Cell wall degradation is a crucial process within the malting process of barley. Therefore the haplotype diversity of a gene for the cell wall degrading enzyme (1→4)-β-Xylan-endohydrolase 1, was investigated and associations to malting quality parameters were performed.
In case of the (1→4)-β-Xylan-endohydrolase 1 (X-1 gene) a fragment of 525 bp was sequenced representing 68 bp of the 5'UTR, the first exon (153 bp), an intron of 91 bp followed by 313 bp of the second exon. Two of four detected SNPs were successfully converted into pyrosequencing markers. One of them (SNP3 with the alleles A/G) leads to an amino acid exchange (AAG = Lysine or AGG = Arginine, respectively) while SNP4 (T/A) is located in the intron.
When genotyping all 454 barley varieties consisting of 218 spring and 236 winter forms with both pyrosequencing markers three haplotypes were detected Generally, haplotype X-1_H1 is the most abundant one with 287 cultivars, and containing nearly all winter cultivars investigated here, whereas the other two haplotypes X-1_H2 and X-1_H3 are predominating in the spring cultivars. All three haplotypes are found to be equally distributed in the spring subpopulation.
In order to reveal significant associations, 141 winter and spring varieties were studied with regard of population structure. The obtained results resembled the significant associations found for a subset consisting of 60 spring varieties only, while all 81 winter cultivars were not significant at all for the malting or kernel quality parameters considered here (data not shown).
Significant relationships were especially detected for SNP3 and X-1_H2 and some malting properties assuming the General Linear Model (GLM).
The malting characters diastatic power, saccharification, and soluble nitrogen content were significant at p < 0.05 for the haplotype X1-1_H2, while the same parameters were even more significant (p < 0.01 and p < 0.001) for SNP3 in the subpopulation of 60 spring varieties (Table 4). The same results were also found in the total set of 141 spring and winter varieties with regard of population structure. Approx. 30-50 % of the total variation in the whole set of 141 cultivars can be explained due to the presence of population structure, which is reflecting mainly the two subpopulations spring and winter barley. This is true for the traits soluble nitrogen and saccharification, while for diastatic power only 5-10 % of the variation were determined by population structure either regarding SNPs or haplotypes of this candidate gene.
In the spring subpopulation, the presence of nucleotide G in SNP3 resulted in a significant increase of diastatic power (DP), as well as saccharification VZ45 compared to the presence of nucleotide A at SNP 3. For the trait soluble nitrogen, the allele A of SNP3 could be shown to be the favourable one leading to a diminuished nitrogen content. A high content of soluble nitrogen is not wanted due to haze formation in beer, while a high saccharification number VZ45 and high diastatic power are desired.
It can be concluded, that the haplotype X-1_H2 is mostly determined by SNP3. Therefore, SNP3 with the favourable allele G can serve as a diagnostic marker for those traits. It occurs predominantly in the two-rowed spring barleys. The significance of the malting parameter diastatic power, which describes the collective activity of starch debranching enzymes in malt is explained by 17 % (X-1_H2) and 18 % (SNP3) of the total genetic variation.
The most significant associations of (1→4)-β-Xylan-endohydrolase 1 gene X-1 were found for diastatic power, saccharification VZ45 and soluble nitrogen with 18 %, 12 % and 8 % of the total variation explained by SNP3 in the spring barleys.