Sequence variation in the barley genes encoding sucrose synthase I and sucrose phosphate synthase II, and its association with variation in grain traits and malting quality

Sequence diversity in the two barley (Hordeum vulgare L.) genes encoding sucrose synthase I (SSI) and sucrose phosphate synthase II (SPSII), both of which are involved in sucrose accumulation and grain filling, was studied by partial resequencing of eight reference genotypes and SNP analysis by pyrosequencing in a panel of 94 spring and 96 winter European barley varieties. The resequencing was based on two adjacent SSI fragments of size 880 and 820 bp, and a 2,322 bp SPSII fragment. In the SSI gene, 26 SNPs were present in the larger fragment, and 25 in the smaller one, and 11 of these were exploited to develop high-throughput SNP assays used for haplotype analysis. An association analysis based on either a general or a mixed linear model suggested that the predominant three haplotypes influenced certain components of both kernel and malting quality. However, the level of phenotype/haplotype association shown with the SPSII gene was rather low. SNP variation of SSI was used to map the locus to chromosome 7H.