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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

ApplicationofmolecularmarkersforcharacterizationoflatviancropplantsApplicationofmolecularmarkersforcharacterizationoflatviancropplants

Nils Rostoks

UniversityofLatvia

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

outline of the talk
Outline of the talk
  • Genomicsandplantbreeding
  • DArT un SNP genotyping systemsforcharacterizationofplant genomes
  • Traitmappingusingassociationwith SNP markers
  • Markersformarkerassistedselection

2012.05.31.

2

conventional plant breeding
Conventionalplantbreeding

FromPoehlman (1959) Breedingfieldcrops

2012.05.31.

2012.05.31.

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3

genomics and plant breeding
Genomicsandplantbreeding

Phenotype

Plantbreeding

Genomics

Geneticmap

Physicalmap

Genomesequence

Allelicdiversity

Genefunction

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2012.05.31.

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4

dna based molecular markers
DNA-basedmolecularmarkers
  • Typeofvariation:

- pointmutations

- insertions/deletions

- repeatnumbervariation

- copynumbervariation

  • Genotypingtechnology:

- RFLP

- AFLP

- RAPD, ISSR

- CAPS

- SSAP, IRAP, REMAP

- SSCP

Variationinanonymousgenomicregionsorvariationintranscribedregions (genes)

Throughputandlevelofautomationofthegenotypingtechnology

slide6
DArT
  • DArTgenotypingavailableasservicefromtheDiversityArrays Technologies, Australia
  • Dominantmarkersystem, basedonrandomlydigestedpolymorphicgenomic DNA clones
  • DArTplatformavailableforbarley, wheat, rice, oatandpotato
  • DArTgenotypingdoneforLatvianbarley, oatandpotatoaccessions
oat dart1
OatDArT

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2012.05.31.

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8

genomics for plant breeding
Genomicsforplantbreeding
  • Identificationofgenesencodingspecifictraitsandcharacterizationofgenefunction
  • Assessmentofallelicdiversityinspecificgenes to linkdiversityandthegenefunction
  • Markersforspecifictraitsallowing to createvarietieswithdefinedproperties
  • Assessmentofgeneticdiversityin germplasm available to plantbreedersfornewvarietieswith novel characteristics
illumina snp genotyping
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
snp diversity in latvian barley germplasm
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
slide14

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2012.05.31.

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

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preliminary results of association mapping
Preliminaryresultsofassociationmapping
  • BOPA1 genotypes, phenotypesfrombiologicalandconventionaltrials 2010 – 2011

Resistance to loosesmut

b-glucan content

6H, 55.7 cM

7H, 34.8 cM

molecular markers and genetic diversity
Molecularmarkersandgeneticdiversity
  • Genetic diversity is both the basisfordevelopmentofvarietieswithdifferenttraits, and a tool to distinguishthevarietiesandmapandtransfertraits
  • DNA-basedmarkersdirectlyassessgeneticdiversityin a genome
  • Gene-basedmolecularmarkersallow to assessallelicdiversityingenesprovidingdirectlink to functionaldiversity
markers for plant breeding
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
markers for breeding
Markersforbreeding
  • Powderymildewresistanceinbarley – Mlacase

Mla18 GB

Mla19 GB

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2012.05.31.

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outlook
Outlook
  • Associationmappinginbarleyusing SNP markersandphenotypingdatacollectedwithinEuropeanSocialFundproject
  • Developmentofassaysforpublishedandnewmolecularmarkersforspecifictraitsthatcanbeusedbybreederswith a focusontraitsimportantinorganicfarming

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2012.05.31.

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acknowledgements
Acknowledgements
  • PlantmoleculargeneticsgroupattheUniversityofLatvia
  • State Priekuli PlantBreedingInstitute
  • State Stende PlantBreedingInstitute
  • Funding – EuropeanSocialFundproject 2009/0218/1DP/1.1.1.2.0/09/APIA/VIAA/099
acknowledgements1
Acknowledgements
  • Collaboratorsatthe James HuttonInstitute

Dr. Robbie Waugh, Dr. William Thomas

  • CollaboratorsatUniversityofCalifornia, Riverside

Dr. Timothy Close

  • DiversityArraysTechnology

Dr. Andrzej Kilian