scholarly journals Amplified Fragment Length Polymorphism Analysis and Internal Transcribed Spacer and coxII Sequences Reveal a Species Boundary Within Pythium irregulare

2005 ◽  
Vol 95 (12) ◽  
pp. 1489-1498 ◽  
Author(s):  
Carla D. Garzón ◽  
David M. Geiser ◽  
Gary W. Moorman
Keyword(s):  
Cryptic Species ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Internal Transcribed Spacer ◽  
Fragment Length Polymorphism ◽  
Amplified Fragment Length Polymorphism ◽  
Its Region ◽  
The United States ◽  
Sensu Stricto ◽  
Pythium Irregulare

Pythium irregulare is a plant-pathogenic oomycete that causes significant damage to a variety of crops, including ornamentals and vegetables. Morphological as well as molecular studies have reported high levels of genetic diversity within P. irregulare sensu lato which has raised the question as to whether it is a single species or is actually a complex of morphologically similar (cryptic) species. In this study, we used amplified fragment length polymorphism (AFLP) fingerprinting and DNA sequence analysis of the internal transcribed spacer (ITS) region of the ribosomal genes (ITS region) and a portion of the mitochondrial cytochrome oxidase II gene and the spacer region between coxI and coxII to characterize 68 isolates of P. irregulare from the United States. The ITS sequence of a P. irregulare neotype at the CBS collection as well as ITS and coxII sequences for P. irregulare, P. spinosum, and P. sylvaticum from previous studies were included in our analysis. Cluster analysis identified a 19-isolate group (IR-II) that separated itself from the rest of the sample (IR-I). Population structure and sequence analyses supported the distinction of IR-I and IR-II and identified IR-II as P. irregulare sensu stricto. IR-I was designated Pythium sp. clade IR-I. Two insertion/deletion mutations and nine nucleotide substitutions in the ITS region and three in the sequence of coxII and the adjacent spacer region separated the two species. Additionally, they differed significantly (P > 0.01) in the frequency of 182 (77%) AFLP alleles. Gene flow results suggested that P. irregulare sensu stricto and Pythium sp. clade IR-I are cryptic species capable of exchanging favorable alleles (Nm = 0.72).

scholarly journals Amplified fragment length polymorphism used for inter- and intraspecific differentiation of screwworms (Diptera: Calliphoridae)

2008 ◽  
Vol 99 (2) ◽  
pp. 139-149 ◽  
Author(s):  
L. Alamalakala ◽  
S.R. Skoda ◽  
J.E. Foster
Keyword(s):  
Length Polymorphism ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Amplified Fragment Length Polymorphism ◽  
The United States ◽  
Bootstrap Support ◽  
Strain Identification ◽  
Correct Identification ◽  
Important Pest ◽  
United States Mexico

AbstractMorphologically, early immature stages of the economically important pest called screwworms, Cochliomyia hominivorax (Coquerel) (Diptera: Calliphoridae), and non-pest secondary screwworms, Cochliomyia macellaria (Fabricius) (Diptera: Calliphoridae), are nearly indistinguishable. Correct identification is crucial to the ongoing eradication and exclusion program protecting the United States, Mexico and Central America from reinvasion of screwworms persistent in South America and the Caribbean. Amplified fragment length polymorphism (AFLP) polymerase chain reaction was used to differentiate populations of C. hominivorax and to discriminate them from C. macellaria. Ten primer pairs screened for interspecific discrimination of C. hominivorax from C. macellaria showed 52 discrete bands, allowing the two species to be readily distinguished; divergent branches on resulting dendrograms showed 100% bootstrap support. C. macellaria populations grouped at the 92% level; C. hominivorax populations grouped at the 68% level. Of the 52 bands, seven were monomorphic for both species, 22 were specific to C. macellaria, ten were present only in C. hominivorax and the remaining 13 bands differentiated C. hominivorax populations. Separate studies using ten strains of C. hominivorax showed a higher level of genetic similarity within than between populations. Analyses using 72 bands (19 monomorphic bands, 53 bands grouped all ten strains at the 58% similarity level) resolved seven mutant strains from Mexico (85% similarity level); all ten strains were resolved at the 72% similarity level. Diagnostic bands were identified for species and strain identification. We conclude that AFLP can be a valuable tool for studies of interspecific and intraspecific genetic variation in screwworm populations.

scholarly journals Analysis of Genetic Variability among Phalaenopsis Species and Hybrids Using Amplified Fragment Length Polymorphism

2009 ◽  
Vol 134 (1) ◽  
pp. 58-66 ◽  
Author(s):  
Yeun-Kyung Chang ◽  
Richard E. Veilleux ◽  
Muhammad Javed Iqbal
Keyword(s):  
Genetic Variability ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Genetic Similarity ◽  
Fragment Length Polymorphism ◽  
Species Conservation ◽  
Amplified Fragment Length Polymorphism ◽  
The United States ◽  
Group Method ◽  
Aflp Analysis

Phalaenopsis is the second most valuable potted plant in the United States. Information on the genetic diversity and relationships among species and hybrids is important for breeding purposes and species conservation. In this study, genetic variability of 16 Phalaenopsis species and hybrids was analyzed using amplified fragment length polymorphism (AFLP) markers. Ten AFLP primer combinations amplified 1353 DNA fragments ranging in size from 100 to 350 bp and 1285 (95%) of them were polymorphic. The genetic similarity among Phalaenopsis species and hybrids ranged from 0.298 to 0.774 based on Dice coefficient. The dendrogram derived by the unweighted pair group method with arithmetic mean analysis clustered the germplasm into two main groups. Bootstrap values for the groups supported 70% of the clustering. A significant linear relationship (r = 0.724, P < 0.0001) was observed between known pedigrees and AFLP-derived genetic similarity for 136 pairwise comparisons of Phalaenopsis species and hybrids. The results of this study demonstrate the usefulness of AFLP analysis in Phalaenopsis and its potential application in breeding and species conservation.

scholarly journals The Origin of Cultivated Citrus as Inferred from Internal Transcribed Spacer and Chloroplast DNA Sequence and Amplified Fragment Length Polymorphism Fingerprints

2010 ◽  
Vol 135 (4) ◽  
pp. 341-350 ◽  
Author(s):  
Xiaomeng Li ◽  
Rangjin Xie ◽  
Zhenhua Lu ◽  
Zhiqin Zhou
Keyword(s):  
Chloroplast Dna ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Internal Transcribed Spacer ◽  
Phylogenetic Trees ◽  
Fragment Length Polymorphism ◽  
Sweet Orange ◽  
Amplified Fragment Length Polymorphism ◽  
Sour Orange ◽  
Rough Lemon

Citrus species are among the most important fruit trees in the world and have a long cultivation history. However, until now, the exact genetic origins of cultivated Citrus such as sweet orange (Citrus sinensis), lemon (C. limon), and grapefruit (C. paradisi) have remained unidentified. In the present study, amplified fragment length polymorphism (AFLP) fingerprints, nuclear internal transcribed spacer (ITS), and three plastid DNA regions (psbH – petB, trnL – trnF, and trnS - trnG) of 30 accessions of the cultivated citrus and their putative wild ancestors were analyzed in an attempt to identify their paternal and maternal origins. Molecular phylogenetic trees were constructed based on the AFLP data, and chloroplast DNA and ITS sequences using the genus Poncirus as the outgroup. Our results indicated that bergamot (C. aurantifolia) and lemon were derived from citron (C. medica) and sour orange (C. aurantium), and grapefruit was a hybrid that originated from a cross between pummelo (C. grandis) and sweet orange. Rough lemon (C. limon) was probable as a parent of rangpur lime (C. limonia) and guangxi local lemon (C. limonia). Our data also demonstrated that sweet orange and sour orange were hybrids of mandarin (C. reticulata) and pummelo, while rough lemon was a cross between citron and mandarin. For mexican lime (C. aurantifolia), our molecular data confirmed a species of Papeda to be the female parent and C. medica as the male. These findings provide new information for future study on the taxonomy, evolution, and genetic breeding of Citrus.

scholarly journals Development of Linkage Maps for Pecan Using Fluorescently Labeled Amplified Fragment Length Polymorphism Markers

HortScience ◽  
2004 ◽  
Vol 39 (4) ◽  
pp. 862A-862 ◽  
Author(s):  
Sudheer Beedanagari* ◽  
Patrick Conner
Keyword(s):  
Length Polymorphism ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Amplified Fragment Length Polymorphism ◽  
The United States ◽  
Mapping Method ◽  
Aflp Markers ◽  
Scab Resistance ◽  
Linkage Maps ◽  
Pecan Scab

Pecan, [Carya illinoinensis (Wangenh.) C. Koch], is a member of Juglandaceae family and is one of the most important nut crops produced in the United States. The objective of this study is to generate the first genetic linkage maps for pecan. Maps were constructed for the cultivars `Elliot' and `Pawnee' using the double pseudo-testcross mapping method whereby a separate linkage map is made for each parent using markers heterozygous in that parent. First generation maps consisted primarily of randomly amplified polymorphic DNA (RAPD) markers. We have now used fluorescently labeled amplified fragment length polymorphism (AFLP) markers to produce more complete maps. In the development of the AFLP markers, 64 primer combinations were originally screened to find the most informative combinations. Ten primer combinations were then chosen to produce markers for the maps. The maps currently consist of approximately 100 RAPD and 100 AFLP markers on each cultivar map. `Pawnee' is a high quality commercial pecan cultivar with a very early ripening date. `Elliot' possesses high levels of resistance to pecan scab, caused by the fungus Cladosporium caryigenum. The maps will be used to find markers linked to scab resistance genes and other traits of interest to the breeding program.

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