Microsatellites and microsynteny in the chloroplast genomes of Oryza and eight other Gramineae species

被引:101
作者
Ishii, T [1 ]
McCouch, SR [1 ]
机构
[1] Cornell Univ, Dept Plant Breeding, Ithaca, NY 14853 USA
关键词
chloroplast microsatellite; simple sequence length polymorphism (SSLP) allelic diversity; rice (Oryza sativa); Gramineae;
D O I
10.1007/s001220051432
中图分类号
S3 [农学(农艺学)];
学科分类号
0901 ;
摘要
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 I-ice 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.
引用
收藏
页码:1257 / 1266
页数:10
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