Diversity of microsatellites derived from genomic libraries and GenBank sequences in rice (Oryza sativa L.) |
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Authors: | Y G Cho T Ishii S Temnykh X Chen L Lipovich S R McCouch W D Park N Ayres S Cartinhour |
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Institution: | (1) Department of Plant Breeding, 252 Emerson Hall, Cornell University, Ithaca, NY 14853–1901, USA, US;(2) Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77845, USA, US |
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Abstract: | The growing number of rice microsatellite markers warrants a comprehensive comparison of allelic variability between the markers
developed using different methods, with various sequence repeat motifs, and from coding and non-coding portions of the genome.
We have performed such a comparison over a set of 323 microsatellite markers; 194 were derived from genomic library screening
and 129 were derived from the analysis of rice-expressed sequence tags (ESTs) available in public DNA databases. We have evaluated
the frequency of polymorphism between parental pairs of six inter- subspecific crosses and one inter-specific cross widely
used for mapping in rice. Microsatellites derived from genomic libraries detected a higher level of polymorphism than those
derived from ESTs contained in the GenBank database (83.8% versus 54.0%). Similarly, the other measures of genetic variability
the number of alleles per locus, polymorphism information content (PIC), and allele size ranges] were all higher in genomic
library-derived microsatellites than in their EST-database counterparts. The highest overall degree of genetic diversity was
seen in GA-containing microsatellites of genomic library origin, while the most conserved markers contained CCG- or CAG-trinucleotide
motifs and were developed from GenBank sequences. Preferential location of specific motifs in coding versus non-coding regions
of known genes was related to observed levels of microsatellite diversity. A strong positive correlation was observed between
the maximum length of a microsatellite motif and the standard deviation of the molecular-weight of amplified fragments. The
reliability of molecular weight standard deviation (SDmw) as an indicator of genetic variability of microsatellite loci is
discussed.
Received: 5 May 1999 / Accepted: 16 August 1999 |
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Keywords: | Allelic diversity Simple sequence repeat (SSR) Microsatellite marker Rice (Oryza sativa L ) |
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