The population structure of domesticated species is influenced by the natural history of the populations of predomesticated ancestors, as well as by the breeding system and complexity of the breeding practices exercised by humans. Within Oryza sativa, there is an ancient and well-established divergence between the two major subspecies, indica and japonica, but finer levels of genetic structure are suggested by the breeding history. In this study, a sample of 234 accessions of rice was genotyped at 169 nuclear SSRs and two chloroplast loci. The data were analyzed to resolve the genetic structure and to interpret the evolutionary relationships between groups. Five distinct groups were detected, corresponding to indica, aus, aromatic, temperate japonica, and tropical japonica rices. Nuclear and chloroplast data support a closer evolutionary relationship between the indica and the aus and among the tropical japonica, temperate japonica, and aromatic groups. Group differences can be explained through contrasting demographic histories. With the availability of rice genome sequence, coupled with a large collection of publicly available genetic resources, it is of interest to develop a population-based framework for the molecular analysis of diversity in O. sativa.

The RAPD (or AP-PCR) DNA fingerprinting method was used to distinguish among clinical isolates of Helicobacter pylori, a bacterium whose long term carriage is associated with gastritis, peptic ulcers and gastric carcinomas. This method uses arbitrarily chosen oligonucleotides to prime DNA synthesis from genomic sites to which they are fortuitously matched, or almost matched. Most 10-nt primers with > or = 60% G + C yielded strain-specific arrays of up to 15 prominent fragments, as did most longer (> or = 17-nt) primers, whereas most 10-nt primers with 50% G+C did not. Each of 64 independent H. pylori isolates, 60 of which were from patients in the same hospital, was distinguishable with a single RAPD primer, which suggests a high level of DNA sequence diversity within this species. In contrast, isolates from initial and followup biopsies were indistinguishable in each of three cases tested.

Simple sequence repeats (SSRs), also known as microsatellites, are highly variable DNA sequences that can be used as markers for the genetic analysis of plants. Three approaches were followed for the development of PCR primers for the amplification of DNA fragments containing SSRs from sorghum [Sorghum bicolor (L.) Moench]: a search for sorghum SSRs in public DNA databases; the use of SSR-specific primers developed in the Poaceae species maize (Zea mays L.) and seashore paspalum grass (Paspalum vaginatum Swartz); and the screening of sorghum genomic libraries by hybridization with SSR oligonucleotides. A total of 49 sorghum SSR-specific PCR primer pairs (two designed from GenBank SSR-containing sequences and 47 from the sequences of genomic clones) were screened on a panel of 17 sorghum and one maize accession. Ten primer pairs from paspalum and 90 from maize were also screened for polymorphism in sorghum. Length polymorphisms among amplification products were detected with 15 of these primer pairs, yielding diversity values ranging from 0.2 to 0.8 with an average diversity of 0.56. These primer pairs are now available for use as markers in crop improvement and conservation efforts.

phisms among 36 sorghum lines were equally low for profiles obtained by means of 30 RAPD primers or 29 DNA markers are being increasingly utilized in cultivar develop- RFLP probes. Vierling et al. (1994) found 73 RAPD ment, quality control of seed production, measurement of genetic diversity for conservation management, varietal identity, and to assist primers discriminated among sorghum lines but those in maintenance of intellectual property protection (IPP). The use of data did not allow lines to be associated into groupings simple sequence repeats (SSRs) for variety profiling can provide high that reflected pedigrees. Associations among 34 lines discrimination, with excellent reproducibility at less cost than for determined by 19 RFLP probes, 21 RAPD primers, and restriction fragment length polymorphisms (RFLPs). The objective 41 ISSRs were markedly different and dependent on of this study was to evaluate the potential utility of SSR technology the source of molecular profile data (Yang et al., 1996). for applications in research, product development, seed production, Ahnert et al. (1996) reported a study of 105 sorghum and genetic resource conservation management for sorghum. Fifty inbreds that used 104 RFLP probes which showed genetically diverse elite sorghum [Sorghum bicolor (L.) Moench]higher levels of polymorphism and associations of lines inbreds were used to compare the discrimination abilities of 15 SSR that were congruent with pedigree information and primers with 104 RFLPs and to compare the associations among lines revealed by these molecular data and by pedigrees. RFLP data allowed

Fourteen microsatellites containing GArepeats were isolated and characterized in cassava (Manihot esculenta Crantz, Euphorbiaceae). Microsatellite heterozygosity (h) was estimated in 48 accessions using (P)-end-labeled primers and in more than 500 accessions using fluorescence-based genotyping. Heterozygosity values ranged from 0.00 to 0.88 and the number of alleles detected varied from 1 to 15. The reproducibility of allele sizing was also assessed using fluorescence-based genotyping. The average inter-gel size difference was 1.03 nucleotides. Chi-square tests ( ) were performed to analyse segregation distortion and the linkage between alleles segregating from either or both parents in an F mapping population. Most microsatellite loci segregated in the expected 1 : 1, 1 : 2 : 1 or 1 : 1 : 1 : 1 ratio. Linkage was detected between loci segregating from either parent, and segregation distortion from the male parent was detected for locus GA-131. Approximately 80% of the microsatellites detected one or two alleles per accession, suggesting a low degree of microsatellite locus duplication, an unexpected finding for a putative allopolyploid, highly