AFLP data and the origins of domesticated crops

Genome ◽  
2003 ◽  
Vol 46 (3) ◽  
pp. 448-453 ◽  
Author(s):  
Robin G Allaby ◽  
Terence A Brown
Keyword(s):  
Population Biology ◽  
Fragment Length Polymorphism ◽  
Plant Domestication ◽  
Neighbor Joining ◽  
Cereal Crop ◽  
Einkorn Wheat ◽  
Aflp Data ◽  
Monophyletic Origin ◽  
Aflp Genotyping ◽  
Domestication Process

Amplified fragment length polymorphism (AFLP) datasets have been used to construct neighbor-joining trees from which monophyletic origins for crops such as einkorn wheat, barley, and emmer wheat have been inferred. We simulated several different multiple domestication scenarios for an imaginary cereal crop and examined the resulting domesticated populations. The simulations showed that the population biology aspects of the domestication process can result in independently domesticated populations merging in such a way that a monophyletic origin is erroneously inferred when the resulting population is examined by AFLP genotyping and neighbor-joining analysis. The results bring into question the use of this method to infer the origins of real crops.Key words: AFLPs, agriculture, neighbor-joining, plant domestication.

Reply to the comment by Salamini et al. on "AFLP data and the origins of domesticated crops"

Genome ◽  
2004 ◽  
Vol 47 (3) ◽  
pp. 621-622 ◽  
Author(s):  
Robin G Allaby ◽  
Terence A Brown
Keyword(s):  
Tetraploid Wheat ◽  
Neighbor Joining ◽  
Crop Domestication ◽  
Critical Question ◽  
Einkorn Wheat ◽  
Aflp Data ◽  
Tetraploid Wheats ◽  
Key Points

We reiterate the key points of a previous paper that showed that neighbor-joining analysis of AFLP datasets can produce erroneous results. The critical question, whether the datasets used to infer the origins of einkorn, barley, and the hulled and hard tetraploid wheats display sufficient linkage to avoid the artifacts that we observed, is not adequately answered by Salamini et al.Key words: AFLPs, crop domestication, einkorn wheat, barley, tetraploid wheat.

Amplified fragment length polymorphism analysis reveals three distinct taxa in Carex digitalis sect. Careyanae (Cyperaceae)

2006 ◽  
Vol 84 (9) ◽  
pp. 1444-1452 ◽  
Author(s):  
Bruce A. Ford ◽  
Robert F.C. Naczi ◽  
Habibollah Ghazvini ◽  
Mahmood Iranpour
Keyword(s):  
North Carolina ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Amplified Fragment Length Polymorphism ◽  
Polymorphism Analysis ◽  
Neighbor Joining ◽  
Aflp Data ◽  
Additional Species ◽  
Pair Group

Unweighted pair-group (UPGMA) cluster, neighbor-joining (NJ), and parsimony analyses using amplified fragment length polymorphism (AFLP) data revealed the presence of three taxa within Carex digitalis Willd. (var. digitalis , var. floridana , var. macropoda ). Even when taxa occur syntopically, genetic distinctiveness is maintained (Hertford Co., North Carolina populations of var. macropoda and var. floridana). Clades or clusters corresponding with vars. digitalis and floridana were well supported in all analyses. However, the var. macropoda clade was poorly supported on most trees. Despite our inability to fully resolve taxon relationships, AFLP data substantiate ongoing morphological and phytogeographic studies that show the presence of additional species diversity within sect. Careyanae and the eastern North American Carex flora.

Systematic relationships in Lathyrus sect. Lathyrus (Fabaceae) based on amplified fragment length polymorphism (AFLP) data

2002 ◽  
Vol 80 (9) ◽  
pp. 962-969 ◽  
Author(s):  
Abdelfattah Badr ◽  
Hanaa El Shazly ◽  
Haddad El Rabey ◽  
Linda E Watson
Keyword(s):  
Phylogenetic Tree ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Neighbor Joining ◽  
Aflp Data ◽  
Length Polymorphisms ◽  
Amplified Fragment Length Polymorphisms ◽  
Close Relationship ◽  
Systematic Relationships

Amplified fragment length polymorphisms (AFLP) were utilized to examine systematic relationships in Lathyrus L. sect. Lathyrus (Fabaceae). In addition to a parsimony-based phylogenetic tree, AFLP-based trees were constructed using Dice, Jaccard, and mean character difference coefficients to produce distance-based trees using the UPGMA and neighbor-joining methods. All trees clearly show a close relationship among accessions of the same species, confirming the monophyly of the species examined. All analyses indicate that species of the section Lathyrus are distinct from species of other sections. These findings confirm the monophyly of the section and contradict proposals to split it. They do not support the segregation of L. gorgoni in the section Gorgonia. Within the section Lathyrus, several relationships are present but are only weakly supported. The use of AFLP data to resolve systematic relationships in the genus Lathyrus is further demonstrated.Key words: Lathyrus, Fabaceae, systematics, AFLP.

Genetic diversity of Echinacea species based upon amplified fragment length polymorphism markers

Genome ◽  
2004 ◽  
Vol 47 (1) ◽  
pp. 102-111 ◽  
Author(s):  
D -H Kim ◽  
D Heber ◽  
D W Still
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Fragment Length ◽  
Echinacea Purpurea ◽  
Morphological Characters ◽  
Pairwise Distance ◽  
Neighbor Joining ◽  
Aflp Data ◽  
Phenetic Relationships ◽  
Length Polymorphisms

The taxonomy of Echinacea is based on morphological characters and has varied depending on the monographer. The genus consists of either nine species and four varieties or four species and eight varieties. We have used amplified fragment length polymorphisms (AFLP) to assess genetic diversity and phenetic relationships among nine species and three varieties of Echinacea (sensu McGregor). A total of 1086 fragments, of which approximately 90% were polymorphic among Echinacea taxa, were generated from six primer combinations. Nei and Li's genetic distance coefficient and the neighbor-joining algorithm were employed to construct a phenetic tree. Genetic distance results indicate that all Echinacea species are closely related, and the average pairwise distance between populations was approximately three times the intrapopulation distances. The topology of the neighbor-joining tree strongly supports two major clades, one containing Echinacea purpurea, Echinacea sanguinea, and Echinacea simulata and the other containing the remainder of the Echinacea taxa (sensu McGregor). The species composition within the clades differs between our AFLP data and the morphometric treatment offered by Binns and colleagues. We also discuss the suitability of AFLP in determining phylogenetic relationships.Key words: Echinacea, AFLP, genetic distance, phylogeny.

Genetic Variability in the Potato Pathogen Colletotrichum coccodes as Determined by Amplified Fragment Length Polymorphism and Vegetative Compatibility Group Analyses

2006 ◽  
Vol 96 (10) ◽  
pp. 1097-1107 ◽  
Author(s):  
Larry J. Heilmann ◽  
Nadav Nitzan ◽  
Dennis A. Johnson ◽  
Julie S. Pasche ◽  
Curt Doetkott ◽  
...  
Keyword(s):  
Length Polymorphism ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Amplified Fragment Length Polymorphism ◽  
Vegetative Compatibility ◽  
Colletotrichum Coccodes ◽  
Aflp Analysis ◽  
Aflp Data ◽  
Bootstrap Analysis ◽  
Nit Mutants

Amplified fragment length polymorphism (AFLP) using three primer sets was used to characterize 211 Colletotrichum coccodes isolates from North America, 112 of which were assigned to six vegetative compatibility groups (VCGs) using nitrate nonutilizing (nit) mutants. These isolates clustered into five corresponding groups by unweighted pairgroup method with arithmetic means-based cluster analysis of AFLP banding patterns. Isolates of C. coccodes belonging to NA-VCG1 and NA-VCG3 were closely related, as were isolates belonging to NA-VCG2 and NA-VCG5. Based on bootstrap analysis of AFLP data, the two isolates originally assigned to NA-VCG4 clustered with isolates belonging to NA-VCG2 and NA-VCG5. C. coccodes isolates that clustered with two isolates belonging to NA-VCG6 were the most diverged from other groups, including seven isolates collected from hosts other than potato. As opposed to the bootstrap analysis, a quadratic discriminant analysis (QDA) of AFLP data correctly categorized the two isolates of NA-VCG4. Furthermore, in isolates where VCG determinations had been made, this model correctly classified isolates of all VCGs. QDA classifications were identical to those made by the bootstrap analysis, with the exception of VCG4. Overall, classifications made by the QDA model were strongly correlated (r = 0.970, P < 0.001) to the VCGs assigned by traditional methods. All 99 C. coccodes isolates evaluated only by AFLP also were subjected to QDA, leading to the assignment of a presumptive VCG for each isolate. No isolates of VCG4 or VCG6 were identified by QDA within this population. Symptoms of black dot developed in plants inoculated with isolates collected from both potato and non-potato hosts. However, total yield was not significantly reduced by infection with non-potato isolates. The lack of any additional groups identified by AFLP analysis may be an indicator of a limited level of genetic variation among North American C. coccodes isolates. AFLP is a much more efficient technique for subspecific characterization in C. coccodes than VCG analysis utilizing nit mutants and will provide an effective means by which the population biology of this pathogen can be further investigated worldwide.

Genetic structure of the Anthyllis vulneraria L. s. l. species complex in Estonia based on AFLPs

2008 ◽  
Vol 3 (4) ◽  
pp. 442-450 ◽  
Author(s):  
Egle Köster ◽  
Elena Bitocchi ◽  
Roberto Papa ◽  
Silvia Pihu
Keyword(s):  
Species Complex ◽  
Fragment Length Polymorphism ◽  
Aflp Analysis ◽  
Data Sets ◽  
Geographic Scale ◽  
Aflp Data ◽  
Anthyllis Vulneraria ◽  
Directional Variation ◽  
Intraspecific Structure ◽  
Cryptic Taxa

AbstractAnthyllis vulneraria L. (Fabaceae) s. lato includes many cryptic taxa, ranging from 25 to 60 subspecies according to different authors. The delimitation of intraspecific taxa of A. vulneraria s. lato has always been complicated and inconsistent. Different data sets (multivariate analyses of morphological variation, allozymes, chloroplast SSRs and ITS) have not resolved the existing problem with distinguishing some subspecies. We used the amplified fragment length polymorphism (AFLP) analysis to describe the differentiation in this species complex and to characterize variation on a geographic scale. Some correlation was found between genetic variability and geographic distribution (western-eastern directional variation), but AFLP data analysis did not reveal clear intraspecific structure of the seven analysed taxa. The analysed specimens did not comprise groups correlated with the subspecies.

scholarly journals Discrimination and Genetic Diversity of Cephalotaxus Accessions Using AFLP Markers

2000 ◽  
Vol 125 (4) ◽  
pp. 404-412 ◽  
Author(s):  
Donglin Zhang ◽  
Michael A. Dirr ◽  
Robert A. Price
Keyword(s):  
Genetic Diversity ◽  
Cluster Analysis ◽  
Shade Tolerance ◽  
Fragment Length Polymorphism ◽  
Genetic Differences ◽  
Aflp Markers ◽  
Base Pairs ◽  
Aflp Data ◽  
Hybrid Species ◽  
Sun And Shade

Cephalotaxus Sieb. and Zucc. (plum yew) species and cultivars have become popular because of their sun and shade tolerance, resistance to deer browsing, disease and insect tolerance, and cold and heat adaptability. Unfortunately, the nomenclature and classification in the literature and nursery trade are confusing due to their extreme similarity in morphology. In this study, amplified fragment-length polymorphism (AFLP) markers were used to discriminate taxa and evaluate genetic differences among 90 Cephalotaxus accessions. A total of 403 useful markers between 75 and 500 base pairs (bps) was generated from three primer-pair combinations. Cluster analysis showed that the 90 accessions can be classified as four species, C. oliveri Mast., C. fortunei Hooker, C. harringtonia (Forbes) Koch., and C. ×sinensis (a hybrid species); four varieties, C. fortunei var. alpina Li, C. harringtonia var. koreana (Nakai) Rehd., C. harringtonia var. nana (Nakai) Hornibr., and C. harringtonia var. wilsoniana (Hayata) Kitamura; and eight cultivars. Suggested names are provided for mislabeled or misidentified taxa. The Cephalotaxus AFLP data serve as a guide to researchers and growers for identification and genetic differences of a taxon, and a model to establish a cultivar library against which later introductions or problematic collections can be cross-referenced.

scholarly journals Comment on "AFLP data and the origins of domesticated crops"

Genome ◽  
2004 ◽  
Vol 47 (3) ◽  
pp. 615-620 ◽  
Author(s):  
F Salamini ◽  
M Heun ◽  
A Brandolini ◽  
H Özkan ◽  
J Wunder
Keyword(s):  
Phylogenetic Tree ◽  
Dna Fingerprinting ◽  
Phylogenetic Analyses ◽  
Tetraploid Wheat ◽  
Aflp Markers ◽  
Crop Domestication ◽  
Einkorn Wheat ◽  
Aflp Data ◽  
Fertile Crescent ◽  
Tree Topologies

We review some concepts and methods of handling and using DNA fingerprinting in phylogenetic analyses related to crop domestication. Particular reference is made to AFLP markers and mode and place of einkorn, barley, and tetraploid wheat domestication in the Neolithic by human communities in the Fertile Crescent. The reconsideration of AFLP databases of domesticated and wild lines demonstrates that phylogenetic tree topologies, originally described for the three species, match closely the new results obtained by principle coordinate analyse.Key words: AFLPs, discontinuous markers, crop domestication, einkorn wheat, barley, tetraploid wheat.

Two distinct AFLP types in three populations of marram grass (Ammophila arenaria) in Wales

2008 ◽  
Vol 6 (3) ◽  
pp. 201-207 ◽  
Author(s):  
W. H. Gera Hol ◽  
Andre W. G. van der Wurff ◽  
Leif Skøt ◽  
Roger Cook
Keyword(s):  
Fragment Length Polymorphism ◽  
Assignment Test ◽  
Sampling Location ◽  
Ammophila Arenaria ◽  
Aflp Data ◽  
Plant Materials ◽  
Marram Grass ◽  
Outlier Loci

The genetic structure of marram grass populations at coastal and inland locations, 200 m apart, was investigated at three sites by means of amplified fragment length polymorphism (AFLP) DNA markers. We expected a genetic differentiation between coastal and inland populations and more genetic variation in the coastal areas as a result of different events of colonization by different plant materials. An assignment test showed that the sampledAmmophila arenariacould be assigned to two groups based on AFLP data. The spatial distribution of the two AFLP types ofA. arenariavaried with sampling location. In two of the three locations, mainly one type (1) was found in the newly formed dunes. This type did also occur further landward, but the second type (2) was preferentially found in inland populations. Genetic diversity was very low and of similar value in both coastal and inland populations. For each site, outlier loci with respect toFSTvalue were identified, which may be indicative of different selection pressures in coastal compared with inland clusters. However, no identical outlier loci were found at all three sites. Possible explanations for the observed difference in distribution of type 1 and 2 populations between coastal and inland sites are discussed.

scholarly journals Separation of the genera in the subtribe Cassiinae (Leguminosae: Caesalpinioidae) using molecular markers

2011 ◽  
Vol 25 (1) ◽  
pp. 223-233 ◽  
Author(s):  
Laxmikanta Acharya ◽  
Arup Kumar Mukherjee ◽  
Pratap Chandra Panda
Keyword(s):  
Molecular Markers ◽  
Simple Sequence Repeat ◽  
Fragment Length Polymorphism ◽  
Molecular Level ◽  
Random Amplified Polymorphic Dna ◽  
Inter Simple Sequence Repeat ◽  
Aflp Data ◽  
High Bootstrap ◽  
Simple Sequence ◽  
Issr Primers

Random amplified polymorphic DNA (RAPD), Inter simple sequence repeat (ISSR) and Amplified fragment length polymorphism (AFLP) markers were used to verify the segregation of the genus Cassia L. senso lato into three distinct genera namely Chamaecrista Moench., Senna P. Mill. and Cassia L. sensostricto Eighteen representatives of the three taxa were characterized using the molecular markers. 25 RAPD, six ISSR primers and six AFLP primer combinations resulted in the amplification of 612, 115 and 622 bands (loci) respectively. Most of the loci are found to be polymorphic, showing high degrees of genetic diversity among the different taxa studied. The dendrogram constructed on the basis of the RAPD, ISSR and AFLP data using SHAN clustering, divided Cassia L. senso lato. into three different clusters as Chamaecrista Moench. Senna P. Mill. and Cassia L. senso stricto High bootstrap value revealed that all the clusters were stable and robust. It was observed from the present investigation that these genera have their identity at molecular level, which supports the elevation of the genus Cassia L. senso lato to the level of subtribe Cassiinae and segregation into three distinct genera instead of intrageneric categories.

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