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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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Genotypic effects of the significant single nucleotide polymorphisms (SNPs) in PtoCesA4 on the same phenotypic trait in association and linkage populations. The marker SNP49 in exon 3 of PtoCesA4, a nonsynonymous mutation, which results in an encoded amino acid change from His to Asn, was significantly associated with α-cellulose content in association and linkage populations. The AA homozygotes were associated with higher α-cellulose values and CC homozygotes were associated with lower α-cellulose values, and mean values in AC heterozygotes were medium in both populations, which are supported by the observation that SNP49 has an additive effect on gene action in cellulose content. The nonsynonymous marker SNP59 in exon 6 of PtoCesA4 significantly associated with fiber width in both populations and shows patterns of gene action consistent with additive effects on fiber width. The A allele at SNP59 causes a Ser-to-Tyr amino acid substitution (d) SNP18 from the promoter of PtoCesA4 and showed significant association with α-cellulose content in both populations. The differences in α-cellulose content among the three genotypes of this marker indicate that patterns of gene action are consistent with overdominance effects. P1 represents the female clone YX01 (Populus alba × Populus glandulosa), P2 represents the male clone LM 50 (Populus tomentosa), and F1 represents the hybrid progeny.
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fig4: Genotypic effects of the significant single nucleotide polymorphisms (SNPs) in PtoCesA4 on the same phenotypic trait in association and linkage populations. The marker SNP49 in exon 3 of PtoCesA4, a nonsynonymous mutation, which results in an encoded amino acid change from His to Asn, was significantly associated with α-cellulose content in association and linkage populations. The AA homozygotes were associated with higher α-cellulose values and CC homozygotes were associated with lower α-cellulose values, and mean values in AC heterozygotes were medium in both populations, which are supported by the observation that SNP49 has an additive effect on gene action in cellulose content. The nonsynonymous marker SNP59 in exon 6 of PtoCesA4 significantly associated with fiber width in both populations and shows patterns of gene action consistent with additive effects on fiber width. The A allele at SNP59 causes a Ser-to-Tyr amino acid substitution (d) SNP18 from the promoter of PtoCesA4 and showed significant association with α-cellulose content in both populations. The differences in α-cellulose content among the three genotypes of this marker indicate that patterns of gene action are consistent with overdominance effects. P1 represents the female clone YX01 (Populus alba × Populus glandulosa), P2 represents the male clone LM 50 (Populus tomentosa), and F1 represents the hybrid progeny.

Mentions: Of these 10 unique SNPs, there were two nonsynonymous, two synonymous, and six noncoding SNPs (Table 3). The nonsynonymous marker SNP49 in exon 3 results in an amino acid change from His to Asn, associated significantly with multiple traits, i.e., α-cellulose (5.3%), lignin (3.0%), and H (2.3%). In this case, the mode of gene action seems additive, with the minor allele (A) conferring a lower lignin content and higher values in α-cellulose and H (Table 3). For the other nonsynonymous marker, SNP59 in exon 6, which has the minor allele (A), results in an amino acid change from Ser to Tyr, associated significantly with fiber width (R2 = 2.6%). The genotypic effects on fiber width were significant (22.38 µm in AA, 23.21 µm for AC, and 23.99 µm for CC), consistent with the additive effect of gene action on fiber width (Table 3 and Figure 4). Also, a synonymous marker SNP45 in exon 2, associated with holocellulose content, showed a difference among three genotypic classes (two significant) (74.62% in AA, 74.55% in AC, and 73.30% in CC), indicating patterns of gene action consistent with dominant effects (Table 3). SNP75 in exon 10, the other synonymous mutation, associated with D and V, explaining 3.2% and 2.6% of the phenotypic variance, respectively (Table 3).


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)

Genotypic effects of the significant single nucleotide polymorphisms (SNPs) in PtoCesA4 on the same phenotypic trait in association and linkage populations. The marker SNP49 in exon 3 of PtoCesA4, a nonsynonymous mutation, which results in an encoded amino acid change from His to Asn, was significantly associated with α-cellulose content in association and linkage populations. The AA homozygotes were associated with higher α-cellulose values and CC homozygotes were associated with lower α-cellulose values, and mean values in AC heterozygotes were medium in both populations, which are supported by the observation that SNP49 has an additive effect on gene action in cellulose content. The nonsynonymous marker SNP59 in exon 6 of PtoCesA4 significantly associated with fiber width in both populations and shows patterns of gene action consistent with additive effects on fiber width. The A allele at SNP59 causes a Ser-to-Tyr amino acid substitution (d) SNP18 from the promoter of PtoCesA4 and showed significant association with α-cellulose content in both populations. The differences in α-cellulose content among the three genotypes of this marker indicate that patterns of gene action are consistent with overdominance effects. P1 represents the female clone YX01 (Populus alba × Populus glandulosa), P2 represents the male clone LM 50 (Populus tomentosa), and F1 represents the hybrid progeny.
© Copyright Policy - open-access
Related In: Results  -  Collection

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fig4: Genotypic effects of the significant single nucleotide polymorphisms (SNPs) in PtoCesA4 on the same phenotypic trait in association and linkage populations. The marker SNP49 in exon 3 of PtoCesA4, a nonsynonymous mutation, which results in an encoded amino acid change from His to Asn, was significantly associated with α-cellulose content in association and linkage populations. The AA homozygotes were associated with higher α-cellulose values and CC homozygotes were associated with lower α-cellulose values, and mean values in AC heterozygotes were medium in both populations, which are supported by the observation that SNP49 has an additive effect on gene action in cellulose content. The nonsynonymous marker SNP59 in exon 6 of PtoCesA4 significantly associated with fiber width in both populations and shows patterns of gene action consistent with additive effects on fiber width. The A allele at SNP59 causes a Ser-to-Tyr amino acid substitution (d) SNP18 from the promoter of PtoCesA4 and showed significant association with α-cellulose content in both populations. The differences in α-cellulose content among the three genotypes of this marker indicate that patterns of gene action are consistent with overdominance effects. P1 represents the female clone YX01 (Populus alba × Populus glandulosa), P2 represents the male clone LM 50 (Populus tomentosa), and F1 represents the hybrid progeny.
Mentions: Of these 10 unique SNPs, there were two nonsynonymous, two synonymous, and six noncoding SNPs (Table 3). The nonsynonymous marker SNP49 in exon 3 results in an amino acid change from His to Asn, associated significantly with multiple traits, i.e., α-cellulose (5.3%), lignin (3.0%), and H (2.3%). In this case, the mode of gene action seems additive, with the minor allele (A) conferring a lower lignin content and higher values in α-cellulose and H (Table 3). For the other nonsynonymous marker, SNP59 in exon 6, which has the minor allele (A), results in an amino acid change from Ser to Tyr, associated significantly with fiber width (R2 = 2.6%). The genotypic effects on fiber width were significant (22.38 µm in AA, 23.21 µm for AC, and 23.99 µm for CC), consistent with the additive effect of gene action on fiber width (Table 3 and Figure 4). Also, a synonymous marker SNP45 in exon 2, associated with holocellulose content, showed a difference among three genotypic classes (two significant) (74.62% in AA, 74.55% in AC, and 73.30% in CC), indicating patterns of gene action consistent with dominant effects (Table 3). SNP75 in exon 10, the other synonymous mutation, associated with D and V, explaining 3.2% and 2.6% of the phenotypic variance, respectively (Table 3).

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