Waxy gene haplotypes: Associations with pasting properties in an international rice germplasm collection

Associations between RVA pasting properties and three single nucleotide polymorphism (SNP) sites in the Waxy gene intron 1, exon 6, and exon 10 were determined using rice genotypes of diverse geographic origin. A total of four SNP-haplotypes (combination of SNP alleles) were identified that explained high proportions of the variation in RVA pasting properties (R2 = 0.574–0.704). A haplotype containing DNA sequence variation in exon 10 (exon 10 cytosine nucleotide) was exclusively found in high-apparent amylose content (AAC) genotypes with a higher RVA viscosity profile compared to the high AAC genotypes with a different haplotype. The exon 10 SNP explained variances in coolpaste and setback (coolpaste–hotpaste) to 0.642 and 0.499, respectively. Across three haplotypes, which contained exon 10 adenine nucleotide, AAC was correlated with peak, hotpaste, breakdown and setback (coolpaste–hotpaste) at r = −0.85, −0.75, −0.79, and 0.49, respectively. Therefore, the exon 10 SNP differentiates high AAC types with a strong RVA profile and thus can be used by molecular breeding programs focused on quality improvement. Additionally, characterizing genotypes by their functional SNPs allowed us to better understand the relationship between the Waxy gene, its chemical product (i.e., AAC) and the functionality created by the product (i.e., pasting properties).