Organization of Microsatellites Differs between Mammals and Cold-water Teleost Fishes

Abstract

1994. Organization of microsatellites differs between mammals and cold-water teleost fishes. Can. 8 . Fish. Aquat. Sci. 51 : 1959-1 966. Microsatellites, in particular (dG-dT), and (dG-dA), dinucleotide repeats, are abundant and display a high degree of length polymorphism and heterozygssity in eukaryotic gewomes. Here, we report the cloning and characterization of 64 microsatellite sequences from Atlantic cod, Gadus moshua. The microsateiBites were classified as perfect, imperfect, and compound repeats. The length and integrity of these repeats were compared with rnicrosatellites characterized from two other teleosts, rainbow trout (Oncorhynchus mykiss) and Atlantic salmon (Salmo salar), and from three mammalian genomes, human, porcine, and canine. Differences were found in the proportions of the repeat classes; however, the most significant difference between rnicrosatellites from teleost fishes and mammals was the propensity of the former to be of greater length: some cod and rainbow trout rnicrosatellites were more than twice the size of the longest microsatellite repeats reported for any mammalian genome. Primers for PCR amplification were constructed for seven of the cod rnicrosatellites. Allele frequencies, degree of polymorphism, and heterozygosity were estimated for a sample population. Amplification with these cod primers was also carried out on a number of related gadids. These polymorphic microsatellite loci have enormous potential utility as genetic markers for use in population, breeding, and evolutionary studies.kes chaines dlADN microsatellite, et plus particuliitrement les sequences repktitives des dinuclbotides (dG-dT),et (dC-dA),, sont abowdantes et Beurs genornes eucaryotes presentent un taux blev6 de polymorphisrne et d'hbtkrozygositk. Dans ce rapport, nous presentons les resultats du clonage et de la caractkrisation de 6Q sequences dfADN microsatellite de la rnorue franche, Gadus rnsrhua. kes ADN rnicrosatellites ktaient classees en trois categories : parfaites, irnparfaites et 3 sequence de repetition cornposke. La longueur et I'intkgritb de ces sequences de rkpetition ont 6te comparees a celles dtADN microsatellite caractbrisee chez deux autres tkl6ostbens, la truite arc-en-ciel (Oncorhynchus mykiss) et le saumon de I'Atlantique (Salrno salar), et chez trois gknomes de mamrnif$res, (hurnain, porcin et canin). On a trouve des differences dans les proportions des categories de sequences de repetition; toutefois, la difference la plus significative entre les ADN microsatellites de t6leosteens et celle de mammif5res etait kmne tendance 5 une longueur superieure chez ces derniers : les ABN microsatellites de certaines morues et truites arcen-ciel etaient deux fois plus Bongues que les skquences repktees d'ADN microsatellite observkes pour tous les genomes de mammiferes. Des amorces pour Itamplification par la PCR ont et6 crkkes pour sept des ADN microsatellites de morue. kes frbquences d'alleles, le degre de polymorphisme et 11het6romygosit6 ont et6 estimks pour une population kchantillon. On a...

Fine-scale spatial and temporal genetic structure of Atlantic cod off the Atlantic coast of the USA

“…DNA was extracted with Qiagen DNeasy tissue kits (Qiagen) or standard phenol/chloroform procedures. A panel of 11 microsatellite markers (Gmo02 and Gmo132, Brooker et al 1994; Gmo19, Gmo35, Gmo36 and Gmo37, Miller et al 2000; PGmo-32, PGmo34, PGmo38, PGmo56 and PGmo58, Jakobs-179 Bigelow Bight and juvenile samples were genotyped entirely at UNH by means of 10 microsatellite loci and the PanI locus. To ensure consistency in the microsatellite allele scores for these samples relative to the remainder of the data set, a subset of samples (n = 123) were genotyped at Gmo132, Gmo35, Gmo37, PGmo32 and PGmo38 in laboratories at both institutions and the microsatellite allele scores at UNH were calibrated to those of NYU.…”

“…DNA was extracted with Qiagen DNeasy tissue kits (Qiagen) or standard phenol/chloroform procedures. A panel of 11 microsatellite markers (Gmo02 and Gmo132, Brooker et al 1994;Gmo19, Gmo35, Gmo36 and Gmo37, Miller et al 2000;PGmo-32, PGmo34, PGmo38, PGmo56 and PGmo58, Jakobs-179 Microsatellite analysis was conducted using procedures in Wirgin et al (2007) or in 12 µl total volumes containing 2 µl DNA template (50 to 200 ng µl -1 ), 0.5 µM of each primer, 1× GoTaq Flexi PCR Buffer (Promega), 0.2 mg ml -1 bovine serum albumin, 1 mM MgCl 2 , 100 µM deoxynucleotide triphosphates (dNTPs) and 0.2 U GoTaq Flexi DNA Polymerase (Promega). At UNH, the forward or reverse primer of each microsatellite was fluorescently labeled with FAM, NED or HEX, and amplification parameters followed those described in the literature for each primer set.…”

Marked genetic structuring in localised spawning populations of cod Gadus morhua in the North Sea and adjoining waters, as revealed by microsatellites

“…Five dinucleotide (GT repeat) cod microsatellite loci were employed in this study, to give a range of allelic diversity and heterozygosity. Two loci, GMO2 and GMO132, were obtained from Brooker et al (1994) and PCR-amplified according to the conditions therein. Three additional loci, GADM1, GADM2 and GADM3, were developed using the PIMA technique described in Lunt et al (1999) (Raymond & Rousset 1995).…”

Worldwide genetic structure of albacore Thunnus alalunga revealed by microsatellite DNA markers

“…Genetic studies of natural populations often use highly polymorphic microsatellite loci because of their high statistical power for population genetics (Brooker et al 1994, O'Connell & Wright 1997, Oleksiak 2010). Thus, nuclear-encoded DNA mi crosatellite markers could shed light on the genetic variability and population genetic structure of albacore, as it has been previously reported for other tuna species, such as bluefin (Riccioni et al 2010) and bigeye tuna (González et al 2008).…”