New SNPs and Indels of Starch Synthesis-Related Genes in Korean Waxy and Dull Rice (Oryza sativa L.)

Starch is composed of amylose and amylopectin and is synthesized under the coordinated action of a wide array of enzymes. The relative contribution of variation in the genes of starch biosynthesis to the nutritional and functional properties of the rice was evaluated in rice breeding population. In the present study, 10 starch synthesis related genes were sequenced in a population of 8 waxy and 3 dull breeding lines.  Totally 23 sequence variations were found in 15 sequenced amplicons, including 15 single-nucleotide polymorphisms (SNPs),7 insertion-deletions (InDels) and one polymorphic simple sequence repeat (SSR). Among them, 16 variations were exon-based, of which 9 should lead to amino acid changes. Eight genes,OsAGPL1, OsAGPL2, OsAGPL3, OsAGPL4, OsAGPS1,PUL3,OsSSⅡChr6 and OsSSⅡChr7 showed no polymorphism. The present results showed the OsGBSSI appear to be the major loci controlling traits under human selection in waxy and dull lines. A unique duplication of 23bp was found to be present only in waxy lines when compared the sequence of OsGBSS1, in addition to that two new deletions (InDel T and InDel CCCGCAG) were found in one waxy cultivar, JS-34. These two deletions resulted in a frameshift mutant and a premature translation stop codon at 190 bp downstream. In addition, We found one unique microsatellite allele in exon 1, (CT)₁₈ and one single nucleotide polymorphisms in exons 6 (A->C) were detected only in dull and waxy lines along with the amylose content about 10 % and 0, respectively. These new findings would provide some new perspectives to understand some starch synthesis-related genes function, especial OsGBSSI, in the process of starch synthesis.