1. APPLICATION OF MOLECULAR MARKERS FOR CHARACTERIZATION OF LATVIAN CROP PLANTS Nils Rostoks University of Latvia 2012.05.31.1 Vienošanās Nr. 2009/0218/1DP/1.1.1.2.0/09/APIA/VIAA/099

2. 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 Markers for marker assisted selection 2012.05.31.2 2

3. Conventional plant breeding 2012.05.31.3 From Poehlman (1959) Breeding field crops 2012.05.31.3 3

4. Genomics and plant breeding 2012.05.31.4 Genomics Plant breeding Phenotype Genetic map Physical map Genome sequence Gene function Allelic diversity 2012.05.31.4 4

5. DNA-based molecular markers Type of variation: - point mutations - insertions/deletions - repeat number variation - copy number variation Genotyping technology: - RFLP - AFLP - RAPD, ISSR - CAPS - SSAP, IRAP, REMAP - SSCP 2012.05.31.5 Variation in anonymous genomic regions or variation in transcribed regions (genes) Throughput and level of automation of the genotyping technology

6. DArT DArT genotyping available as service from the Diversity Arrays Technologies, Australia Dominant marker system, based on randomly digested polymorphic genomic DNA clones DArT platform available for barley, wheat, rice, oat and potato DArT genotyping done for Latvian barley, oat and potato accessions 2012.05.31.6

7. Oat DArT 2012.05.31.7

8. Oat DArT 2012.05.31.8 8 8

9. Genomics for plant breeding Identification of genes encoding specific traits and characterization of gene function Assessment of allelic diversity in specific genes to link diversity and the gene function Markers for specific traits allowing to create varieties with defined properties Assessment of genetic diversity in germplasm available to plant breeders for new varieties with novel characteristics 9

10. 2012.05.31.10

11. Illumina SNP genotyping Genotyping technology developed by Illumina Barley genotyping assays (BOPA1 and BOPA2) developed by The James Hutton Institute, University of California, Riverside and The Leibniz Institute of Plant Genetics and Crop Plant Research 2 x 1536 SNP Most of the SNPs mapped 2012.05.31.11

12. SNP diversity in Latvian barley germplasm 95 Latvian barley varieties and breeding lines genotyped with BOPA1 (1536 SNP) 96 Latvian and foreign accessions genotyped with BOPA1 and BOPA2 (2 x 1536 SNP) Assessement of genetic diversity based on BOPA1 Association mapping in a set of 153 accessions genotyped with BOPA1 2012.05.31.12

13. SNP diversity in Latvian barley germplasm 2012.05.31.13

14. 2012.05.31.142012.05.31.142012.05.31.14 Vienošanās Nr. 2009/0218/1DP/1.1.1.2.0/09/APIA/VIAA/099

15. Preliminary results of association mapping BOPA1 genotypes, phenotypes from biological and conventional trials 2010 – 2011 2012.05.31. 15  -glucan content 7H, 34.8 cM Resistance to loose smut 6H, 55.7 cM

16. Molecular markers and genetic diversity Genetic diversity is both the basis for development of varieties with different traits, and a tool to distinguish the varieties and map and transfer traits DNA-based markers directly assess genetic diversity in a genome Gene-based molecular markers allow to assess allelic diversity in genes providing direct link to functional diversity 2012.05.31.16

17. Markers for plant breeding Any marker that allows to select for a specific trait is useful in plant breeding Molecular markers detect differences between individuals or varieties at molecular (protein and DNA) level Molecular markers that are linked to certain traits form the basis for marker-assisted selection (MAS) Essentially, molecular markers are just another way of achieving what breeders have been doing for years – combine traits of interest in a novel variety in the most efficient way 2012.05.31.17

18. Markers for breeding Powdery mildew resistance in barley – Mla case 2012.05.31.18 Mla19 GBMla18 GB 2012.05.31.182012.05.31.18

19. Outlook Association mapping in barley using SNP markers and phenotyping data collected within European Social Fund project Development of assays for published and new molecular markers for specific traits that can be used by breeders with a focus on traits important in organic farming 2012.05.31.192012.05.31.192012.05.31.19

20. Acknowledgements Plant molecular genetics group at the University of Latvia State Priekuli Plant Breeding Institute State Stende Plant Breeding Institute Funding – European Social Fund project 2009/0218/1DP/1.1.1.2.0/09/APIA/VIAA/099 2012.05.31.20

21. Acknowledgements Collaborators at the James Hutton Institute Dr. Robbie Waugh, Dr. William Thomas Collaborators at University of California, Riverside Dr. Timothy Close Diversity Arrays Technology Dr. Andrzej Kilian 2012.05.31.21