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GrainGenes Reference Report: TAG-100-1257

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Reference	TAG-100-1257
Title	Microsatellites and microsynteny in the chloroplast genomes of Oryza and eight other Gramineae species
Journal	Theoretical and Applied Genetics
Year	2000
Volume	100
Pages	1257-1266
Author	Ishii T McCouch SR
Abstract	Summary: Primer pairs flanking ten chloroplast microsatellite loci, originally identified in Oryza sativa cv Nipponbare, were evaluated for amplification and allelic diversity using a panel of 13 diverse cultivars of rice (O. sativa), 19 accessions of wild rice (three O. officinalis, five O. latifolia, five O. minuta, four O. australiensis, one O. brachyantha and one O. ridleyi) and eight other Gramineae species (maize, teosinte, wheat, oat, barley, pearl millet, sorghum and sugarcane). Amplified products were obtained for all samples at nine out of ten loci. Among the rice cultivars, the number of alleles per locus ranged from one to four, with monomorphic patterns observed at five loci. The average polymorphism information content (PIC) value at the other five (polymorphic) loci was 0.54 among the 13 cultivars. When wild rice and the other Gramineae species were compared based on the proportion of shared alleles, their phylogenetic relationships were in agreement with previous studies using different types of markers; however, the magnitude of the differences based on chloroplast microsatellites underestimated the genetic distance separating these divergent species and genera. A sequence-based comparison of homologous regions of the rice and maize chloroplast genomes revealed that, while a high level of microsynteny is evident, the occurrence of actively evolving microsatellite motifs in specific regions of the rice chloroplast genome appears to be mainly a species or genome-specific phenomenon. Thus the chloroplast primer pairs used in this study bracketed mutationally active microsatellite motifs in rice but degenerate, interrupted motifs or highly conserved, mutationally inert motifs in distantly related genera
External Databases	http://link.springer-ny.com/link/service/journals/00122/bibs/0100008/01001257.htm"
Keyword	[ Hide all but 1 of 41 ] accessions alleles amplification animal barley chloroplast chloroplast genome chloroplast microsatellite comprehensive genetic-map cultivated rice distance diversity dna marker genera genetic distance genome genus oryza gramineae linkage map loci locus maize marker microsatellite microsatellite loci millet oat oryza sativa pattern pearl millet phylogenetic relationships polymorphism rice sequence simple sequence length polymorphism (sslp) allelic diversity simple sequence repeat sorghum sugarcane teosinte wild wild rice

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