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Characterization of phenylpropanoid pathway genes within European maize (Zea mays L.) inbreds.

Andersen JR, Zein I, Wenzel G, Darnhofer B, Eder J, Ouzunova M, Lübberstedt T - BMC Plant Biol. (2008)

Bottom Line: A 1-bp indel in 4CL1 was associated with in vitro digestibility of organic matter (IVDOM), a non-synonymous SNP in C3H was associated with IVDOM, and an intron SNP in F5H was associated with neutral detergent fiber.However, the C3H and F5H associations did not remain significant when controlling for multiple testing.While the number of lines included in this study limit the power of the association analysis, our results imply that genetic variation for forage quality traits can be mined in phenylpropanoid pathway genes of elite breeding lines of maize.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Genetics and Biotechnology, University of Aarhus, Research Center Flakkebjerg, 4200 Slagelse, Denmark. jepper.andersen@agrsci.dk

ABSTRACT

Background: Forage quality of maize is influenced by both the content and structure of lignins in the cell wall. Biosynthesis of monolignols, constituting the complex structure of lignins, is catalyzed by enzymes in the phenylpropanoid pathway.

Results: In the present study we have amplified partial genomic fragments of six putative phenylpropanoid pathway genes in a panel of elite European inbred lines of maize (Zea mays L.) contrasting in forage quality traits. Six loci, encoding C4H, 4CL1, 4CL2, C3H, F5H, and CAD, displayed different levels of nucleotide diversity and linkage disequilibrium (LD) possibly reflecting different levels of selection. Associations with forage quality traits were identified for several individual polymorphisms within the 4CL1, C3H, and F5H genomic fragments when controlling for both overall population structure and relative kinship. A 1-bp indel in 4CL1 was associated with in vitro digestibility of organic matter (IVDOM), a non-synonymous SNP in C3H was associated with IVDOM, and an intron SNP in F5H was associated with neutral detergent fiber. However, the C3H and F5H associations did not remain significant when controlling for multiple testing.

Conclusion: While the number of lines included in this study limit the power of the association analysis, our results imply that genetic variation for forage quality traits can be mined in phenylpropanoid pathway genes of elite breeding lines of maize.

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Linkage disequilibrium between haplotypes of individual genes in the phenylpropanoid pathway in maize.
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Figure 3: Linkage disequilibrium between haplotypes of individual genes in the phenylpropanoid pathway in maize.

Mentions: Extended LD was identified at the 4CL1 locus at which all polymorphisms, with the exception of two 1-bp deletions, were in high LD (P > 0.001) across the entire amplified sequence (~1.3 kb; Figure 2). At the C4H, C3H, 4CL2, and F5H loci, breakdown of LD was observed within ~200 bp. Inter-locus LD was examined by estimating LD between SNP haplotypes of the six loci as well as PAL (32 lines), COMT (42 lines), CCoAOMT1 (40 lines) and CCoAOMT2 (34 lines) ([18,21], unpublished results). This revealed that C4H were in high (P < 0.0001) LD with CCoAOMT2 and intermediate (P < 0.001) LD with CCoAOMT1 and CAD. Significant LD was not observed between any other pairs of loci (Figure 3). Examining LD between individual SNPs at these three loci pinpointed that a single non-synonymous SNP, changing the 27th amino acid of the C4H enzyme from Threonine to Serine, was in high LD with several SNPs at the CCoAOMT1 and CCoAOMT2 locus, respectively (data not shown).


Characterization of phenylpropanoid pathway genes within European maize (Zea mays L.) inbreds.

Andersen JR, Zein I, Wenzel G, Darnhofer B, Eder J, Ouzunova M, Lübberstedt T - BMC Plant Biol. (2008)

Linkage disequilibrium between haplotypes of individual genes in the phenylpropanoid pathway in maize.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2265712&req=5

Figure 3: Linkage disequilibrium between haplotypes of individual genes in the phenylpropanoid pathway in maize.
Mentions: Extended LD was identified at the 4CL1 locus at which all polymorphisms, with the exception of two 1-bp deletions, were in high LD (P > 0.001) across the entire amplified sequence (~1.3 kb; Figure 2). At the C4H, C3H, 4CL2, and F5H loci, breakdown of LD was observed within ~200 bp. Inter-locus LD was examined by estimating LD between SNP haplotypes of the six loci as well as PAL (32 lines), COMT (42 lines), CCoAOMT1 (40 lines) and CCoAOMT2 (34 lines) ([18,21], unpublished results). This revealed that C4H were in high (P < 0.0001) LD with CCoAOMT2 and intermediate (P < 0.001) LD with CCoAOMT1 and CAD. Significant LD was not observed between any other pairs of loci (Figure 3). Examining LD between individual SNPs at these three loci pinpointed that a single non-synonymous SNP, changing the 27th amino acid of the C4H enzyme from Threonine to Serine, was in high LD with several SNPs at the CCoAOMT1 and CCoAOMT2 locus, respectively (data not shown).

Bottom Line: A 1-bp indel in 4CL1 was associated with in vitro digestibility of organic matter (IVDOM), a non-synonymous SNP in C3H was associated with IVDOM, and an intron SNP in F5H was associated with neutral detergent fiber.However, the C3H and F5H associations did not remain significant when controlling for multiple testing.While the number of lines included in this study limit the power of the association analysis, our results imply that genetic variation for forage quality traits can be mined in phenylpropanoid pathway genes of elite breeding lines of maize.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Genetics and Biotechnology, University of Aarhus, Research Center Flakkebjerg, 4200 Slagelse, Denmark. jepper.andersen@agrsci.dk

ABSTRACT

Background: Forage quality of maize is influenced by both the content and structure of lignins in the cell wall. Biosynthesis of monolignols, constituting the complex structure of lignins, is catalyzed by enzymes in the phenylpropanoid pathway.

Results: In the present study we have amplified partial genomic fragments of six putative phenylpropanoid pathway genes in a panel of elite European inbred lines of maize (Zea mays L.) contrasting in forage quality traits. Six loci, encoding C4H, 4CL1, 4CL2, C3H, F5H, and CAD, displayed different levels of nucleotide diversity and linkage disequilibrium (LD) possibly reflecting different levels of selection. Associations with forage quality traits were identified for several individual polymorphisms within the 4CL1, C3H, and F5H genomic fragments when controlling for both overall population structure and relative kinship. A 1-bp indel in 4CL1 was associated with in vitro digestibility of organic matter (IVDOM), a non-synonymous SNP in C3H was associated with IVDOM, and an intron SNP in F5H was associated with neutral detergent fiber. However, the C3H and F5H associations did not remain significant when controlling for multiple testing.

Conclusion: While the number of lines included in this study limit the power of the association analysis, our results imply that genetic variation for forage quality traits can be mined in phenylpropanoid pathway genes of elite breeding lines of maize.

Show MeSH