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Haplotype diversity in the endosperm specific β-amylase gene Bmy1 of cultivated barley (Hordeum vulgare L.)


Haplotype diversity in the endosperm specific β-amylase gene Bmy1 of cultivated barley (Hordeum vulgare L.)


L. V. Malysheva-Otto1,*, M. S. Röder1


1 Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)
   Corrensstraße 3
   06466 Gatersleben

* corresponding author

Molecular Breeding (2006)


The amylolytic enzyme β-amylase (1,4-α-D-glucan maltohydrolase; EC catalyses the release of maltose from starch which is an important biochemical pathway during germination and the malting process. Four alleles of the endosperm specific β-amylase gene giving rise to proteins with different thermostability and electrophoretic characteristics, Bmy1-Sd1, Bmy1-Sd2L Bmy1-Sd2H and Bmy1-Sd3, were identified in cultivated and wild barley (Allison and Swanston 1974; Eglington et al. 1998; Paris et al. 2002).The gene Bmy1 is 3825 bp in length without promoter region and contains seven exons and six introns, the deduced protein contains approximately 550 amino acids (AAs) (Yoshigi et al. 1995). For several barley varieties AAs substitutions, resulting from corresponding single nucleotide polymorphisms (SNPs), were described at positions 115, 165, 233, 347 and 430 (Yoshigi et al. 1994; Erkkilä et al. 1998; Li et al. 2000; Ma et al. 2001; Paris et al. 2002; Clark et al. 2003). The effects of several specific point mutations causing AA exchanges on the thermostability and kinetic properties of the enzyme were investigated by Ma et al. (2001) and Clark et al. (2003). The use of a CAPS marker for distinguishing the presence of a codon for valine (in Bmy1-Sd1 and Bmy1-Sd2L) or alanine (in Bmy1-Sd2H and Bmy1-Sd3) allowed the evaluation of a worldwide collection of barley varieties (Malysheva et al. 2004). The thermostable alleles Bmy1-Sd2H and Bmy1-Sd3 were predominantly discovered in 6-rowed Asian spring barleys with the highest frequency in Japanese varieties. Only low frequencies of Bmy1-Sd2H were found in European 2-rowed spring barleys and the origin of this allele was traced back to the cross Binder x Gull (Malysheva et al. 2004; Sjakste and Röder, 2004).

In the present study five SNP sites corresponding to substitutions in the protein sequence of the β-amylase gene Bmy1 at AA positions 115, 165, 233, 347 and 430 were genotyped in 493 cultivated barley accessions by Pyrosequencing and a CAPS assay. A total of 6 different haplotypes for the Bmy1 gene were discovered of which 4 haplotypes were identified as previously described alleles Bmy1-Sd1, Bmy1-Sd2L, Bmy1-Sd2H and Bmy1-Sd3, while 2 haplotypes were new (Malysheva-Otto & Röder, 2006). Previously described alleles were assigned to specific SNP patterns according to Ma et al. (2001) and Paris et al. (2002). Two new haplotypes were called Bmy1-Sd1b and Bmy1-Sd4.


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