@article{kirst_basten_myburg_zeng_sederoff_2005, title={Genetic architecture of transcript-level variation in differentiating xylem of a eucalyptus hybrid}, volume={169}, ISSN={["1943-2631"]}, DOI={10.1534/genetics.104.039198}, abstractNote={Abstract
               Species diversity may have evolved by differential regulation of a similar set of genes. To analyze and compare the genetic architecture of transcript regulation in different genetic backgrounds of Eucalyptus, microarrays were used to examine variation in mRNA abundance in the differentiating xylem of a E. grandis pseudobackcross population [E. grandis × F1 hybrid (E. grandis × E. globulus)]. Least-squares mean estimates of transcript levels were generated for 2608 genes in 91 interspecific backcross progeny. The quantitative measurements of variation in transcript abundance for specific genes were mapped as expression QTL (eQTL) in two single-tree genetic linkage maps (F1 hybrid paternal and E. grandis maternal). EQTL were identified for 1067 genes in the two maps, of which 811 were located in the F1 hybrid paternal map, and 451 in the E. grandis maternal map. EQTL for 195 genes mapped to both parental maps, the majority of which localized to nonhomologous linkage groups, suggesting trans-regulation by different loci in the two genetic backgrounds. For 821 genes, a single eQTL that explained up to 70% of the transcript-level variation was identified. Hotspots with colocalized eQTL were identified in both maps and typically contained genes associated with specific metabolic and regulatory pathways, suggesting coordinated genetic regulation.}, number={4}, journal={GENETICS}, author={Kirst, M and Basten, CJ and Myburg, AA and Zeng, ZB and Sederoff, RR}, year={2005}, month={Apr}, pages={2295–2303} }
 @article{kirst_meyer_gibbon_jung_boston_2005, title={Identification and characterization of endoplasmic reticulum-associated degradation proteins differentially affected by endoplasmic reticulum stress}, volume={138}, ISSN={["1532-2548"]}, DOI={10.1104/pp.105.060087}, abstractNote={Abstract
               The disposal of misfolded proteins from the lumen of the endoplasmic reticulum (ER) is one of the quality control mechanisms present in the protein secretory pathway. Through ER-associated degradation, misfolded substrates are targeted to the cytosol where they are degraded by the proteasome. We have identified four maize (Zea mays) Der1-like genes (Zm Derlins) that encode homologs of Der1p, a yeast (Saccharomyces cerevisiae) protein implicated in ER-associated degradation. Zm Derlins are capable of functionally complementing a yeast Der1 deletion mutant. Such complementation indicates that the Der1p function is conserved among species. Zm Derlin genes are expressed at low levels throughout the plant, but appear prevalent in tissues with high activity of secretory protein accumulation, including developing endosperm cells. Expression of three of the four Zm Derlin genes increases during ER stress, with Zm Derlin1-1 showing the strongest induction. Subcellular fractionation experiments localized Zm Derlin proteins to the membrane fraction of microsomes. In maize endosperm, Zm Derlin proteins were found primarily associated with ER-derived protein bodies regardless of the presence of an ER stress response.}, number={1}, journal={PLANT PHYSIOLOGY}, author={Kirst, ME and Meyer, DJ and Gibbon, BC and Jung, R and Boston, RS}, year={2005}, month={May}, pages={218–231} }
 @article{kirst_myburg_de leon_kirst_scott_sederoff_2004, title={Coordinated genetic regulation of growth and lignin revealed by quantitative trait locus analysis of cDNA microarray data in an interspecific backcross of eucalyptus}, volume={135}, ISSN={["1532-2548"]}, DOI={10.1104/pp.103.037960}, abstractNote={AbstractPhenotypic, genotypic, and transcript level (microarray) data from an interspecific backcross population of Eucalyptus grandis and Eucalyptus globulus were integrated to dissect the genetic and metabolic network underlying growth variation. Transcript abundance, measured for 2,608 genes in the differentiating xylem of a 91 (E. grandis × E. globulus) × E. grandis backcross progeny was correlated with diameter variation, revealing coordinated down-regulation of genes encoding enzymes of the lignin biosynthesis and associated methylation pathways in fast growing individuals. Lignin analysis of wood samples confirmed the content and quality predicted by the transcript levels measured on the microarrays. Quantitative trait locus (QTL) analysis of transcript levels of lignin-related genes showed that their mRNA abundance is regulated by two genetic loci, demonstrating coordinated genetic control over lignin biosynthesis. These two loci colocalize with QTLs for growth, suggesting that the same genomic regions are regulating growth, and lignin content and composition in the progeny. Genetic mapping of the lignin genes revealed that most of the key biosynthetic genes do not colocalize with growth and transcript level QTLs, with the exception of the locus encoding the enzyme S-adenosylmethionine synthase. This study illustrates the power of integrating quantitative analysis of gene expression data and genetic map information to discover genetic and metabolic networks regulating complex biological traits.}, number={4}, journal={PLANT PHYSIOLOGY}, author={Kirst, M and Myburg, AA and De Leon, JPG and Kirst, ME and Scott, J and Sederoff, R}, year={2004}, month={Aug}, pages={2368–2378} }
 @article{egertsdotter_zyl_mackay_peter_kirst_clark_whetten_sederoff_2004, title={Gene Expression during Formation of Earlywood and Latewood in Loblolly Pine: Expression Profiles of 350 Genes}, volume={6}, ISSN={1435-8603 1438-8677}, url={http://dx.doi.org/10.1055/s-2004-830383}, DOI={10.1055/s-2004-830383}, abstractNote={Abstract:  The natural variability of wood formation in trees affords opportunities to correlate transcript profiles with the resulting wood properties. We have used cDNA microarrays to study transcript abundance in developing secondary xylem of loblolly pine (Pinus taeda) over a growing season. The cDNAs were selected from a collection of 75 000 ESTs that have been sequenced and annotated (http:web.ahc.umn.edubiodatansfpine). Cell wall thickness and climatic data were related to earlywood and latewood formation at different time points during the growing season. Seventy‐one ESTs showed preferential expression in earlywood or latewood, including 23 genes with no significant similarity to genes in GenBank. Seven genes involved in lignin synthesis were preferentially expressed in latewood. The studies have provided initial insights into the variation of expression patterns of some of the genes related to the wood formation process.}, number={6}, journal={Plant Biology}, publisher={Wiley}, author={Egertsdotter, U. and Zyl, L. M. and MacKay, J. and Peter, G. and Kirst, M. and Clark, C. and Whetten, R. and Sederoff, R.}, year={2004}, month={Nov}, pages={654–663} }