Allelic variation in PtGA20Ox associates with growth and wood properties in Populus spp

Populus tomentosa is an economically important tree crop that produces wood for lumber, pulp, paper, and biofuels. Wood quality traits are likely to be strongly affected by the plant hormone gibberellic acid (GA), which regulates growth. GA20Ox encodes one of the major regulatory enzymes of GA biosynthesis and may therefore play a large role in growth and wood quality. Here, linkage disequilibrium (LD) studies were used to identify significant associations between single nucleotide polymorphisms (SNPs) within PtGA20Ox and growth and wood-quality traits of P. tomentosa. We isolated a full-length GA20Ox cDNA from Populus tomentosa by reverse transcription (RT)-PCR; this 1401 bp cDNA clone had an open reading frame of 1158 bp and encoded a protein of 385 amino acids. PtGA20Ox transcripts were maximally expressed in the mature xylem of vascular tissues, suggesting that PtGA20Ox is highly expressed and specifically associated with secondary xylem formation. Resequencing the PtGA20Ox locus of 36 individuals identified 55 SNPs, and the frequency of SNPs was 1/31 bp. The 29 most common SNPs (frequency>0.1) were genotyped in an association population (426 individuals) that was also phenotyped for key growth and wood quality traits. LD did not extend over the entire gene (r(2)<0.1, within 500 bp), demonstrating that a candidate-gene-based LD approach may the best way to understand the molecular basis underlying quantitative variation in this species. SNP- and haplotype-based association analyses indicated that four SNPs (false discovery rate Q<0.05) and 14 haplotypes (P<0.05) were significantly associated with growth and wood properties. The phenotypic variance explained by each SNP ranged from 3.44% to 14.47%. The SNP markers identified in this study can be applied to breeding programs for the improvement of growth and wood-property traits by marker-assisted selection.