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Title: Waxy gene haplotypes: Associations with amylose content and the effect by the environment 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: 6/13/2007
Publication Date: 5/1/2008
Citation: Chen, M., Bergman, C.J., Pinson, S.R., Fjellstrom, R.G. 2008. Waxy gene haplotypes: Associations with amylose content and the effect by the environment in an international rice germplasm collection. Journal of Cereal Science. 47:536-545.

Interpretive Summary: Apparent amylose content is the key determinant of rice end-use quality attributes and is primarily controlled by the Waxy gene which codes for synthesis of the granule bound starch synthase enzyme. We examined the combination of the sequence variation in the Waxy gene and environmental effects and their associations with apparent amylose content using 171 rice accessions originated from 43 countries. Several sequence variation sites were identified in the Waxy gene. The combination of the two sites of the DNA sequence variations allows the discrimination of rice accessions into three market classes of low-, intermediate- and high-amylose rice. These Waxy gene DNA sequence variations studied appear to be useful molecular markers for selecting the apparent amylose content of breeding lines developed from the world’s rice germplasm.

Technical Abstract: Apparent amylose content (AAC), the key determinant of rice end-use quality attributes, is primarily controlled by the Waxy gene which codes for granule bound starch synthase. We examined the combination of sequence variation in the Waxy gene and environmental effects and their associations with AA using 171 rice accessions originating from 43 countries. The combination of two single-nucleotide-polymorphism (SNP) markers in the Waxy gene allows the identification of three marker haplotypes in this gene. The first SNP is at the leader intron splice site (intron 1 SNP), and the second polymorphism is in exon 6. The haplotypes explained 86.9% of the variation in AAC and discriminated the three market classes of low-, intermediate- and high-amylose rice from each other. The environment significantly affected the AAC of the low- and intermediate-amylose, but not the high-amylose types. We hypothesize the exon 6 polymorphism unique to the intermediate-amylose haplotype affects the stability or the activity of granule bound starch synthase. The association of AAC with several Waxy RM190 microsatellite-(CTn) alleles in combination with the intron 1 SNP was also examined. In conclusion, the Waxy haplotypes studied appear to be useful markers for selecting the apparent amylose content of breeding lines developed from the world’s rice germplasm.