Transcription regulation and plant diversity

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 pseudo-backcross 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. (Abstract shortened by UMI.)...