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Application of molecular markers for characterization of latvian crop plants

Application of molecular markers for characterization of latvian crop plants. Nils Rostoks University of Latvia. Outline of the talk . Genomics and plant breeding DArT un SNP genotyping systems for characterization of plant genomes Trait mapping using association with SNP markers

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Application of molecular markers for characterization of latvian crop plants

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  1. ApplicationofmolecularmarkersforcharacterizationoflatviancropplantsApplicationofmolecularmarkersforcharacterizationoflatviancropplants Nils Rostoks UniversityofLatvia Vienošanās Nr. 2009/0218/1DP/1.1.1.2.0/09/APIA/VIAA/099

  2. Outline of the talk • Genomicsandplantbreeding • DArT un SNP genotyping systemsforcharacterizationofplant genomes • Traitmappingusingassociationwith SNP markers • Markersformarkerassistedselection 2012.05.31. 2

  3. Conventionalplantbreeding FromPoehlman (1959) Breedingfieldcrops 2012.05.31. 2012.05.31. 3 3

  4. Genomicsandplantbreeding Phenotype Plantbreeding Genomics Geneticmap Physicalmap Genomesequence Allelicdiversity Genefunction 2012.05.31. 2012.05.31. 4 4

  5. DNA-basedmolecularmarkers • Typeofvariation: - pointmutations - insertions/deletions - repeatnumbervariation - copynumbervariation • Genotypingtechnology: - RFLP - AFLP - RAPD, ISSR - CAPS - SSAP, IRAP, REMAP - SSCP Variationinanonymousgenomicregionsorvariationintranscribedregions (genes) Throughputandlevelofautomationofthegenotypingtechnology

  6. DArT • DArTgenotypingavailableasservicefromtheDiversityArrays Technologies, Australia • Dominantmarkersystem, basedonrandomlydigestedpolymorphicgenomic DNA clones • DArTplatformavailableforbarley, wheat, rice, oatandpotato • DArTgenotypingdoneforLatvianbarley, oatandpotatoaccessions

  7. OatDArT

  8. OatDArT 2012.05.31. 2012.05.31. 8 8

  9. Genomicsforplantbreeding • Identificationofgenesencodingspecifictraitsandcharacterizationofgenefunction • Assessmentofallelicdiversityinspecificgenes to linkdiversityandthegenefunction • Markersforspecifictraitsallowing to createvarietieswithdefinedproperties • Assessmentofgeneticdiversityin germplasm available to plantbreedersfornewvarietieswith novel characteristics

  10. Illumina SNP genotyping • GenotypingtechnologydevelopedbyIllumina • Barleygenotypingassays (BOPA1 and BOPA2) developedby The James HuttonInstitute, UniversityofCalifornia, RiversideandThe Leibniz Institute of Plant Genetics and Crop Plant Research • 2 x 1536 SNP • MostoftheSNPsmapped

  11. SNP diversityinLatvianbarley germplasm • 95 Latvianbarleyvarietiesandbreedinglinesgenotypedwith BOPA1 (1536 SNP) • 96 Latvianandforeignaccessionsgenotypedwith BOPA1 and BOPA2 (2 x 1536 SNP) • Assessementofgeneticdiversitybasedon BOPA1 • Associationmappingin a setof 153 accessionsgenotypedwith BOPA1

  12. SNP diversityinLatvianbarley germplasm

  13. 2012.05.31. 2012.05.31. Vienošanās Nr. 2009/0218/1DP/1.1.1.2.0/09/APIA/VIAA/099 14 14

  14. Preliminaryresultsofassociationmapping • BOPA1 genotypes, phenotypesfrombiologicalandconventionaltrials 2010 – 2011 Resistance to loosesmut b-glucan content 6H, 55.7 cM 7H, 34.8 cM

  15. Molecularmarkersandgeneticdiversity • Genetic diversity is both the basisfordevelopmentofvarietieswithdifferenttraits, and a tool to distinguishthevarietiesandmapandtransfertraits • DNA-basedmarkersdirectlyassessgeneticdiversityin a genome • Gene-basedmolecularmarkersallow to assessallelicdiversityingenesprovidingdirectlink to functionaldiversity

  16. Markersforplantbreeding • Anymarkerthatallows to selectfor a specifictraitisusefulinplantbreeding • Molecularmarkersdetectdifferencesbetweenindividualsorvarietiesatmolecular (proteinand DNA) level • Molecularmarkersthatarelinked to certaintraitsformthebasisformarker-assistedselection (MAS) • Essentially, molecular markers arejust another way of achieving what breeders have been doing for years – combine traits of interest in a novel varietyinthemostefficientway

  17. Markersforbreeding • Powderymildewresistanceinbarley – Mlacase Mla18 GB Mla19 GB 2012.05.31. 2012.05.31. 18 18

  18. Outlook • Associationmappinginbarleyusing SNP markersandphenotypingdatacollectedwithinEuropeanSocialFundproject • Developmentofassaysforpublishedandnewmolecularmarkersforspecifictraitsthatcanbeusedbybreederswith a focusontraitsimportantinorganicfarming 2012.05.31. 2012.05.31. 19 19

  19. Acknowledgements • PlantmoleculargeneticsgroupattheUniversityofLatvia • State Priekuli PlantBreedingInstitute • State Stende PlantBreedingInstitute • Funding – EuropeanSocialFundproject 2009/0218/1DP/1.1.1.2.0/09/APIA/VIAA/099

  20. Acknowledgements • Collaboratorsatthe James HuttonInstitute Dr. Robbie Waugh, Dr. William Thomas • CollaboratorsatUniversityofCalifornia, Riverside Dr. Timothy Close • DiversityArraysTechnology Dr. Andrzej Kilian

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