Agrobacterium-mediated floral-dip transformation of the obligate outcrosser Capsella grandiflora

AbstractPlant transformation by floral dip has been essential for research on plant genetics. The plant family Brassicaceae is one of the most well studied plant families and contains both established and emerging genetic model species. Two emerging model species that bear on the evolution of the selfing syndrome are Capsella grandiflora, an obligate outcrosser, and C. rubella, an inbreeder. While the selfing syndrome has been well characterized at the genomic level the genetic mechanisms underlying it remain elusive, in part due to the challenges of establishing mutation lines in C. grandiflora. Here, we describe an efficient method for transforming C. grandiflora by Agrobacterium-mediated floral-dip while simultaneously tracking self-incompatibility loci. With the ability to transform both C. grandiflora and C. rubella, researchers have gained a valuable tool to study the progression to selfing at the genetic level.

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Do s genes or deleterious recessives control late-acting self-incompatibility in Handroanthus heptaphyllus (Bignoniaceae)? A diallel study with four full sib progeny arrays

Annals of Botany ◽

10.1093/aob/mcab031 ◽

2021 ◽

Author(s):

Marta B Bianchi ◽

Thomas R Meagher ◽

Peter E Gibbs

Keyword(s):

Genetic Control ◽

Inbreeding Depression ◽

Fruit Set ◽

Genetic Model ◽

Pollen Tubes ◽

Self Incompatibility ◽

Significant Difference ◽

Partial Embryo ◽

Ovule Penetration ◽

S Genes

Abstract Background and Aims Genetically controlled self-incompatibility (SI) mechanisms constrain selfing and thus have contributed to the evolutionary diversity of flowering plants. In homomorphic gametophytic SI (GSI) and homomorphic sporophytic SI (SSI), genetic control is usually by a single multi-allelic locus S. Both GSI and SSI prevent self pollen tubes reaching the ovary and so are pre-zygotic in action. In contrast, in taxa with late-acting self-incompatibility (LSI), rejection is often post-zygotic, since self-pollen tubes grow to the ovary where fertilization may occur prior to floral abscission. Alternatively, lack of self fruit set could be due to early-acting inbreeding depression (EID). The aim of our study was to investigate mechanisms underlying lack of selfed fruit set in Handroanthus heptaphyllus in order to assess the likelihood of LSI versus EID. Methods We employed four full sib diallels to study the genetic control of LSI in Handroanthus heptaphyllus using a precociously flowering variant. We also used fluorescence microscopy to study the incidence of ovule penetration by pollen tubes in pistils that abscised following pollination or initiated fruits. Key Results All diallels showed reciprocally cross-incompatible full-sibs (RCI), reciprocally cross compatible full-sibs (RCC), and non-reciprocally compatible full-sibs (NRC) in almost equal proportions. There was no significant difference between the incidence of ovule penetrations in abscised pistils following self- and cross-incompatible pollinations, but those in successful cross pollinations were around twofold greater. Conclusions A genetic model postulating a single S locus with four s alleles, one of which, in the maternal parent, is dominant to the other three, will produce RCI, RCC and NRC situations each at 33 %, consistent with our diallel results. We favour this simple genetic control over an early-acting inbreeding depression (EID) explanation since none of our pollinations, successful or unsuccessful, resulted in partial embryo development, as would be expected under a whole genome EID effect.

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Homology-Based Interactions between Small RNAs and Their Targets Control Dominance Hierarchy of Male Determinant Alleles of Self-Incompatibility in Arabidopsis lyrata

International Journal of Molecular Sciences ◽

10.3390/ijms22136990 ◽

2021 ◽

Vol 22 (13) ◽

pp. 6990

Author(s):

Shinsuke Yasuda ◽

Risa Kobayashi ◽

Toshiro Ito ◽

Yuko Wada ◽

Seiji Takayama

Keyword(s):

Dominance Hierarchy ◽

Male Dominance ◽

Self Incompatibility ◽

Arabidopsis Halleri ◽

Plant Family ◽

Arabidopsis Lyrata ◽

Multiple Networks ◽

Target Sites ◽

Gains And Losses ◽

Linear Dominance Hierarchy

Self-incompatibility (SI) is conserved among members of the Brassicaceae plant family. This trait is controlled epigenetically by the dominance hierarchy of the male determinant alleles. We previously demonstrated that a single small RNA (sRNA) gene is sufficient to control the linear dominance hierarchy in Brassica rapa and proposed a model in which a homology-based interaction between sRNAs and target sites controls the complicated dominance hierarchy of male SI determinants. In Arabidopsis halleri, male dominance hierarchy is reported to have arisen from multiple networks of sRNA target gains and losses. Despite these findings, it remains unknown whether the molecular mechanism underlying the dominance hierarchy is conserved among Brassicaceae. Here, we identified sRNAs and their target sites that can explain the linear dominance hierarchy of Arabidopsis lyrata, a species closely related to A. halleri. We tested the model that we established in Brassica to explain the linear dominance hierarchy in A. lyrata. Our results suggest that the dominance hierarchy of A. lyrata is also controlled by a homology-based interaction between sRNAs and their targets.

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Neural and genetic degeneracy underlies Caenorhabditis elegans feeding behavior

Journal of Neurophysiology ◽

10.1152/jn.00150.2014 ◽

2014 ◽

Vol 112 (4) ◽

pp. 951-961 ◽

Cited By ~ 28

Author(s):

Nicholas F. Trojanowski ◽

Olivia Padovan-Merhar ◽

David M. Raizen ◽

Christopher Fang-Yen

Keyword(s):

Caenorhabditis Elegans ◽

Neural Circuit ◽

Dependent Manner ◽

State Dependent ◽

Excitatory Pathways ◽

Genetic Mechanisms ◽

Genetic Level ◽

Pharyngeal Pumping ◽

Robust Network

Degenerate networks, in which structurally distinct elements can perform the same function or yield the same output, are ubiquitous in biology. Degeneracy contributes to the robustness and adaptability of networks in varied environmental and evolutionary contexts. However, how degenerate neural networks regulate behavior in vivo is poorly understood, especially at the genetic level. Here, we identify degenerate neural and genetic mechanisms that underlie excitation of the pharynx (feeding organ) in the nematode Caenorhabditis elegans using cell-specific optogenetic excitation and inhibition. We show that the pharyngeal neurons MC, M2, M4, and I1 form multiple direct and indirect excitatory pathways in a robust network for control of pharyngeal pumping. I1 excites pumping via MC and M2 in a state-dependent manner. We identify nicotinic and muscarinic receptors through which the pharyngeal network regulates feeding rate. These results identify two different mechanisms by which degeneracy is manifest in a neural circuit in vivo.

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FlyRNAi.org—the database of the Drosophila RNAi screening center and transgenic RNAi project: 2021 update

Nucleic Acids Research ◽

10.1093/nar/gkaa936 ◽

2020 ◽

Vol 49 (D1) ◽

pp. D908-D915

Author(s):

Yanhui Hu ◽

Aram Comjean ◽

Jonathan Rodiger ◽

Yifang Liu ◽

Yue Gao ◽

...

Keyword(s):

Drosophila Melanogaster ◽

Functional Genomics ◽

Protein Interactions ◽

Protein Modification ◽

Genetic Model ◽

Online Resources ◽

Model Species ◽

Rnai Screening ◽

Transcriptomics Data

Abstract The FlyRNAi database at the Drosophila RNAi Screening Center and Transgenic RNAi Project (DRSC/TRiP) provides a suite of online resources that facilitate functional genomics studies with a special emphasis on Drosophila melanogaster. Currently, the database provides: gene-centric resources that facilitate ortholog mapping and mining of information about orthologs in common genetic model species; reagent-centric resources that help researchers identify RNAi and CRISPR sgRNA reagents or designs; and data-centric resources that facilitate visualization and mining of transcriptomics data, protein modification data, protein interactions, and more. Here, we discuss updated and new features that help biological and biomedical researchers efficiently identify, visualize, analyze, and integrate information and data for Drosophila and other species. Together, these resources facilitate multiple steps in functional genomics workflows, from building gene and reagent lists to management, analysis, and integration of data.

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Genome size variation and endopolyploidy in the diverse succulent plant family Aizoaceae

Botanical Journal of the Linnean Society ◽

10.1093/botlinnean/boaa034 ◽

2020 ◽

Vol 194 (1) ◽

pp. 47-68

Author(s):

Robyn F Powell ◽

Laura Pulido Suarez ◽

Anthony R Magee ◽

James S Boatwright ◽

Maxim V Kapralov ◽

...

Keyword(s):

Genome Size ◽

Size Variation ◽

Cape Floristic Region ◽

Genome Size Variation ◽

Rapid Radiation ◽

Plant Family ◽

Succulent Plant ◽

The Family ◽

The World ◽

Plant Families

Abstract Aizoaceae are one of the most diverse succulent plant families in the world, with c. 2 400 species, and they are a major component of the Greater Cape Floristic Region of South Africa. Despite this diversity, genome size (GS) has only been recorded in three of the c. 144 genera of Aizoaceae. This study provides the first comprehensive assessment of GS in the family with 109 genera measured (76% of genera). GS (2C) is conserved in Aizoaceae, varying from 0.54 to 6.34 pg (0.53–6.20 Gbp), with a mean of 2.6 pg. No significant differences between GS and the ecological and environmental traits tested were recovered. Infrageneric GS was explored in the most diverse stoneplant genus, Conophytum, and was found to be extremely conserved [0.98–2.24 pg (1C)]. Furthermore, the extent of endoreduplication in Conophytum was determined across 46 species. Leaf and flower tissues of Conophytum are highly polysomatic and ploidy states of 2C–64C were typically observed across the genus, with some instances of 128C. The relatively conserved and small GS measured across Aizoaceae and in Conophytum is possibly linked to the recent and rapid radiation of the family.

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Current Status of Green Space and Plant Disposition in the Urban Road Landscape Design

Applied Mechanics and Materials ◽

10.4028/www.scientific.net/amm.209-211.352 ◽

2012 ◽

Vol 209-211 ◽

pp. 352-356

Author(s):

Xu Zhou ◽

Lin Zhang ◽

Zhao Fei Zhang

Keyword(s):

Green Space ◽

Relative Concentration ◽

Ornamental Plants ◽

Plant Species Richness ◽

Current Status ◽

Plant Family ◽

Urban Road ◽

Regional Landscape ◽

Plant Families ◽

Pedestrian Street

This study conducts investigations on the plants and plant landscaping in the two regions - Huangxing Commercial Pedestrian Street and Furong Road, which are representative and with relative concentration of population flow and traffic flow. The statistics results show that there are a total of 21 families and 25 species of ornamental plants applied in Huangxing Pedestrian Street, of which arbors and shrubs are widely used with 11 species of arbors, and 11 species of small arbors and shrubs; in terms of plant families, plants from Oleaceae, Pinaceae and Celastraceae families are more frequently used. There are a total of 12 families and 15 species of ornamental plants applied in the Furong Road, of which shrubs are more extensively used with 10 species; in terms of plant family and genera, plants from Oleaceae, Rosaceae and Theaceae families are more frequently used. On this basis, and combining with the different plant combinations and collocations, this paper conducts comparative analysis on the regional landscape arrangement modes and features, and points out the shortcomings of plant species richness and landscape levels in the plant landscapes of the two regions.

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Seed plant families with diverse mycorrhizal states have higher diversification rates

10.1101/824441 ◽

2019 ◽

Author(s):

María Isabel Mujica ◽

Gustavo Burin ◽

María Fernanda Pérez ◽

Tiago Quental

Keyword(s):

Soil Fungi ◽

Plant Evolution ◽

Ancestral State ◽

Seed Plant ◽

Plant Family ◽

Symbiotic Interaction ◽

Evolutionary Transitions ◽

Diversification Rates ◽

Plant Families ◽

The Relationship

AbstractA crucial innovation in plant evolution was the association with soil fungi during land colonization. Today, this symbiotic interaction is present in most plants species and can be classified in four types: arbuscular (AM), Ecto (EM), Orchid (OM) and Ericoid Mycorrhiza (ER). Since the AM ancestral state, some plants lineages have switched partner (EM, OM and ER) or lost the association (no-association: NM). Evolutionary transitions to a novel mycorrhizal state (MS) might allow plant lineages to access new resources, enhancing diversification rates. However, some clades are not restricted to one MS, and this variability might promote diversification. In this study we address the relationship between MS and diversification rates of seed plant families. For this, we used the recently published FungalRoot database, which compiled data for 14,870 species and their mycorrhizal partners. We assigned a MS to each plant family, calculated the MS heterogeneity and estimated their diversification rates using the method-of-moments. Families with mixed MS had the highest diversification rates and there was a positive relationship between MS heterogeneity and diversification rates. These results support the hypothesis that MS lability promotes diversification and highlight the importance of the association with soil fungi for the diversification of plants.

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Improved contiguity of the threespine stickleback genome using long-read sequencing

10.1101/2020.06.30.170787 ◽

2020 ◽

Cited By ~ 1

Author(s):

Shivangi Nath ◽

Daniel E. Shaw ◽

Michael A. White

Keyword(s):

Gasterosteus Aculeatus ◽

Genetic Model ◽

Threespine Stickleback ◽

Model Species ◽

Long Distance ◽

Sequencing Technologies ◽

A Genome ◽

Long Read ◽

The Cost ◽

Stickleback Genome

AbstractWhile the cost and time for assembling a genome have drastically reduced, it still remains a challenge to assemble a highly contiguous genome. These challenges are rapidly being overcome by the integration of long-read sequencing technologies. Here, we use long sequencing reads to improve the contiguity of the threespine stickleback fish (Gasterosteus aculeatus) genome, a prominent genetic model species. Using Pacific Biosciences sequencing, we were able to fill over 76% of the gaps in the genome, improving contiguity over five-fold. Our approach was highly accurate, validated by 10X Genomics long-distance linked-reads. In addition to closing a majority of gaps, we were able to assemble segments of telomeres and centromeres throughout the genome. This highlights the power of using long sequencing reads to assemble highly repetitive and difficult to assemble regions of genomes. This latest genome build has been released through a newly designed community genome browser that aims to consolidate the growing number of genomics datasets available for the threespine stickleback fish.

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Genetic interaction between two unlinked loci underlies the loss of self-incompatibility in Arabidopsis lyrata

10.1101/830414 ◽

2019 ◽

Author(s):

Yan Li ◽

Mark van Kleunen ◽

Marc Stift

Keyword(s):

Breeding System ◽

Genetic Basis ◽

Genetic Model ◽

Genetic Interaction ◽

Current Knowledge ◽

Breeding Systems ◽

Self Incompatibility ◽

Arabidopsis Lyrata ◽

Loss Of Self ◽

Selfing Species

AbstractAs the first step towards the evolution of selfing from obligate outcrossing, identifying the key mutations underlying the loss of self-incompatibility is of particular interest. However, our current knowledge is primarily based on sequence-based comparisons between selfing species and their self-incompatible relatives, which makes it hard to distinguish causal from secondary mutations. To by-pass this problem, we inferred the genetic basis of the loss of self-incompatibility by intercrossing plants from twelve geographically interspersed outcrossing and selfing populations of North-American Arabidopsis lyrata and determining the breeding system of 1,580 progeny. Self-incompatibility was not restored after crosses between different self-compatible populations. Equal frequencies of self-compatible and self-incompatible progeny emerged from crosses between parents with different breeding systems. We propose a two-locus genetic model for the loss of self-incompatibility in which specific S-locus haplotypes (S1 and S19) are associated with loss of self-incompatibility through their interaction with an unlinked modifier.

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