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Background  Apparent Amylose Content (AAC), regulated by the  Waxy  gene, represents the key determinant of rice cooking properties. In occidental countries high AAC rice represents the most requested market class but the availability of molecular markers allowing specific selection of high AAC varieties is limited.    Results  In this study, the effectiveness of available molecular markers in predicting AAC was evaluated in a collection of 127 rice accessions (125  japonica  ssp. and 2  indica  ssp.) characterized by AAC values from glutinous to 26%. The analyses highlighted the presence of several different allelic patterns identifiable by a few molecular markers, and two of them, i.e., the SNPs at intron1 and exon 6, were able to explain a maximum of 79.5% of AAC variation. However, the available molecular markers haplotypes did not provide tools for predicting accessions with AAC higher than 24.5%. To identify additional polymorphisms, the re-sequencing of the  Waxy  gene and 1kbp of the putative upstream regulatory region was performed in 21 genotypes representing all the AAC classes identified. Several previously un-characterized SNPs were identified and four of them were used to develop dCAPS markers.    Conclusions  The addition of the SNPs newly identified slightly increased the AAC explained variation and allowed the identification of a haplotype almost unequivocally associated to AAC higher than 24.5%. Haplotypes at the  waxy  locus were also associated to grain length and length/width (L/W) ratio. In particular, the SNP at the first intron, which identifies the  Wx    a    and  Wx    b    alleles, was associated with differences in the width of the grain, the L/W ratio and the length of the kernel, most likely as a result of human selection.

Improvement of marker-based predictability of Apparent Amylose Content in japonica rice through GBSSI allele mining