Polymorphisms in cinnamoyl CoA reductase (CCR) are associated with variation in microfibril angle in Eucalyptus spp

Abstract

Linkage disequilibrium (LD) mapping using natural populations results in higher resolution of marker-trait associations compared to family-based quantitative trait locus (QTL) studies. Depending on the extent of LD, it is possible to identify alleles within candidate genes associated with a trait. Analysis of a natural mutant in Arabidopsis has shown that mutations in cinnamoyl CoA reductase (CCR), a key lignin gene, affect physical properties of the secondary cell wall such as stiffness and strength. Using this gene, we tested whether LD mapping could identify alleles associated with microfibril angle (MFA), a wood quality trait affecting stiffness and strength of wood. We identified 25 common single-nucleotide polymorphism (SNP) markers in the CCR gene in Eucalyptus nitens. Using single-marker and haplotype analyses in 290 trees from a E. nitens natural population, two haplotypes significantly associated with MFA were found. These results were confirmed in two full-sib families of E. nitens and Eucalyptus globulus. In an effort to understand the functional significance of the SNP markers, we sequenced the cDNA clones and identified an alternatively spliced variant from the significant haplotype region. This study demonstrates that LD mapping can be used to identify alleles associated with wood quality traits in natural populations of trees.

Figure 1.

Pairwise linkage disequilibrium (r²) between the SNP markers.

Figure 2.

Expression of CCR. (A) Schematic of the CCR gene showing the positions of exons and introns. Exons are shown as boxes and introns as lines. Positions of SNP markers from the significant haplotype region are shown. Alternative splicing is caused by skipping part of exon 4 and all of exon 5. Alternative stop codon in 3′-UTR has been included in the splice variant. (B) Amino acid sequence of the CCR gene. The boxed motif NWYCY (bottom) is conserved in all plant CCR genes and is thought be the catalytic site of the gene. Amino acid sequences (boldface type) are deleted and a new sequence of six amino acids is added to the splice variant. “*SNP 120” is from the E. globulus full-sib family.