Restriction Fragment Length Polymorphism Assessment of the Heterogeneous Nature of Maize Population GT-MAS:gk and Field Evaluation of Resistance to Aflatoxin Production by Aspergillus flavus

2002 ◽  
Vol 65 (1) ◽  
pp. 167-171 ◽  
Author(s):  
B. Z. GUO ◽  
A. BUTRON ◽  
H. LI ◽  
N. W. WIDSTROM ◽  
R. E. LYNCH
Keyword(s):  
Cluster Analysis ◽  
Restriction Fragment Length Polymorphism ◽  
Length Polymorphism ◽  
Fragment Length Polymorphism ◽  
Field Evaluation ◽  
Aflatoxin Production ◽  
Inbred Lines ◽  
Rflp Markers ◽  
Maize Population ◽  
Restriction Fragment Length

Aflatoxin, produced by Aspergillus flavus, is one of the most toxic and carcinogenic substances known and contaminates many agricultural commodities such as corn, peanuts, cottonseed, and tree nuts. The challenge to breeders/plant pathologists is to identify lines that have resistance to aflatoxin production. Maize population GT-MAS:gk has been identified and released as a germplasm with resistance to aflatoxin contamination. In the present study, we assessed genetic divergence in the GT-MAS:gk population using restriction fragment length polymorphism (RFLP) DNA markers to survey 11 selfed inbred lines and conducted field evaluations for the dissimilarities in aflatoxin production among these inbred lines in comparison with a sister population, GT-MAS:pw,nf. The 11 selfed inbred lines were assayed for DNA polymorphism using 113 RFLP markers in 10 linkage groups covering 1,518.2 centimorgans (cM; unit of gene or chromosome size). Considerable variation among the inbreds was detected with RFLP markers, of which 42 probe-enzyme combinations gave 102 polymorphic bands. Cluster analysis based on genetic similarities revealed associations and variations among the tested lines. Three polymorphic groups were distinguished by cluster analysis. Two years of field evaluation data showed that aflatoxin concentrations among the lines were significantly different in both years (P < 0.001). Maturity data were also different. Thus, this study demonstrates that the maize population GT-MAS:gk is heterogeneous and that individuals may be different in resistance to A. flavus infection and aflatoxin production. Therefore, the most resistant lines should be inbred to increase homogeneity, and resistance should be confirmed through progeny testing.

scholarly journals Terminal Restriction Fragment Length Polymorphism Data Analysis for Quantitative Comparison of Microbial Communities

2003 ◽  
Vol 69 (2) ◽  
pp. 926-932 ◽  
Author(s):  
Christopher B. Blackwood ◽  
Terry Marsh ◽  
Sang-Hoon Kim ◽  
Eldor A. Paul
Keyword(s):  
Cluster Analysis ◽  
Data Analysis ◽  
Restriction Fragment Length Polymorphism ◽  
Restriction Fragment ◽  
Length Polymorphism ◽  
Redundancy Analysis ◽  
Fragment Length Polymorphism ◽  
Peak Height ◽  
Relative Peak Height ◽  
Restriction Fragment Length

ABSTRACT Terminal restriction fragment length polymorphism (T-RFLP) is a culture-independent method of obtaining a genetic fingerprint of the composition of a microbial community. Comparisons of the utility of different methods of (i) including peaks, (ii) computing the difference (or distance) between profiles, and (iii) performing statistical analysis were made by using replicated profiles of eubacterial communities. These samples included soil collected from three regions of the United States, soil fractions derived from three agronomic field treatments, soil samples taken from within one meter of each other in an alfalfa field, and replicate laboratory bioreactors. Cluster analysis by Ward's method and by the unweighted-pair group method using arithmetic averages (UPGMA) were compared. Ward's method was more effective at differentiating major groups within sets of profiles; UPGMA had a slightly reduced error rate in clustering of replicate profiles and was more sensitive to outliers. Most replicate profiles were clustered together when relative peak height or Hellinger-transformed peak height was used, in contrast to raw peak height. Redundancy analysis was more effective than cluster analysis at detecting differences between similar samples. Redundancy analysis using Hellinger distance was more sensitive than that using Euclidean distance between relative peak height profiles. Analysis of Jaccard distance between profiles, which considers only the presence or absence of a terminal restriction fragment, was the most sensitive in redundancy analysis, and was equally sensitive in cluster analysis, if all profiles had cumulative peak heights greater than 10,000 fluorescence units. It is concluded that T-RFLP is a sensitive method of differentiating between microbial communities when the optimal statistical method is used for the situation at hand. It is recommended that hypothesis testing be performed by redundancy analysis of Hellinger-transformed data and that exploratory data analysis be performed by cluster analysis using Ward's method to find natural groups or by UPGMA to identify potential outliers. Analyses can also be based on Jaccard distance if all profiles have cumulative peak heights greater than 10,000 fluorescence units.

Physical mapping of restriction fragment length polymorphism (RFLP) markers in homoeologous groups 1 and 3 chromosomes of wheat by in situ hybridization

Genome ◽  
2001 ◽  
Vol 44 (3) ◽  
pp. 401-412 ◽  
Author(s):  
X -F. Ma ◽  
K Ross ◽  
J P Gustafson
Keyword(s):  
In Situ Hybridization ◽  
Restriction Fragment Length Polymorphism ◽  
Restriction Fragment ◽  
Physical Mapping ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Rflp Markers ◽  
Restriction Fragment Length

Using wheat ditelosomic lines and in situ hybridization of biotin-labelled DNA probes, 18 restriction fragment length polymorphism (RFLP) markers were physically located on homoeologous groups 1 and 3 chromosomes of wheat. Most of the markers hybridized to chromosome arms in a physical order concordant with the genetic maps. A majority of the markers studied were clustered in non-C-banded, distal euchromatic areas, indicating the presence of recombination hot spots and cold spots in those regions. However, on 1BS the markers were well dispersed, which could be due to the abundance of heterochromatin throughout the arm. An inversion between Xpsr653 and Xpsr953 was observed on 1AL. One new Xpsr688 locus, approximately 20–26% from the centromere, was found on 1AS and 1BS. The physical location of Xpsr170 on group 3 chromosomes probably represents an alternative to the loci on the genetic map. Finally, Xpsr313 was mapped to two physical loci on 1DL. Five markers were located to bins consistent with the deletion-based physical maps.Key words: wheat, physical mapping, in situ hybridization.

scholarly journals New restriction fragment length polymorphism (RFLP) markers forAspergillus fumigatus

2001 ◽  
Vol 31 (1) ◽  
pp. 15-19 ◽  
Author(s):  
Camile Pizeta Semighini ◽  
Guillaume Delmas ◽  
Steven Park ◽  
Donald Amstrong ◽  
David Perlin ◽  
...  
Keyword(s):  
Restriction Fragment Length Polymorphism ◽  
Restriction Fragment ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Rflp Markers ◽  
Restriction Fragment Length

Identification of X chromosomal restriction fragment length polymorphism markers and their use in a gene localization study in Drosophila virilis and D. littoralis

Genome ◽  
2001 ◽  
Vol 44 (2) ◽  
pp. 242-248 ◽  
Author(s):  
Seliina Päällysaho ◽  
Susanna Huttunen ◽  
Anneli Hoikkala
Keyword(s):  
Restriction Fragment Length Polymorphism ◽  
Restriction Fragment ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Drosophila Virilis ◽  
Rflp Markers ◽  
Male Courtship ◽  
Restriction Fragment Length

We have identified six restriction fragment length polymorphism (RFLP) markers based on unique gene sequences on the X chromosome of Drosophila virilis and D. littoralis. The markers were localized by in situ hybridization on larval polytene chromosomes, and the conjugation of the X chromosomes of the two species was studied in salivary glands of interspecific hybrid female larvae. The gene arrangement of D. virilis and D. littoralis appeared to be very different at the proximal end of the X chromosome preventing recombination between RFLP markers located in this area. Simple quantitative trait loci (QTL) analysis showed that five of our marker genes (including nonA and Dmca1A, previously found to affect male courtship song in D. melanogaster) are linked with a gene(s) having a major effect on species differences in the male courtship song between D. virilis and D. littoralis. This shows that the song gene(s) may be located inside a large X-chromosomal inversion in D. littoralis (as previously suggested), but that it may also be located on an area between this inversion and the centromere, close to nonA and Dmca1A. Localization of this gene or gene complex will be continued with the aid of our newly identified RFLP markers by making interspecific crosses between D. virilis group species with more similar X chromosomes.Key words: restriction fragment length polymorphism (RFLP), in situ hybridization, Drosophila virilis.

scholarly journals Single Cystosorus Isolate Production and Restriction Fragment Length Polymorphism Characterization of the Obligate Biotroph Spongospora subterranea f. sp. subterranea

2006 ◽  
Vol 96 (10) ◽  
pp. 1157-1163 ◽  
Author(s):  
Xinshun Qu ◽  
Barbara J. Christ
Keyword(s):  
North America ◽  
Restriction Fragment Length Polymorphism ◽  
Restriction Fragment ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Rflp Markers ◽  
Spongospora Subterranea ◽  
Geographic Locations ◽  
Restriction Fragment Length

Spongospora subterranea f. sp. subterranea causes powdery scab in potatoes and is distributed worldwide. Genetic studies of this pathogen have been hampered due, in part, to its obligate parasitism and the lack of molecular markers for this pathogen. In this investigation, a single cystosorus inoculation technique was developed to produce large amounts of S. subterranea f. sp. subterranea plasmodia or zoosporangia in eastern black nightshade (Solanum ptycanthum) roots from which DNA was extracted. Cryopreservation of zoosporangia was used for long-term storage of the isolates. S. subterranea f. sp. subterranea-specific restriction fragment length polymorphism (RFLP) markers were developed from randomly amplified polymorphic DNA (RAPD) fragments. Cystosori of S. subterranea f. sp. subterranea were used for RAPD assays and putative pathogen-specific RAPD fragments were cloned and sequenced. The fragments were screened for specificity by Southern hybridization and subsequent DNA sequence BLAST search. Four polymorphic S. subterranea f. sp. subterranea-specific probes containing repetitive elements, and one containing single copy DNA were identified. These RFLP probes were then used to analyze 24 single cystosorus isolates derived from eight geographic locations in the United States and Canada. Genetic variation was recorded among, but not within, geographic locations. Cluster analysis separated the isolates into two major groups: group I included isolates originating from western North America, with the exception of those from Colorado, and group II included isolates originating from eastern North America and from Colorado. The techniques developed in this study, i.e., production of single cystosorus isolates of S. subterranea f. sp. subterranea and development of RFLP markers for this pathogen, provide methods to further study the genetic structure of S. subterranea f. sp. subterranea.

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