ARS | Publication request: Inheritance of starch paste viscosity is directly associated with a rice Waxy gene exon 10 SNP marker

Submitted to: Journal of Cereal Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: August 19, 2010
Publication Date: January 1, 2011
Citation: Traore, K., McClung, A.M., Chen, M., Fjellstrom, R.G. 2011. Inheritance of starch paste viscosity is directly associated with a rice Waxy gene exon 10 SNP marker. Journal of Cereal Science. 53:37-44.

Interpretive Summary: The amount of amylose within a rice variety’s seed or flour is a key element for characterizing its cooking quality. However, rice varieties with similar amylose content can have widely varying quality attributes, including starch stiffness, also known as paste viscosity. It has been previously seen that the presence of a specific DNA marker at the rice Waxy gene, which encodes a starch synthesizing gene, appears to be correlated with starch paste viscosities in high amylose rice varieties. It was further postulated that the inheritance of this marker would be directly associated with the inheritance of paste viscosity differences, which is what this research study tried to verify. A genetic mapping population of 200 progeny lines derived from an intercross between two varieties, Cocodrie and Dixiebelle, having similarly high amylose contents, but with different paste viscosity properties and Waxy gene markers, was analyzed for the inheritance of various pasting properties. Accompanying marker inheritance analyses of this same genetic mapping population revealed that the Waxy gene marker could accurately predict most of the differences in starch pasting properties within the progeny lines. This research proved that Waxy gene markers can be used to efficiently improve the selection of rice with desirable characteristics, particularly for superior parboiling and canning quality.

Technical Abstract: Apparent amylose content is a key element for characterizing a rice cultivar for cooking quality. However, cultivars with similar apparent amylose content can have widely varying quality attributes, including major parameters of starch paste viscosity. It has been postulated that the presence of a rice Waxy gene single nucleotide polymorphism (SNP) marker appearing to be correlated with elevated Rapid Visco Analyzer (RVA) paste viscosities in specific high amylose rice cultivars is directly associated with these for these quality differences. A mapping population derived from a cross between two varieties, Cocodrie and Dixiebelle, having similarly high apparent amylose contents, but with different paste viscosity properties and Waxy gene markers was analyzed for the genetic segregation of various pasting properties, measured with RVA instrumentation. Marker inheritance analyses revealed that the Waxy exon 10 SNP marker was associated with the proportion of soluble to insoluble apparent amylose and most RVA pasting measurements. Waxy gene markers can be used to efficiently improve the selection of rice with desirable characteristics, particularly for superior parboiling and canning quality.