Project

Back to overview

Sequencing, assembly, and annotation of the highly heterozygous genome of the apomictic plant Boechera divaricarpa

English title Sequencing, assembly, and annotation of the highly heterozygous genome of the apomictic plant Boechera divaricarpa
Applicant Grossniklaus Ueli
Number 163885
Funding scheme Russia
Research institution Institut für Pflanzen- und Mikrobiologie Universität Zürich
Institution of higher education University of Zurich - ZH
Main discipline Genetics
Start/End 01.08.2016 - 31.12.2019
Approved amount 233'503.00
Show all

All Disciplines (4)

Discipline
Genetics
Agricultural and Forestry Sciences
Embryology, Developmental Biology
Botany

Keywords (8)

highly heterozygous genome; reproduction; apomixis; genome organization; hybrid seed production; genome annotation; genome assembly; Boechera

Lay Summary (German)

Lead
Apomixis, die asexuelle Fortpflanzung durch Samen, kommt natürlicherweise in ungefähr 500 Pflanzen aus mehr als 40 Familien vor. Seit vielen Jahren gilt die Einführung von Apomixis in Nutzpflanzen, bei denen diese Art der Fortpflanzung nicht vorkommt, als grosses Ziel der landwirtschaftlichen Forschung. Apomixis ermöglicht die Herstellung von Klonen, also Nachkommen die genetisch identisch mit der Mutterpflanze sind. So könnte Apomixis genutzt werden, um Heterosis in Hybridpflanzen zu fixieren. Hybridpflanzen produzieren einen höheren Ertrag und sind widerstandsfähiger, aber der Effekt lässt sich nicht über mehrere Generationen aufrechterhalten. Dies wäre mittels Apomixis möglich und könnte die Landwirtschaft revolutionieren.
Lay summary

In den letzten Jahren hat die Genomforschung enorm viele Fortschritte gemacht, aber das Genom einer apomiktischen Art wurde bisher nicht sequenziert. Ziel dieses Projektes ist es, das Genom der apomiktischen Pflanzen Boechera divaricarpa komplett zu entschlüsseln, um daraus Informationen über die Evolution und die Mechanismus von Apomixis zu erhalten. Boechera ist verwandt mit Arabidopsis thaliana, der Modellpflanze der Grundlagenforschung.

Obschon das Boechera Genom mit 230 Milliarden Basenpaaren für Pflanzen relativ klein ist, hat sich das Entziffern dieses Genoms als enorm schwierig herausgestellt. Dies kommt daher, dass das Genom apomiktischer Pflanzen extrem heterozygot oder sogar aneuploid sein kann. Die bioinformatischen Methoden zum Zusammensetzen von Genomen aus kleinen Sequenzstücken haben damit grosse Mühe und das Genom kann nicht assembliert werden. In dieser Schweizerisch-Russichen Kollaboration werden wir neue bioinformatische Methoden entwickeln, um dieses Problem, das für viele Organismen mit grosser Heterozygosie und nicht nur für Apomikten gilt, zu lösen. Zudem werden zusätzliche genomische Daten erhoben, zum Beispiel durch die Identifikation benachbarter Fragmente mittels neuer molekularer Ansätze, um das Assemblieren zu vereinfachen und das Genom besser zu annotieren.

Das Genom einer apomiktischen Pflanze wird nicht nur neue Erkenntnisse über die Mechanismen der Apomixis ermöglichen, sondern auch Einblicke in die Evoltution von Genomen in der Absenz von sexueller Fortpflanzung gewähren.

Das Projekt befasst sich mit Grundlagenforschung, aber die erwarteten Resultate könnten auch für die angewandte Forschung von Bedeutung sein. Heutzutage nutzen die meisten Subsitenzbauern keine  Hybridpflanzen, da sie deren Samen nicht von Jahr zu Jahr aufbewahren können. Apomixis würde dies ermöglichen und könnte so einen wichtigen Beitrag zur Verbesserung der Lebensumstände von Kleinbauern in Entwicklungsländern leisten.

Direct link to Lay Summary Last update: 15.07.2016

Responsible applicant and co-applicants

Employees

Publications

Publication
The Boechera Genus as a Resource for Apomixis Research
Brukhin Vladimir, Osadtchiy Jaroslaw V., Florez-Rueda Ana Marcela, Smetanin Dmitry, Bakin Evgeny, Nobre Margarida Sofia, Grossniklaus Ueli (2019), The Boechera Genus as a Resource for Apomixis Research, in Frontiers in Plant Science, 10, 392.
Assembly of the Boechera retrofracta Genome and Evolutionary Analysis of Apomixis-Associated Genes
Kliver Sergei, Rayko Mike, Komissarov Alexey, Bakin Evgeny, Zhernakova Daria, Prasad Kasavajhala, Rushworth Catherine, Baskar R., Smetanin Dmitry, Schmutz Jeremy, Rokhsar Daniel, Mitchell-Olds Thomas, Grossniklaus Ueli, Brukhin Vladimir (2018), Assembly of the Boechera retrofracta Genome and Evolutionary Analysis of Apomixis-Associated Genes, in Genes, 9(4), 185-185.

Collaboration

Group / person Country
Types of collaboration
Wicker, Thomas, University of Zurich Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
- Research Infrastructure
Szczuka, Ewa, University Maria Curie Sklodowska, Lublin Poland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
Baskar, Ramamurthy, Indian Institute of Technology, Madras India (Asia)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
- Research Infrastructure
Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University Russia (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
Mitchell-Olds, Tom, Duke University United States of America (North America)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
Lyzak, Martin, Masaryk University, Brno Czech Republic (Europe)
- in-depth/constructive exchanges on approaches, methods or results

Scientific events

Active participation

Title Type of contribution Title of article or contribution Date Place Persons involved
Apomixis Consortium Meeting Individual talk Apomixis for Clonal Seed Production and Fixation of Hybrid Vigor 07.01.2020 Einbeck, but participated remotely , Germany Grossniklaus Ueli;
Seminar at Graduate School for Bioagricultural Sciences of Nagoya University Individual talk The Quest for Clonal Seeds: Towards Engineering Apomixis in Maize 29.11.2019 Nagoya, Japan Grossniklaus Ueli;
Seminar at Tokyo Science University Individual talk The Quest for Clonal Seeds: towards Engineering Apomixis in Crops 12.11.2019 Noda, Japan Grossniklaus Ueli;
VII Congress and Associate Symposiums of Vavilov Society of Geneticists and Breeders Talk given at a conference Evolutionary and ecological role of apomixis and asexual reproduction 18.06.2019 St. Petersburg, Russia Brukhin Vladimir;
Seminar at KWS Saat SE Individual talk The Quest for Clonal Seeds - Engineering of Apomixis in Crops 02.05.2019 Einbeck, Germany Grossniklaus Ueli;
Mendel Centre CEITEC, Masaryk University, Seminar Series Spring 2019 Individual talk Sexual and Apomictic Development: From Biology to Genomics 03.04.2019 Brno, Czech Republic Brukhin Vladimir;
Plant and Animal Genome XXVII Conference Talk given at a conference Genome of some apomictic Boechera species and evolution of apomixis associated genes 12.01.2019 San Diego, United States of America Brukhin Vladimir;
11th International Conference on Bioinformatics of Genome Regulation and Structure Talk given at a conference Assembly and annotation of genomes of some species from the apomictic genus Boechera and evolutionary analysis of apomixis-associated genes 20.08.2018 Novosibirsk, Russia Brukhin Vladimir;
25th International Conference on Sexual Plant Reproduction Talk given at a conference Assembly and annotation of the Boechera retrofracta genome and evolutionary analysis of apomixis-associated genes 11.06.2018 Gifu, Japan Brukhin Vladimir;
Farewell Symposium Helmut Bäumlein, IPK Gatersleben Individual talk The quest for clonal seed 04.06.2018 Gatersleben, Germany Grossniklaus Ueli;
3rd International and 15th Iranian Genetics Congress Talk given at a conference The Quest for Clonal Seeds: Engineering of Apomixis in Crops 13.05.2018 Tehran, Iran Grossniklaus Ueli;
Plant and Animal Genome XXVI Conference Talk given at a conference Boechera species: de novo assembly of genomes of sexual and apomictic accessions and apomixis associated genes analysis 13.01.2018 San Diego, United States of America Brukhin Vladimir;
Seminar Tsukuba University Individual talk Engineering Apomixis in Crops: Concepts, Progress, and Challenges in the Quest for Asexual Seeds 15.12.2017 Tsukuba, Japan Grossniklaus Ueli;
Plant & Animal Genome XXV Conference Poster Genome Assembly and Annotation of Boechera holboellii (fam. Brassicaceae) 14.01.2017 San Diego, United States of America Grossniklaus Ueli; Smetanin Dmitry; Brukhin Vladimir; Schmid Marc;


Knowledge transfer events

Active participation

Title Type of contribution Date Place Persons involved
KWS Saat SE: The Quest for Clonal Seeds - Engineering of Apomixis in Crops Talk 02.05.2019 Einbeck, Germany Grossniklaus Ueli;


Communication with the public

Communication Title Media Place Year
Media relations: print media, online media Die Weltverbesserer - Er will die Landwirtschaft revolutionieren Beobachter German-speaking Switzerland 2017
Talks/events/exhibitions Grüne Gentechnik und Nachhaltigkeit in der Landwirtschaft German-speaking Switzerland 2017
Media relations: print media, online media Porträt - Natürlich Klonen Vierteljahresschrift, Naturforschende Gesellschaft in Zürich German-speaking Switzerland 2017
Video/Film Wissenschaftsdoku: Welt ohne Männer International 2017

Abstract

Apomixis, defined as the asexual reproduction of plants through seed, could become a key ‘enabling technology’ of immense benefit to agriculture, because it would enable the permanent fixation of heterosis in crop plants.A better understanding of the molecular basis of apomixis is crucial for yield increases that are required for the sustainable production of biofuels, biomaterials, fibers, food, and feed. Despite the fact that apomixis is considered as one of the key technologies for the improvement of agriculture, it is currently not known what genes control this important trait, nor has the genome of any apomictic species been sequenced (Grossniklaus et al., 2001; Bicknell & Koltunow, 2004; Koltunow & Grossniklaus, 2003, Rodriguez-Leal and Vielle-Calzada, 2012).We propose sequencing of the genome of Boechera divaricarpa, a member of the Brassicaceae (mustard family). The species Boechera divaricarpa includes both apomictic and sexual accessions. We will use the well characterized accession ES517, because it is a diploid apomict (Schranz et al., 2005), characterized by 98-100% formation of seeds with a 2:6 embryo:endosperm ratio (Aliyu, 2010), indicating apomeiosis (absence or omission of meiosis), parthenogenetic development of the unreduced (2n) egg cell, and pseudogamous fertilization of the central cell with unreduced (2n) pollen (self-fertilization).The genome size of Boechera divaricarpa is relatively small, estimated to be around 230 Mb (Oyama et al., 2008; Sharbel & Mitchell-Olds, 2001). However, due to the highly heterozygous nature of apomictic genomes, the production of a high quality draft genome is not a trivial task. Thus, in this project we will develop novel approaches and bioinformatics tools that will be generally applicable to highly heterozygous genomes as they are often found in genetically diverse outcrossing species or in asexual lineages. We will use a combination of sequencing technologies (Illumina, Pacific Bioscience) and a novel approach for genome assembly based on topological chromatin interaction (Hi-C) data (Grob et al., 2014) that permits assembling a genome up to chromosomal level without need of a detailed genetic map or the sequencing of BAC clones.B. divaricarpa is hypothesized to have arisen through hybridization between sexual B. stricta and B. holboellii. Genomic resources for both parental species are available. We will apply comparative approaches to identify apomixis-related genomic regions through a genomic comparison with the ancestral species.Apomictic B. divaricarpa likely represents a group of lines arisen through independent hybridisation events (Katama et al., 2007) and we plan to re-sequence another apomictic diploid line of B. divaricarpa in addition to our reference accession ES517. This will allow us to look into peculiarities of hybridisation events, the chromosomal organisation, and the stability of apomictic genomes.
-