Development of SSR DNA Markers for Variety Identification of Rice Varieties from Different Geographic Origins
Date Issued
2009
Date
2009
Author(s)
Chang, Hsing-Yi
Abstract
Molecular markers are potentially useful for crop variety identification. International Seed Testing Association is currently developing DNA-based markers system of variety identification for four major crops including Zea mays (maize), Oryza sativa (rice), Triticum durum and Triticum aestivum (wheat), and Glycine max L Mer. (soybean). Previous researches conducted on rice variety identification focused on particular regions or countries. The object of this study was to select simple sequence repeat (SSR) markers from 54 fluorescently-labeled SSR markers in 11 multiplex panels for rice, using 192 lines originated from geographically diverse regions. After excluding 6 markers which were poorly amplified or difficult to score due to strong stutter with incomplete effect of adding terminal adenine, a group of 12 unlinked makers were selected based on their easiness to score, absent of null alleles, and polymorphic information content (PIC) value. Numbers of alleles per locus of the selected markers ranged from 5 to 26, with an average of 12.8. PIC values ranged from 0.64 to 0.9, with an average of 0.79. Principal coordinate analysis (PCoA) result of the 192 rice lines showed that there were two groups. All Taiwan japonica varieties and four Italian varieties were assigned to the smaller group, which consist of 56 lines. The larger group contained the other 136 lines, including three Taiwan indica varieties. The first three dimensions account for 17.7%, 6.44% and 5.41% of total variability respectively. The larger group was more diverse on the third dimension, indicating its higher genetic diversity. Cluster analysis result was similar to PCoA result. There were 27 unresolved pairs, including 39 lines, by using these 12 selected markers. The best combination analysis indicated that if choose properly, the number of markers may be further reduced to 9 with no effect on the resolution
Subjects
rice
simple sequence repeat (SSR)
variety identification
principal coordinate analysis
cluster analysis
Type
thesis
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