: 10.1111/j.1469-8137.2009.03089.x