Markers derived from amplified fragment length polymorphism gels for plant ecology and evolution studies

McLenachan, Patricia A.; Stöckler, Karen; Winkworth, Richard C.; McBreen, Kim; Zauner, Stefan; Lockhart, P. J.

doi:10.1046/j.1365-294x.2000.01075.x

Cited by 23 publications

(18 citation statements)

References 11 publications

(13 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…This study and an earlier one which reported on AFLP-derived SCAR markers for other New Zealand plants (McLenachan et al 2000) suggest that standard conventional markers, such as the nuclear ITS region, provide limited resolution for characterising closely related selections of even morphologically diverse genera such as Phormium. Our results show that higher levels of resolution can be found using marker systems such as ISSR and AFLP.…”

Section: Discussionmentioning

confidence: 62%

“…Amplified fragment length polymorphisms (AFLP) and intersimple sequence repeats (ISSR) have also been applied to distinguish closely related taxa in natural populations of plants (e.g., Esselman et al 1999;Perrie et al 2000). Some concern has been raised over the use of fingerprinting methods for testing phylogenetic relationships (e.g., Swofford et al 1996;Yang et al 1996;McLenachan et al 2000). For example, presence or absence of particular bands may be non-independent, and amplification of fragments may be influenced by quality and quantity of DNA template, rendering results unrepeatable.…”

Section: Introductionmentioning

confidence: 99%

“…Once identified, these regions can be amplified and characterised using PCR primers specific for these regions (Lockhart & McLenachan 1997;Shan et al 1999). Often such regions show elevated substitution rates (Lockhart et al 2001) and are useful for studying the relationships between closely related taxa (McLenachan et al 2000). This implementation of AFLP was used in the present work.…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

The use of molecular techniques to resolve relationships among traditional weaving cultivars ofPhormium

McBreen¹,

Lockhart²,

McLenachan³

et al. 2003

New Zealand Journal of Botany

View full text Add to dashboard Cite

Molecular techniques -sequencing of the nuclear internal transcribed spacer region (ITS), and fingerprinting of amplified fragment length polymorphisms (AFLP) and intersimple sequence repeats (ISSR) -were investigated for their potential to characterise genetic variation in harakeke (Phormium spp., family Hemerocallidaceae) in New Zealand. ITS showed no variation between species of Phormium. However, both AFLP and ISSR identified genome regions that were polymorphic among intraspecific accessions of Phormium obtained from the National New Zealand Flax Collection. When used as a direct sequencing marker, one AFLP fragment distinguished two major groups of nuclear haplotypes. The partitioning of taxa into these groups was supported by phylogenetic analysis of ISSR fingerprinting profiles. Split decomposition, a network-building technique, was shown to be useful in representing the sorts of relationships present in this study of intraspecific variation. Further sampling of natural populations is required to understand the origins and present-day distributions of these accessions; however, the present results show the usefulness of these methods for addressing such ethnobotanic questions.

show abstract

Section: Discussionmentioning

confidence: 62%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

The use of molecular techniques to resolve relationships among traditional weaving cultivars ofPhormium

McBreen¹,

Lockhart²,

McLenachan³

et al. 2003

New Zealand Journal of Botany

View full text Add to dashboard Cite

show abstract

“…(b) The SCAR-based approach where screening for variability in RAPD-generated DNA fragments among closely related species precedes design of primers (modified from Bailey et al 2004). regions (SCARs; Melotto et al 1996) that can be screened as potentially useful sequence loci prior to development of specific primers (Shaw et al 2003;Bailey et al 2004). This strategy is a modified version of the AFLP-based method of McLenachan et al (2000) for characterizing population level gel-based markers. Under this method, PCR products of equal length amplified across a subset of species using commercially available random primers are excised, cloned, sequenced and aligned to evaluate variability (figure 4b; Bailey et al 2004).…”

Section: Strategies For Selecting Nuclear Sequence Locimentioning

confidence: 99%

From famine to feast? Selecting nuclear DNA sequence loci for plant species-level phylogeny reconstruction

Hughes

Eastwood

Bailey

2005

Phil. Trans. R. Soc. B

120

View full text Add to dashboard Cite

Phylogenetic analyses of DNA sequences have prompted spectacular progress in assembling the Tree of Life. However, progress in constructing phylogenies among closely related species, at least for plants, has been less encouraging. We show that for plants, the rapid accumulation of DNA characters at higher taxonomic levels has not been matched by conventional sequence loci at the species level, leaving a lack of well-resolved gene trees that is hindering investigations of many fundamental questions in plant evolutionary biology. The most popular approach to address this problem has been to use low-copy nuclear genes as a source of DNA sequence data. However, this has had limited success because levels of variation among nuclear intron sequences across groups of closely related species are extremely variable and generally lower than conventionally used loci, and because no universally useful low-copy nuclear DNA sequence loci have been developed. This suggests that solutions will, for the most part, be lineage-specific, prompting a move away from 'universal' gene thinking for species-level phylogenetics. The benefits and limitations of alternative approaches to locate more variable nuclear loci are discussed and the potential of anonymous nongenic nuclear loci is highlighted. Given the virtually unlimited number of loci that can be generated using these new approaches, it is clear that effective screening will be critical for efficient selection of the most informative loci. Strategies for screening are outlined.

show abstract

“…Also, the reproducibility of AFLP markers is lower than for single locus markers and homoplasy of equal-sized fragments cannot be excluded. Finally, the application of AFLP markers for wood identification faces difficulties because of the need for goodquality genomic DNA (McLenachan et al 2000), whereas quality and quantity of DNA from wood is generally low (De Filippis and Magel 1998;Dumolin-Lapègue et al 1999;Deguilloux et al 2002;Rachmayanti et al 2006Rachmayanti et al , 2009. Thus, AFLP markers need to be converted into locus-specific markers [sequence characterized amplified region (SCAR markers)].…”

Section: Introductionmentioning

confidence: 99%

Development of a diagnostic DNA marker for the geographic origin of Shorea leprosula

2016

View full text Add to dashboard Cite

Abstract:The development of sequence characterized amplified region (SCAR) markers derived from amplified fragment length polymorphisms (AFLPs) is described for Shorea leprosula. An AFLP fragment that showed nearly complete differentiation between Borneo and Sumatra was gel-extracted, sequenced, and converted into a SCAR marker using the inverse polymerase chain reaction (PCR) technique. The single nucleotide polymorphism (SNP) that originally caused the AFLP was found in the MseI restriction site. Differentiation between islands was detected either as size variation of the codominant SCAR marker or after digestion of the PCR products with the restriction enzyme MseI (PCR-RFLP). Size variation was due to insertions/deletions found within the sequenced region that flanked the original AFLP fragment. After genotyping 151 samples of S. leprosula from 14 populations in Sumatra and Borneo, all but one sample from Sumatra were homozygous for one size variant (427 bp), while S. leprosula populations from Borneo showed different genotypes than Sumatra populations and variation not only among populations but also within populations. Complete differentiation and fixation on alternative variants was found for the geographic regions of Sumatra and Borneo by the PCR-RFLP method. The SCAR marker did not amplify in Shorea parvifolia and thus can also be used to distinguish between S. leprosula and S. parvifolia. The marker was successfully amplified from wood DNA extracts suggesting its applicability to track the geographic origin of timber.

show abstract

Markers derived from amplified fragment length polymorphism gels for plant ecology and evolution studies

Cited by 23 publications

References 11 publications

The use of molecular techniques to resolve relationships among traditional weaving cultivars ofPhormium

The use of molecular techniques to resolve relationships among traditional weaving cultivars ofPhormium

From famine to feast? Selecting nuclear DNA sequence loci for plant species-level phylogeny reconstruction

Development of a diagnostic DNA marker for the geographic origin of Shorea leprosula

Contact Info

Product

Resources

About