Genomics and Bioinformatics

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Genomics and Bioinformatics

• Tatjana Sjakste
• 2006

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• www.lubi.edu.lv
• Departments
• Genomics and bioinformatics
• Plant genetics
• Plant mineral nutrition
• Bioindication
• Botany
• Animal physiology

• Miera street 3, Salaspils
• Experimental entomology
• Hydrobiology
• Hydrobiont biochemistry
• Ornitology
• Phychophysiology

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Main directions of scientific work

• Research and rational usage of Latvian nature
  recourses, problems of ecology and environment,
  nature protection
• entomology, zoology of soil, systematics of
  higher plants, studies on Latvian flora, ecology,
  hydrobiology, hydrochemistry, ornithology
• Research of plant and animal life processes and
  their biological productivity
• genomics and bioinformatics, plant genetics,
  plant physiology, biochemistry of hormones,
  physiology of animal digestion, chemistry of soil
  and mineral nutrition of plants, psychophysiology
  of humans

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Genomics and bioinformatics

• Genotyping of genes and genomic polymorphisms in
  plants, animals and humans
• Development of the molecular markers
  (microsatellite, SNPs, etc.) with emphasis on
  their high quality and reproducibility

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Genomics and bioinformatics

• Construction and analysis of haplotypes of the
  genes encoding the economically important traits
  in plants and animals
• Association studies on gene-candidate
  polymorphisms and diseases of humans and animals
• Development of the simple and highly reproducible
  biotechnological approaches to be applied in
  plant and animal breeding programs in Latvia

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Professional skills

• Molecular marker development and mapping

Genetics, 2000, 156, 1997-2005
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Professional skills

• Molecular marker development and mapping

T.Sjakste, J.-Z. Li, M. Ganal Gerstenmikrosatellit
en (GBMS barley microsatellites). 2002/01 AZ
150901 IPK, Gatersleben, Germany
Theoretical and Applied Genetics, 2003, 107 1021
- 1027 Development and genetic mapping of 127
new micrrosatellite markers in barley J. Z. Li1.,
T. G. Sjakste2, M. S. Röder1 and M. W.
Ganal1,3  1Institut fur Pflanzengenetik und
Kulturpflanzenforschung (IPK), Correnstrasse 3,
D-06466, Gatersleben, Germany 2University of
Latvia, Institute of Biology, Miera str. 3, LV
2169, Salaspils, Latvia
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Professional skills

• Molecular marker development and mapping

Immunogenetics. 2004 56238-43
HSMS006 Latvijas populacija
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Professional skills
2. Genotyping of polymorphisms
Theor Appl Genet. 2003, 106539-49.
Inheritance of microsatellite alleles in
pedigrees of Latvian barley varieties and related
European ancestors T. Sjakste, I. Rashal, M.
Röder  Institute of Biology, Miera str. 3, LV
2169, Salaspils, Latvia Institut für
Pflanzengenetik und Kulturpflanzenforschung
(IPK), Correnstrasse 3, D-06466, Gatersleben,
Germany
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Professional skills
3. Application of molecular markers
Genome 2003 46314-322 Molecular cytogenetic
analysis of wheat-barley hybrids using genomic in
situ hybridization and barley microsatellite
markers Malysheva L, Sjakste T, Matzk F, Roder M,
Ganal M.
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Professional skills
4. Application of molecular markers in plant
breeding programs
Hereditas (2004), 14139-45

• Distribution and inheritance of ß-amylase
  alleles in North European barley varieties
• 1Sjakste T., 2Röder M.

1Institute of Biology, Salaspils, Latvia,
2Institut für Pflanzengenetik und
Kulturpflanzenforschung (IPK), Gatersleben,
Germany
SNPs, microsatellite and INDEL variability of the
beta-amylase gene alleles
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Professional skills
5. Search for new polymorphisms in
genes-candidates
2006
Novel data on the intron III nucleotide sequences
of the Bmy1 gene of Latvian barley varieties were
deposited in the GenBank (http//www.ncbi.nlm.nih.
gov/) under accession numbers DQ316895
DQ316905.
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2006
Professional skills
5. Haplotype construction and analysis
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From single genes to genomes
Genomics is the study of genes and their function
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Functional
Structural
Post-genomic era
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Science
Medicine
Society
Agriculture and Industry
Business

• Food
• - production
• quality
• safety

Farmacogenomics
Plant and animal breeding
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NCBI Entrez Genome Project database
is a collection of complete and incomplete large
scale sequencing, assembly, annotation and
mapping projects for cellular organisms. The
database is organized into organisms-specific
overviews that function as portals from which all
projects in the database pertaining to that
organism can be browsed and retrieved
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RH (radiation hybrid map) ILTX map

• This is a third generation map of the
  Illinois-Texas 5,000-rad RH map that contains
  3,484 ordered markers, of which 3,204 are
  anchored in the human genome.

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GET-READY FOR FRAMEWORK PROGRAMME 7

• We can work on plant, animal and human
  genes-candidates
• We can develop new molecular markers
• We can genotype polymorphisms of gene encoding
  the economically important traits in plants and
  animals
• We can analyze inheritance of polymorphic loci
  through the generations
• We can apply genotyping and bioinformatics
  approaches to control and/or predict the breeding
  process

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Thank you for your attention