Submitted to: Plant and Animal Genome Conference Proceedings
Publication Type: Proceedings
Publication Acceptance Date: November 15, 2002
Publication Date: January 11, 2003
Citation: Chen, M.H., Bergman, C.J., Fjellstrom, R.G. 2003. SSSIIA locus genetic variation 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. 153.
Gelatinization temperature is predicted using the alkali spreading test and is an important aspect of rice cooking quality. The alkali spreading has been mapped to chromosome 6 (alk locus) loosely linked to the waxy locus. The alk locus reportedly encodes a soluble starch synthase (SSSIIa) that controls amylopectin structure variation between japonica- and indica-type rice. SSSIIa sequence comparison between the japonica variety Nipponbare and the indica breeding line 93-11 indicates the SSSIIa gene is highly conserved, even in intron regions. We have identified five polymorphic nucleotides, with two of them causing amino acid changes, both in exon eight. We are surveying 200 diverse rice accessions with broad variation in gelatinization temperature and determining sequence variation at the SSSIIa locus to identify trait/genotype associations. Preliminary data indicates that high alkali spreading value is associated with amino acid changes at either of the two exon 8 polymorphic regions in SSSIIa. Low and intermediate alkali spreading values appear to have no sequence variation at these two sites, suggesting another polymorphic region or locus may be involved in controlling this phenotype.