Polymorphic simple sequence repeat (SSR) loci within cellulose synthase (PtoCesA) genes are associated with growth and wood properties in Populus tomentosa

Abstract

SummaryChinese white poplar (Populus tomentosa), an important commercial tree species for timber and pulp production in northern China, has been used to examine the individual genes and allelic diversity responsible for complex traits controlling growth and lignocellulosic biosynthesis. Taking advantage of the low degree of linkage disequilibrium (LD) within P. tomentosa association populations, we examined associations between 15 cellulose synthase (PtoCesA) genes and traits including growth and wood properties.Thirty-six novel simple sequence repeat (SSR) markers within PtoCesA genes were detected by re-sequencing and genotyped in an association population (460 individuals). Single-marker and haplotype-based LD approaches were used to identify significant marker-trait associations. Family-based linkage studies and real-time PCR testing were conducted to validate the functional significance of SSR variation.Fifteen single-marker associations from seven PtoCesA genes and nine haplotype-based associations within six genes were identified in the association population (false discovery rate Q < 0.05). Next, five SSR marker-trait associations (Q < 0.05) from four PtoCesA genes were successfully validated in a linkage mapping population (1200 individuals).The results imply a functional role for these genes in mediating wood properties, demonstrating the potential of combining single-marker and haplotype-based LD approaches to detect functional allelic variation underlying quantitative traits in a low-LD population.

The Interactions between the Long Non-coding RNA NERDL and Its Target Gene Affect Wood Formation in Populus tomentosa

“…Phenotypic data for 10 growth and wood property traits were obtained from the 435 selected individuals in 2011 as previously described (Du et al, 2013b). Trees of this age are in a stable growth and developmental phase and can therefore be used to reflect the natural growth and developmental state of trees.…”

“…Seven wood property traits and three tree growth traits were investigated: LC (lignin content, %), HC (holocellulose content, %), HEMC (hemicellulose content, %), AC (α-cellulose content, %), FL (fiber length, mm), FW (fiber width, μm), Angle (microfibril angle, °), H (tree height, m), D (tree diameter at breast, cm), and V (volume of wood, m 3 ). The correlations of these phenotypic data in the association population were calculated as previously described (Du et al, 2013b). …”

Single nucleotide polymorphisms in a cellulose synthase gene (PtoCesA3) are associated with growth and wood properties in Populus tomentosa

“…Table S1. The details of ANOVA and Pearson's correlation coefficients for these traits have been reported by Tian et al (2012) and Du et al (2013).…”

Association mapping for morphological and physiological traits in Populus simonii

“…It can exploits all the recombination events that have occurred during the history of the population, allowing fine-scale QTL mapping [2-4]. Moreover, it bypasses the expense and shortens the duration of mapping studies by making the crossing cycles in population development unnecessary and enabling the mapping of many traits in one set of genotypes [2,5,6]. A concern about association mapping is that marker-trait associations may arise from confounding population structure, which may cause spurious correlations, leading to an elevated both Type I and II errors between molecular markers and traits of interest.…”