The spotted rose snapper Lutjanus guttatus is a fishery relevant species from the eastern Pacific Ocean, with aquaculture potential. Species-specific genetic markers are needed for the genetic characterization of wild and cultivated populations to help management strategies. Eighteen hypervariable microsatellites were developed by Next Generation Sequencing and characterized in a wild population sample. Genetic diversity was high (observed heterozygosity = 0.88 ± 0.050; the number of alleles per locus = 13.4 ± 1.3) and few loci departed from the Hardy-Weinberg Equilibrium, leaving 14 loci potentially suitable for population genetic studies. A reduced panel of five loci was tested in a cultivated stock to determine the parentage of progeny (embryonated eggs; n = 413), to estimate the temporal contribution of each parental broodstock. The above resulted in the successful assignment of 95.6% of the progeny to its parental couple, representing 17 out of the 24 possible families. Two of the four females produced most of those progeny (97.3%). These females, which reproduced throughout the season, did not spawn on consecutive days. The contribution of males was evenly distributed during the season and occurred on successive days. Some microsatellites can be used in other lutjanids (L. peru, L. argentiventris, and Hoplopagrus guentherii).
Release or escapes of aquaculture organisms may impact the genetic composition and variability of wild populations, leading to diverse issues that may compromise long-term wild stock fitness. Therefore, it is relevant to determine if farmed stocks are currently interacting with wild populations. Shrimp farming is an aquaculture activity taking place along the tropical Pacific coast of the Americas, and represents the most important culture bussiness of Northwestern Mexico. In this study, wild and farmed whiteleg shrimp Litopenaeus vannamei from the State of Sinaloa were genetically evaluated to determine admixture levels. A newly developed set of 14 microsatellite markers (mean number of alleles per locus 11.8, and 0.836 expected heterozygosity) was obtained by Next Generation Sequencing to characterize samples. Sampling consisted of 32 wild shrimps collected during three years (2002, 2012, and 2013) and three different sites, and two hatchery stocks from 2007. No significant differences were observed among years in the wild samples, but cluster analyses showed that hatchery-produced individuals were different from wild specimens. Deviations from Hardy-Weinberg Equilibrium and genotype assignment tests indicated that a fraction from each sample could contain individuals from hatchery origin. Even though the estimated fraction of escaped farmed individuals in the most recent samples (2012-2013; mean = 7.1 %) is considered of low genetic risk, management recommendations for hatcheries and farms were provided. Besides, the reasons that explain the intended and unintended farmed shrimp release into the wild were discussed.
Pedigree traceability in whiteleg shrimp (Litopenaeus vannamei) using genetic markers: A comparison between microsatellites and SNPsRastreabilidad del pedigrí en camarón blanco (Litopenaeus vannamei) mediante marcadores genéticos: Una comparación entre microsatélites y SNP ABSTRACT. To increase productivity, genetic improvement in cultivated shrimp is of much interest. Evaluation of genetic parameters (e.g., heritability, genotype-environment interaction, inbreeding) and the design of appropriate breeding plans are necessary steps towards genetic improvement. Pedigree traceability by genetic markers is relevant to these objectives. The aim of this study was to compare the performance of 2 genetic marker panels (microsatellites and single nucleotide polymorphisms [SNPs]) for pedigree traceability of a cultivated stock of whiteleg shrimp (Litopenaeus vannamei). Pedigree of a stock from 81 full-sib families reared in a common environment was assessed with microsatellites and SNPs as genetic markers. The panel of 76 SNPs performed better than microsatellites, allowing 94-96% of parentage assignment of the tested progeny (n = 192). A minimum number of 50 SNPs with a proportion of 60% loci with a minimum allele frequency of 0.3 is suitable for successful pedigree assignment. SNP markers are suggested for confidently testing the pedigree of shrimp from known parental broodstock.Key words: shrimp farming, parentage assignment, genetic identification, assignment likelihood, exclusion probability. RESUMEN.El mejoramiento genético en el camarón cultivado es de amplio interés para incrementar la productividad. La evaluación de parámetros genéticos (e.g., heredabilidad, interacción entre genotipo y ambiente, endogamia) y el diseño de planes de apareamiento son elementos necesarios para el mejoramiento genético. La rastreabilidad del pedigrí con marcadores genéticos es importante para estos objetivos. El objetivo de este trabajo fue comparar el desempeño de 2 paneles de marcadores genéticos (microsatélites y polimorfismos de nucleótido sencillo [SNP]) para rastrear el pedigrí en una población de camarón blanco (Litopenaeus vannamei) de cultivo. Se determinó el pedigrí de la progenie de 81 familias de hermanos completos mediante el uso de microsatélites y SNP como marcadores genéticos. Un panel de 76 SNP probó tener un mejor desempeño que los microsatélites para la asignación de parentesco, obteniéndose un 94-96% de asignación en una muestra de la progenie (n = 192). Un número mínimo de 50 SNP con una proporción de 60% de loci con una frecuencia alélica mínima de 0.3 es adecuado para una asignación exitosa de pedigrí. Se sugiere utilizar los marcadores SNP para determinar el parentesco de la progenie de camarón proveniente de padres conocidos.Palabras clave: cultivo de camarón, asignación de parentesco, identificación genética, probabilidad de asignación, probabilidad de exclusión.
Cherax quadricarinatus is a decapod crustacean of interest to the aquaculture industry. In Mexico, a significant effort has been made to improve biological requirements, but the genetic characteristics are unknown. We examined the genetic diversity and differentiation in four populations in Mexico (three commercial farms and one feral population), as well as one research line from Argentina, used as reference. To initiate a founder stock in a genetic improvement program, we analyzed five microsatellite markers. The genetic diversity in terms of the number of alleles was low to moderate (2.8-6.2) in Mexican populations than the Argentinean sample (8.8). A pairwise Wright's Fst analysis showed that all populations were significantly different (P < 0.5). Cross-breeding organisms from a different population are suggested to increase genetic variability before initiating a founder stock with higher genetic variation.
Twenty-four new tetranucleotide microsatellite loci, obtained by 454 pyrosequencing, were found in the green abalone Haliotis fulgens. Genetic diversity ranged from 6 to 27 alleles per locus with 0.653-0.912 expected heterozygosity. This provides polymorphic markers for population genetics and parentage analysis focusing on the management and conservation of this species. Crossamplification in H. corrugata and H. rufescens showed polymorphism in five and four loci, respectively.
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