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Single-nucleotide polymorphisms in the 5′ UTR of UDP-glucose dehydrogenase (PtUGDH) associate with wood properties in Populus tomentosa

Tian, Jiaxing, Du, Qingzhang, Li, Bailian, Zhang, Deqiang
Tree genetics & genomes 2014 v.10 no.2 pp. 339-354
Populus tomentosa, amino acids, cell walls, complementary DNA, forest trees, gene expression, gene frequency, genes, genetic markers, haplotypes, leaves, linkage disequilibrium, loci, marker-assisted selection, phenotypic variation, quantitative traits, single nucleotide polymorphism, wood properties, wood quality, xylem
Association studies have emerged as a powerful tool for identification of markers associated with quantitative traits in forest trees. The cytosolic enzyme uridine 5′ diphosphate-glucose dehydrogenase (UGDH) converts UDP-glucose to UDP-glucuronate and affects cell wall formation in higher plants. Here, we used association genetics to identify UDP-glucose dehydrogenase (PtUGDH) allelic variation that associates with wood quality traits in Populus tomentosa. We isolated a 1,828 bp PtUGDH cDNA encoding a polypeptide of 481 amino acids. Expression analysis revealed that PtUGDH was expressed predominantly in young root, developing xylem from vascular tissues, and young leaves, suggesting that UGDH functions in cell wall formation. We identified 59 single-nucleotide polymorphisms (SNPs; π T = 0.00475) by resequencing the PtUGDH locus of 40 individuals and genotyped the 22 most common SNPs (minor allele frequency >10 %) in a discovery population (n = 426). Linkage disequilibrium (LD) analysis showed that LD did not extend over the entire gene (r² < 0.1, within 300 bp). Association studies indicated that three SNPs (false discovery rate, Q < 0.05) and 12 haplotypes (Q < 0.05) were significantly associated with wood properties. The three significant SNPs are all in the 5′ untranslated regions of PtUGDH, and the phenotypic variance explained by each SNP ranged from 5.37 to 11.97 %. We validated one association in a validation population (n = 1,200) and validated another association by examining its effect on gene expression. The present study provided molecular markers associated with fiber length and holocellulose content, markers that have potential applications in marker-assisted breeding.