Polyploid genome evolution : a thesis presented in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Plant Biology, Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand

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Genome duplication is a major force influencing plant genome evolution. Many plant species have shown multiple rounds of whole genome duplications in the past. Duplicated genes show variable rate of retention, silencing, subfunctionalization and neofunctionalization which are pronounced outcomes of genome duplication. This thesis addresses polyploid genome evolution focusing on the genetic and epigenetic consequences of genome duplication. Tragopogon dubius, T. pratensis and T. porrifolius (diploid progenitors) and their polyploids T. miscellus and T. mirus were employed as an ideal system to examine the outcomes of polyploidy. An investigation of cytonuclear coordination in T. miscellus polyploids showed a maternal influence which was evident from the biased retention and expression of the maternally inherited homeolog of rbcS possibly to facilitate its interaction with the maternally derived rbcL in independently formed T. miscellus natural polyploids. The second study involved the genetic characterization of synthetic T. miscellus and T. mirus polyploids in the context of their relationship with each other. Results showed the presence of the same multilocus genotypes reported previously in natural T. miscellus and T. mirus and also suggested that there are certain genetic rules to the formation of polyploids; that is, only some progenitor genotypes are successful in producing polyploids. In the third study, a comparative transcriptome analysis of the reciprocally formed synthetic and natural T. miscellus polyploids was conducted. This study demonstrated additivity in the expression of progenitor orthologs of floral identity genes in reciprocally formed T. miscellus polyploids, suggesting other genetic factors are responsible for the differing inflorescence and flora morphologies in T. miscellus. The fourth study explored the epigenetic consequences of polyploidy. The DNA methylation status of homeologous loci previously reported to be silenced in T. miscellus natural polyploids was investigated. This study revealed silencing of two out of five homeologous loci by DNA methylation, suggesting other mechanisms may be responsible for silencing of the remaining three homeologous loci. In short, collectively these studies significantly contribute to our knowledge of polyploid genome evolution in Tragopogon in particular and in plants in general.
Genome evolution, Tragopogon miscellus, Genome duplication, Polyploids, Evolutionary genetics, Gene silencing