From microsatellites to single nucleotide polymorphisms for the genetic monitoring of a critically endangered sturgeon

Abstract

The use of genetic information is crucial in conservation programs for the establishment of breeding plans and for the evaluation of restocking success. Short tandem repeats (STRs) have been the most widely used molecular markers in such programs, but next‐generation sequencing approaches have prompted the transition to genome‐wide markers such as single nucleotide polymorphisms (SNPs). Until now, most sturgeon species have been monitored using STRs. The low diversity found in the critically endangered European sturgeon (Acipenser sturio), however, makes its future genetic monitoring challenging, and the current resolution needs to be increased. Here, we describe the discovery of a highly informative set of 79 SNPs using double‐digest restriction‐associated DNA (ddRAD) sequencing and its validation by genotyping using the MassARRAY system. Comparing with STRs, the SNP panel proved to be highly efficient and reproducible, allowing for more accurate parentage and kinship assignments' on 192 juveniles of known pedigree and 40 wild‐born adults. We explore the effectiveness of both markers to estimated relatedness and inbreeding, using simulated and empirical datasets. Interestingly, we found significant correlations between STRs and SNPs at individual heterozygosity and inbreeding that give support to a reasonable representation of whole genome diversity for both markers. These results are useful for the conservation program of A. sturio in building a comprehensive studbook, which will optimize conservation strategies. This approach also proves suitable for other case studies in which highly discriminatory genetic markers are needed to assess parentage and kinship.

Parentage Analysis in Giant Grouper (Epinephelus lanceolatus) Using Microsatellite and SNP Markers from Genotyping-by-Sequencing Data

“…A recent rising molecular tool for parentage analysis is single nucleotide polymorphisms (SNPs), since the availability of genomic resources and multiplexed detecting methods have been greatly enhanced by NGS and bioinformatic techniques [ 13 ]. Over the last decade, SNPs have been used in parentage assignment [ 14 ], relatedness analysis [ 15 ], sibship assessment [ 3 ], population structure [ 16 ] or mating system research [ 17 ] in about 20 fish species [ 13 ]. Compared to microsatellites, SNPs are superior in their abundance over genomes [ 12 ], lower mutation rates [ 18 ], higher automation and easier standardization across laboratories [ 19 ], which effectively reduce the cost of time and genotyping errors caused by human factors.…”

Genetic Diversity and Genetic Structure of the Wild Tsushima Leopard Cat from Genome-Wide Analysis

“…Moreover, more economical and efficient approaches using NGS have been developed, such as restriction site-associated DNA sequencing (RADSeq) [ 14 ], double digest RADSeq (ddRADSeq) [ 15 ], MIG-Seq (multiplexed ISSR genotyping by sequencing) [ 16 ], genotyping-in-thousands by sequencing (GT-Seq) [ 17 , 18 ], and genotyping by random amplicon sequencing, direct (GRAS-Di) [ 19 , 20 ]. These approaches enable simultaneous sequencing and genotyping of thousands of SNP markers, and they have been used in various species, including endangered species [ 18 , 21 ]. Although GRAS-Di has few applications thus far, GRAS-Di is useful in characterizing wildlife because it can function with the available low-quality DNA in a polymerase chain reaction (PCR)-based method and does not require a reference genome, similar to MIG-seq [ 19 , 20 ].…”

Genetic admixture despite ecological segregation in a North African sparrow hybrid zone (Aves, Passeriformes, Passer domesticus × Passer hispaniolensis)

“…On the one hand, cautious interpretation of admixture proportions inferred from microsatellites has been recommended for a number of reasons. Pitfalls associated with the use of short tandem repeats (STRs) for population genetic studies relate to their particular mechanism of mutation (Putman & Carbone, 2014), a generally assumed inferiority of neutral markers compared to functional markers (Liebl, Schrey, Andrew, Sheldon, & Griffith, 2015), possible over- (Fernández et al, 2013;Ljungqvist, Åkeson, & Hansson, 2010;Narum et al, 2008;Roques, Chancerel, Boury, Pierre, & Acolas, 2019). Moreover, we stress that in our sparrow data set, there is a considerable difference between patterns of admixture in Algeria compared to the situation in the European area of sympatry where only limited asymmetrical allelic introgression occurs (i.e., on the Iberian Peninsula: this study in accordance with Hermansen et al, 2014).…”

“…Pitfalls associated with the use of short tandem repeats (STRs) for population genetic studies relate to their particular mechanism of mutation (Putman & Carbone, ), a generally assumed inferiority of neutral markers compared to functional markers (Liebl, Schrey, Andrew, Sheldon, & Griffith, ), possible overestimate of gene flow (Balloux, Brünner, Lugon‐Moulin, Hausser, & Goudet, ; Balloux, Lugon‐Moulin, & Hausser, ), and to the fact that STRs do not represent genome‐wide variation as, for example, inferred from single nucleotide polymorphisms (SNPs) (Lemopoulus et al, ). On the other hand, several comparative studies have concluded that despite all limitations, microsatellite data are not generally less informative or less suitable for detection of patterns of divergence and admixture than genome‐wide data, for example, SNPs (Fernández et al, ; Ljungqvist, Åkeson, & Hansson, ; Narum et al, ; Roques, Chancerel, Boury, Pierre, & Acolas, ). Moreover, we stress that in our sparrow data set, there is a considerable difference between patterns of admixture in Algeria compared to the situation in the European area of sympatry where only limited asymmetrical allelic introgression occurs (i.e., on the Iberian Peninsula: this study in accordance with Hermansen et al, ).…”