Nils Rostoks

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Augu molekularas genetikas perspektivas

• Nils Rostoks

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Lekciju saraksts
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From green revolution to gene revolution

• Informacija par augu genomu sekvencem, geniem,
  genu regulacijas elementiem un alelisko
  daudzveidibu dos iespejas merktiecigakai un
  precizakai selekcijai, objektivakai genetiskas
  daudzveidibas analizei u.t.t.

Genomika
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Augu molekularas genetikas sasniegumi

• Pilnas genomu sekvences
• Genotipeanas platformas
• Transkriptoma, proteoma un metaboloma analizes
  platformas
• Molekularo markieru datubazes
• Informacija par genu alelisko daudzveidibu un
  funkciju
• Kada veida pielietot is zinaanas un rikus, lai
  panaktu praktiskus rezultatus lauksaimnieciba,
  mesaimnieciba un vides saglabaana?

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Zinatniskie izaicinajumi

• Heterozes mehanismu izpete
• Kvantitativas pazimes nosakoo genu
  identifikacija un raksturojums
• Genu strukturas un ekspresijas loma adaptacija
  noteiktiem vides apstakliem
• Epigenoma loma augu fenotipa veidoana
• Genu inenierijas metou talaka attistiba
• Augi ka biomedicina pielietojamu preparatu avots
• Augu kolekcijas genu bankas un to raksturojums

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Lielakie sagaidamie sasniegumi

• Genomisko sekvencu skaita pieaugums miljardiem
  bazu paru dau dienu laika. Bet ari cDNS un
  molekularie markieri, kas kopa lauj iegut
  arkartigi precizu un bagatigu informaciju par
  konkreto genomu un ta ekspresiju
• Fenotipeana ir aurais posms. Fenotipeana ir
  laikietilpiga, darga un biei vien atkariga no
  cilveku subjektiva viedokla. Jaunas,
  automatizetas fenotipeanas sistemas, piemeram,
  LemnaTec
• Proteomika un metabolomika

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DNS sekvencu pieaugums GenBank
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Jaunas DNS sekveneanas tehnologijas

• Roche 454 sekvenators

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Shendure and Ji (2008) Next-generation DNA
sequencing. Nat Biotech, 26 1135
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454 Roche
Illumina/Solexa
ABI Solid
Heliscope
Shendure and Ji (2008) Next-generation DNA
sequencing. Nat Biotech, 26 1135
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Jauno sekveneanas tehnologiju salidzinajums
Shendure and Ji (2008) Next-generation DNA
sequencing. Nat Biotech, 26 1135
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Jauno sekveneanas tehnologiju pielietojums
Shendure and Ji (2008) Next-generation DNA
sequencing. Nat Biotech, 26 1135
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• 454 sekveneanas tehnologija - 106.5 miljoni
  augstas kvalitates sekvencu ar kopejo garumu 24.5
  miljardi bazu paru
• 93.2 miljoni sekvencu kartetas uz cilveka
  references genoma sekvences
• 7.4-kartigs genoma nosegums

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Mieu genoma analize ar Illumina sekveneanas
tehnologiju

• Sekvene 574 miljonus bazu paru (10) mieu genoma
  (15 950 203 sekvences, katra 36 nukleotidi gara)
• Veido mieu genoma DNS atkartojumu indeksu

Wicker et al. (2008) Low-pass shotgun sequencing
of the barley genome facilitates rapid
identification of genes, conserved non-coding
sequences and novel repeats. BMC Genomics, 9 518
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Genu bankas
Svalbardas Genu banka
IPK Genu banka
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Jauni fenotipi

• Augu saknu fenotips

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Jauni fenotipi
Redzama gaisma
UV gaisma ar GFP3 filtru
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Jaunas fenotipeanas tehnologijas
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Jaunas fenotipeanas tehnologijas
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Augu genetikas petijumu koordineana un
finanseana

• ES 7. ietvara programma
• ES tehnologiju platformas
• EPSO, ERA-PG
• Daadas starptautiskas organizacijas un
  iniciativas

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7. Ietvara programma

• Cooperation
• Ideas
• People
• Capacities
• Euratom, JRC
• http//cordis.europa.eu/home_en.html
• http//cordis.europa.eu/fp7/home_en.html

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ES tehnologijas platformas

• TP platformas daadu prioritaro nozaru ilgtermina
  attistibai
• http//cordis.europa.eu/technology-platforms/

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Plants for the Future

• The SRA establishes a road map for guiding and
  integrating plant research over the next 20 years
  such that the full potential of European human
  capital and knowledge in this field can be
  realised. We articulate five distinct challenges
  that will enable Europe to make key
  contributions
• Challenge one Healthy, safe and sufficient food
  and feed
• Challenge two Plant-based products chemicals
  and energy
• Challenge three Sustainable agriculture,
  forestry and landscape
• Challenge four Vibrant and competitive basic
  research
• Challenge five Consumer choice and governance

http//www.epsoweb.org/Catalog/TP/Launch_25June07/
TP_SRA_Summary.pdf
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C1 Healthy, safe and sufficient food and feed

• Develop and produce sufficient, diversified and
  affordable high quality plant raw materials for
  food products
• Produce, trace and control safe plant raw
  materials for feed and food
• Tailor plant raw materials for certain health
  benefits and specific consumer groups
• High-quality, sufficient, affordable and
  sustainable feed

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C2 Plant-based products chemicals and energy

• Biochemical production
• Bio-energy production
• Enabling research for plant-based products

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C3 Sustainable agriculture, forestry and
landscape

• Improve plant productivity and quality
• Reduce and optimise the environmental impact of
  agriculture
• Enhance biodiversity

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C5 Consumer choice and governance

• Public and consumer involvement
• Ethics and food security
• Legal and financial environment

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C4 Vibrant and competitive basic research

• Genome sequences of European crops and major
  pathogens
• Detailing the parts list of genomes
• From gene to phenotype
• Systems biology and prediction of novel traits
• Building human resources, infrastructure and
  networking

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Genome sequences of European crops and major
pathogens

• Five years
• Acquisition of genome sequences from selected
  model species and important European crops
• Large scale re-sequencing of crop and reference
  genomes
• Determination of the genome sequences of major
  plant pathogens affecting major European crops
• Development of next generation databases for
  model plants, selected crops and major pathogens
• Construction of physical maps of major European
  crops with large genomes (e.g. wheat, barley)
• Ten Years
• Acquisition of genome sequences from selected
  crops with large genomes (e.g. wheat, barley)

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Detailing the parts list of genomes

• Five years
• Acquisition of platforms for transcriptome
  analysis of the newly sequenced genomes of major
  European crops and their pathogens
• Development of efficient proteomics and
  metabolomics platforms
• Development of technologies to assay protein
  functions
• Development of software and database systems to
  handle multi-level genomics datasets
• Ten years
• Development and application of technologies for
  observing biological processes at the subcellular
  level in real time and applying these
  systematically to understanding plant growth,
  development and environmental interactions
• Acquisition of platforms for transcriptome
  analysis of European crops with large genomes

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From gene to phenotype

• Five years
• Establishment of phenotyping platforms for major
  crops
• Development of tilling collections for major
  European crops
• Application of re-sequencing technologies for
  high throughput genetic analysis
• Ten years
• Establishment of phenotyping platforms for major
  crops with large genomes
• Development of tilling collections for major
  European crops with large genome sizes
• Availability of site-specific integration systems
  for all major crops
• Extensive combinations of mutations to reveal
  major new levels of control and integration of
  biological processes

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Systems biology and prediction of novel traits

• Five years
• The definition of the regulatory logic of simple
  biological systems
• Development of modelling tools for plant growth
  and architecture
• Ten years
• The modelling of all basic biological processes
  in plants
• Twenty years
• The understanding of the regulatory logic of all
  fundamental processes in plants why and how this
  logic permits trait plasticity during evolution
  and domestication, within and across species.
  Ultimately, models should allow the definition of
  which genes and processes needs to be modified in
  order to obtain a given desired trait

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Building human resources, infrastructure and
networking

• Five years
• Establish the virtual training centre in plant
  science for PhD students
• Exchange grants for a transition between academia
  and industry established in selected Member
  States
• First landing grants for scientists from new
  Member States
• Ten years
• Virtual training centre in plant science for PhD
  students and post-docs operating with national
  funding
• Extended landing grants for scientists from new
  Member States
• Twenty years
• European graduate schools in plant science
• Landing grants become a common scheme to promote
  science in less advanced regions in Europe

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ERA-PG

• ERA-NET Plant Genomics (ERA-PG) ir sadarbibas
  tikls starp nacionalajam parvaldes un
  finanseanas agenturam augu genomikas joma
• ERA-PG merkis ir stimulet augstas kvalitates
  zinatniskos petijumus, veicinat inovacijas un
  radit augligu vidi zinatnisko sasniegumu
  komercializacijai Eiropa
• ERA-PG patlaban piedalas 23 partneri no 17
  valstim
• Latvija (un parejas Baltijas valstis ) ERA-PG
  nepiedalas
• http//www.erapg.org

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The European Plant Science Organization

• EPSO ir neatkariga, akademiska organizacija, kas
  apvieno 59 dalibniekus, kuri parstav 185
  petnieciskos institutus un universitates no 27
  valstim, kas darbojas augu biologijas joma
• EPSO merkis ir uzlabot augu biologijas (plant
  science) ietekmi un atpazistamibu Eiropa.
• Pie EPSO uzdevumiem pieder izpratnes par augu
  biologiju veicinaana, fundamentalo petiju
  finansejuma palielinaana un zinatnisko petijumu
  koordineana nacionala un Eiropas limeni
• http//www.epsoweb.org

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ITMI International Triticeae mapping Initiative

• ITMI ir starptautiska organizacija, kura koordine
  genetikas, molekularas genetikas un genomikas
  petijumus Triticeae grupa. Tas merki ir sekojoi
  
• - nodroinat informacijas un zinatnisko datu par
  Triticeae izplatianu zinatnieku vidu
• - palidzet izvairities no paraleliem petijumiem
  par vienu temu
• - nodroinat vidi starptautiskas sadarbibas
  veidoanai
• - nodroinat Triticeae petijumu augsto
  zinatnisko limeni
• Darbibas jomas Triticeae augu kolekcijas,
  rekombinacijas kartes un populacijas, fiziskas
  kartes, genu ekspresijas profileana, funkcionala
  analize (tai skaita transgenie augi),
  bioinformatika un pielietojama genomika
• http//wheat.pw.usda.gov/ITMI/

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ETGI - European Triticeae Genomics Initiative

• ETGI koordine Triticeae genoma petijumus Eiropa
  un nodroina saikni ar starptautiskajiem
  petijumiem, kurus parstav ITMI
• http//pgrc.ipk-gatersleben.de/etgi/

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• Zinatnes finansejums ES dalibvalstis

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Zinatnes finansejums Latvija
Centralas statistikas parvaldes dati (29.04.2009)
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Ar augu genetiku saistiti projekti Latvija

• Valsts petijumu programma agrobiotehnologija
• 1. projekts Latvijas laukaugu sugu
  daudzveidibas izvertejums un selekcijas
  optimizacija, pielietojot modernas
  biotehnologijas metodes
• 2. projekts Augstvertigas Latvijas ogas no
  kirnes lidz kvalitativam, veseligam un droam
  produktam
• LZP projekti

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Seminars 07.05.2009

• Nils Rostoks