title: Association of allelic variation in PtoXET16A with growth and wood properties in Populus tomentosa.
abstract: Xyloglucan endo-transglycosylases (XETs) modify the xyloglucan-cellulose framework of plant cell walls and, thus, affect cell wall expansion and strength. Dissecting the mechanism by which natural variation in XETs affects wood properties can inform breeding efforts to improve wood quality and yield traits. To this end, we isolated a full-length PtoXET16A cDNA clone from Populus tomentosa. Real-time PCR analysis showed that PtoXET16A was maximally expressed in the root, followed by phloem, cambium, and developing xylem, suggesting that PtoXET16A plays important roles in the development of vascular tissues. Nucleotide diversity and linkage disequilibrium analysis revealed that PtoXET16A has high single nucleotide polymorphism (SNP) diversity (π = 0.01266 and θ(w) = 0.01392) and low linkage disequilibrium (r² ≥ 0.1, within 900 bp). SNP- and haplotype-based association analyses of 426 individuals from a natural population indicated that nine SNPs (including two non-synonymous markers and one splicing variant) (p ≤ 0.05, false discovery rate Q ≤ 0.01), and nine haplotypes (p ≤ 0.05) were significantly associated with growth and wood properties, each explaining from 3.40%-10.95% of phenotypic variance. This work shows that examination of allelic variation and linkage disequilibrium by a candidate-gene-based approach can help to decipher the genetic basis of wood formation. Moreover, the SNP markers identified in this study can potentially be applied for marker-assisted selection to improve growth and wood-property traits in Populus.
authors.affiliation: National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China. 15210908561@yeah.net.
authors.forename: Bowen
authors.initials: B
authors.lastname: Wang
authors.affiliation: National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China. deqiangzhang@bjfu.edu.cn.
authors.forename: Deqiang
authors.initials: D
authors.lastname: Zhang
mesh_terms: D000483:Alleles; D000595:Amino Acid Sequence; D001483:Base Sequence; D020134:Catalytic Domain; D002473:Cell Wall / Q000737:chemistry / Q000648:ultrastructure; D005091:Exons; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D056726:Genetic Association Studies; D014644:Genetic Variation; D005838:Genotype; D016695:Glycosyltransferases / Q000096:biosynthesis / Q000235:genetics*; D006239:Haplotypes / Q000235:genetics; D007438:Introns; D015810:Linkage Disequilibrium; D008969:Molecular Sequence Data; D009928:Organ Specificity; D010802:Phylogeny; D010940:Plant Proteins / Q000096:biosynthesis / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide; D032107:Populus / Q000235:genetics* / Q000254:growth & development; D020033:Protein Isoforms / Q000235:genetics; D014158:Transcription, Genetic; D014934:Wood / Q000166:cytology
chemical_list: D010940:Plant Proteins; D020033:Protein Isoforms; D016695:Glycosyltransferases; C473049:xyloglucan - xyloglucosyltransferase