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Screening of Mhc variation in Atlantic salmon (Salmo salar): a comparison of restriction fragment length polymorphism (RFLP), denaturing gradient gel electrophoresis (DGGE) and sequencing

Langefors, Åsa LU ; Lohm, Jakob LU ; von Schantz, Torbjörn LU and Grahn, Mats LU (2000) In Molecular Ecology 9(2). p.215-219
Abstract
We compared three different molecular methods currently used for screening of Mhc variation in population studies of Atlantic salmon. Restriction fragment length polymorphism (RFLP) of the entire class II gene detected 22 haplotypes. Seventeen exon 2 sequences were obtained from individuals carrying the 22 haplotypes, two of which had not been detected by RFLP. The six alleles (27%) detected by RFLP and not by exon 2 sequencing probably resulted from sequence variation outside exon 2. Within exon 2, RFLP differentiated 88% of the sequences. Alternatively, denaturing gradient gel electrophoresis (DGGE) performed under two run conditions detected 94% of the sequence variation. Both RFLP using different probes, and the two PCR-based methods... (More)
We compared three different molecular methods currently used for screening of Mhc variation in population studies of Atlantic salmon. Restriction fragment length polymorphism (RFLP) of the entire class II gene detected 22 haplotypes. Seventeen exon 2 sequences were obtained from individuals carrying the 22 haplotypes, two of which had not been detected by RFLP. The six alleles (27%) detected by RFLP and not by exon 2 sequencing probably resulted from sequence variation outside exon 2. Within exon 2, RFLP differentiated 88% of the sequences. Alternatively, denaturing gradient gel electrophoresis (DGGE) performed under two run conditions detected 94% of the sequence variation. Both RFLP using different probes, and the two PCR-based methods using three different primer pairs, suggest that there is only a single Mhc class II B gene in the Baltic populations of Atlantic salmon. (Less)
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author
organization
publishing date
type
Contribution to journal
publication status
published
subject
in
Molecular Ecology
volume
9
issue
2
pages
215 - 219
publisher
Wiley-Blackwell
external identifiers
  • scopus:0034144342
ISSN
0962-1083
DOI
10.1046/j.1365-294x.2000.00838.x
language
English
LU publication?
yes
id
070daf63-953d-424a-9037-4e4d21747b78 (old id 146060)
date added to LUP
2007-06-26 09:06:11
date last changed
2017-07-30 03:50:37
@article{070daf63-953d-424a-9037-4e4d21747b78,
  abstract     = {We compared three different molecular methods currently used for screening of Mhc variation in population studies of Atlantic salmon. Restriction fragment length polymorphism (RFLP) of the entire class II gene detected 22 haplotypes. Seventeen exon 2 sequences were obtained from individuals carrying the 22 haplotypes, two of which had not been detected by RFLP. The six alleles (27%) detected by RFLP and not by exon 2 sequencing probably resulted from sequence variation outside exon 2. Within exon 2, RFLP differentiated 88% of the sequences. Alternatively, denaturing gradient gel electrophoresis (DGGE) performed under two run conditions detected 94% of the sequence variation. Both RFLP using different probes, and the two PCR-based methods using three different primer pairs, suggest that there is only a single Mhc class II B gene in the Baltic populations of Atlantic salmon.},
  author       = {Langefors, Åsa and Lohm, Jakob and von Schantz, Torbjörn and Grahn, Mats},
  issn         = {0962-1083},
  language     = {eng},
  number       = {2},
  pages        = {215--219},
  publisher    = {Wiley-Blackwell},
  series       = {Molecular Ecology},
  title        = {Screening of Mhc variation in Atlantic salmon (Salmo salar): a comparison of restriction fragment length polymorphism (RFLP), denaturing gradient gel electrophoresis (DGGE) and sequencing},
  url          = {http://dx.doi.org/10.1046/j.1365-294x.2000.00838.x},
  volume       = {9},
  year         = {2000},
}