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Single nucleotide polymorphism (SNP) detection in the red rice α-amylase gene amy1: effect on seedling vigour

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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.
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Document Type: Research Article

Publication date: July 1, 2008

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  • Seed Science and Technology (SST) is one of the leading international journals featuring original papers and review articles on seed quality and physiology as related to seed production, harvest, processing, sampling, storage, distribution and testing. This widely recognised journal is designed to meet the needs of researchers, advisers and all those involved in the improvement and technical control of seed quality.
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