Ribosomal DNA spacer-length polymorphisms in barley: mendelian inheritance, chromosomal location, and population dynamics.
01 Dec 1984-Proceedings of the National Academy of Sciences of the United States of America (National Academy of Sciences)-Vol. 81, Iss: 24, pp 8014-8018
TL;DR: It is concluded that the rDNA sl variants and/or associated loci are under selection in CCII, which demonstrates that Rrn1 and Rrn2 are useful as new genetic markers.
Abstract: Spacer-length (sl) variation in ribosomal RNA gene clusters (rDNA) was surveyed in 502 individual barley plants, including samples from 50 accessions of cultivated barley, 25 accessions of its wild ancestor, and five generations of composite cross II (CCII), an experimental population of barley. In total, 17 rDNA sl phenotypes, made up of 15 different rDNA sl variants, were observed. The 15 rDNA sl variants comprise a complete ladder in which each variant differs in length from adjacent variants by approximately equal to 115 nucleotide pairs. Studies of four rDNA sl variants in an F2 population showed that these variants are located at two unlinked loci, Rrn1 and Rrn2, each with two codominant alleles. Using wheat-barley addition lines, we determined that Rrn1 and Rrn2 are located on chromosomes 6 and 7, respectively. The nonrandom distribution of sl variants between loci suggests that genetic exchange occurs much less frequently between than within the two loci, which demonstrates that Rrn1 and Rrn2 are useful as new genetic markers. Frequencies of rDNA sl phenotypes and variants were monitored over 54 generations in CCII. A phenotype that was originally infrequent in CCII ultimately became predominant, whereas the originally most frequent phenotype decreased drastically in frequency, and all other phenotypes originally present disappeared from the population. We conclude that the sl variants and/or associated loci are under selection in CCII.
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TL;DR: An analysis of aligned sequences of the four nuclear and two mitochondrial rRNA genes identified regions of these genes that are likely to be useful to address phylogenetic problems over a wide range of levels of divergence.
Abstract: Ribosomal DNA (rDNA) sequences have been aligned and compared in a number of living organisms, and this approach has provided a wealth of information about phylogenetic relationships. Studies of rDNA sequences have been used to infer phylogenetic history across a very broad spectrum, from studies among the basal lineages of life to relationships among closely related species and populations. The reasons for the systematic versatility of rDNA include the numerous rates of evolution among different regions of rDNA (both among and within genes), the presence of many copies of most rDNA sequences per genome, and the pattern of concerted evolution that occurs among repeated copies. These features facilitate the analysis of rDNA by direct RNA sequencing, DNA sequencing (either by cloning or amplification), and restriction enzyme methodologies. Constraints imposed by secondary structure of rRNA and concerted evolution need to be considered in phylogenetic analyses, but these constraints do not appear to impede seriously the usefulness of rDNA. An analysis of aligned sequences of the four nuclear and two mitochondrial rRNA genes identified regions of these genes that are likely to be useful to address phylogenetic problems over a wide range of levels of divergence. In general, the small subunit nuclear sequences appear to be best for elucidating Precambrian divergences, the large subunit nuclear sequences for Paleozoic and Mesozoic divergences, and the organellar sequences of both subunits for Cenozoic divergences. Primer sequences were designed for use in amplifying the entire nuclear rDNA array in 15 sections by use of the polymerase chain reaction; these "universal" primers complement previously described primers for the mitochondrial rRNA genes. Pairs of primers can be selected in conjunction with the analysis of divergence of the rRNA genes to address systematic problems throughout the hierarchy of life.
2,439 citations
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...In addition, variation in the spacer regions has been used to identify species or strains, to study hybridization, and as markers in population genetic studies (Toivonen et al., 1983; Saghai-Maroof et al., 1984; Rogers et al., 1986; Learn and Schaal, 1987; Schaal et al., 1987; Baker et al., 1989; King and Schaal, 1989; Sites and Davis, 1989; Hillis, Moritz, Porter, and Baker, 1991)....
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TL;DR: Results show that with the software tool developed, EST databases can be efficiently exploited for the development of cDNA-SSRs, EST-derived SSRs are significantly less polymorphic than those derived from genomic regions, a considerable portion of the developed SSRs can be transferred to related species, and compared to RFLP-markers, c DNA- SSRs yield similar patterns of genetic diversity.
Abstract: A software tool was developed for the identification of simple sequence repeats (SSRs) in a barley (Hordeum vulgare L.) EST (expressed sequence tag) database comprising 24,595 sequences. In total, 1,856 SSR-containing sequences were identified. Trimeric SSR repeat motifs appeared to be the most abundant type. A subset of 311 primer pairs flanking SSR loci have been used for screening polymorphisms among six barley cultivars, being parents of three mapping populations. As a result, 76 EST-derived SSR-markers were integrated into a barley genetic consensus map. A correlation between polymorphism and the number of repeats was observed for SSRs built of dimeric up to tetrameric units. 3′-ESTs yielded a higher portion of polymorphic SSRs (64%) than 5′-ESTs did. The estimated PIC (polymorphic information content) value was 0.45 ± 0.03. Approximately 80% of the SSR-markers amplified DNA fragments in Hordeum bulbosum, followed by rye, wheat (both about 60%) and rice (40%). A subset of 38 EST-derived SSR-markers comprising 114 alleles were used to investigate genetic diversity among 54 barley cultivars. In accordance with a previous, RFLP-based, study, spring and winter cultivars, as well as two- and six-rowed barleys, formed separate clades upon PCoA analysis. The results show that: (1) with the software tool developed, EST databases can be efficiently exploited for the development of cDNA-SSRs, (2) EST-derived SSRs are significantly less polymorphic than those derived from genomic regions, (3) a considerable portion of the developed SSRs can be transferred to related species, and (4) compared to RFLP-markers, cDNA-SSRs yield similar patterns of genetic diversity.
2,093 citations
Cites methods from "Ribosomal DNA spacer-length polymor..."
...Genomic DNA from the above plants was isolated from young leaves using the CTAB method described by Saghai-Maroof et al. (1984)....
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TL;DR: This is the first procedure for the isolation of DNA from mature strawberry leaf tissue that produces consistent results for a variety of different species, both octoploid and diploid, and is both stable and PCR amplifiable before and after extended storage.
Abstract: A relatively quick, inexpensive and consistent protocol for extraction of DNA from expanded leaf material containing large quantities of polyphenols, tannins and polysaccharides is described. Mature strawberry leaves, which contain high levels of these secondary components, were used as a study group. The method involves a modified CTAB extraction, employing high salt concentrations to remove polysaccharides, the use of polyvinyl pyrrolidone (PVP) to remove polyphenols, an extended RNase treatment and a phenol-chloroform extraction. Average yields range from 20 to 84 μg/g mature leaf tissue for both wild and cultivated octoploid and diploidFragaria species. Results from 60 plants were examined, and were consistently amplifiable in the RAPD reaction with as little as 0.5 ng DNA per 25-μL reaction. Presently, this is the first procedure for the isolation of DNA from mature strawberry leaf tissue that produces consistent results for a variety of different species, both octoploid and diploid, and is both stable and PCR amplifiable before and after extended storage. This procedure may prove useful for other difficult species in the family Rosaceae.
1,869 citations
TL;DR: SSR technology presents the potential advantages of reliability, reproducibility, discrimination, standardization and cost effectiveness over RFLPs, and represents the optimum approach for the identification and pedigree validation of maize genotypes compared to other currently available methods.
Abstract: The utility of 131 simple sequence repeat (SSR) loci to characterize and identify maize inbred lines, validate pedigree, and show associations among inbred lines was evaluated using a set of 58 inbred lines and four hybrids. Thirteen sets of inbred parent-progeny triplet pedigrees together with four hybrids and their parental lines were used to quantify incidences of scoring that departed from expectations based upon simple Mendelian inheritance. Results were compared to those obtained using 80 restriction fragment length polymorphism (RFLP) probes. Over all inbred triplets, 2.2% of SSRs and 3.6% of RFLP loci resulted in profiles that were scored as having segregated in a non-Mendelian fashion. Polymorphic index content (PIC, a measure of discrimination ability) values ranged from 0.06 to 0.91 for SSRs and from 0.10 to 0.84 for RFLPs. Mean values for PIC for SSRs and RFLPs were similar, approximately 0.62. However, PIC values for nine SSRs exceeded the maximum PIC for RFLPs. Di-repeats gave the highest mean PIC scores for SSRs but this class of repeats can result in “stutter” bands that complicate accurate genotyping. Associations among inbreds were similar for SSR and RFLP data, closely approximating expectations from known pedigrees. SSR technology presents the potential advantages of reliability, reproducibility, discrimination, standardization and cost effectiveness over RFLPs. SSR profiles can be readily interpreted in terms of alleles at mapped loci across a broad range of maize germ plasm. Consequently, SSRs represent the optimum approach for the identification and pedigree validation of maize genotypes compared to other currently available methods.
877 citations
Cites methods from "Ribosomal DNA spacer-length polymor..."
...Initial DNA extractions were made using the CTAB procedure (Saghai-Maroof et al. 1984)....
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...Initial DNA extractions were made using the CTAB procedure ( Saghai-Maroof et al. 1984 )....
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TL;DR: Results are presented, comparing total cellular DNA samples extracted from a set of fresh and silica-gel dried samples of the same species, as well as examining the efficiency of endonuclease restriction and intactness of DNA from of aSet of field-collected leaves preserved with silica gel.
Abstract: Silica gels an inexpensive and reliable substance to preserve field-collected leaves for molecular studies of variation in DNA. A method for its utilization is explained, and results are presented, comparing total cellular DNA samples extracted from a set of fresh and silica-gel dried samples of the same species, as well as examining the efficiency of endonuclease restriction and intactness of DNA from of a set of field-collected leaves preserved with silica gel.
799 citations
References
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TL;DR: This paper describes a method of transferring fragments of DNA from agarose gels to cellulose nitrate filters that can be hybridized to radioactive RNA and hybrids detected by radioautography or fluorography.
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Abstract: A method is presented for the rapid isolation of high molecular weight plant DNA (50,000 base pairs or more in length) which is free of contaminants which interfere with complete digestion by restriction endonucleases. The procedure yields total cellular DNA (i.e. nuclear, chloroplast, and mitochondrial DNA). The technique is ideal for the rapid isolation of small amounts of DNA from many different species and is also useful for large scale isolations.
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TL;DR: Comparison of Hae III and Hpa II digestion of cereal rDNAs and the cloned repeats suggests that most methylated cytosines in natural rDNA are in -CpG-.
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