Development of an Identification System for Rice Varieties Based on Simple Sequence Repeats
Date Issued
2014
Date
2014
Author(s)
Ko, Yu-Shan
Abstract
Rice (Oryza sativa L.) is the most important food crop in Taiwan. The goal of this study is to develop a set of simple sequence repeat (SSR) markers for rice variety identification. By screening SSRs with four-nucleotide repeat units from the published rice whole genome sequence, we have successfully developed a set of 12 SSR markers that are distributed over the 12 rice chromosomes. The complete set of 12 SSR markers are arranged into 4 non-overlapping groups that are labeled with 4 different fluorophores and may be combined into a multiplex-PCR reaction and analyzed concurrently with multiplex capillary electrophoresis. A total of 315 varieties from a wide geographical area were evaluated with these 12 SSR markers, polymorphism information contents (PICs) of the markers ranged from 0.49 to 0.84. The probability of identity (PID) value for this set is 1.91x10-7. Compared with SSR markers with three-nucleotide repeat units, the set of markers developed in the study have significantly lower stutter ratio and more uniform signal strength. These 12 selected markers having high discriminatory power allow to discriminate all of Taiwan rice varieties except 18 unresolved pairs of Taiwan rice varieties with high kinship. We have also selected 12 Taiwan rice varieties as the reference varieties, which effectively cover 96.2% of the alleles of 53 Taiwan rice varieties.
Subjects
品種檢查
簡單重複序列
遺傳純度
Type
thesis
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