caa a22 4500 475796586 CHVBK 20180406123726.0 cr unu---uuuuu 170329e20000301xx s 000 0 eng 10.1007/s001220051343 doi (NATIONALLICENCE)springer-10.1007/s001220051343 Diversity of microsatellites derived from genomic libraries and GenBank sequences in rice ( Oryza sativa L.) [Elektronische Daten] [Y. G. Cho, T. Ishii, S. Temnykh, X. Chen, L. Lipovich, S. R. McCouch, W. D. Park, N. Ayres, S. Cartinhour] 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. Springer-Verlag Berlin Heidelberg, 2000 Key words Allelic diversity nationallicence Simple sequence repeat (SSR) nationallicence Microsatellite marker nationallicence Rice (Oryza sativa L.) nationallicence Cho Y. G. Department of Plant Breeding, 252 Emerson Hall, Cornell University, Ithaca, NY 14853-1901, USA, US aut Ishii T. Department of Plant Breeding, 252 Emerson Hall, Cornell University, Ithaca, NY 14853-1901, USA, US aut Temnykh S. Department of Plant Breeding, 252 Emerson Hall, Cornell University, Ithaca, NY 14853-1901, USA, US aut Chen X. Department of Plant Breeding, 252 Emerson Hall, Cornell University, Ithaca, NY 14853-1901, USA, US aut Lipovich L. Department of Plant Breeding, 252 Emerson Hall, Cornell University, Ithaca, NY 14853-1901, USA, US aut McCouch S. R. Department of Plant Breeding, 252 Emerson Hall, Cornell University, Ithaca, NY 14853-1901, USA, US aut Park W. D. Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77845, USA, US aut Ayres N. Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77845, USA, US aut Cartinhour S. Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77845, USA, US aut https://doi.org/10.1007/s001220051343 text/html Onlinezugriff via DOI 1 research-article jats NATIONALLICENCE 856 40 https://doi.org/10.1007/s001220051343 text/html Onlinezugriff via DOI NATIONALLICENCE 700 1- Cho Y. G. Department of Plant Breeding, 252 Emerson Hall, Cornell University, Ithaca, NY 14853-1901, USA, US aut NATIONALLICENCE 700 1- Ishii T. Department of Plant Breeding, 252 Emerson Hall, Cornell University, Ithaca, NY 14853-1901, USA, US aut NATIONALLICENCE 700 1- Temnykh S. Department of Plant Breeding, 252 Emerson Hall, Cornell University, Ithaca, NY 14853-1901, USA, US aut NATIONALLICENCE 700 1- Chen X. Department of Plant Breeding, 252 Emerson Hall, Cornell University, Ithaca, NY 14853-1901, USA, US aut NATIONALLICENCE 700 1- Lipovich L. Department of Plant Breeding, 252 Emerson Hall, Cornell University, Ithaca, NY 14853-1901, USA, US aut NATIONALLICENCE 700 1- McCouch S. R. Department of Plant Breeding, 252 Emerson Hall, Cornell University, Ithaca, NY 14853-1901, USA, US aut NATIONALLICENCE 700 1- Park W. D. Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77845, USA, US aut NATIONALLICENCE 700 1- Ayres N. Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77845, USA, US aut NATIONALLICENCE 700 1- Cartinhour S. Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77845, USA, US aut Metadata rights reserved Springer special CC-BY-NC licence nationallicence BK010053 XK010053 XK010000 NATIONALLICENCE NATIONALLICENCE NL-springer