Silver staining DNA in polyacrylamide gels

Bassam, Brant J.; Gresshoff, Peter M.

doi:10.1038/nprot.2007.330

Cited by 171 publications

(113 citation statements)

References 17 publications

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“…DNA fragments were visualized by silver staining (Bassam and Gresshoff 2007). The specificity of SSAP reaction was confirmed by sequencing 17 random bands which were excised from BARE-1 gel-separated products and reamplified in the same conditions as the 2nd PCR step described above.…”

Section: Ssap Protocolmentioning

confidence: 99%

Molecular markers based on LTR retrotransposons BARE-1 and Jeli uncover different strata of evolutionary relationships in diploid wheats

et al. 2010

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Molecular markers based on retrotransposon insertions are widely used for various applications including phylogenetic analysis. Multiple cases were described where retrotransposon-based markers, namely sequence-specific amplification polymorphism (SSAP), were superior to other marker types in resolving the phylogenetic relationships due to their higher variability and informativeness. However, the patterns of evolutionary relationships revealed by SSAP may be dependent on the underlying retrotransposon activity in different periods of time. Hence, the proper choice of retrotransposon family is essential for obtaining significant results. We compared the phylogenetic trees for a diverse set of diploid A-genome wheat species (Triticum boeoticum, T. urartu and T. monococcum) based on two unrelated retrotransposon families, BARE-1 and Jeli. BARE-1 belongs to Copia class and has a uniform distribution between common wheat (T. aestivum) genomes of different origin (A, B and D), indicating similar activity in the respective diploid genome donors. Gypsy-class family Jeli was found by us to be an A-genome retrotransposon with >70% copies residing in A genome of hexaploid common wheat, suggesting a burst of transposition in the history of A-genome progenitors. The results indicate that a higher Jeli transpositional activity was associated with T. urartu versus T. boeoticum speciation, while BARE-1 produced more polymorphic insertions during subsequent intraspecific diversification; as an outcome, each retrotransposon provides more informative markers at the corresponding level of phylogenetic relationships. We conclude that multiple retroelement families should be analyzed for an image of evolutionary relationships to be solid and comprehensive.

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Section: Ssap Protocolmentioning

confidence: 99%

Molecular markers based on LTR retrotransposons BARE-1 and Jeli uncover different strata of evolutionary relationships in diploid wheats

et al. 2010

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“…Genomic DNA (*500 ng) was digested with 5 U each of EcoR1 for 30 s, 72°C for 1 min, and finishing with 72°C for 2 min. 2 ll of the final AFLP PCR product were separated on 6% polyacrylamide gels and visualized by staining with silver nitrate using the protocol described by Switzer et al (1979) as modified by Bassam and Gresshoff (2007). All samples were replicated from the pre-amplification step onward, with miss-matches in replicates resulting in that sample being excluded from the analysis.…”

Section: Dna Isolationmentioning

confidence: 99%

Patterns of genetic variation in invasive populations of Gunnera tinctoria: an analysis at three spatial scales

Fennell

Gallagher

2010

Biol Invasions

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While there is evidence that the genetic structure of invasive populations may be distinct from native populations, it has proved difficult to establish the causes of any variation owing in part to the range of evolutionary processes involved. In order to assess differences in the genetic structure of invasive populations of Gunnera tinctoria, five native populations were compared to 23 geographically widely dispersed invasive populations using amplified fragment length polymorphic markers (AFLPs). In total, 221 individuals were sampled at three spatial scales: inter-regional, within-region, and at a high-resolution local scale. It was observed that there were high levels of genetic variation between most populations, that invasive populations were generally distinct from both native populations and from each other and that genetic variation away from founding populations can occur relatively quickly and within a small geographic area. Changes in the pattern of genetic variation observed in invasive populations strongly indicated that founder effects and genetic drift played a significant role in shaping their genetic structure. It was further concluded that gene flow had a homogenizing effect on the structure of invasive populations occurring in close proximity, increasing their allele content and potentially contributing to their successful establishment.

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“…Products were separated on 8% polyacrylamide gel electrophoresis run at a constant 55 watts for 1 h 45 min. PCR product was visualized by silver staining using the method described by Bassam and Caetano-Anolles (1993).…”

Section: Dna Testingmentioning

confidence: 99%

Screening for grain dormancy in segregating generations of dormant × non-dormant crosses in white-grained wheat (Triticum aestivum L.)

et al. 2009

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Pre-harvest sprouting (PHS) in wheat (Triticum aestivum L.) is a significant problem. Introgression of genes controlling grain dormancy into white-grained bread wheat is one means of improving resistance to PHS. In this study seven dormant (containing the SW95-50213 and AUS1408 sources) 9 non-dormant crosses were produced to investigate the effectiveness of selection for grain dormancy in early segregating generations. Each generation (F 1 -F 4 ) was grown in a temperature controlled glasshouse with an extended photoperiod (i.e. continuous light). F 2 and F 3 generations were subject to selection. Five hundred harvest-ripe grains were tested for germination over a 14 day period, and the 100 most dormant grains were retained and grown-on to produce the next generation within each cross. The response to selection was assessed through analysis of the time to 50% germination (G 50 ) in the F 2 , F 3 and F 4 generations. In addition, changes in marker class frequencies for two SSR markers (barc170 and gpw2279) flanking a known quantitative trait locus (QTL) for grain dormancy on chromosome 4A were assessed in DNA from F 2 plants selected from early germinating (nondormant) and late germinating (dormant) phenotypic extremes within each cross. Selection for grain dormancy in the F 2 and F 3 generations effectively recovered the dormant phenotype in all seven crosses, i.e. the F 4 generation was not significantly different from the dormant parent. Further, selection based on individual F 2 grains changed marker class frequencies for the 4A dormancy QTL; in most cases eliminating the marker class homozygous for the non-dormant alleles. Application of this screening method will enable breeders to better select for grain dormancy and may lead to development of new cultivars offering effective resistance to PHS in the near future.

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Silver staining DNA in polyacrylamide gels

Cited by 171 publications

References 17 publications

Molecular markers based on LTR retrotransposons BARE-1 and Jeli uncover different strata of evolutionary relationships in diploid wheats

Molecular markers based on LTR retrotransposons BARE-1 and Jeli uncover different strata of evolutionary relationships in diploid wheats

Patterns of genetic variation in invasive populations of Gunnera tinctoria: an analysis at three spatial scales

Screening for grain dormancy in segregating generations of dormant × non-dormant crosses in white-grained wheat (Triticum aestivum L.)

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