Proceedings of the XLVII Italian Society of Agricultural Genetics - SIGA Annual Congress

Verona, Italy - 24/27 September, 2003

ISBN 88-900622-4-X

Poster Abstract - 2.33

GENOTYPING SINGLE NUCLEOTIDE POLYMORPHISMS (SNPs) FOR SCREENING OF BETA-AMYLASE ALLELES IN BARLEY CULTIVARS

E. Chiapparino*, P. Donini*, R. Tuberosa**, D. O’Sullivan*

*) NIAB, Huntingdon Road, CB3 0LE, Cambridge - UK

**) DiSTA, University of Bologna, Viale Fanin 44, 40127 Bologna, Italy

beta-amylase, SNPs, functional polymorphisms, barley

Beta-amylase (1, 4-alpha-glucan maltohydrolase; EC 3.2.1.2) is a key enzyme in the degradation of starch in germinating barley, and its activity, in combination with the activities of limit dextrinase, alpha amylase and alpha-glucosidase, is a measure of the total starch degrading activity of barley malt, which is an important characteristic for estimating the quality of malt for beer production.

However, in most commercial malts, beta-amylase activity is insufficient, and the enzyme appears to be rate-limiting for starch hydrolysis during mashing. The lack of activity is due to its thermolability during the mashing proccess which is perfomed at elevated temperature.

Investigation of natural variation in beta-amylase thermostability within cultivated barley led to the identification of 3 alleles, termed Bmy1-Sd1, Bmy1-Sd2L, Bmy1-Sd2H at the Bmy1 locus on chromosome 4H, and the corresponding enzymes (Sd1, Sd2L and Sd2H) possess low, intermediate and high thermostability respectively.

The functional differences between these three allelic forms reside mainly in three amino acid substitutions (R115C, V233A and L347S) therefore, by genotyping for the three single nucleotide polymorphisms (SNPs) which cause the respective amino acid substitutions, it is possible to identify which allele is present in the variety under study.

More than 500 cultivated barley varieties, representing a large proportion of the acreage sown to barley in the EU over the last 60 years, have been surveyed for the three known beta-amylase alleles by genotyping the varieties the three SNPs described above. In addition to the previously described Sd1, Sd2L and Sd2H alleles, novel haplotypes (previously undescribed combinations of the three functional mutations) were observed, and these were confirmed by resequencing the relevant fragments of the coding sequence. The predicted functional significance of the observed new haplotypic diversity will be discussed. We conclude that genotyping known functional polymorphisms shows some promise for the early detection of barley lines which carry superior beta-amylase alleles, and may represent a powerful tool for selection strategies for breeders.