Limits...
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.

Show MeSH

Related in: MedlinePlus

PtoCesA4 transcript abundance varies among genotypic classes for significant SNP associations. (A) Transcript abundance variation of three genotypic classes for SNP49 in both association and linkage populations. The black and gray lines represent the transcript levels among three genotypic classes in association and linkage populations, respectively. (B) The relative mRNA transcript levels of PtoCesA4 among three genotypic classes for SNP41, a significant noncoding marker in the 5′UTR region of PtoCesA4. The error bars represent ±SD.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC3815066&req=5

fig6: PtoCesA4 transcript abundance varies among genotypic classes for significant SNP associations. (A) Transcript abundance variation of three genotypic classes for SNP49 in both association and linkage populations. The black and gray lines represent the transcript levels among three genotypic classes in association and linkage populations, respectively. (B) The relative mRNA transcript levels of PtoCesA4 among three genotypic classes for SNP41, a significant noncoding marker in the 5′UTR region of PtoCesA4. The error bars represent ±SD.

Mentions: To determine whether these significant allelic SNPs affect the PtoCesA4 RNA transcript abundance, transcript levels were compared among the different genotypic classes for the 10 significant SNPs (Q < 0.10, Table 3) in the association population and seven (Q < 0.10) (Table 5) in the linkage population using RT–qPCR with gene-specific primers. Measurement of differential transcript abundance across three or two genotypic classes (10 trees for each genotype) for each of the 17 SNPs indicated that two markers (SNP41 and 49) exhibited significant differences in the RNA transcript levels among the three genotypes in the association population, but only SNP49 was detected in the linkage population (Figure 6). The genotypic abundance ratio estimates for these SNPs had very low SEs, suggesting that these estimates are robust (Figure 6).


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 transcript abundance varies among genotypic classes for significant SNP associations. (A) Transcript abundance variation of three genotypic classes for SNP49 in both association and linkage populations. The black and gray lines represent the transcript levels among three genotypic classes in association and linkage populations, respectively. (B) The relative mRNA transcript levels of PtoCesA4 among three genotypic classes for SNP41, a significant noncoding marker in the 5′UTR region of PtoCesA4. The error bars represent ±SD.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

fig6: PtoCesA4 transcript abundance varies among genotypic classes for significant SNP associations. (A) Transcript abundance variation of three genotypic classes for SNP49 in both association and linkage populations. The black and gray lines represent the transcript levels among three genotypic classes in association and linkage populations, respectively. (B) The relative mRNA transcript levels of PtoCesA4 among three genotypic classes for SNP41, a significant noncoding marker in the 5′UTR region of PtoCesA4. The error bars represent ±SD.
Mentions: To determine whether these significant allelic SNPs affect the PtoCesA4 RNA transcript abundance, transcript levels were compared among the different genotypic classes for the 10 significant SNPs (Q < 0.10, Table 3) in the association population and seven (Q < 0.10) (Table 5) in the linkage population using RT–qPCR with gene-specific primers. Measurement of differential transcript abundance across three or two genotypic classes (10 trees for each genotype) for each of the 17 SNPs indicated that two markers (SNP41 and 49) exhibited significant differences in the RNA transcript levels among the three genotypes in the association population, but only SNP49 was detected in the linkage population (Figure 6). The genotypic abundance ratio estimates for these SNPs had very low SEs, suggesting that these estimates are robust (Figure 6).

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