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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).

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Structures of the sequenced phenylalanine ammonia-lyase (PAL) gene fragments PAL_1 and PAL_2. Comparison of both fragments revealed differing SNP patterns indicating to belong to different gene copies of the PAL gene family. Exons are depicted as light grey boxes. Blue – CAPS marker available, green – high-throughput SNP marker developed, red arrows – shared SNP-positions of both investigated gene fragments.
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Figure 2: Structures of the sequenced phenylalanine ammonia-lyase (PAL) gene fragments PAL_1 and PAL_2. Comparison of both fragments revealed differing SNP patterns indicating to belong to different gene copies of the PAL gene family. Exons are depicted as light grey boxes. Blue – CAPS marker available, green – high-throughput SNP marker developed, red arrows – shared SNP-positions of both investigated gene fragments.

Mentions: Two fragments of the gene encoding PAL were amplified resulting in a total of 877 bp of the sequenced exonic region. Both fragments have an overlapping identical region of 322 bp. Within this area a completely different SNP pattern was observed with only two identical SNPs between both sequenced fragments (SNP 1 and SNP 2 of PAL_1 with SNPs 16 and 17 of PAL_2, illustrated in Figure 2). Thus, both fragments must belong to different gene copies of the PAL gene family. Kervinen et al. [25] also observed at least five copies of a PAL gene family in barley. The consensus sequences for both fragments generated from 16 reference genotypes were 99% identical to the cDNA clone AB367438 [26].


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)

Structures of the sequenced phenylalanine ammonia-lyase (PAL) gene fragments PAL_1 and PAL_2. Comparison of both fragments revealed differing SNP patterns indicating to belong to different gene copies of the PAL gene family. Exons are depicted as light grey boxes. Blue – CAPS marker available, green – high-throughput SNP marker developed, red arrows – shared SNP-positions of both investigated gene fragments.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 2: Structures of the sequenced phenylalanine ammonia-lyase (PAL) gene fragments PAL_1 and PAL_2. Comparison of both fragments revealed differing SNP patterns indicating to belong to different gene copies of the PAL gene family. Exons are depicted as light grey boxes. Blue – CAPS marker available, green – high-throughput SNP marker developed, red arrows – shared SNP-positions of both investigated gene fragments.
Mentions: Two fragments of the gene encoding PAL were amplified resulting in a total of 877 bp of the sequenced exonic region. Both fragments have an overlapping identical region of 322 bp. Within this area a completely different SNP pattern was observed with only two identical SNPs between both sequenced fragments (SNP 1 and SNP 2 of PAL_1 with SNPs 16 and 17 of PAL_2, illustrated in Figure 2). Thus, both fragments must belong to different gene copies of the PAL gene family. Kervinen et al. [25] also observed at least five copies of a PAL gene family in barley. The consensus sequences for both fragments generated from 16 reference genotypes were 99% identical to the cDNA clone AB367438 [26].

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
Related in: MedlinePlus