Abstract
We have used the polymorphic chloroplast (cp) and nuclear simple sequence repeats (SSRs) to analyse levels of cytoplasmic and nuclear diversity in the gene pool of the European cultivated potato (Solanum tuberosum ssp. tuberosum). Primers designed from the complete chloroplast sequence of tobacco (Nicotiana tabacum) were used to amplify polymorphic products in a range of potato cultivars. Combining the data from seven polymorphic cpSSR loci gave 26 haplotypes, one of which (haplotype A) accounted for 151 out of the 178 individuals studied and corresponded to the T-type cytoplasm previously identified in cultivated potatoes using chloroplast restriction fragment length polymorphism analysis. Phylogenetic and diversity analyses of the relationships between cpSSR haplotypes confirmed much higher levels of cytoplasmic diversity outwith the T-type group. Diversity levels at eight nuclear SSR loci, however, were not significantly different between cytoplasmic groups, suggesting a severe maternal bottleneck in the evolution of the modern cultivated potato. These results highlight the importance in quantifying levels of cytoplasmic as well as nuclear diversity and confirm the need for a change in breeding practices to increase levels of non-T-type cytoplasm in the cultivated gene pool, thus helping reduce problems associated with pollen sterility. This may be facilitated by germplasm analysis using cpSSRs, which will allow efficient selection of diverse cytoplasm donors.
Full Text
The Full Text of this article is available as a PDF (145.8 KB).
Selected References
These references are in PubMed. This may not be the complete list of references from this article.
- Goldstein D. B., Ruiz Linares A., Cavalli-Sforza L. L., Feldman M. W. Genetic absolute dating based on microsatellites and the origin of modern humans. Proc Natl Acad Sci U S A. 1995 Jul 18;92(15):6723–6727. doi: 10.1073/pnas.92.15.6723. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Michalakis Y., Excoffier L. A generic estimation of population subdivision using distances between alleles with special reference for microsatellite loci. Genetics. 1996 Mar;142(3):1061–1064. doi: 10.1093/genetics/142.3.1061. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Milbourne D., Meyer R. C., Collins A. J., Ramsay L. D., Gebhardt C., Waugh R. Isolation, characterisation and mapping of simple sequence repeat loci in potato. Mol Gen Genet. 1998 Aug;259(3):233–245. doi: 10.1007/s004380050809. [DOI] [PubMed] [Google Scholar]
- Morgante M., Olivieri A. M. PCR-amplified microsatellites as markers in plant genetics. Plant J. 1993 Jan;3(1):175–182. [PubMed] [Google Scholar]
- Powell W., Morgante M., Andre C., McNicol J. W., Machray G. C., Doyle J. J., Tingey S. V., Rafalski J. A. Hypervariable microsatellites provide a general source of polymorphic DNA markers for the chloroplast genome. Curr Biol. 1995 Sep 1;5(9):1023–1029. doi: 10.1016/s0960-9822(95)00206-5. [DOI] [PubMed] [Google Scholar]
- Powell W., Morgante M., Doyle J. J., McNicol J. W., Tingey S. V., Rafalski A. J. Genepool variation in genus Glycine subgenus Soja revealed by polymorphic nuclear and chloroplast microsatellites. Genetics. 1996 Oct;144(2):793–803. doi: 10.1093/genetics/144.2.793. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Powell W., Morgante M., McDevitt R., Vendramin G. G., Rafalski J. A. Polymorphic simple sequence repeat regions in chloroplast genomes: applications to the population genetics of pines. Proc Natl Acad Sci U S A. 1995 Aug 15;92(17):7759–7763. doi: 10.1073/pnas.92.17.7759. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Provan J., Corbett G., McNicol J. W., Powell W. Chloroplast DNA variability in wild and cultivated rice (Oryza spp.) revealed by polymorphic chloroplast simple sequence repeats. Genome. 1997 Feb;40(1):104–110. doi: 10.1139/g97-014. [DOI] [PubMed] [Google Scholar]
- Provan J., Corbett G., Waugh R., McNicol J. W., Morgante M., Powell W. DNA fingerprints of rice (Oryza sativa) obtained from hypervariable chloroplast simple sequence repeats. Proc Biol Sci. 1996 Oct 22;263(1375):1275–1281. doi: 10.1098/rspb.1996.0187. [DOI] [PubMed] [Google Scholar]
- Saghai-Maroof M. A., Soliman K. M., Jorgensen R. A., Allard R. W. Ribosomal DNA spacer-length polymorphisms in barley: mendelian inheritance, chromosomal location, and population dynamics. Proc Natl Acad Sci U S A. 1984 Dec;81(24):8014–8018. doi: 10.1073/pnas.81.24.8014. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Shinozaki K., Ohme M., Tanaka M., Wakasugi T., Hayashida N., Matsubayashi T., Zaita N., Chunwongse J., Obokata J., Yamaguchi-Shinozaki K. The complete nucleotide sequence of the tobacco chloroplast genome: its gene organization and expression. EMBO J. 1986 Sep;5(9):2043–2049. doi: 10.1002/j.1460-2075.1986.tb04464.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Slatkin M. A measure of population subdivision based on microsatellite allele frequencies. Genetics. 1995 Jan;139(1):457–462. doi: 10.1093/genetics/139.1.457. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Tanksley S. D., McCouch S. R. Seed banks and molecular maps: unlocking genetic potential from the wild. Science. 1997 Aug 22;277(5329):1063–1066. doi: 10.1126/science.277.5329.1063. [DOI] [PubMed] [Google Scholar]
- Wolfe K. H., Li W. H., Sharp P. M. Rates of nucleotide substitution vary greatly among plant mitochondrial, chloroplast, and nuclear DNAs. Proc Natl Acad Sci U S A. 1987 Dec;84(24):9054–9058. doi: 10.1073/pnas.84.24.9054. [DOI] [PMC free article] [PubMed] [Google Scholar]