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GENETIC ANALYSIS of the GROUP IV Rht LOCI in WHEAT

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GENETIC ANALYSIS of the GROUP IV Rht LOCI in WHEAT GENETIC ANALYSIS OF THE GROUP IV Rht LOCI IN WHEAT Edward Paul Wilhelm A thesis submitted for the degree of Doctor of Philosophy University of East Anglia John Innes Centre June 2011 © This copy of the thesis has been supplied on condition that anyone who consults it is understood to recognise that its copyright rests with the author and that no quotation from the thesis, nor any information derived there from, may be published without the author‟s prior, written consent ABSTRACT The introduction of the group IV semi-dwarf Rht alleles, Rht-B1b (formerly Rht1) and Rht-D1b (formerly Rht2) into bread wheat varieties from the donor line „Norin 10‟ that began in the 1960s was a major contributor to the „green revolution‟. Rht-B1b and Rht-D1b were characterised and cloned over a decade ago (Gale and Youssefian 1985; Peng et al. 1999), however the Rht- A1 locus has not been isolated and little is known regarding the genetic diversity of the group IV Rht loci or the genetic composition of the contiguous sequence surrounding Rht that was presumably introgressed into wheat varieties along with the dwarfing alleles. To investigate the contiguous region around Rht, a hexaploid wheat („Chinese Spring‟ (CS)) BAC library was screened using a PCR-based technique (Febrer et al. 2009). This identified several Rht-containing BAC clones, three of which (representing the A, B, and D genomes) were sequenced and found to contain one to two genes upstream of Rht in conserved order. Gene synteny was also highly conserved in rice, Brachypodium distachyon, sorghum, and maize. The previously unidentified Rht-A1 homoeologue was physically mapped to the long arm of chromosome 4A using aneuploid lines and mapped relative to genetic markers. To estimate genetic diversity, the entire coding regions of Rht-A1, Rht-B1, and Rht-D1 and the flanking regions (approximately 1800 bp 5‟ and 450 bp 3‟) were sequenced in 40 diverse wheat accessions. Little polymorphism and few haplotypes were identified on the A and D genomes, but on the B genome a relative abundance of haplotypes and polymorphism were present, including insertions (relative to CS) of 160 bp and 197 bp within 600 nucleotides of the ORF. The Rht-B1 insertions did not have a pronounced effect on RNA transcript level when assessed in seedlings. In an analysis of 368 lines from the INRA bread wheat core collection (BWCC) (Balfourier et al., 2007), lines with the Rht-B1 insertions were associated with reduced heights and reduced GA sensitivity relative to lines without an insertion, but only the height reductions associated with the 197 bp insertion were significant (p < 0.05). GA sensitivity tests of the INRA BWCC did not reveal any novel GA insensitive mutants. An investigation of the origin of the „Norin 10‟ alleles revealed potential discrepancies between the published pedigree and of „Norin 10‟ and the genotypes of seed stocks. Sequence, annotation, and comparative genomics of the Rht-containing BAC clones, the mapping of Rht-A1, and the discovery and investigation of novel genetic diversity provides greater insight into the Rht region and also provides tools for further analysis of this region and for the potential improvement of bread wheat. ii ACKNOWLEDGEMENTS I am indebted to my supervisor Margaret Boulton for her generous help and fantastic support throughout the thesis. Special thanks also to my co- supervisor Wayne Powell who made this thesis possible. I gratefully acknowledge support from the NIAB trust and the BBSRC for a studentship for research funding. Thank you to Andy Greenland and all my colleagues at NIAB for their technical help (especially Rhian Howells, bioinformatics) and for providing a wonderful working environment. Thanks also to the rest of my PhD committee: Nadia Al-Kaff, JIC, for her encouragement and help; Ian Mackay, NIAB, for statistical advice; Simon Griffiths, JIC, and his lab (notably Michelle Leverington-Waite and Catherine Baker) for help with genetic mapping. I‟d also like to thank the members of Margaret Boulton‟s lab (in particular Andrey Korolev) for their help in performing experiments and Robert Saville for his help and fruitful discussions on Rht. Thanks also to collaborators Francois Balfourier (Clermont-Ferrand, INRA) and Jizeng Jia (Chinese Academy of Agricultural Sciences, P.R. China) Finally, I‟m indebted to my wife for not divorcing me during this process, and to my wife and son for reminding me that life existed outside of the PhD. iii TABLE OF CONTENTS 1. GENERAL INTRODUCTION 1 1.1. INTRODUCTION 1 1.2. DELLA PROTEINS IN PLANTS 1 1.2.1. DELLA loci in dicots and monocots 1 1.2.2. Conserved DELLA domains 3 1.2.3. DELLA protein characterisation 4 1.2.4. Regulation of DELLA protein levels 5 1.2.5. DELLA protein function 7 1.2.6. Role of DELLAs in response to plant stress 8 1.3. GROUP IV RHT-1 LOCI AND DWARFING ALLELES IN WHEAT 10 1.3.1. Rht-1 loci 10 1.3.2. Rht-B1b and Rht-D1b 11 1.3.3. Alternative Rht-B1 dwarfing alleles 13 1.3.4. Alternative Rht-D1 dwarfing alleles 14 1.4. ADDITIONAL RHT LOCI AFFECTING PLANT HEIGHT IN WHEAT 15 1.5. Physiological effects of Rht-B1b and Rht-D1b 17 1.5.1. Rht-B1b and Rht-D1b effects on wheat morphology and yield 17 1.5.2. Rht-B1b and Rht-D1b effects on wheat abiotic stress performance 18 1.5.3. Rht-B1b and Rht-D1b associations with Fusarium Head Blight 19 1.6. EVOLUTIONARY HISTORY AND GENETIC DIVERSITY OF WHEAT AND POACEAE SPECIES 21 1.7. Origin and distribution of Rht-B1b and Rht-D1b 25 1.7.1. Origin and spread of ‘Norin 10’ 25 1.7.2. Alternative sources of Rht-B1b and Rht-D1b 26 1.7.3. Rht-B1b and Rht-D1b prevalence in the world 27 1.8. LINKAGE DISEQUILIBRIUM AND SELECTIVE SWEEPS IN PLANTS 29 1.9. PHD OBJECTIVES 30 2. IDENTIFICATION AND CHARACTERISATION OF BAC CLONES CONTAINING RHT-1 32 2.1. INTRODUCTION 32 2.2. MATERIALS AND METHODS 33 2.2.1. The Triticum aestivum (cv Chinese Spring) BAC library 33 2.2.2. Screening of the French component of the CS BAC library by radioactive hybridization 34 2.2.2.1. Screening strategy and probe construction 34 2.2.2.2. Screening of BAC library filters using radioactive probes 36 2.2.2.3. Extraction of plasmid DNA 37 2.2.2.4. Gel analysis of BAC clones 37 2.2.2.5. PCR amplification and sequencing of Rht-1 38 2.2.3. Screening of the UK component of the CS BAC library by PCR 39 2.3. RESULTS 41 2.3.1. Identification and characterisation of Rht-1-containing BAC clones from the French component of the CS library 41 2.3.2. Identification and characterisation of Rht-1-containing BAC clones from the UK component of the CS library 47 iv 2.3.3. Summary of Rht-1-containing BAC clones identified in the French and UK components of the CS library 53 2.4. DISCUSSION 54 3. GENETIC COMPOSITION AND COMPARATIVE ANALYSIS OF THE RHT-1 LOCI AND ADJOINING SEQUENCE 56 3.1. INTRODUCTION 56 3.2. MATERIALS AND METHODS 58 3.2.1. Sequencing of Rht-1-containing BAC clones 58 3.2.2. Annotation of the five Rht-1 containing wheat BAC sequences 58 3.2.3. Comparative analysis of BAC sequences 59 3.3. RESULTS 61 3.3.1. Genetic composition and comparative analysis of the Rht-1 containing wheat BACs 61 3.3.2. Comparative analyses of Rht-1 and the surrounding region in wheat and Poaceae 67 3.3.2.1. Comparative analysis of the Rht-1 ORF in wheat and Poaceae 69 3.3.2.2. Comparative analysis of the Rht-1 flanking region (10 kb 5’ and 10kb 3’) in wheat and Poaceae 74 3.3.2.3. Comparative analysis of ZnF in wheat and Poaceae 79 3.3.2.4. Comparative analysis of DUF6 among wheat BACs and Poaceae 84 3.3.3. Predicted genes on the CS wheat BAC sequences 90 3.4. DISCUSSION 90 4. PHYSICAL AND GENETIC MAPPING OF RHT-A1 97 4.1. INTRODUCTION 97 4.2. MATERIALS AND METHODS 100 4.2.1. Plant Materials 100 4.2.2. DNA extraction 102 4.2.3. PCR amplification 103 4.2.4. SSR linkage mapping 104 4.3. RESULTS 104 4.3.1 Physical mapping of Rht-1 loci using aneuploid lines 104 4.3.2 Rht-A1 mapping in the ‘SS7010073 × Paragon’ F5 population 108 4.4. DISCUSSION 113 5. GENETIC DIVERSITY AT THE RHT-1 LOCI IN WHEAT 117 5.1. INTRODUCTION 117 5.2. MATERIALS AND METHODS 119 5.2.1. Sources of accessions used for sequencing the Rht-1 region 119 5.2.2. Diversity sets 122 5.2.2.1. Bread Wheat 1 (BW1) set: Accessions and experimental design 122 5.2.2.2. Bread Wheat 2 (BW2) set: Accessions and experimental design 122 5.2.2.3. Tetraploid/Diploid Wheat (TDW) set: Accessions and experimental design 123 5.2.3. Rht-B1a/Rht-B1b and Rht-D1a/Rht-D1b PCR assays 124 5.2.4. PCR amplification and sequencing of Rht-1 and the flanking region 125 5.2.5. Assembly of Rht-1 contigs and bioinformatic analyses 127 5.2.6. Rht-1 Transcript analysis 128 v 5.3. RESULTS 130 5.3.1. PCR amplification and sequencing 130 5.3.2. Genetic diversity of the Rht-1+flank region of the BW1 set 132 5.3.2.1.
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