447 EFFECT OF α-AMYLASE GENE AMY1 IN RICE SEED GERMINATION Malone, G., Peske, S.T., Zimmer, P.D., Malone, E., Meneghello, G.E. and Costa de Oliveira, A. (2008), Seed Sci. & Technol., 36, 447-455 Single nucleotide polymorphism (SNP) detection in the red rice α-amylase gene amy1: effect on seedling vigour G. MALONE 1 , S.T. PESKE 1 , P.D. ZIMMER 1 , E. MALONE 2 , G.E. MENEGHELLO 1 AND A. COSTA DE OLIVEIRA 2 1 Laboratório de Bio-sementes, Departamento de Fitotecnia, Faculdade de Agronomia “Eliseu Maciel”, sala 608, Campus Universitário s/n, Universidade Federal de Pelotas, Caixa Postal 354, CEP 96010-900, Pelotas (RS), Brasil (E-mail: gmalone@ufpel.edu.br) 2 Centro de Genômica e Fitomelhoramento, Faculdade de Agronomia “Eliseu Maciel”, 3 Andar, Campus Universitário s/n, Cx Postal 354, CEP 96010-900, Pelotas (RS), Brasil (Accepted November 2007) Summary Red rice genotypes are part of a very valuable gene pool lost in the rice domestication and breeding. Therefore, genetic, phenotypic and physiological studies in red rice could aid the elucidation of important characters in cultivated rice. A wide range of variability both at the genetic and physiological levels has been identified in red rice ecotypes from Southern Brazil, regarding the germination process. In this work, we revealed Single Nucleotide Polymorphisms (SNPs) in three internal regions (483 pb from intron 1, 460 pb from intron 1 and 461 pb from exon 2) of the α-amylase gene AMY1 in an collection of 30 red rice ecotypes from the germplasm bank of the Federal University of Pelotas - Brazil. Eight of them presented mutant haplotypes in the codifying region. Changes on the amino acid sequence were estimated, and the putative impact of aminoacid substitutions on seedling vigour was discussed.. Three out of five SNPs were detected in the same region of exon 2, suggesting the presence of a “hot spot”. Physiological tests of some variants indicated changes in vigour attributes. Introduction The germination process in seeds is composed of several physiological and developmental events, which are not yet fully understood. Enzymes, such as α-amylases (α-1,4-D-glucan glucan-hydrolase, EC3.2.1.1) hydrolyze internal α-1,4-glucosidic bonds in starch, malt dextrins and malt oligosaccharides (Yamamoto, 1995). Several nomenclatures for α- amylase isoforms and their genes are found in the literature. Jones and Jacobsen (1991) classified AMY1 as a group of low-pI α-amylases and AMY2 as a group of high-pI α- amylases. Rogers (1985) described high-pI and low-pI α-amylases as AMYA and AMYB, respectively. In the triticeae, α-amylase genes were divided into three subfamilies (Amy1, Amy2 and Amy3), clustering Amy1 and Amy2 into AmyA and Amy3 into AmyB classes, respectively (Huang et al., 1992). An additional subfamily of α-amylase genes (Amy3) has been identified in wheat (Huang et al., 1992). Low-pI isoenzyme genes have been named as type A and high pI as type B (Rogers and Milliman, 1984; Whittier et al.,