Natural variation in expression of genes involved in xylem development in loblolly pine (Pinus taeda L.)

Abstract

Gene expression analyses using native populations can contribute to the understanding of plant development and adaptation in multiple ways. These include the identification of candidate genes and genetic polymorphisms affecting expression and phenotypic traits and characterization of transcriptional networks. We analyzed the expression of 111 genes with probable roles in xylem/wood development in a population of loblolly pine (Pinus taeda L.) covering much of the natural range. Loblolly pine is one of the most commercially important forest tree species in the United States, and the discovery of genes and alleles contributing to desirable wood properties would be valuable. Of the 111 genes analyzed using quantitative reverse transcriptionpolymerase chain reaction, there were significant differences in gene expression between clones for 106 genes.Genes encoding lignin biosynthetic enzymes and arabinogalactan proteins were more variable than those encoding cellulose synthases or those involved in signal transduction. Several groups of genes with related functions form clusters. A network analysis identified transcription factors that may be key regulators of xylem development in pine. Secondary wall-associated NAC domain protein 1 (SND1) in particular appears to be involved in the regulation of many other genes. The cluster analysis using clones did not result in discrete populations but did identify some expression differences between regions. In the future, the gene expression data will be used for association analyses and promoter studies to understand how these gene expression differences are associated with specific genetic polymorphisms in other genes and promoters.

Expression of three phenylpropanoid pathway genes in Scots pine (Pinus sylvestris L.) in open-pollinated families with differing relative wood densities during early and late wood formation

“…It is possible that elevated PAL1 activity provides more substrate for CCR, and therefore the expression of the CCR gene increases. Correlation between expression levels of PAL and CCR was found in other studies as well (PALLE et al, 2010). A positive correlation was also found between PAL1 expression and wood density.…”

“…The expression of candidate genes related to xylem development has been studied in 400 unrelated loblolly pine clones, where significant variation was found for 106 of the 111 genes examined. The gene expression differences between high and low expressing clones ranged from 4.3 to 362 fold (average 20.8) (PALLE et al, 2010). The results from this study also exhibit a large variation in gene expression between individuals, with the PAL1 gene showing the largest expression differences between low and high expressing individuals, followed by CCR and then CAD.…”

“…Correlations that can be established between individuals from different families with such large natural variation must be taken in consideration as important clues for understanding wood formation related molecular processes within trees. PALLE et al (2010) found large differences in gene expression between P. taeda clones for lignin biosynthesis genes (11-27 fold differences) and found that there was greater variation between clones in gene expression for lignin biosynthesis genes than for genes involved in cellulose biosynthesis. Results from this study also found a large amount of variation between individuals, while also detecting significant differences in mean values of gene expression between groups of individuals with high and low wood density, and between early wood and late wood formation time points.…”

“…Gene expression patterns have been studied in many organisms in response to a wide range of conditions and treatments, and gene expression differences are important for phenotypic variation within species. Gene expression levels can vary between cell types within a single plant and also between individuals (PALLE et al, 2010). Expression of specific candidate genes has been studied as well as a more general profiling of expression using sequencing, microarrays and other techniques.…”

Combining Genotype, Phenotype, and Environment to Infer Potential Candidate Genes

“…Authors of several studies collected the phenotypic trait data. First, Palle et al (2011) mapped the expression of 111 genes involved in the production of lignin, which has important consequences for tree growth and survival (Palle et al 2011) for 246 trees (87% of the trees in the SNP dataset; between 1 and 10 per county). We used these gene expression data, along with the SNP genotypic data for the same individual trees, in our study as a first dataset (referred to as EXP for ease of reference).…”