title: Single nucleotide polymorphisms in a cellulose synthase gene (PtoCesA3) are associated with growth and wood properties in Populus tomentosa.
abstract: In plants, the composition and organization of the cell wall determine cell shape, enable cell expansion, and affect the properties of woody tissues. Cellulose synthase (CesA) genes encode the enzymes involved in the synthesis of cellulose which is the major component of plant primary and secondary cell walls. Here, we isolated a full-length PtoCesA3 cDNA from the stem cambium tissue of Populus tomentosa. Tissue-specific expression profiling showed that PtoCesA3 is highly expressed during primary cell wall formation. Estimation of single nucleotide polymorphism (SNP) diversity and linkage disequilibrium (LD) revealed that PtoCesA3 harbors high SNP diversity (π(T) = 0.00995 and θ(w) = 0.0102) and low LD (r(2) ≥ 0.1, within 1,280 bp). Association analysis in a P. tomentosa association population (460 individuals) showed that seven SNPs (false discovery rate Q < 0.10) and five haplotypes (Q < 0.10) were significantly associated with growth and wood properties, explaining 4.09-7.02% of the phenotypic variance. All significant marker-trait associations were validated in at least one of the three smaller subsets (climatic regions) while five associations were repeated in the linkage population. Variation in RNA transcript abundance among genotypic classes of significant loci was also confirmed in the association or linkage populations. Identification of PtoCesA3 and examining its allelic polymorphisms using association studies open an avenue to understand the mechanism of cellulose synthesis in the primary cell wall and its effects on the properties of woody tissues.
authors.affiliation: National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, People's Republic of China.
authors.forename: Baohua
authors.initials: B
authors.lastname: Xu
authors.forename: Jiaxing
authors.initials: J
authors.lastname: Tian
authors.forename: Qingzhang
authors.initials: Q
authors.lastname: Du
authors.forename: Chenrui
authors.initials: C
authors.lastname: Gong
authors.forename: Wei
authors.initials: W
authors.lastname: Pan
authors.forename: Deqiang
authors.initials: D
authors.lastname: Zhang
mesh_terms: D020869:Gene Expression Profiling; D015971:Gene Expression Regulation, Enzymologic; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D056726:Genetic Association Studies; D056426:Genetic Loci; D005819:Genetic Markers; D005964:Glucosyltransferases / Q000737:chemistry / Q000235:genetics*; D006239:Haplotypes / Q000235:genetics; D015810:Linkage Disequilibrium / Q000235:genetics; D008969:Molecular Sequence Data; D009711:Nucleotides / Q000235:genetics; D009928:Organ Specificity / Q000235:genetics; D010641:Phenotype; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D032107:Populus / Q000201:enzymology* / Q000235:genetics* / Q000254:growth & development; D019655:Quantitative Trait, Heritable; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D014934:Wood / Q000201:enzymology / Q000235:genetics* / Q000254:growth & development*
chemical_list: D005819:Genetic Markers; D009711:Nucleotides; D012333:RNA, Messenger; D005964:Glucosyltransferases; C478648:cellulose synthase