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The Plant Cell Jul 2022Bread wheat (Triticum aestivum, genome BBAADD) is a young hexaploid species formed only 8,500-9,000 years ago through hybridization between a domesticated...
Bread wheat (Triticum aestivum, genome BBAADD) is a young hexaploid species formed only 8,500-9,000 years ago through hybridization between a domesticated free-threshing tetraploid progenitor, genome BBAA, and Aegilops tauschii, the diploid donor of the D subgenome. Very soon after its formation, it spread globally from its cradle in the fertile crescent into new habitats and climates, to become a staple food of humanity. This extraordinary global expansion was probably enabled by allopolyploidy that accelerated genetic novelty through the acquisition of new traits, new intergenomic interactions, and buffering of mutations, and by the attractiveness of bread wheat's large, tasty, and nutritious grain with high baking quality. New genome sequences suggest that the elusive donor of the B subgenome is a distinct (unknown or extinct) species rather than a mosaic genome. We discuss the origin of the diploid and tetraploid progenitors of bread wheat and the conflicting genetic and archaeological evidence on where it was formed and which species was its free-threshing tetraploid progenitor. Wheat experienced many environmental changes throughout its evolution, therefore, while it might adapt to current climatic changes, efforts are needed to better use and conserve the vast gene pool of wheat biodiversity on which our food security depends.
Topics: Bread; Diploidy; Evolution, Molecular; Genome, Plant; Hybridization, Genetic; Polyploidy; Tetraploidy; Triticum
PubMed: 35512194
DOI: 10.1093/plcell/koac130 -
Cell May 2023Hybrid potato breeding will transform the crop from a clonally propagated tetraploid to a seed-reproducing diploid. Historical accumulation of deleterious mutations in...
Hybrid potato breeding will transform the crop from a clonally propagated tetraploid to a seed-reproducing diploid. Historical accumulation of deleterious mutations in potato genomes has hindered the development of elite inbred lines and hybrids. Utilizing a whole-genome phylogeny of 92 Solanaceae and its sister clade species, we employ an evolutionary strategy to identify deleterious mutations. The deep phylogeny reveals the genome-wide landscape of highly constrained sites, comprising ∼2.4% of the genome. Based on a diploid potato diversity panel, we infer 367,499 deleterious variants, of which 50% occur at non-coding and 15% at synonymous sites. Counterintuitively, diploid lines with relatively high homozygous deleterious burden can be better starting material for inbred-line development, despite showing less vigorous growth. Inclusion of inferred deleterious mutations increases genomic-prediction accuracy for yield by 24.7%. Our study generates insights into the genome-wide incidence and properties of deleterious mutations and their far-reaching consequences for breeding.
Topics: Diploidy; Mutation; Phylogeny; Plant Breeding; Solanum tuberosum
PubMed: 37146612
DOI: 10.1016/j.cell.2023.04.008 -
Trends in Neurosciences Dec 2018The benefits of diploidy are considered to involve masking partially recessive mutations and increasing genetic diversity. Here, we review new studies showing evidence... (Review)
Review
The benefits of diploidy are considered to involve masking partially recessive mutations and increasing genetic diversity. Here, we review new studies showing evidence for diverse allele-specific expression and epigenetic states in mammalian brain cells, which suggest that diploidy expands the landscape of gene regulatory and expression programs in cells. Allele-specific expression has been thought to be restricted to a few specific classes of genes. However, new studies show novel genomic imprinting effects that are brain-region-, cell-type- and age-dependent. In addition, novel forms of random monoallelic expression that impact many autosomal genes have been described in vitro and in vivo. We discuss the implications for understanding the benefits of diploidy, and the mechanisms shaping brain development, function, and disease.
Topics: Alleles; Animals; Brain; Diploidy; Epigenomics; Gene Expression Regulation; Humans
PubMed: 30098802
DOI: 10.1016/j.tins.2018.07.005 -
Genome Biology Apr 2021High-quality chromosome-scale haplotype sequences of diploid genomes, polyploid genomes, and metagenomes provide important insights into genetic variation associated... (Review)
Review
High-quality chromosome-scale haplotype sequences of diploid genomes, polyploid genomes, and metagenomes provide important insights into genetic variation associated with disease and biodiversity. However, whole-genome short read sequencing does not yield haplotype information spanning whole chromosomes directly. Computational assembly of shorter haplotype fragments is required for haplotype reconstruction, which can be challenging owing to limited fragment lengths and high haplotype and repeat variability across genomes. Recent advancements in long-read and chromosome-scale sequencing technologies, alongside computational innovations, are improving the reconstruction of haplotypes at the level of whole chromosomes. Here, we review recent and discuss methodological progress and perspectives in these areas.
Topics: Chromosomes; Computational Biology; Diploidy; Genomics; Haplotypes; High-Throughput Nucleotide Sequencing; Humans; Metagenome; Metagenomics; Polyploidy; Sequence Analysis, DNA
PubMed: 33845884
DOI: 10.1186/s13059-021-02328-9 -
The New Phytologist Jun 2020The wheat group offers an outstanding system to address the interplay between hybridization, chromosomal evolution and biological diversification. Most diploid wild... (Review)
Review
The wheat group offers an outstanding system to address the interplay between hybridization, chromosomal evolution and biological diversification. Most diploid wild wheats originated following hybridization between the A-genome lineage and the B-genome lineage some 4 Myr ago, resulting in an admixed D-genome lineage that presented dramatic radiation accompanied by considerable changes in genome size and chromosomal rearrangements. Comparative profiling of low-copy genes, repeated sequences and transposable elements among those divergent species characterized by different karyotypes highlights high genome dynamics and sheds new light on the processes underlying chromosomal evolution in wild wheats. One of the hybrid clades presents upsizing of metacentric chromosomes going along with the proliferation of specific repeats (i.e. 'genomic obesity'), whereas other species show stable genome size associated with increasing chromosomal asymmetry. Genetic and ecological variation in those specialized species suggest that genome restructuring was coupled with adaptive processes to support the evolution of a majority of acrocentric chromosomes. This synthesis of current knowledge on genome restructuring across the diversity of wild wheats paves the way towards surveys based on latest sequencing technologies to characterize valuable resources and address the significance of chromosomal evolution in species with complex genomes.
Topics: DNA Transposable Elements; Diploidy; Genome, Plant; Hybridization, Genetic; Karyotype; Triticum
PubMed: 31913521
DOI: 10.1111/nph.16415 -
Philosophical Transactions of the Royal... May 2022Plants have characteristic features that affect the expression of sexual function, notably the existence of a haploid organism in the life cycle, and in their... (Review)
Review
Plants have characteristic features that affect the expression of sexual function, notably the existence of a haploid organism in the life cycle, and in their development, which is modular, iterative and environmentally reactive. For instance, primary selection (the first filtering of the products of meiosis) is via gametes in diplontic animals, but via gametophyte organisms in plants. Intragametophytic selfing produces double haploid sporophytes which is in effect a form of clonal reproduction mediated by sexual mechanisms. In homosporous plants, the diploid sporophyte is sexless, sex being only expressed in the haploid gametophyte. However, in seed plants, the timing and location of gamete production is determined by the sporophyte, which therefore has a sexual role, and in dioecious plants has genetic sex, while the seed plant gametophyte has lost genetic sex. This evolutionary transition is one that E.J.H. Corner called 'the transference of sexuality'. The iterative development characteristic of plants can lead to a wide variety of patterns in the distribution of sexual function, and in dioecious plants poor canalization of reproductive development can lead to intrasexual mating and the production of YY supermales or WW superfemales. Finally, plant modes of asexual reproduction (agamospermy/apogamy) are also distinctive by subverting gametophytic processes. This article is part of the theme issue 'Sex determination and sex chromosome evolution in land plants'.
Topics: Animals; Diploidy; Germ Cells, Plant; Plants; Reproduction
PubMed: 35306890
DOI: 10.1098/rstb.2021.0213 -
Protein & Cell Jan 2020Diploidy is the typical genomic mode in all mammals. Haploid stem cells are artificial cell lines experimentally derived in vitro in the form of different types of stem... (Review)
Review
Diploidy is the typical genomic mode in all mammals. Haploid stem cells are artificial cell lines experimentally derived in vitro in the form of different types of stem cells, which combine the characteristics of haploidy with a broad developmental potential and open the possibility to uncover biological mysteries at a genomic scale. To date, a multitude of haploid stem cell types from mouse, rat, monkey and humans have been derived, as more are in development. They have been applied in high-throughput genetic screens and mammalian assisted reproduction. Here, we review the generation, unique properties and broad applications of these remarkable cells.
Topics: Animals; Cell Line; Diploidy; Genomics; Haploidy; Humans; Macaca mulatta; Mice; Rats; Stem Cells
PubMed: 31004328
DOI: 10.1007/s13238-019-0625-0 -
Nature Communications Jun 2023Monocots are a major taxon within flowering plants, have unique morphological traits, and show an extraordinary diversity in lifestyle. To improve our understanding of...
Monocots are a major taxon within flowering plants, have unique morphological traits, and show an extraordinary diversity in lifestyle. To improve our understanding of monocot origin and evolution, we generate chromosome-level reference genomes of the diploid Acorus gramineus and the tetraploid Ac. calamus, the only two accepted species from the family Acoraceae, which form a sister lineage to all other monocots. Comparing the genomes of Ac. gramineus and Ac. calamus, we suggest that Ac. gramineus is not a potential diploid progenitor of Ac. calamus, and Ac. calamus is an allotetraploid with two subgenomes A, and B, presenting asymmetric evolution and B subgenome dominance. Both the diploid genome of Ac. gramineus and the subgenomes A and B of Ac. calamus show clear evidence of whole-genome duplication (WGD), but Acoraceae does not seem to share an older WGD that is shared by most other monocots. We reconstruct an ancestral monocot karyotype and gene toolkit, and discuss scenarios that explain the complex history of the Acorus genome. Our analyses show that the ancestors of monocots exhibit mosaic genomic features, likely important for that appeared in early monocot evolution, providing fundamental insights into the origin, evolution, and diversification of monocots.
Topics: Tetraploidy; Acorus; Phylogeny; Diploidy; Genome
PubMed: 37339946
DOI: 10.1038/s41467-023-38829-3 -
Theoretical Population Biology Dec 2017Our focus here is on the infinitesimal model. In this model, one or several quantitative traits are described as the sum of a genetic and a non-genetic component, the... (Review)
Review
Our focus here is on the infinitesimal model. In this model, one or several quantitative traits are described as the sum of a genetic and a non-genetic component, the first being distributed within families as a normal random variable centred at the average of the parental genetic components, and with a variance independent of the parental traits. Thus, the variance that segregates within families is not perturbed by selection, and can be predicted from the variance components. This does not necessarily imply that the trait distribution across the whole population should be Gaussian, and indeed selection or population structure may have a substantial effect on the overall trait distribution. One of our main aims is to identify some general conditions on the allelic effects for the infinitesimal model to be accurate. We first review the long history of the infinitesimal model in quantitative genetics. Then we formulate the model at the phenotypic level in terms of individual trait values and relationships between individuals, but including different evolutionary processes: genetic drift, recombination, selection, mutation, population structure, …. We give a range of examples of its application to evolutionary questions related to stabilising selection, assortative mating, effective population size and response to selection, habitat preference and speciation. We provide a mathematical justification of the model as the limit as the number M of underlying loci tends to infinity of a model with Mendelian inheritance, mutation and environmental noise, when the genetic component of the trait is purely additive. We also show how the model generalises to include epistatic effects. We prove in particular that, within each family, the genetic components of the individual trait values in the current generation are indeed normally distributed with a variance independent of ancestral traits, up to an error of order 1∕M. Simulations suggest that in some cases the convergence may be as fast as 1∕M.
Topics: Biological Evolution; Diploidy; Epistasis, Genetic; Haploidy; Humans; Models, Genetic; Mutation; Selection, Genetic; Wills
PubMed: 28709925
DOI: 10.1016/j.tpb.2017.06.001 -
Cell Research Nov 2015To maintain homeostasis, organs replace cells lost through normal cellular turnover, often through the straightforward replication of existing cells. A recent paper in...
To maintain homeostasis, organs replace cells lost through normal cellular turnover, often through the straightforward replication of existing cells. A recent paper in Nature shows that cells in the liver are not equivalent when it comes to their replicative capacity; rather, a subset of hepatocytes defined by the maintenance of active Wnt signaling bears the brunt of responsibility for maintaining liver mass.
Topics: Animals; Axin Protein; Diploidy; Female; Hepatocytes; Homeostasis; Liver; Male
PubMed: 26403190
DOI: 10.1038/cr.2015.117