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Transcription regulation and plant diversity

by 1973- Kirst, Matias

Abstract (Summary)
KIRST, MATIAS. Transcription Regulation and Plant Diversity. (Under the supervision of Dr. Ronald R. Sederoff.) Comparative genomics of yeast, nematodes, flies and humans demonstrate that the developmental, morphological and behavioral diversity of multicellular eukaryotes evolved primarily from differential regulation of a similar core set of genes. In the first part of this study, a comparative analysis of the functional genome of higher plants was carried out by analyzing the gene sequence similarity from the angiosperm Arabidopsis thaliana to a unigene set derived from 59,797 expressed sequence tags (ESTs) from wood-forming tissues of the coniferous Pinus taeda L. (loblolly pine). Both species last shared a common ancestor 300 million years ago and differ greatly in morphology, life-span and genome size. A detailed analysis of long, high-quality sequence contigs, generated by clustering the loblolly pine ESTs, demonstrated that over 90% have an apparent Arabidopsis homolog (E-value < 10-10). Substantial conservation of gene sequence in seed plants suggests that morphological and developmental diversity arose by differential regulation of expression of a common core set of genes, rather than acquisition or creation of new ones. Evolution of the genetic regulation of gene expression can be studied on a genome-wide scale using microarrays to analyze the genetic architecture of transcript variation in different genetic backgrounds. Gene expression variation was studied in the genus Eucalyptus by microarray analysis of mRNA abundance in the differentiating xylem of a E. grandis pseudobackcross population (F1 hybrid [E. grandis x E. globulus] x E. grandis). Relative estimates of transcript levels were generated for 2608 genes in 91 individuals of the progeny and mapped as gene expression QTLs (eQTLs) in two single-tree genetic maps. The F1 hybrid paternal map describes the effects of the E. globulus and E. grandis alleles in the backcross population and the E. grandis map describes the effect of the pure species. eQTLs were identified for 1067 genes in both maps and typically displayed a simple genetic architecture. eQTLs for functionally related genes frequently clustered in the same genomic regions, suggesting trans-regulation by common transcription regulators. For 195 genes, eQTLs could be mapped to both single-tree maps but did not typically localize to homologous linkage groups, indicating that variation of transcript regulation occurs normally in trans-, with low conservation of points of regulation in different genetic backgrounds. E. grandis and E. globulus have contrasting wood properties and growth. Crosses between the two species have resulted in wide genetic and phenotypic segregation and are useful to study the genetic architecture of quantitative variation in wood quality and growth traits. Phenotypic and genotypic data collected from the segregating progeny of the E. grandis pseudobackcross population were integrated with transcript level (microarray) information, collected in the differentiating xylem, to identify genes associated with variation in diameter and wood density. Candidate genes were identified by detecting differential transcript abundance between individuals inheriting alternative QTL genotypes for the phenotypic traits. Genes differentially expressed, in this case, are a representation of the effect of genotypic variation at the phenotypic trait QTL region on gene expression. Candidate genes were confirmed by the analysis of correlation between gene expression and phenotypic variation. This allowed the identification of one candidate gene whose transcript level explains ΒΌ of the variation in wood density and several genes of the phenylpropanoid and associated methylation pathways that explain ? of the growth variation. For wood density and growth, transcript abundance of the candidate genes describe a substantially higher proportion of the phenotypic variation than the trait QTL itself.
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School:North Carolina State University

School Location:USA - North Carolina

Source Type:Master's Thesis

Keywords:north carolina state university

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