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

Author
item Chen, Ming Hsuan
item BERGMAN, CHRISTINE - UNIV. OF NV, LAS VEGAS
item Pinson, Shannon
item Fjellstrom, Robert

Submitted to: Journal of Cereal Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/19/2008
Publication Date: 10/31/2008
Citation: Chen, M., Bergman, C.J., Pinson, S.R., Fjellstrom, R.G. 2008. Waxy gene haplotypes: Associations with pasting properties in an international rice germplasm collection. Journal of Cereal Science. 48:781-788.

Interpretive Summary: Apparent amylose content is one of the key predictors of rice end-use quality used during varietal development. However, there are certain quality traits among high apparent-amylose types that apparent amylose content cannot discriminate. The RVA pasting viscosity is an additional tool used for this purpose. However, RVA viscosity curves were affected by the growing environment, and post-harvest handling and storage. Both apparent amylose content and pasting properties have been associated with the DNA sequence changes in the Waxy gene of rice. We investigated these sequence variations and their associations with pasting properties using 146 non-glutinous rice accessions of diverse origin. Three DNA-sequence-variation sites in the Waxy gene in intron 1, exon 6, and exon 10 were determined. Together, a total of four Waxy gene variants were identified in this germplasm collection. These four variants explained high proportions of the variations in RVA viscosity parameters (R square ranged from 0.574 to 0.704) and were able to discriminate low-, intermediate-, high-apparent-amylose-, and high-apparent-amylose strong RVA-profile-type rice. These Waxy gene DNA sequence variations studied appear to be useful molecular markers for selecting the apparent amylose content and pasting properties of breeding lines developed from the world’s rice germplasm.

Technical Abstract: Apparent amylose content is one of the key predictors of rice end-use quality used during varietal development. However, there are quality attributes among high apparent-amylose types that apparent amylose content cannot identify. RVA pasting viscosity is an additional tool used for this purpose. 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 pasting properties using 146 non-glutinous rice accessions of diverse geographic origin. Three single nucleotide polymorphic sites in the Waxy gene in intron 1, exon 6, and exon 10 were genotyped. Together, a total of four haplotypes or alleles were identified in this germplasm collection. These haplotypes explained high proportions of the variations in RVA viscosity parameters (R square ranged from 0.574 to 0.704) and were able to discriminate low-, intermediate-, high-apparent-amylose-, and high-apparent-amylose strong RVA profile-type rice. By characterizing rice accessions by their haplotypes, the contributions from AAC versus the Ex10 mutation to pasting viscosity properties are now better understood.