Natural variation in the serially duplicated Production of Anthocyanin Pigment loci and anthocyanin accumulation in Arabidopsis thaliana (Brassicaceae) : a thesis presented in partial fulfilment of the requirements for the degree of Masters of Science in Plant Biology at Massey University, Palmerston North, New Zealand

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The TTG1-regulatory gene network regulates the development of all epidermal cell fates in Arabidopsis thaliana. Four members of the TTG1 complex, the serially duplicated R2R3-MYB PRODUCTION OF ANTHOCYANIN PIGMENT (PAP) genes, have previously been implicated in regulating the late stages of anthocyanin bionsynthesis in Arabidopsis thaliana. To study the effects of gene duplication, we sought to determine the extent of variation in each PAP gene compared to a single copy gene of the TTG1 network, WEREWOLF, using 48 naturally occurring A. thaliana accessions. It appears that the predominantly expressed PAP1 gene demonstrates a biallelic pattern, consistent with other A. thaliana genes. All four genes fall below the average nucleotide diversity levels observed across A. thaliana; however, WEREWOLF demonstrates almost complete sequence conservation across the 48 accessions used in this study. We attempted to determine the relative ages of the four PAP genes, though this does not appear to correlate with accumulation of genetic variation. To investigate the genetic architecture of anthocyanin accumulation in A. thaliana, we performed an heritability and quantitative trait loci mapping analysis using a recombinant inbred line population derived from 19 natural A. thaliana accessions. While QTL were mapped for anthocyanin accumulation near several of the PAP genes, we observed a number of loci with no obvious candidate genes, providing novel insights into the genetic architecture of anthocyanin accumulation in A. thaliana. This work contributes to a greater understanding of the roles of regulatory genes in biosynthesis and the molecular basis of regulation as well as the effects of gene duplication on nucleotide variation in the resulting genes.
Arabidopsis thaliana, Genetics, Anthocyanins