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Developmental Cell Jun 2017Although haploidy has not been observed in vertebrates, its natural occurrence in various eukaryotic species that had diverged from diploid ancestors suggests that there... (Review)
Review
Although haploidy has not been observed in vertebrates, its natural occurrence in various eukaryotic species that had diverged from diploid ancestors suggests that there is an innate capacity for an organism to regain haploidy and that haploidy may confer evolutionary benefits. Haploid embryonic stem cells have been experimentally generated from mouse, rat, monkey, and humans. Haploidy results in major differences in cell size and gene expression levels while also affecting parental imprinting, X chromosome inactivation, and mitochondrial metabolism genes. We discuss here haploidy in evolution and the barriers to haploidy, in particular in the human context.
Topics: Animals; Diploidy; Embryonic Stem Cells; Genomic Imprinting; Haploidy; Humans; Pluripotent Stem Cells; X Chromosome Inactivation
PubMed: 28633015
DOI: 10.1016/j.devcel.2017.04.019 -
Current Protocols in Bioinformatics 2013This unit describes how to use BWA and the Genome Analysis Toolkit (GATK) to map genome sequencing data to a reference and produce high-quality variant calls that can be...
This unit describes how to use BWA and the Genome Analysis Toolkit (GATK) to map genome sequencing data to a reference and produce high-quality variant calls that can be used in downstream analyses. The complete workflow includes the core NGS data processing steps that are necessary to make the raw data suitable for analysis by the GATK, as well as the key methods involved in variant discovery using the GATK.
Topics: Calibration; Databases, Genetic; Genetic Variation; Genome, Human; Haploidy; Haplotypes; Humans; Molecular Sequence Annotation; Polymorphism, Single Nucleotide; Sequence Alignment; Software
PubMed: 25431634
DOI: 10.1002/0471250953.bi1110s43 -
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 -
Stem Cell Research & Therapy Sep 2017Haploid cells are excellent tools to study gene function as they contain a single copy of the genome and are thus unable to mask the effect of mutations. Recently,... (Review)
Review
Haploid cells are excellent tools to study gene function as they contain a single copy of the genome and are thus unable to mask the effect of mutations. Recently, haploid embryonic stem cells, which are capable of self-renewal and potentially differentiating into other cell types despite having only one set of chromosomes, have been established in several species. These unique haploid cells allow us to seek recessive gene functions in mammals, and have had a profound influence on the field of genetic screening and drug target identification. In this review, we briefly introduce advances and breakthroughs in haploid cell line research and broadly discuss the versatile application thereof.
Topics: Animals; Embryonic Stem Cells; Genetic Techniques; Haploidy; Humans; Pluripotent Stem Cells
PubMed: 28962667
DOI: 10.1186/s13287-017-0657-4 -
The Plant Genome Jun 2023Cross bred species such as switchgrass may benefit from advantageous breeding strategies requiring inbred lines. Doubled haploid production methods offer several ways...
Cross bred species such as switchgrass may benefit from advantageous breeding strategies requiring inbred lines. Doubled haploid production methods offer several ways that these lines can be produced that often involve uniparental genome elimination as the rate limiting step. We have used a centromere-mediated genome elimination strategy in which modified CENH3 is expressed to induce the process. Transgenic tetraploid switchgrass lines coexpressed Cas9, a poly-cistronic tRNA-gRNA tandem array containing eight guide RNAs that target two CENH3 genes, and different chimeric versions of CENH3 with alterations to the N-terminal tail region. Genotyping of CENH3 genes in transgenics identified edits including frameshift mutations and deletions in one or both copies of the two CENH3 genes. Flow cytometry of T seedlings identified two T lines that produced five haploid individuals representing an induction rate of 0.5% and 1.4%. Eight different T lines produced aneuploids at rates ranging from 2.1 to 14.6%. A sample of aneuploid lines were sequenced at low coverage and aligned to the reference genome, revealing missing chromosomes and chromosome arms.
Topics: Haploidy; Panicum; Histones; Plant Breeding; Aneuploidy
PubMed: 35470589
DOI: 10.1002/tpg2.20209 -
Current Biology : CB Nov 2013
Topics: Allergens; Haploidy; Plant Physiological Phenomena; Pollen; Pollen Tube
PubMed: 24262831
DOI: 10.1016/j.cub.2013.08.016 -
Current Biology : CB Sep 2009
Topics: Fungi; Genome, Fungal; Haploidy; Phylogeny; Species Specificity
PubMed: 19788875
DOI: 10.1016/j.cub.2009.07.004 -
Plant Biotechnology Journal Nov 2017haploid inducer line can be transferred (DH) technology can not only shorten the breeding process but also increase genetic gain. Haploid induction and subsequent genome... (Review)
Review
haploid inducer line can be transferred (DH) technology can not only shorten the breeding process but also increase genetic gain. Haploid induction and subsequent genome doubling are the two main steps required for DH technology. Haploids have been generated through the culture of immature male and female gametophytes, and through inter- and intraspecific via chromosome elimination. Here, we focus on haploidization via chromosome elimination, especially the recent advances in centromere-mediated haploidization. Once haploids have been induced, genome doubling is needed to produce DH lines. This study has proposed a new strategy to improve haploid genome doubling by combing haploids and minichromosome technology. With the progress in haploid induction and genome doubling methods, DH technology can facilitate reverse breeding, cytoplasmic male sterile (CMS) line production, gene stacking and a variety of other genetic analysis.
Topics: Centromere; Chromosomes, Plant; Crosses, Genetic; Genetic Engineering; Genome, Plant; Germ Cells, Plant; Haploidy; Hybridization, Genetic; Plant Breeding; Plants; Transformation, Genetic
PubMed: 28796421
DOI: 10.1111/pbi.12805 -
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 -
International Journal of Biological... Apr 2011Stem cells have the potential for self-renewal and differentiation. First stem cell cultures were derived 30 years ago from early developing mouse embryos. These are... (Review)
Review
Stem cells have the potential for self-renewal and differentiation. First stem cell cultures were derived 30 years ago from early developing mouse embryos. These are pluripotent embryonic stem (ES) cells. Efforts towards ES cell derivation have been attempted in other mammalian and non-mammalian species. Work with stem cell culture in fish started 20 years ago. Laboratory fish species, in particular zebrafish and medaka, have been the focus of research towards stem cell cultures. Medaka is the second organism that generated ES cells and the first that gave rise to a spermatogonial stem cell line capable of test-tube sperm production. Most recently, the first haploid stem cells capable of producing whole animals have also been generated from medaka. ES-like cells have been reported also in zebrafish and several marine species. Attempts for germline transmission of ES cell cultures and gene targeting have been reported in zebrafish. Recent years have witnessed the progress in markers and procedures for ES cell characterization. These include the identification of fish homologs/paralogs of mammalian pluripotency genes and parameters for optimal chimera formation. In addition, fish germ cell cultures and transplantation have attracted considerable interest for germline transmission and surrogate production. Haploid ES cell nuclear transfer has proven in medaka the feasibility of semi-cloning as a novel assisted reproductive technology. In this special issue on "Fish Stem Cells and Nuclear Transfer", we will focus our review on medaka to illustrate the current status and perspective of fish stem cells in research and application. We will also mention semi-cloning as a new development to conventional nuclear transfer.
Topics: Animals; Biomarkers; Cell Culture Techniques; Cell Line; Cloning, Organism; Embryonic Stem Cells; Germ Cells; Haploidy; Oryzias
PubMed: 21547056
DOI: 10.7150/ijbs.7.392