Whole genome association mapping of beta-glucan content ir barley Ieva Mežaka, Nils Rostoks Advances in Plant Biotechnology in Baltic Sea region1 State Priekuli Plant Breeding Institute Faculty of Biology, University of Latvia

(1 →3)(1 →4 )-β-D-glucan is a major constitutent of barley cell wall Its content in barley grain determins it’s end use  Low β-glucan content is favourable for malt and feed  High β-glucan content is favourable for food as it helps to lower blood sugar level and cholesterol therefore reduces risk of coronary heart disease and type II diabetes. It is necessary to know the genetic basis of inheritance of the trait to have a success in breeding   -glucan content before has been mapped only in bi- parental mapping populations, results have been dependent on population Advances in Plant Biotechnology in Baltic Sea region 2 Introduction

Advances in Plant Biotechnology in Baltic Sea region 3 Published QTLs for beta-glucan content in barley grain Kim et al. 2004Molina-Cano et al Han et al. 1995Li et al. 2008

To map  -glucan content in Latvian barley varieties and breeding lines using association (linkage disequilibrium– LD) mapping approach Advances in Plant Biotechnology in Baltic Sea region 4 Aim

23 Latvian barley varieties Selections from local landraces, crosses with Nordic, German and Czech varieties and breeding lines 72 Latvian barley breeding lines Crosses of Latvian barley varieties with diverse germplasm from Europe and North America (hulless barley, donors of resistance to loose smut and mildew) Advances in Plant Biotechnology in Baltic Sea region 5 (Latvian) Barley germplasm

State Priekuļi plant breeding institute, State Stende cereal breeding institute years replicates β- glucan content detected by Infratec™ 1241 Grain Analyzer from Foss Advances in Plant Biotechnology in Baltic Sea region 6 Phenotyping Stende Priekuļi

Illumina GoldenGate platform  1536 SNP – each SNP corresponds to a single gene  Most of SNPs have been mapped (Close et al., 2009, BMC Genomics) 1325 polimorfic SNP have been used for association mapping Average distance between SNP markers ~1 cM Average distance between SNPs with significant (P 0.5) linkage disequilibrium cM Advances in Plant Biotechnology in Baltic Sea region 7 Genotyping

 Computer programm for plant associationn mapping “Tassel” implementing four statistical models: ◦ GLM (general linear model) ◦ GLM+Q ◦ MLM (mixed linear model)+Q+K tassel ◦ MLM+Q+K spagedi  Q – infomation on structured association, calculated with computer program “Structure”.  K – kinship matrix, calculated with computer program “Tassel” or “Spagedi”  SNPs with minor allele frequency> 0.1  β- glucan content – average over three replications, two locations (Stende and Priekuļi) and three years ( )  QTL were declaired significant only if they were significant in all 6 environments after p-value correction by Bonferoni method Advances in Plant Biotechnology in Baltic Sea region 8 Association mapping

Advances in Plant Biotechnology in Baltic Sea region 9 Principal coordinates analysis

Advances in Plant Biotechnology in Baltic Sea region 10  -glucan content in grain

Advances in Plant Biotechnology in Baltic Sea region 11 Genotype and environment effect on β- glucan content in grain

Advances in Plant Biotechnology in Baltic Sea region 12 Statistical models P-value Cumulative frequencies

Advances in Plant Biotechnology in Baltic Sea region 13  SSCBI  2007  SPPBI  2009  2008

Advances in Plant Biotechnology in Baltic Sea region 14

nud locus determines hullless genotype All accessions were genotyped at nud locus with indel marker developed by Taketa (2008) Advances in Plant Biotechnology in Baltic Sea region 15 Influence of nud gene on  -glucan content in hulled and hulles genotypes

Advances in Plant Biotechnology in Baltic Sea region 16  SSCBI  2007  SPPBI  2009  2008

Advances in Plant Biotechnology in Baltic Sea region 17  SSCBI  2007  SPPBI  2009  2008

Major QTL for beta-glucan content in hulled and hulless barley has been mapped on chromosome 7H 7 BIN, at the same location where nud gene has been mapped before. Association mapping shows good agreement with the previously mapped β- glucan QTL in bi-parental population CDC Bold x TR251 on chromosome 7H. To map the minor QTLs for beta-glucan content, it is necessary to enlarge the size of population and number of molecular markers Advances in Plant Biotechnology in Baltic Sea region 18 Conclusions

SCRI (Robbie Waugh) and UCR (Tim Close) for SNP genotyping Funding: EU Structural Funds, Latvian Council of Science, Latvian National Programme in Agrobiotechnology Advances in Plant Biotechnology in Baltic Sea region 19 Acknowledgements