Sequence Variation and Phylogenetic Relationship Analysis of Starch Branching Enzyme I Gene (SBEI) in Rice Varieties from China, Laos and Thailand

Abstract

The coding sequence of starch branching enzyme I gene (SBEI) of 30 rice varieties from China, Laos and Thailand were cloned. All thirty sequences contain 2,463 bp and 14 exons and encode for 820 amino acids. Three sites of Single Nucleotide Polymorphisms (SNPs) A > C, T > C, and T > C were found at positions 1,107, 2,156 and 2,271 in Exon with 6, 13 and 14 respectively. The SNPs at position 1,107 A > C and position 2,271 T > C were silent mutations. The SNP at position 2,156 T > C was a missense mutation and induced a mutation from valine (GTG) to alanine (GCG). Three haplotypes A/T/T, C/T/C and C/C/C were observed. The phylogenetic analysis of 81 SBEI CDS sequences, out of which 30 are from this study and 51 are from previous, classifies them into 2 major groups using 4 sequences as outgroup. The group of monocot comprised of rice, barley, wheat, sorghum whereas maize and the group of dicot comprised of potato, cassava, poplar, Chinese chestnut, bean, legumes and apple. The group of rice SBEI CDS was a major clade in monocot group with high bootstrap value. SBEI gene of rice from China, Laos and Thailand, wheat, apple and poplar contain 14 exons while SBEI gene of rice from Japan and Korea contained only 12 exons. The GC content of SBEI gene of rice varieties was lower than that of wheat and apple but higher than that of poplar.