Taxonomy of Hill's Oak (Quercus ellipsoidalis: Fagaceae): Evidence from AFLP Data

Malus toringoides (Rehd.) Hughes was suggested to have originated from hybridization between Malus transitoria Schneid. and Malus kansuensis Rehd., followed by repeated backcrossing to one of the putative parents. In the present study, the sequence information of the internal transcribed spacer (ITS) of nuclear ribosomal DNA (nrDNA) was used to re-examine the origin of this species. A total of 69 accessions from three natural populations (Maerkang, Xiaba and Kehe, Aba Autonomous Region, Sichuan, China) of M. toringoides and 10 accessions of its putative parents were analyzed. Using Malus angustifolia (Ait.) Michx., Malus ioensis (Wood) Britt. and Malus doumeri Chev. as outgroups, our phylogenetic analysis of the ITS sequences of M. toringoides and its putative parents showed that M. toringoides was not monophyletic, and two different types of ITS sequences which were obtained from each of the six accessions of M. toringoides were found to have clustered separately with those of the two putative parent species on the gene tree. A comparison of the sequence variation between M. toringoides and its putative parents revealed an additive variation pattern of ITS sequences in the putative hybrid species. These results are consistent with the previous morphological and amplified fragment length polymorphism (AFLP) data which suggested that M. toringoides was of hybrid origin. Our ITS data provide new molecular evidence for the hybrid origin hypothesis of M. toringoides and these results are of great importance for future study on hybridization, polyploid speciation and evolution of the genus Malus Miller.

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Genetic variation in Eruca vesicaria (L.) Cav.

Plant Genetic Resources ◽

10.1017/s1479262107842675 ◽

2007 ◽

Vol 5 (03) ◽

pp. 142-153 ◽

Cited By ~ 15

Author(s):

S. I. Warwick ◽

R. K. Gugel ◽

C. Gómez-Campo ◽

T. James

Keyword(s):

Field Trial ◽

Seed Quality ◽

Quality Data ◽

Oilseed Crop ◽

Aflp Data ◽

Cruciferous Vegetable ◽

Western Africa ◽

Length Polymorphisms ◽

Western Asia ◽

Agronomic Potential

Eruca vesicariasubsp.sativa(syn.E. sativa) is a cruciferous vegetable and oilseed crop that is high in erucic acid. It occurs throughout the Mediterranean region and western Asia, and has been naturalized elsewhere as a crop/weed escape. It is closely related to subsp.vesicariaand subsp.pinnatifida, which are endemic to Spain and north-western Africa, respectively. This study evaluated patterns and levels of diversity in the three subspecies based on 234 amplified fragment length polymorphisms (AFLP), and evaluated agronomic and seed quality data in a field trial in western Canada. AFLP data revealed three main clusters: ‘Sativa’ (33 accessions of subsp.sativa), ‘Vesicaria’ (nine accessions of subsp.vesicaria) and a ‘Pinnatifida’ cluster (one accession of subsp.pinnatifidaand three Moroccan accessions of subsp.sativa). The Sativa cluster separated into Mediterranean and Asian groups, likely reflecting differences in origin (wild versus cultivated) or primary usage, vegetable versus seed oil. The origin of the introduced Mexican population was confirmed as subsp.sativa. The highest levels of diversity were found in the Sativa cluster (88% AFLP polymorphisms) and the least in the Vesicaria (56%) and Pinnatifida (39%) clusters. Extensive variation was observed among the 159 subsp.sativaaccessions evaluated in the field trial, and overall findings indicated a favourable agronomic potential.

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Species Boundaries in Pyrrocoma liatriformis and Pyrrocoma scaberula (Asteraceae) Based on AFLP Data

Madroño ◽

10.3120/0024-9637-57.2.95 ◽

2010 ◽

Vol 57 (2) ◽

pp. 95-105

Author(s):

James F. Smith ◽

Dusty N. Perkins ◽

Curtis R. Björk ◽

Gina Glenne

Keyword(s):

Species Boundaries ◽

Aflp Data

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

Genome ◽

10.1139/g03-086 ◽

2004 ◽

Vol 47 (1) ◽

pp. 102-111 ◽

Cited By ~ 17

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.

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Additional information on Meloidogyne polycephannulata and its proposal as a junior synonym of M. incognita

Nematology ◽

10.1163/15685411-00003202 ◽

2019 ◽

Vol 21 (2) ◽

pp. 129-146

Author(s):

Jessica M.S. Monteiro ◽

Vanessa S. Mattos ◽

Marcilene F.A. Santos ◽

Ana C.M.M. Gomes ◽

Valdir R. Correa ◽

...

Keyword(s):

Morphological Variability ◽

Junior Synonym ◽

Valid Species ◽

Bootstrap Support ◽

Nominal Species ◽

Aflp Data ◽

Morphometric Characters ◽

Additional Information ◽

Phylogenetic Studies ◽

Type Population

Summary The type population of Meloidogyne polycephannulata is synonymised with M. incognita based on morphological and morphometric characters, as well as biochemical, molecular and phylogenetic studies. Morphological variability and a wide host range were reported for M. incognita during its first description and later re-description. Meloidogyne polycephannulata was described in Brazil from specimens collected in a carrot field (type population). The esterase phenotype (Est) characterised for this species was identical to the phenotype Est I2 of M. incognita, the most ubiquitous phenotype used for diagnostics. Morphological and morphometric characters of the descriptions of the two nominal species showed major similarities, as well as variability within the range of variation detected in M. incognita. In PCR assays, three SCAR markers species-specific for M. incognita (incK14 F/R, Mi/FR and incB06 F/R) amplified the same fragments of 399 bp, 955 bp and 1200 bp, respectively, for populations in both species. In phylogenetic studies based either on concatenated sequences of ITS1-5.8S-ITS2, D2-D3 rRNA, mitochondrial COII regions or on RAPD and AFLP data, the populations of both species grouped in the same clade with high bootstrap support. Altogether, these results provide congruent evidence that the M. polycephannulata type isolate deposited at the Embrapa Cryopreserved National Collection of Root-knot Nematodes is not a valid species but rather a junior synonym of M. incognita.

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Reciprocal hybridization between diploid Ficaria calthifolia and tetraploid Ficaria verna subsp. verna: evidence from experimental crossing, genome size and molecular markers

Botanical Journal of the Linnean Society ◽

10.1093/botlinnean/boy085 ◽

2019 ◽

Vol 189 (3) ◽

pp. 293-310 ◽

Cited By ~ 1

Author(s):

Ondřej Popelka ◽

Michal Sochor ◽

Martin Duchoslav

Keyword(s):

Genome Size ◽

Morphological Variability ◽

Plastid Dna ◽

Genotypic Diversity ◽

Hybrid Origin ◽

Aflp Analysis ◽

Sympatric Populations ◽

Aflp Data ◽

Evolutionary Forces ◽

Genetic Clusters

Abstract Ficaria is a taxonomically intriguing polyploid complex with high morphological variability. Both hybridization and polyploidization have been suggested as the main evolutionary forces behind the high morphological variability in this genus; however, detailed studies are lacking. In Central Europe, two Ficaria taxa (diploid F. calthifolia and tetraploid F. verna subsp. verna) occasionally co-occur in local sympatry, which might result in hybridization. We investigated sympatric populations of the two Ficaria taxa using flow cytometry, chromosome counts, AFLP analysis and plastid DNA sequencing; we also performed experimental homoploid and heteroploid crosses to determine the frequency and direction of hybrid triploid formation, an alternative route of triploid origin (autopolyploidy) and the possibility of a one-step neoallotetraploid origin. Sympatric populations were composed of three genetic clusters corresponding to diploid F. calthifolia (2n = 16), tetraploid F. verna subsp. verna (2n = 32) and triploid plants (2n = 24). The holoploid genome size and AFLP data suggest a hybrid origin of the triploids, thereby making their formation via autopolyploidization in F. calthifolia unlikely. The triploid populations are monoclonal and of independent origin. In contrast, the parental populations exhibit high genotypic diversity and frequent sexual reproduction, including those of predominantly asexual F. verna subsp. verna. Experimental crossing confirmed that both parental taxa produce fertile seeds via a sexual pathway, but not by apomixis, and that both serve as pollen acceptors in heteroploid crosses, which is consistent with the plastid sequencing. However, hybridization is asymmetric, with maternal-excess crosses being significantly more successful. No signs of neoautotetraploidization or neoallotetraploidization were detected. In summary, recent gene flow between the studied Ficaria taxa is either limited or absent.

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Genetic diversity among flue-cured tobacco cultivars on the basis of AFLP markers

Czech Journal of Genetics and Plant Breeding ◽

10.17221/15/2009-cjgpb ◽

2009 ◽

Vol 45 (No. 4) ◽

pp. 155-159 ◽

Cited By ~ 1

Author(s):

X.Z. Liu ◽

C.S. He ◽

Y.M. Yang ◽

H.Y. Zhang

Keyword(s):

Genetic Diversity ◽

Yunnan Province ◽

Southwest China ◽

Germplasm Conservation ◽

Research Centre ◽

Aflp Data ◽

Breeding Research ◽

Polymorphic Bands ◽

Relationship Of ◽

The Relationship

AFLP analyses were used to assess the genetic similarity among selected accessions at the South China Tobacco Breeding Research Centre (Yunnan province, Southwest China). 154 AFLP polymorphic fragments out of 561 fragments were used to assess the genetic diversity among 28 tobacco accessions. The average number of polymorphic bands per AFLP primer pair was 15.4. AFLPs seemed to be an effective classification tools for germplasm conservation and breeding. Limited genetic variation was detected within this group of accessions. The relationship of cultivars was estimated by cluster analysis based on AFLP data.

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Evaluating the Relationship between Evolutionary Divergence and Phylogenetic Accuracy in AFLP Data Sets

Molecular Biology and Evolution ◽

10.1093/molbev/msp315 ◽

2009 ◽

Vol 27 (5) ◽

pp. 988-1000 ◽

Cited By ~ 30

Author(s):

María Jesús García-Pereira ◽

Armando Caballero ◽

Humberto Quesada

Keyword(s):

Evolutionary Divergence ◽

Data Sets ◽

Aflp Data ◽

The Relationship

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

Phytopathology ◽

10.1094/phyto-96-1097 ◽

2006 ◽

Vol 96 (10) ◽

pp. 1097-1107 ◽

Cited By ~ 17

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.

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