Limits...
Development of SNP markers for genes of the phenylpropanoid pathway and their association to kernel and malting traits in barley.

Peukert M, Weise S, Röder MS, Matthies IE - BMC Genet. (2013)

Bottom Line: The resulting SNP and haplotype patterns were used to calculate associations with kernel and malting quality parameters.SNP patterns were found to be highly variable for the investigated genes.The candidate genes PAL, C4H and F3H were shown to be associated to several malting properties like glassiness (PAL), viscosity (C4H) or to final attenuation (F3H).

View Article: PubMed Central - HTML - PubMed

Affiliation: Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstr, 3, 06466 Stadt Seeland, Germany. roder@ipk-gatersleben.de.

ABSTRACT

Background: Flavonoids are an important class of secondary compounds in angiosperms. Next to certain biological functions in plants, they play a role in the brewing process and have an effect on taste, color and aroma of beer. The aim of this study was to reveal the haplotype diversity of candidate genes involved in the phenylpropanoid biosynthesis pathway in cultivated barley varieties (Hordeum vulgare L.) and to determine associations to kernel and malting quality parameters.

Results: Five genes encoding phenylalanine ammonia-lyase (PAL), cinnamate 4-hydroxylase (C4H), chalcone synthase (CHS), flavanone 3-hydroxylase (F3H) and dihydroflavonol reductase (DFR) of the phenylpropanoid biosynthesis pathway were partially resequenced in 16 diverse barley reference genotypes. Their localization in the barley genome, their genetic structure, and their genetic variation e.g. single nucleotide polymorphism (SNP) and Insertion/Deletion (InDel) patterns were revealed. In total, 130 SNPs and seven InDels were detected. Of these, 21 polymorphisms were converted into high-throughput pyrosequencing markers. The resulting SNP and haplotype patterns were used to calculate associations with kernel and malting quality parameters.

Conclusions: SNP patterns were found to be highly variable for the investigated genes. The developed high-throughput markers are applicable for assessing the genetic variability and for the determination of haplotype patterns in a set of barley accessions. The candidate genes PAL, C4H and F3H were shown to be associated to several malting properties like glassiness (PAL), viscosity (C4H) or to final attenuation (F3H).

Show MeSH
Level of kernel raw protein assigned to a) F3H haplotypes 1 and 3 and b) to the allelic distribution of SNP38 detected in the F3H encoding gene. ┴ = minimum values, ┬ = maximum values, boxes are 0.25 to 0.75 quartiles including ─ = median.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC3852699&req=5

Figure 7: Level of kernel raw protein assigned to a) F3H haplotypes 1 and 3 and b) to the allelic distribution of SNP38 detected in the F3H encoding gene. ┴ = minimum values, ┬ = maximum values, boxes are 0.25 to 0.75 quartiles including ─ = median.

Mentions: Final attenuation and fermentable extract were significantly associated with the haplotype 4 of F3H, which occurs only in two-rowed spring barleys (Table 5). The final attenuation describes the enzymatic activity of amylases and is correlated to dilution properties of the malt extract. A close correlation exists with the malting parameter fermentable extract [37]. Combining SNPs to haplotype patterns can provide more information than single SNPs. This is illustrated by the significant association results of F3H_H4 with these traits, which was not found considering their single SNPs. The haplotypes 1 and 3 of F3H showed associations to kernel raw protein (KRP), kernel yield (KY) and pH (Table 8). The haplotype 3 (F3H_H3) is associated to a lower raw kernel protein content (K_RP) and is mainly found in the 2-rowed spring cultivars (Table 5). Differences in raw kernel protein (K_RP) assigned to different SNP alleles (a) or haplotypes (b) for F3H are shown in Figure 7. For a good malting and brewing quality, a low raw protein concentration in kernels is desired.


Development of SNP markers for genes of the phenylpropanoid pathway and their association to kernel and malting traits in barley.

Peukert M, Weise S, Röder MS, Matthies IE - BMC Genet. (2013)

Level of kernel raw protein assigned to a) F3H haplotypes 1 and 3 and b) to the allelic distribution of SNP38 detected in the F3H encoding gene. ┴ = minimum values, ┬ = maximum values, boxes are 0.25 to 0.75 quartiles including ─ = median.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3852699&req=5

Figure 7: Level of kernel raw protein assigned to a) F3H haplotypes 1 and 3 and b) to the allelic distribution of SNP38 detected in the F3H encoding gene. ┴ = minimum values, ┬ = maximum values, boxes are 0.25 to 0.75 quartiles including ─ = median.
Mentions: Final attenuation and fermentable extract were significantly associated with the haplotype 4 of F3H, which occurs only in two-rowed spring barleys (Table 5). The final attenuation describes the enzymatic activity of amylases and is correlated to dilution properties of the malt extract. A close correlation exists with the malting parameter fermentable extract [37]. Combining SNPs to haplotype patterns can provide more information than single SNPs. This is illustrated by the significant association results of F3H_H4 with these traits, which was not found considering their single SNPs. The haplotypes 1 and 3 of F3H showed associations to kernel raw protein (KRP), kernel yield (KY) and pH (Table 8). The haplotype 3 (F3H_H3) is associated to a lower raw kernel protein content (K_RP) and is mainly found in the 2-rowed spring cultivars (Table 5). Differences in raw kernel protein (K_RP) assigned to different SNP alleles (a) or haplotypes (b) for F3H are shown in Figure 7. For a good malting and brewing quality, a low raw protein concentration in kernels is desired.

Bottom Line: The resulting SNP and haplotype patterns were used to calculate associations with kernel and malting quality parameters.SNP patterns were found to be highly variable for the investigated genes.The candidate genes PAL, C4H and F3H were shown to be associated to several malting properties like glassiness (PAL), viscosity (C4H) or to final attenuation (F3H).

View Article: PubMed Central - HTML - PubMed

Affiliation: Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstr, 3, 06466 Stadt Seeland, Germany. roder@ipk-gatersleben.de.

ABSTRACT

Background: Flavonoids are an important class of secondary compounds in angiosperms. Next to certain biological functions in plants, they play a role in the brewing process and have an effect on taste, color and aroma of beer. The aim of this study was to reveal the haplotype diversity of candidate genes involved in the phenylpropanoid biosynthesis pathway in cultivated barley varieties (Hordeum vulgare L.) and to determine associations to kernel and malting quality parameters.

Results: Five genes encoding phenylalanine ammonia-lyase (PAL), cinnamate 4-hydroxylase (C4H), chalcone synthase (CHS), flavanone 3-hydroxylase (F3H) and dihydroflavonol reductase (DFR) of the phenylpropanoid biosynthesis pathway were partially resequenced in 16 diverse barley reference genotypes. Their localization in the barley genome, their genetic structure, and their genetic variation e.g. single nucleotide polymorphism (SNP) and Insertion/Deletion (InDel) patterns were revealed. In total, 130 SNPs and seven InDels were detected. Of these, 21 polymorphisms were converted into high-throughput pyrosequencing markers. The resulting SNP and haplotype patterns were used to calculate associations with kernel and malting quality parameters.

Conclusions: SNP patterns were found to be highly variable for the investigated genes. The developed high-throughput markers are applicable for assessing the genetic variability and for the determination of haplotype patterns in a set of barley accessions. The candidate genes PAL, C4H and F3H were shown to be associated to several malting properties like glassiness (PAL), viscosity (C4H) or to final attenuation (F3H).

Show MeSH