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Allelic variation in a cellulose synthase gene (PtoCesA4) associated with growth and wood properties in Populus tomentosa.

Du Q, Xu B, Pan W, Gong C, Wang Q, Tian J, Li B, Zhang D - G3 (Bethesda) (2013)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, People's Republic of China.

ABSTRACT
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.

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PtoCesA4 gene structure and the positions of common SNPs (minor allele frequencies > 0.10). All common SNPs are represented by dark spots; putative transcription factor binding sites around SNPs in the PtoCesA4 promoter were predicted and numbers above the promoter region indicate the positions of putative transcription factor binding sites in base pairs relative to the predicted transcription start site. (A) Zinc-binding domain. (B–I) Two transmembrane helices in the N-terminal region and six in the C-terminal region.
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fig1: PtoCesA4 gene structure and the positions of common SNPs (minor allele frequencies > 0.10). All common SNPs are represented by dark spots; putative transcription factor binding sites around SNPs in the PtoCesA4 promoter were predicted and numbers above the promoter region indicate the positions of putative transcription factor binding sites in base pairs relative to the predicted transcription start site. (A) Zinc-binding domain. (B–I) Two transmembrane helices in the N-terminal region and six in the C-terminal region.

Mentions: We used reverse-transcription PCR to isolate a full-length cDNA of PtoCesA4 from a cDNA library prepared from the developing xylem zone of P. tomentosa. The cDNA clone PtoCesA4 (GenBank Accession no. KC762292) is 3757 bp in length, and the open reading frame (3129 bp) encodes a polypeptide of 1042 amino acids with an estimated molecular mass of 118.4 kD and a pI of 7.60, flanked by 297 bp of 5′untranslated leader region (5′UTR) and 331 bp of 3′UTR (Figure 1). Nucleotide sequence comparison of PtoCesA4 cDNAs with known full-length Arabidopsis CesA cDNA sequences revealed that PtoCesA4 is a member of the CesA gene family because it contains all of the conserved features (Holland et al. 2000; Chen et al. 2010), such as a putative zinc-binding domain (at amino acid residues 31–76), two transmembrane helices (at residues 217–238 and 250–267) in the N-terminal region, and six transmembrane helices in the C-terminal region (Figure 1).


Allelic variation in a cellulose synthase gene (PtoCesA4) associated with growth and wood properties in Populus tomentosa.

Du Q, Xu B, Pan W, Gong C, Wang Q, Tian J, Li B, Zhang D - G3 (Bethesda) (2013)

PtoCesA4 gene structure and the positions of common SNPs (minor allele frequencies > 0.10). All common SNPs are represented by dark spots; putative transcription factor binding sites around SNPs in the PtoCesA4 promoter were predicted and numbers above the promoter region indicate the positions of putative transcription factor binding sites in base pairs relative to the predicted transcription start site. (A) Zinc-binding domain. (B–I) Two transmembrane helices in the N-terminal region and six in the C-terminal region.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3815066&req=5

fig1: PtoCesA4 gene structure and the positions of common SNPs (minor allele frequencies > 0.10). All common SNPs are represented by dark spots; putative transcription factor binding sites around SNPs in the PtoCesA4 promoter were predicted and numbers above the promoter region indicate the positions of putative transcription factor binding sites in base pairs relative to the predicted transcription start site. (A) Zinc-binding domain. (B–I) Two transmembrane helices in the N-terminal region and six in the C-terminal region.
Mentions: We used reverse-transcription PCR to isolate a full-length cDNA of PtoCesA4 from a cDNA library prepared from the developing xylem zone of P. tomentosa. The cDNA clone PtoCesA4 (GenBank Accession no. KC762292) is 3757 bp in length, and the open reading frame (3129 bp) encodes a polypeptide of 1042 amino acids with an estimated molecular mass of 118.4 kD and a pI of 7.60, flanked by 297 bp of 5′untranslated leader region (5′UTR) and 331 bp of 3′UTR (Figure 1). Nucleotide sequence comparison of PtoCesA4 cDNAs with known full-length Arabidopsis CesA cDNA sequences revealed that PtoCesA4 is a member of the CesA gene family because it contains all of the conserved features (Holland et al. 2000; Chen et al. 2010), such as a putative zinc-binding domain (at amino acid residues 31–76), two transmembrane helices (at residues 217–238 and 250–267) in the N-terminal region, and six transmembrane helices in the C-terminal region (Figure 1).

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, People's Republic of China.

ABSTRACT
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.

Show MeSH
Related in: MedlinePlus