Genetic variation at the waxy locus associated with alkali spreading value in international rice germplasm

Authors: Chen, Ming Hsuan; Bergman, Christine; Fjellstrom, Robert

Submitted to: Plant and Animal Genome Conference Proceedings
Publication Type: Proceedings
Publication Acceptance Date: 11/15/2002
Publication Date: 1/11/2003
Citation: Chen, M.J., Bergman, C.J., Fjellstrom, R.G. 2003. Genetic variation at the waxy locus associated with alkali spreading value in international rice germplasm. In: Proceedings of the Plant and Animal Genome Conference, January 11-15, 2003, San Diego, CA. p. 152.

Interpretive Summary:

Technical Abstract: Rice end-use quality is strongly impacted by amylose content. The waxy locus on chromosome 6 encodes the granule bound starch synthase enzyme (GBSS) which controls much of the variation in rice amylose content. A microsatellite in the non-coding region of GBSS exon 1 containing a CT repeats and a G/T polymorphic intron/exon splicing site at this exon are reportedly associated with the amylose contents of US rice cultivars. We studied the association between these two polymorphic regions and the amylose content among international germplasm collection. High amylose content was seen in germplasm with 8, 10, 11 and 20 dimeric CT repeats in the first exon region and all had a G nucleotide at the first intron splice site. Intermediate amylose content was found in germplasm with 14, 16, 17, 18, 19, and 20 dimeric repeats, and all had a G at the intron splice site. Low amylose was found in germplasm with 17, 18, and 19 CT repeats that characteristacally had a T at the intron splice site. Since the G/T polymorphism explains amylose content variation in the 17, 18, and 19 CT repeat accessions, allele specific oligonucleotide primers are being developed to discriminate these genotypes for marker assisted selection of amylose content.