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A Genome-Wide Association Study to Genetically Dissect Yield Related Traits in a Diverse Collection of Spring Barley Landraces

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A Genome-Wide Association Study to Genetically Dissect Yield Related Traits in a Diverse Collection of Spring Barley Landraces Aus dem Institut für Agrar- und Ernährungswissenschaften der Naturwissenschaftlichen Fakultät III der Martin-Luther-Universität Halle-Wittenberg A genome-wide association study to genetically dissect yield related traits in a diverse collection of spring barley landraces Dissertation zur Erlangung des Doktorgrades der Agrarwissenschaften (Dr. agr.) vorgelegt von Herrn Celestine Wabila Geb. am 08.08.1981 in Bamenda-Cameroon Gutachter: Prof. Dr. Andreas Graner (IPK Gatersleben) Prof. Dr. Volker Mohler (Lfl Freising-Weihenstephan) Verteidigung am: 07/05/2018 Contents Contents....................................................................................................................................ii 1 General introduction……………………………………………………………………1 1.1 Barley taxonomy and geographical distribution ......................................................... 1 1.2 Barley domestication ................................................................................................... 2 1.3 Early and modern use of barley and its economic importance ................................... 3 1.4 The genepool of barley and its genetic diversity......................................................... 5 1.5 Barley landraces and their importance ........................................................................ 7 1.6 Barley breeding ........................................................................................................... 8 1.7 Barley as a model crop for genetic research ............................................................... 9 1.8 Barley genomic resources ......................................................................................... 10 1.9 Quantitative trait loci (QTL) analysis ....................................................................... 10 1.9.1 Linkage mapping vs linkage disequilibrium mapping ....................................... 11 1.9.2 Genome-wide association mapping and linkage disequilibrium decay (LD) .... 12 1.9.3 Practical approaches for genome-wide association analysis ............................. 14 1.9.4 Genome-wide association scans and challenges ................................................ 15 1.9.5 Sample size and statistical power for GWAS .................................................... 15 1.10 Research objectives ................................................................................................... 17 2 Materials and methods………………………………………………………………...18 2.1 Plant material............................................................................................................. 18 2.2 Sowing ....................................................................................................................... 19 2.3 Phenotyping ............................................................................................................... 20 2.4 Evaluation of phenotypic data ................................................................................... 23 2.5 Broad sense heritability ............................................................................................. 24 2.6 Genotyping ................................................................................................................ 24 2.7 Comparison of SSR and SNP makers in genetic relatedness study .......................... 25 2.8 Polymorphic information content.............................................................................. 25 2.9 Population structure................................................................................................... 26 2.10 Linkage disequilibrium (LD) decay .......................................................................... 28 2.11 Genome-wide association analysis............................................................................ 29 3 Results………………………………………………………………………………………….31 3.1 Heading date .............................................................................................................. 31 3.1.1 Other agronomic traits ....................................................................................... 33 ii 3.2 Variance components explained by Genotype, Genotype x year.............................. 35 3.3 Comparison of SSR and SNP makers in genetic relatedness study .......................... 36 3.4 Marker distribution and polymorphic information content ....................................... 38 3.5 Population structure................................................................................................... 39 3.6 Linkage disequilibrium (LD) decay .......................................................................... 43 3.7 Genome-wide association analyses – model selection .............................................. 44 3.8 GWAS results ............................................................................................................ 45 3.8.1 Heading date, grains per spike, plant height and harvest index ......................... 46 3.8.2 Thousand kernel weight, Seed Area, seed width and seed length ..................... 48 3.8.3 Spike density and ear length .............................................................................. 50 3.8.4 Awn length, Awn roughness and stigma hairiness ............................................ 52 3.8.5 Presence or absence of hulls .............................................................................. 53 4 Discussion………………………………………………………………………………56 4.1 Phenotypic variation and trait heritability ................................................................. 56 4.2 Population structure................................................................................................... 57 4.3 Linkage disequilibrium decay ................................................................................... 58 4.4 Comparison of SSR and SNP markers in genetic relatedness study ......................... 59 4.5 GWA analysis ........................................................................................................... 61 5 Summary and outlook......................………………………………………………….75 6 Zusammenfassung……………………………………………………………………..78 7 Supplementary Tables………………………………………………………………............81 7.1 Supplementary Figure: ............................................................................................ 107 8 References…………………………………………………………………………….109 Acknowledgements……………………………………………………………………129 iii List of figures Figure 1.1. Genepools in cultivated barley ............................................................................... 6 Figure 2.1. World map showing the geographic origin of all 261 accessions.. ...................... 18 Figure 2.2. Barley field trial at four months after sowing in 2013.. ....................................... 20 Figure 2.3. Images of stigma taken under a binocular microscope at magnification x25.. .... 21 Figure 2.4. Images of barley awns showing different densities of barbs.. .............................. 22 Figure 2.5. Images of barley seeds.. ........................................................................................ 23 Figure 3.1. Neighbour joining tree of all 199 accessions generated based on heading date data from 2013 and 2014 field trials.. ...................................................................................... 32 Figure 3.2. Interactive circos plot showing the influence of five factors, Genotype (G), Environment (year), Genotype x Environment (G.E) and Replicate (rep) on ten quantitative traits.......................................................................................................................................... 35 Figure 3.3. Neighbor joining tree of 88 barley accessions representing 30 potential duplicate groups.. ..................................................................................................................................... 37 Figure 3.4. Distribution of SNP frequencies within the population of 199 spring barley landraces considered for GWAS. ............................................................................................. 39 Figure 3.5. Population structure analysis of 199 spring barley landraces based on principal component analysis (PCA). ..................................................................................................... 40 Figure 3.6. Neighbor joining net of all 199 spring barley accessions generated with splits tree software.. .................................................................................................................................. 41 Figure 3.7. Plot of mean likelihood of delta K against the number of K groups.. .................. 42 Figure 3.8. Q-matrix plot of STRUCTURE analysis at K=2.. ................................................ 43 Figure 3.9. Average genome wide linkage disequilibrium (r2) decay over genetic distance. 44 Figure 3.10. Quantile-Quantile plots showing of GWAS for harvest index. .......................... 45 Figure 3.11. GWAS results for heading date (Hd), Grains per spike (GPS), plant height (Pht) and harvest index (HI).. ........................................................................................................... 48 Figure 3.12. GWAS result for thousand kernel weight (TKW), seed area (SDA), seed length (SDL) and seed width (SDW).. ................................................................................................ 50 Figure 3.13. GWAS result for spike density (SPD), and earl length (EL).. ............................ 51 Figure 3.14. GWAS result across stigma
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