http://auburn.edu/academic/agriculture/fisheries/genomics/FISH7660%202006/DNA%20marker%20review%20paper-Aquaculture.pdf

DNA marker technologies and their applications in aquaculture genetics.

Few studies have yet addressed the functional aspects of MHC molecules in fish. To lay the foundation for this, we evaluated the association between disease resistance and MHC class I and class II polymorphism in Atlantic salmon. Standardized disease challenge trials were performed on a semi-wild Atlantic salmon population with subsequent MHC typing and statistical analysis. The pathogens employed were infectious salmon anaemia virus (ISAV) causing infectious salmon anaemia and the Aeromonas salmonicida bacteria causing furunculosis. The material consisted of 1,182 Atlantic salmon from 33 families challenged with A. salmonicida and 1,031 Atlantic salmon from 25 families challenged with ISAV. We found highly significant associations between resistance towards infectious diseases caused by both pathogens and MH class I and class II polymorphism in Atlantic salmon. The observed associations were detected due to independently segregating MH class I and class II single loci, and inclusion of a large number of fish allowing an extensive statistical analysis.

MHC polymorphism and disease resistance in Atlantic salmon (Salmo salar); facing pathogens with single expressed major histocompatibility class I and class II loci

http://www.gen.tcd.ie/molpopgen/link%20files/Norris%20et%20al%20variation.pdf

Microsatellite genetic variation between and within farmed and wild Atlantic salmon (Salmo salar) populations

The major histocompatibility complex (MHC) is the center of the immune universe. Genes in the MHC determine which antigens are processed and presented. Not surprisingly, the MHC contributes the major genetic component to important autoimmune diseases and will no doubt, although evidence is limited, contribute to resistance to infectious disorders. Vertebrates all seem to have MHC genes and it should be possible to determine, within the next few years, whether the clustering of antigen processing and presenting genes in this region is a conserved feature. One could imagine an evolutionary advantage to maintaining the MHC as a unit, either to coordinate expression of the genes in different tissues, or to coordinate T-cell selection during thymic ontogeny, since inheriting a linked set of polymorphic gene products may help to avoid conflicts during positive and negative selection. 153 refs., 9 figs., 3 tabs.

“Both man & bird & beast”: comparative organization of MHC genes

The rainbow trout (Oncorhynchus mykiss) is one of the most widely studied of model fish species. Extensive basic biological information has been collected for this species, which because of their large size relative to other model fish species are particularly suitable for studies requiring ample quantities of specific cells and tissue types. Rainbow trout have been widely utilized for research in carcinogenesis, toxicology, comparative immunology, disease ecology, physiology and nutrition. They are distinctive in having evolved from a relatively recent tetraploid event, resulting in a high incidence of duplicated genes. Natural populations are available and have been well characterized for chromosomal, protein, molecular and quantitative genetic variation. Their ease of culture, and experimental and aquacultural significance has led to the development of clonal lines and the widespread application of transgenic technology to this species. Numerous microsatellites have been isolated and two relatively detailed genetic maps have been developed. Extensive sequencing of expressed sequence tags has begun and four BAC libraries have been developed. The development and analysis of additional genomic sequence data will provide distinctive opportunities to address problems in areas such as evolution of the immune system and duplicate genes.

Status and opportunities for genomics research with rainbow trout.

The major histocompatibility complex (Mhc) has attracted much attention because of its immense polymorphism, its importance in transplantation, and its indisputable role in disease susceptibility in humans (Chen and Parham 1989; Hill et al. 1991) and in animals (Lie 1990). Previously, typical Mhc features reflected in allograft rejection and mixed leucocyte reactivity were the only indications that an Mhc also existed in teleost fish (Stet and Egberts 1991). The use of polymerase chain reaction (PCR) with degenerate oligonucleotides from conserved Mhc regions provided the first direct evidence for Mhc class I and class II genes in a fish, the teleost carp (Hashimoto et al. 1990). The primary aim of our study was to isolate and characterize expressed Mhc molecules in Atlantic salmon, and thereby provide data for further studies on evolutionary and disease aspects of the Mhc and its polymorphism. An Atlantic salmon-specific Mhc probe from leucocyte RNA was generated by PCR based on primers from conserved regions of known Mhc genes. The oligonucleotides and detailed strategies are described in an accompanying paper by Hordvik and co-workers (this issue). This salmon-specific probe was employed to screen a leucocyte )~gtl0 cDNA library based on a few individuals, from which Mhc-positive cDNAs were derived. The cDNAs analyzed in this report were established as subclones in pGEM-7z(+)R (Promega, Madison, WI) and sequencing was performed on double-stranded DNA with SP6, T7, and internal primers, using the procedure supplied by Multi-Pol TM DNA

Molecular cloning of major histocompatibility complex class I cDNAs from Atlantic salmon ( Salmo salar )

A genetic marker map of Atlantic salmon would facilitate the identification of loci influencing economically important traits. In the present paper we describe five new Atlantic salmon microsatellites. Segregation studies and linkage analysis of these and previously published microsatellites were carried out in pedigrees consisting of diploid dams and haploid gynogenetic offspring. We confirm earlier reports that salmon microsatellites tend to have a higher number of repeat units than those of mammals. Linkage analysis revealed that three microsatellites belong to a linkage group spanning approximately 50 cM of the genome, whereas the remaining 10 markers seem to be unlinked.

/pdf/segregation-studies-and-linkage-analysis-of-atlantic-salmon-2uhw7vfz6t.pdf

Segregation studies and linkage analysis of Atlantic salmon microsatellites using haploid genetics

Variability in the most extracellular exons of Atlantic salmon MHC-Sasa class I and class II was studied by polymerase chain reaction (PCR) amplification followed by sequencing The domains studied were class I alpha 2 and class II beta 1 The material used was genomic DNA of fish, mainly derived from the major Norwegian breeding pool, supplemented with some material from a minor breeder and a local river strain The analysis revealed extensive variation, most individuals being heterozygous with at least two variants

A study of variability in the MHC class II beta 1 and class I alpha 2 domain exons of Atlantic salmon, Salmo salar L.

The human pathogenic Neisseria species N. gonorrhoeae and N. meningitidis are closely related. In contrast to N. meningitidis, however, almost all clinical isolates of N. gonorrhoeae harbour a phenotypically cryptic plasmid. In some gonococcal strains regions of the cryptic plasmid have been found in the gonococcal genome and it has been suggested that large segments of the cryptic plasmid can be integrated into the gonococcal chromosome of both plasmid-bearing and plasmid-free strains. Here we report homology between parts of the cryptic gonococcal plasmid and genomic DNA from four different N. meningitidis strains from systemic disease isolates in which no plasmids have been found with the applied methods. Serogroup B strains, causing many of the cases of meningococcal disease in Norway, hybridized strongly to the cryptic plasmid probe, in contrast to serogroup A and C strains. Clones hybridizing to the cryptic plasmid were isolated from a meningococcal genomic lambda EMBL3 DNA library and characterized by restriction mapping. When using one such clone as a probe the parts of the cryptic plasmid showing homology to the genomic meningococcal DNA were confined to two small separate regions of 420 and 88 bp.

Homology between cryptic plasmid from Neisseria gonorrhoeae and genomic DNA from Neisseria meningitidis

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Molecular cloning of major histocompatibility complex class I cDNAs from Atlantic salmon ( Salmo salar )

Segregation studies and linkage analysis of Atlantic salmon microsatellites using haploid genetics

A study of variability in the MHC class II beta 1 and class I alpha 2 domain exons of Atlantic salmon, Salmo salar L.

Homology between cryptic plasmid from Neisseria gonorrhoeae and genomic DNA from Neisseria meningitidis