Functional genomics and cell wall biosynthesis in loblolly pine

Abstract

Loblolly pine (Pinus taeda L.) is the most widely planted tree species in the USA and an important tree in commercial forestry world-wide. The large genome size and long generation time of this species present obstacles to both breeding and molecular genetic analysis. Gene discovery by partial DNA sequence determination of cDNA clones is an effective means of building a knowledge base for molecular investigations of mechanisms governing aspects of pine growth and development, including the commercially relevant properties of secondary cell walls in wood. Microarray experiments utilizing pine cDNA clones can be used to gain additional information about the potential roles of expressed genes in wood formation. Different methods have been used to analyze data from first-generation pine microarrays, with differing degrees of success. Disparities in predictions of differential gene expression between cDNA sequencing experiments and microarray experiments arise from differences in the nature of the respective analyses, but both approaches provide lists of candidate genes which should be further investigated for potential roles in cell wall formation in differentiating pine secondary xylem. Some of these genes seem to be specific to pine, while others also occur in model plants such as Arabidopsis, where they could be more efficiently investigated.

Comparative Mapping in the Pinaceae

“…Total RNA was extracted from linkage analysis because recombination estimators are still valid when distortion is observed at only one locus of a from ‫5ف‬ g of ground tissue following the protocol of Chang et al (1993). Double-stranded cDNA was prepared using the linked pair of loci (Bailey 1961;Ott 1991). ESTP markers were added to the existing segregation data ( Jermstad et al Universal RiboClone cDNA Synthesis System (Promega, Madison, WI), filtered through a Sephacryl S-400 column, ligated 1998) and the linkage analysis was repeated.…”

“…To overcome this problem a computational apspecies, loblolly pine has rich genetic resources, welldeveloped genetic and QTL maps (Sewell et al 1999; proach was used to identify Douglas fir ESTs with high homology, and putative orthology, to ESTPs mapped in Brown et al 2001Brown et al , 2003Temesgen et al 2001), and expressed sequence tag (EST) databases (Allona et al loblolly pine. A similar approach was used in recent comparative mapping studies between tomato, potato, 1998; Whetten et al 2001;Kirst et al 2003). Douglas fir (Pseudotsuga menziesii [Mirb.]…”

Microarray Analyses of Gene Expression during Adventitious Root Development in Pinus contorta

“…Currently, Pinus taeda is the only conifer species for which extensive sequence information is available (http://pine.ccgb.umn.edu). Microarray analysis has previously been used for identifying genes involved in cell wall biosynthesis during xylogenesis in P. taeda (Whetten et al, 2001). Recently, we showed that arrays from P. taeda can be used for studying gene expression in Picea abies and Pinus sylvestris (van Zyl et al, 2002a(van Zyl et al, , 2002bStasolla et al, 2003).…”

Oxidative stress proteins as an indicator of a low quality of eucalyptus clones for the pulp and paper industry

“…There has been extensive research on genes expressed in wood, identifying key genes in the process of xylogenesis (such as the myb transcription factor, phenylalanine ammonia lyase, glycine hydroxymethyltransferase) and contributing to building an accessible database of genes involved in the genetic control of the properties of wood, including metabolic routes (Whetten et al, 2001). However, the process of wood formation is still not well characterized.…”