ARS | Publication request: Rice Waxy gene SNPs: Associations with amylose content and structure and pasting properties

Submitted to: American Association of Cereal Chemists Meetings
Publication Type: Abstract Only
Publication Acceptance Date: June 19, 2007
Publication Date: October 15, 2007
Citation: Chen, M.H., Bergman, C.J., Fjellstrom, R.G. 2007. Rice Waxy gene SNPs: Associations with amylose content and structure and pasting properties [abstract]. American Association of Cereal Chemists Meetings. Paper No. 52:A16.

Technical Abstract: Apparent amylose content (AAC) strongly impacts rice end-use quality, and thus is used as a predictor of end-use quality traits during varietal development. Pasting properties are an additional tool used for predicting certain quality traits that AAC cannot discriminate. Both AAC and pasting properties have been mapped to the Waxy gene on rice chromosome 6. Several DNA sequence variations in this gene have been associated with these traits. We investigated these sequence variations and their associations with AAC and pasting properties using 171 rice accessions originating from 43 countries. In addition, amylase structure was determined using size-exclusion chromatography coupled with multiple angle laser light scattering and differential refractive index detection. Three single nucleotide polymorphic sites (SNP) in the Waxy gene, In1G/T (in intron 1), Ex6A/C (in exon 6), and Ex10C/T (in exon 10) were genotyped. Together, a total of four haplotypes or alleles were identified in this germplasm. These four haplotypes were: In1T_Ex6A_Ex10C, In1G_Ex6C_Ex10C, In1G_Ex6A_Ex10C, and In1G_Ex6A_Ex10T, and were associated with low, intermediate, high AAC-types, and high AAC/strong pasting-property-type, respectively. For the rice accessions with the Ex10C allele, the AAC was negatively correlated with the RVA peak, hot paste, and breakdown (r= -0.85, -0.75 and -0.79, respectively), and was positively correlated with the setback viscosity (r= 0.76). Three different hydrodynamic-volume mass fractions of amylase were observed, and the ratios of each mass fraction to total AAC differed among haplotypes. In conclusion, the Waxy haplotypes studied appear to be useful markers for selecting the AAC and strong pasting-property of breeding lines developed from the world’s rice germplasm. The AAC associated with several pasting parameters of the rice accessions with Waxy Ex10C allele.