Albinism in animals is generally a recessive trait, but in Japan a dominant oculocutaneous albino (OCA) mutant strain has been isolated in rainbow trout (Oncorhyncus mykiss). After confirming that this trait is not due to a tyrosinase gene mutation that causes OCA1 (tyrosinase-negative OCA), we combined the amplified fragment length polymorphism (AFLP) technique with bulked segregant analysis (BSA) to map the gene involved in dominant oculocutaneous albinism. Four AFLP markers tightly linked to the dominant albino locus were identified. One of these markers was codominant and we have it converted into a GGAGT-repeat microsatellite marker, OmyD-AlbnTUF. Using this pentanucleotide-repeat DNA marker, the dominant albino locus has been mapped on linkage group G of a reference linkage map of rainbow trout. The markers identified here will facilitate cloning of the dominant albino gene in rainbow trout and contribute to a better understanding of tyrosinase-negative OCA in animals.
"The bulked segregant analysis (BSA), developed by Michelmore et al. (1991), has been proved to be an effective method for detecting markers that are tightly linked with genes in many aquatic species (Nakamura et al. 2001; Araneda et al. 2005, 2009; Felip et al. 2005; Liu et al. 2011; Ge et al. 2014; Wang et al. 2014). Nakamura et al. (2001) obtained four AFLP markers linked to the dominant albino locus in rainbow trout after a screening of 64 AFLP primer combinations . Felip et al. (2005) identified 19 AFLP markers linking to the sexuality of rainbow trout after a screening of 486 AFLP primer combinations. "
[Show abstract][Hide abstract] ABSTRACT: A number of Pacific oyster (Crassostrea gigas) with golden shell background color were obtained which show great potential to develop a niche market. To improve the selective breeding progress of true-breeding strains with complete golden oysters, research was conducted to identify genetic markers linked to the shell color locus. An F1-segregating population was obtained by crossing two oysters with golden shell and white shell. Genomic DNA from eight progenies with golden shell and eight progenies with white shell were equally pooled for amplified fragment length polymorphism (AFLP) screening. In bulked segregant analysis, six out of 225 selective primer pair combinations produced seven polymorphic fragments tightly linked to shell color across the segregating population. The seven AFLP markers were all derived from the golden dam and mapped onto a single linkage group flanking the shell color locus. In conversion of the AFLPs into single-locus PCR-based markers, a sequence-characterized amplified region (SCAR) marker, named SCARJ8-2, a single nucleotide polymorphism (SNP) marker, named SNPL2-4, and a simple sequence repeat (SSR) marker, named SSRO11-2, were obtained. These markers obtained in this study will be useful for marker-assisted selection of the Pacific oyster.
"An evolutionarily recent whole genome duplication event is estimated to have occurred 25–100 mya , and the genome is estimated to be 1/3 of the way along the process of re-diploidization, . Several laboratories have constructed genetic maps including AFLPs, microsatellites, and SNPs to identify quantitative trait loci (QTL) affecting time to hatch, development rate, growth, thermal tolerance, natural killer cell-like activity, albinism and disease resistance [47-56]. The first genetic map based on molecular markers was constructed by Young et al.  who observed the inheritance of 476 loci (332 AFLPs) on 76 doubled haploid fish. "
[Show abstract][Hide abstract] ABSTRACT: Background
Genetic maps characterizing the inheritance patterns of traits and markers have been developed for a wide range of species and used to study questions in biomedicine, agriculture, ecology and evolutionary biology. The status of rainbow trout genetic maps has progressed significantly over the last decade due to interest in this species in aquaculture and sport fisheries, and as a model research organism for studies related to carcinogenesis, toxicology, comparative immunology, disease ecology, physiology and nutrition. We constructed a second generation genetic map for rainbow trout using microsatellite markers to facilitate the identification of quantitative trait loci for traits affecting aquaculture production efficiency and the extraction of comparative information from the genome sequences of model fish species.
A genetic map ordering 1124 microsatellite loci spanning a sex-averaged distance of 2927.10 cM (Kosambi) and having 2.6 cM resolution was constructed by genotyping 10 parents and 150 offspring from the National Center for Cool and Cold Water Aquaculture (NCCCWA) reference family mapping panel. Microsatellite markers, representing pairs of loci resulting from an evolutionarily recent whole genome duplication event, identified 180 duplicated regions within the rainbow trout genome. Microsatellites associated with genes through expressed sequence tags or bacterial artificial chromosomes produced comparative assignments with tetraodon, zebrafish, fugu, and medaka resulting in assignments of homology for 199 loci.
The second generation NCCCWA genetic map provides an increased microsatellite marker density and quantifies differences in recombination rate between the sexes in outbred populations. It has the potential to integrate with cytogenetic and other physical maps, identifying paralogous regions of the rainbow trout genome arising from the evolutionarily recent genome duplication event, and anchoring a comparative map with the zebrafish, medaka, tetraodon, and fugu genomes. This resource will facilitate the identification of genes affecting traits of interest through fine mapping and positional cloning of candidate genes.
"Linkage maps have been published for a large number of economically important animal species, such as bovine (Kappes et al., 1997), swine (Ellegren et al., 1994), sheep (Crawford et al., 1995), chicken (Groenen et al., 1998), as well as for some aquaculturally important fish species, such as the rainbow trout (Sakamoto et al., 2000), the tilapia (Kocher et al., 1998) and the catfish (Liu and Dunham, 1998). Among these, the genetic linkage map of the rainbow trout represents the effort of an international consortium , the SALMAP (http://dbs.cordis.lu/cordis-cgi/srchidadb?CALLER = FAIR _ 5.3), which has permitted the identification of QTLs for spawning season (Sakamoto et al., 1999; Fishback et al., 2000), temperature tolerance (Jackson et al., 1998) and IPN disease resistance (Ozaki et al., 2001), as well as single gene traits, like the dominant albino locus (Nakamura et al., 2001). "
[Show abstract][Hide abstract] ABSTRACT: The Japanese flounder constitutes one of the most important reared fish species in Asia, with a major stock enhancement program
in Japan to support decreases in industrial catches. Research on pond management, nutrition, immunity, sex manipulation, and
population genetics has assisted flounder aquaculture over the past decades, but genetic programs to improve selection for
complex traits, such as disease resistance, rapid growth rate, temperature tolerance, salinity tolerance, better meat quality,
and high feed conversion ratio are at the beginning. Recently developed techniques in molecular biology have made it possible
to dissect such complex traits controlled by several genes. Genetic linkage maps based on molecular markers at a large number
of sites in the genome constitute an essential prerequisite to identify individual loci controlling these traits (QTLs). A
ten-year effort was conducted toward the construction of genetic linkage maps and the dissection of lymphocystis disease resistance
and pseudo-albinism. In 1999, the first genetic linkage map was constructed based on AFLP and microsatellite markers genotyped
on F1 individuals, revealing 25 linkage groups for the male and 27 linkage groups for the female map and a great sex recombination
rate in males. These sex-specific differences in recombination regions were later characterized by centromere mapping in 2002,
showing that recombination events tend to occur more frequently in centromeric regions in the female, and conversely, in telomeric
regions in the male. These maps were used in 2003 for QTL attempts. A backcross family originated from two contrasting inbred
lines, resistant versus susceptible to lymphocystis disease, was genotyped for previously mapped microsatellite markers. A
QTL that explained 50% of the total phenotypic variation was found in the individuals screened, and now, it is being used
in commercially selective breeding programs. Two other QTLs associated with pseudo-albinism were also identified based on
the previous maps. As more detailed maps are needed to achieve more precise results, a high-density, sex-specific genetic
linkage map is currently being constructed for this species.
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