Application of fluorescence-based semi-automated AFLP analysis in barley and wheat

Schwarz, Gerhard; Herz, Markus; Huang, Xiong-Ying; Michalek, Wolfgang; Jahoor, A.; Wenzel, G.; Mohler, Volker

doi:10.1007/s001220050071

Cited by 43 publications

(32 citation statements)

References 20 publications

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“…This obviously led to high error rates during scoring. These results are supported by the observations of Schwarz et al (2000), showing greater inter-gel differences in the band size of identical samples than intra-gel differences for fluorescence-based semi-automated AFLP analysis in barley and wheat. Sneath and Sokal (1973) noted the usefulness of testing the significance of the difference between similarity coefficients.…”

Section: Error Estimationsupporting

confidence: 89%

Genetic diversity in recent elite faba bean lines using AFLP markers

2003

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Amplified fragment length polymorphism (AFLP) markers were used to study the genetic diversity among a large set (n = 79) of inbred lines of recent elite faba bean ( Vicia faba L.) cultivars with Asian, European (Northern and Southern) and North African origin. The inbred lines were analyzed using eight selected AFLP primer combinations that produced 477 polymorphic fragments. Errors when scoring repeated lanes of one pre-amplification reaction on one gel were negligible, whereas errors when scoring lanes of two individuals of the same inbred line run on different gels were markedly higher. Scoring across gels should be backed by replicates and several appropriate check entries. Based on clustering with Jaccard's similarity coefficient and Principal Coordinate Analysis, only the Asian lines were distinct as a group, the other lines showed no marked further grouping. Nevertheless, several known pedigree relationships were verified. A priori grouping of inbred lines (geographic origin and seed size) and AFLP data corroborate available information on the history of spread and cultivation of faba bean in the studied regions. Based on the diversity observed, studies especially concerning the relationship between genetic similarity based on AFLP markers and hybrid performance within the European elite germplasm have been launched.

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Section: Error Estimationsupporting

confidence: 89%

Genetic diversity in recent elite faba bean lines using AFLP markers

2003

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“…Amplified fragment length polymorphism (AFLP) marker analysis was performed using fluorescent labeled primers essentially as described by Schwarz et al (2000), with the following modifications. The adaptor sequences were: 5′-CTCGTAGACTGCGTACC-3′, 3′-CTGACGCATGGTTAA-5′ (EcoRI adaptors), 5′-GACGATG-AGTCCTGA-3′, 3′-TACTCAGGACTCAT-5′ (MseI adaptors).…”

Section: Aflp Analysismentioning

confidence: 99%

An AFLP and RFLP linkage map and quantitative trait locus (QTL) analysis of growth traits in Salix

2002

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A genetic linkage map of Salix (2n = 38), composed of 325 AFLP and 38 RFLP markers has been constructed. The map was based on a population ( n = 87) derived from a cross between the male hybrid clone "Björn" ( Salix viminalis x Salix schwerinii) and the female clone "78183" ( S. viminalis). Three hundred fifty seven AFLPs corresponding to DNA polymorphisms heterozygous in one parent and null in the other were scored. A total of 87 RFLP probes, most (83) derived from the Populus genome, yielded 39 and 11 polymorphic loci segregating in a 1:1 and 1:2:1 ratio respectively. Two maps, one for each parent, were constructed according to the "two-way pseudo-testcross" mapping strategy. The S. viminalis x S. schwerinii map (2,404 cM) included 217 markers and formed 26 major linkage groups while S. viminalis (1,844 cM) consisted of 146 markers placed on 18 major groups. In addition, eight and 14 additional minor linkage groups composed of less than four markers (doubles and triplets) were obtained in the S. viminalis x S. schwerinii and the S. viminalis maps, respectively. Both maps provided 70-80% genome coverage with an average density of markers of 14 cM. To investigate possible homologies between the parental maps, 20 AFLPs and 11 RFLPs segregating in 3:1 or 1:2:1 ratios were included in the linkage analysis. Eight linkage groups homologous between the two maps were detected. The present genetic map was used to identify quantitative trait loci (QTLs) affecting growth-related traits. Eleven QTLs were identified; seven QTLs for height growth, one QTL for stem diameter, one QTL for the height: diameter ratio, one QTL for the number of vegetative buds during flowering time and one QTL for the number of shoots. The estimated magnitude of the QTL effect ranged from 14 to 22% of the total phenotypic variance. One QTL associated with height growth and one affecting the height: diameter ratio were overlapping in the same marker interval with the QTL affecting stem diameter. QTL stability over years was estimated for traits measured in multiple years. Generally, QTLs were only significant in a single year although two QTLs for height growth were close to reaching the significance level in 2 consecutive years.

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“…These methods recently have been shown to provide higher resolution than conventional radio-detection techniques (Schwarz et al 2000). For multi-fluorophore fragment analysis (multiplexing), EcoRI (or PstI) primers were labeled with either 6-carboxyfluorescein (6-FAM) or 4,7,2′,7′-tetrachloro-6-carboxyfluorescein (TET), and the MseI primer was unlabeled.…”

Section: Multi-fluorophore Aflp Analysismentioning

confidence: 99%

Polyploid formation in cotton is not accompanied by rapid genomic changes

Liu¹,

Brubaker²,

Mergeai³

et al. 2001

Genome

297

118

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Recent work has demonstrated that allopolyploid speciation in plants may be associated with non-Mendelian genomic changes in the early generations following polyploid synthesis. To address the question of whether rapid genomic changes also occur in allopolyploid cotton (Gossypium) species, amplified fragment length polymorphism (AFLP) analysis was performed to evaluate nine sets of newly synthesized allotetraploid and allohexaploid plants, their parents, and the selfed progeny from colchicine-doubled synthetics. Using both methylation-sensitive and methylationinsensitive enzymes, the extent of fragment additivity in newly combined genomes was ascertained for a total of approximately 22 000 genomic loci. Fragment additivity was observed in nearly all cases, with the few exceptions most likely reflecting parental heterozygosity or experimental error. In addition, genomic Southern analysis on six sets of synthetic allopolyploids probed with five retrotransposons also revealed complete additivity. Because no alterations were observed using methylation-sensitive isoschizomers, epigenetic changes following polyploid synthesis were also minimal. These indications of genomic additivity and epigenetic stasis during allopolyploid formation provide a contrast to recent evidence from several model plant allopolyploids, most notably wheat and Brassica, where rapid and unexplained genomic changes have been reported. In addition, the data contrast with evidence from repetitive DNAs in Gossypium, some of which are subject to non-Mendelian molecular evolutionary phenomena in extant polyploids. These contrasts indicate polyploid speciation in plants is accompanied by a diverse array of molecular evolutionary phenomena, which will vary among both genomic constituents and taxa.Key words: polyploidy, genome evolution, cotton, Gossypium, amplified fragment length polymorphism (AFLP).Résumé : De récents travaux ont démontré que la spéciation via l'allopolyploïdisation chez les plantes s'accompagne parfois de changements génomiques non-mendéliens au cours des premières générations. Afin de déterminer si des changements génomiques rapides surviennent chez des espèces allopolyploïdes du cotonnier (Gossypium), une analyse AFLP (polymorphisme de longueur des fragments amplifiés) a été faite pour évaluer neuf jeux d'hybrides synthétiques allotétraploïdes ou allohexaploïdes, leurs parents et la progéniture obtenue par autofécondation suite au doublement chromosomique induit par la colchicine. À l'aide d'enzymes sensibles ou insensibles à la méthylation, le degré d'additivité des fragments a été évalué chez les génomes nouvellement combinés pour environ 22 000 locus génomi-ques. L'additivité des fragments a été observée dans presque tous les cas et les quelques rares exceptions reflétaient vraisemblablement une hétérozygotie parentale ou une erreur expérimentale. De plus, des analyses Southern sur six jeux d'allopolyploïdes examinés à l'aide de sondes constituées de rétrotransposons ont également révélé une complète additivité. Comm...

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Application of fluorescence-based semi-automated AFLP analysis in barley and wheat

Cited by 43 publications

References 20 publications

Genetic diversity in recent elite faba bean lines using AFLP markers

Genetic diversity in recent elite faba bean lines using AFLP markers

An AFLP and RFLP linkage map and quantitative trait locus (QTL) analysis of growth traits in Salix

Polyploid formation in cotton is not accompanied by rapid genomic changes

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