Cloning and mapping of variety-specific rice genomic DNA sequences: amplified fragment length polymorphisms (AFLP) from silver-stained Polyacrylamide gels

Genome ◽  
1996 ◽  
Vol 39 (2) ◽  
pp. 373-378 ◽  
Author(s):  
Yong Gu Cho ◽  
Matthew W. Blair ◽  
Olivier Panaud ◽  
Susan R. McCouch
Keyword(s):  
Restriction Fragment ◽  
Dna Sequences ◽  
Fragment Length ◽  
Silver Staining ◽  
Indica Rice ◽  
Rice Genome ◽  
Polyacrylamide Gels ◽  
Rice Varieties ◽  
Length Polymorphisms ◽  
Amplified Fragment Length Polymorphisms

An efficient technique for cloning DNA from silver-stained denaturing Polyacrylamide gels was developed to allow the isolation of specific bands obtained from selective restriction fragment amplification (SRFA). This method proved as reliable as cloning radioactively labelled SRFA bands from the same gels. Rice DNA was used as a template, both with and without [32P]dCTP, using the same PCR profiles. Amplified products were separated using denaturing polyacryamide gel electrophoresis and visualized either by silver staining of gels or by autoradiography of 32P-labelled products. We cloned specific polymorphic SRFA bands directly from the denaturing polyacrylamide gels with one round of PCR amplification and confirmed that the sequences of the bands from silver-stained gels were identical to the corresponding 32P-labelled bands. The bands that were chosen represented amplified fragment length polymorphisms (AFLPs) between japonica and indica rice varieties. We studied the ability of two cloned AFLP bands to serve as heritable genetic markers by mapping them as RFLPs in an interspecific rice population and found that they represented single-copy DNA at unique loci in the rice genome. Key words : amplified fragment length polymorphism, AFLP, selective restriction fragment amplification, SRFA, PCR cloning, silver staining.

scholarly journals Amplified fragment length polymorphisms (AFLP's)

2017 ◽  
pp. 119 ◽  
Author(s):  
June Simpson
Keyword(s):  
Molecular Marker ◽  
Restriction Fragment ◽  
Restriction Enzyme ◽  
Fragment Length ◽  
Polymorphic Loci ◽  
Length Polymorphisms ◽  
Amplified Fragment Length Polymorphisms ◽  
Pcr Conditions

AFLP is a combination restriction fragment/PCR molecular marker technique which detects polymorphisms due to changes at or in the vicinity of restriction enzyme sites. The technique detects multiple polymorphic loci throughout the genome and may be used for fingerprinting and mapping purposes. The main advantages of the method are the consistency and reliability of the technique due to stringent PCR conditions and the ability to rapidly detect many polymorphic loci.

scholarly journals Ochratoxin A Production and Amplified Fragment Length Polymorphism Analysis of Aspergillus carbonarius, Aspergillus tubingensis, and Aspergillus niger Strains Isolated from Grapes in Italy

2006 ◽  
Vol 72 (1) ◽  
pp. 680-685 ◽  
Author(s):  
Giancarlo Perrone ◽  
Giuseppina Mulè ◽  
Antonia Susca ◽  
Paola Battilani ◽  
Amedeo Pietri ◽  
...  
Keyword(s):  
Ochratoxin A ◽  
Dna Sequences ◽  
Fragment Length ◽  
Strain Identification ◽  
Polymorphism Analysis ◽  
Aspergillus Carbonarius ◽  
Grape Berries ◽  
Tubulin Genes ◽  
Length Polymorphisms ◽  
Amplified Fragment Length Polymorphisms

ABSTRACT Ochratoxin A is a potent nephrotoxin and a possible human carcinogen that can contaminate various agricultural products, including grapes and wine. The capabilities of species other than Aspergillus carbonarius within Aspergillus section Nigri to produce ochratoxin A from grapes are uncertain, since strain identification is based primarily on morphological traits. We used amplified fragment length polymorphisms (AFLPs) and genomic DNA sequences (rRNA, calmodulin, and β-tubulin genes) to identify 77 black aspergilli isolated from grape berries collected in a 2-year survey in 16 vineyards throughout Italy. Four main clusters were distinguished, and they shared an AFLP similarity of <25%. Twenty-two of 23 strains of A. carbonarius produced ochratoxin A (6 to 7,500 μg/liter), 5 of 20 strains of A. tubingensis produced ochratoxin A (4 to 130 μg/liter), 3 of 15 strains of A. niger produced ochratoxin A (250 to 360 μg/liter), and none of the 19 strains of Aspergillus “uniseriate” produced ochratoxin A above the level of detection (4 μg/liter). These findings indicate that A. tubingensis is able to produce ochratoxin and that, together with A. carbonarius and A. niger, it may be responsible for the ochratoxin contamination of wine in Italy.

scholarly journals Extensive movement of LINES ONE sequences in beta-globin loci of Mus caroli and Mus domesticus.

1988 ◽  
Vol 8 (11) ◽  
pp. 4669-4674 ◽  
Author(s):  
N C Casavant ◽  
S C Hardies ◽  
F D Funk ◽  
M B Comer ◽  
M H Edgell ◽  
...  
Keyword(s):  
Gene Conversion ◽  
Restriction Fragment ◽  
Dna Sequences ◽  
Fragment Length ◽  
Concerted Evolution ◽  
Beta Globin ◽  
Mus Caroli ◽  
Length Polymorphisms ◽  
L1 Element ◽  
Restriction Fragment Length

LINES ONE (L1) is a family of movable DNA sequences found in mammals. To measure the rate of their movement, we have compared the positions of L1 elements within homologous genetic loci that are separated by known divergence times. Two models that predict different outcomes of this analysis have been proposed for the behavior of L1 sequences. (i) Previous theoretical studies of concerted evolution in L1 have indicated that the majority of the 100,000 extant L1 elements may have inserted as recently as within the last 3 million years. (ii) Gene conversion has been proposed as an alternative to a history of prolific recent insertions. To distinguish between these two models, we cloned and characterized two embryonic beta-globin haplotypes from Mus caroli and compared them with those of M. domesticus. In 9 of 10 instances, we observed an L1 element to be present in one chromosome and absent at the same site in a homologous chromosome. This frequency is quantitatively consistent with the known rate of concerted evolution. Therefore, we conclude that gene conversion is not required for concerted evolution of the L1 family in the mouse. Furthermore, we show that the extensive movement of L1 sequences contributes to restriction fragment length polymorphism. L1 insertions may be the predominant cause of restriction fragment length polymorphisms in closely related haplotypes.

scholarly journals Extensive movement of LINES ONE sequences in beta-globin loci of Mus caroli and Mus domesticus

1988 ◽  
Vol 8 (11) ◽  
pp. 4669-4674
Author(s):  
N C Casavant ◽  
S C Hardies ◽  
F D Funk ◽  
M B Comer ◽  
M H Edgell ◽  
...  
Keyword(s):  
Gene Conversion ◽  
Restriction Fragment ◽  
Dna Sequences ◽  
Fragment Length ◽  
Concerted Evolution ◽  
Beta Globin ◽  
Mus Caroli ◽  
Length Polymorphisms ◽  
L1 Element ◽  
Restriction Fragment Length

LINES ONE (L1) is a family of movable DNA sequences found in mammals. To measure the rate of their movement, we have compared the positions of L1 elements within homologous genetic loci that are separated by known divergence times. Two models that predict different outcomes of this analysis have been proposed for the behavior of L1 sequences. (i) Previous theoretical studies of concerted evolution in L1 have indicated that the majority of the 100,000 extant L1 elements may have inserted as recently as within the last 3 million years. (ii) Gene conversion has been proposed as an alternative to a history of prolific recent insertions. To distinguish between these two models, we cloned and characterized two embryonic beta-globin haplotypes from Mus caroli and compared them with those of M. domesticus. In 9 of 10 instances, we observed an L1 element to be present in one chromosome and absent at the same site in a homologous chromosome. This frequency is quantitatively consistent with the known rate of concerted evolution. Therefore, we conclude that gene conversion is not required for concerted evolution of the L1 family in the mouse. Furthermore, we show that the extensive movement of L1 sequences contributes to restriction fragment length polymorphism. L1 insertions may be the predominant cause of restriction fragment length polymorphisms in closely related haplotypes.

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