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Genetic Diversity in Puroindolines and Grain Softness Proteins in Australian and Overseas Wheat Germplasm and Implications for Grain Texture

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Genetic Diversity in Puroindolines and Grain Softness Proteins in Australian and Overseas Wheat Germplasm and Implications for Grain Texture Genetic Diversity in Puroindolines and Grain Softness Proteins in Australian and Overseas Wheat Germplasm and Implications for Grain Texture Paul Anthony Pickering BAppSci (Hon) Submitted in fulfilment of the degree of Doctor of Philosophy May 2012 Department of Life and Social Sciences Swinburne University Abstract This thesis is focussed on the genes relating to grain texture or hardness, in the hexaploid wheat species Triticum aestivum. Grain hardness is one of the most important factors that determines the end-use quality and volumes and commercial value of the world trade of wheat. Typically, hard wheat is used for breads, while soft wheat is used for cakes and pastries. While mutations in the two puroindoline genes (Pina-D1 and Pinb-D1) have been associated with grain hardness, currently there is insufficient understanding regarding genetic factors associated with grain texture. The puroindolines are considered to be key genes that determine grain texture, the ‘soft’ texture being wild-type, and hard texture being determined by diverse types mutations in either puroindoline gene deletion or a number of separate point mutations in Pinb- D1. Information on Australian wheats is particularly scanty, with only a handful of varieties having been analysed. This study focussed on Australia’s leading commercial wheat varieties, and addressed the nature of puroindoline mutations in hard wheats. This was achieved using various techniques including amplification of full-length Pina- D1 and Pinb-D1 genes, Cleaved Amplified Polymorphic Sequences (CAPS) analysis of the Pinb-D1 gene, and sequencing of the Pin gene PCR amplification products. The results demonstrate that the Australian hard wheat stocks have only the hardness mutations Pina-D1b or Pinb-D1b, and do not have any other mutations, either singly or in combination. The results show that the Australian hard wheat germplasm offers only limited genetic variability at the Ha loci, with only the two most commonly distributed types of hardness alleles, Pina-D1b and Pinb-D1b. This is most likely due to the shared parental lines shown to be in the pedigree stocks of the majority of the Australian cultivars. The second focus of this work was the assessment of the variability in the puroindoline genes from landrace accessions from countries of early wheat cultivation. Four puroindoline genotypes of known relation to grain hardness were observed in the wheat landrace accessions, including alleles not seen in the Australian hard wheat germplasm. The variety of puroindoline alleles found demonstrates the genetic diversity of landraces, which offer a potential genetic source for invigorating the Australian wheat breeding program with new germplasm to cope with future market demands. Novel variation in the Pin genes was also assessed in the polyploid Triticeae species T. timopheevii and T. zhukovskyi. Puroindoline-a was successfully isolated from accessions of both polyploid species, yet both failed to amplify a PCR product for Puroindoline-b. Null Pina/Pinb haplotypes were also found in both species, and one accession of the T. timopheevii was shown to possess both genes. As found in bread wheat (T. aestivum) and the durum wheats (T. turgidum), it appears that the Ha locus has undergone significant deletions in this lineage of polyploid wheat. The assessment of the genetic variability of the Gsp-1 gene, including copy number and sequence diversity, and potential for influence on grain texture in bread wheat was the focus of the third results component of the thesis. The results showed evidence that a diversity of Gsp-1 haplotypes was to be found in both hard wheats and soft. In total, from three accessions including two hard and one soft wheat, thirty-one distinct haplotypes were identified leading to twenty-five unique deduced mature GSP-1 proteins This suggests significant duplication and rearrangement has been undergone by Gsp-1 in the course of its evolution, producing a multigene family. With genetic factors other than puroindolines known to account for minor differences in grain texture, it may be that the variation of Gsp-1 haplotypes in differing accessions, as observed in this study, may explain the minor differences found in bread wheat lines of identical puroindoline genotype. This investigation has resulted in the identification of: the limited puroindoline diversity present in the Australian hard wheat germplasm; the potential variation and diversity of the puroindoline genes in overseas landraces and the polyploid wheats T. timopheevii and T. zhukovskyi; the diverse variation in sequence and gene copy number of the Gsp-1 genes which have potential for a similar structure and roll as the grain hardness related puroindolines genes. Statement of Originality I hereby declare to the best of my knowledge, this thesis contains no material previously published or written by another person, except where due reference is made in the text of this thesis. I also declare that the material has not been submitted, either in whole or in part, for any degree at this or any other university. ................................................. Paul A. Pickering Acknowledgements I would like to thank my supervisor Professor Mrinal Bhave, for her endless encouragement, patience and support throughout my entire PhD, and for her valuable knowledge, feedback and advice. Mrinal, you have been a fantastic mentor, and I am grateful for everything that you’ve done for me. I will continue to utilize the knowledge that you have instilled in me throughout the rest of my career. I was also fortunate enough to have Associate Professor Enzo Palombo as my co-supervisor for whom I thank for his encouragement and assistance. I would like to acknowledge the people who have helped me throughout my PhD, Chris Key and Soula Mougos not only for their ongoing technical advice but also for their moral support. Thank you also to Dr Greg Grimes and Dr Robyn McLean for seed samples were kindly supplying the seed samples used in this study. I appreciate the financial support from the GRS scholarship through Grains Research and Development Corporation (GRDC). Finally a special thank you to my mother and family, Donna and friends, for their constant support and encouragement throughout my PhD. Table of Contents CHAPTER 1. INTRODUCTION AND LITERATURE REVIEW ....... 1! 1.1 Importance of Bread Wheat ...................................................................................... 1! 1.2 Anatomy of the Wheat Grain ..................................................................................... 2! 1.3 Evolution of the Genome of Bread Wheat (Triticum aestivum L.) ............................ 3! 1.4 Classification of Wheat .............................................................................................. 5! 1.5 Grain Hardness and the Discovery of Friabilin or Grain Softness Protein (GSP) ..... 6! 1.5.1 Impact of hard and soft wheat textures on flour and food tech properties ........... 7! 1.5.2 Identification of the biochemical marker for texture ........................................... 8! 1.6 The Ha Locus and Puroindoline Genes ...................................................................... 9! 1.7 Biochemical Properties of Puroindoline Proteins and Relevance to Grain Texture 10! 1.8 Antimicrobial Properties of Puroindoline Proteins .................................................. 12! 1.9 Grain Softness Protein-1, a Third Component of Friabilin ...................................... 13! 1.10 Organisation of Pina-D1, Pinb-D1 and Gsp-1 Genes at the Ha Locus ................ 15! 1.11 Mutations in Puroindolines affect Kernel Texture ................................................ 17! 1.12 Grain Hardness Studies in Australia ..................................................................... 24! 1.13 Puroindoline Genes in Tetraploid and Diploid Wheat Species ............................. 25! 1.14 Puroindoline Promoters ......................................................................................... 26! 1.15 Measuring Grain Hardness .................................................................................... 27! 1.16 Other Factors Influencing Grain Hardness ........................................................... 28! 1.17 Wheat Landrace Accessions: A Further Source of Genetic Diversity .................. 30! 1.18 Aims of the Project ................................................................................................ 32! CHAPTER 2. MATERIALS AND METHODS .................................... 33! 2.1 Chemicals, Molecular Biological Reagents and Kits ............................................... 33! 2.1.1 Commercially Available Kits and Reagents .................................................... 33! 2.1.2 Molecular Biological Reagents and Solutions .................................................. 34! 2.1.3 Enzymes ............................................................................................................ 35! i 2.2 Plant Materials and Genomic DNA Extractions ...................................................... 35! 2.2.1 Selection of Wheat Accessions ......................................................................... 35! 2.2.2 Growth of Plants ............................................................................................... 39! 2.3 Molecular Methods .................................................................................................. 40! 2.3.1 Isolation of Genomic DNA ..............................................................................
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