Pedigree traceability in whiteleg shrimp (Litopenaeus vannamei) using genetic markers: A comparison between microsatellites and SNPs

Abstract

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.

Genetic tracing of farmed shrimp (Decapoda, Penaeidae) in wild populations from a main aquaculture region in Mexico

“…In the present study, the two loci showing null alleles (Livan13, Livan60) were also recently reported of having this problem in parentage testing (Perez-Enriquez & Max-Aguilar, 2016). It has been recognized that the presence of null alleles may influence the results of population genetic studies (Pompanon, Bonin, Bellemain, & Taberlet, 2005).…”

Effectiveness of SNPs for Sibship Assignment in Farmed Banana Shrimp (Penaeus merguiensis)

“…Using 60-100 SNPs was reported to be sufficient for parentage assignment in Chinook salmon [32]. It was estimated that 59-122 SNPs were sufficient for correct parentage assignment over 99% in black tiger shrimp [18] similar to the high assignment accuracy (>98%) when using 50 SNPs (MAF ≥ 0.3, 162 broodstock) for parentage assignment in Pacific white shrimp [9]. Perez-Enriquez and Max-Aguilar (2016) also demonstrated that using 76 SNPs for parentage assignment resulted in higher assignment rates than microsatellites (SSR), both in simulated data (SSR: 23-83%, SNP: 85-98%) and empirical data (SSR: 15-76%, SNP: 94-96%).…”

“…Pedigree reconstructions in penaeid shrimp have used microsatellites due to their high polymorphism and accuracy to resolve genealogical relationships between individuals and has been commonly used for parentage assignment in framed shrimp [8,9]. However, the development of microsatellites is rather costly and time-consuming; microsatellites need to be developed de novo for species newly examined as their locations are usually within non-coding regions where the nucleotide substitution rates are high [10].…”

“…Effective applications of SNPs have led to the recent development of SNP arrays in high-value farmed species, including Atlantic salmon [21], rainbow trout [22] and Pacific white shrimp [23,24]. In farmed shrimp, SNPs have been reported to show better performances than microsatellites for parentage assignment in black tiger shrimp (Penaeus monodon) [18] and Pacific white shrimp (Penaeus vannamei) [9]; however, comparisons between microsatellite and SNP markers for parentage assignment in banana shrimp remained unknown.…”

Characterization of microsatellite markers in the coding regions of the Penaeus vannamei genome

“…The association of STR markers with specific phenotypes in marine shrimp Penaeus vannamei has been relatively unexplored, primarily due to the availability of new SNP-based genotyping methods [ 18 ]. Unlike SNPs, which typically require around 60 to 100 markers for genotyping individuals, a small number of STRs (sometimes even fewer) can accomplish the same task [ 19 , 20 ]. This difference opens up a range of possibilities for discoveries, considering that approximately 24% of the P .…”