Allelic variation in a cellulose synthase gene (PtoCesA4) associated with growth and wood properties in Populus tomentosa.
Lignocellulosic biomass from trees provides a renewable feedstock for biofuels, lumber, pulp, paper, and other uses. Dissecting the mechanism underlying natural variation of the complex traits controlling growth and lignocellulose biosynthesis in trees can enable marker-assisted breeding to improve wood quality and yield. Here, we combined linkage disequilibrium (LD)-based association analysis with traditional linkage analysis to detect the genetic effect of a Populus tomentosa cellulose synthase gene, PtoCesA4. PtoCesA4 is strongly expressed in developing xylem and leaves. Nucleotide diversity and LD in PtoCesA4, sampled from the P. tomentosa natural distribution, revealed that PtoCesA4 harbors high single nucleotide polymorphism (SNP) diversity (πT = 0.0080 and θw = 0.0098) and low LD (r(2) ≥ 0.1, within 1400 bp), demonstrating that the potential of a candidate-gene-based LD approach in understanding the molecular basis underlying quantitative variation in this species. By combining single SNP, multi-SNP, and haplotype-based associations in an association population of 460 individuals with single SNP linkage analysis in a family-based linkage populations (1200 individuals), we identified three strong associations (false discovery rate Q < 0.05) in both populations. These include two nonsynonymous markers (SNP49 associated with α-cellulose content and SNP59 associated with fiber width) and a noncoding marker (SNP18 associated with α-cellulose content). Variation in RNA transcript abundance among genotypic classes of SNP49 was confirmed in these two populations. Therefore, combining different methods allowed us to examine functional PtoCesA4 allelic variation underlying natural variation in complex quantitative traits related to growth and lignocellulosic biosynthesis.
National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, People's Republic of China.
Qingzhang
Q
Du
Baohua
B
Xu
Wei
W
Pan
Chenrui
C
Gong
Qingshi
Q
Wang
Jiaxing
J
Tian
Bailian
B
Li
Deqiang
D
Zhang
D000483:Alleles; D001483:Base Sequence; D017343:Genes, Plant; D056726:Genetic Association Studies; D056426:Genetic Loci; D014644:Genetic Variation; D005838:Genotype; D005964:Glucosyltransferases / Q000145:classification / Q000235:genetics*; D006239:Haplotypes; D008031:Lignin / Q000096:biosynthesis; D015810:Linkage Disequilibrium; D008969:Molecular Sequence Data; D010641:Phenotype; D010802:Phylogeny; D018515:Plant Leaves / Q000201:enzymology; D010940:Plant Proteins / Q000145:classification / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide; D032107:Populus / Q000235:genetics* / Q000254:growth & development; D014934:Wood / Q000378:metabolism
D010940:Plant Proteins; C036909:lignocellulose; D008031:Lignin; D005964:Glucosyltransferases; C478648:cellulose synthase
Populus tomentosa; RNA transcript analysis; linkage analysis; linkage disequilibrium; multi-locus association models; single nucleotide polymorphism