Genotyping‐by‐sequencing of genome‐wide microsatellite loci reveals fine‐scale harvest composition in a coastal Atlantic salmon fishery

Abstract

Individual assignment and genetic mixture analysis are commonly utilized in contemporary wildlife and fisheries management. Although microsatellite loci provide unparalleled numbers of alleles per locus, their use in assignment applications is increasingly limited. However, next‐generation sequencing, in conjunction with novel bioinformatic tools, allows large numbers of microsatellite loci to be simultaneously genotyped, presenting new opportunities for individual assignment and genetic mixture analysis. Here, we scanned the published Atlantic salmon genome to identify 706 microsatellite loci, from which we developed a final panel of 101 microsatellites distributed across the genome (average 3.4 loci per chromosome). Using samples from 35 Atlantic salmon populations (n = 1,485 individuals) from coastal Labrador, Canada, a region characterized by low levels of differentiation in this species, this panel identified 844 alleles (average of 8.4 alleles per locus). Simulation‐based evaluations of assignment and mixture identification accuracy revealed unprecedented resolution, clearly identifying 26 rivers or groups of rivers spanning 500 km of coastline. This baseline was used to examine the stock composition of 696 individuals harvested in the Labrador Atlantic salmon fishery and revealed that coastal fisheries largely targeted regional groups (<300 km). This work suggests that the development and application of large sequenced microsatellite panels presents great potential for stock resolution in Atlantic salmon and more broadly in other exploited anadromous and marine species.

SSR‐seq: Genotyping of microsatellites using next‐generation sequencing reveals higher level of polymorphism as compared to traditional fragment size scoring

“…They reviewed different NGS methods of SSR identification and primer development and discussed the pros and cons of using genotyping‐by‐sequencing (GBS) or restriction site‐associated DNA sequencing (RAD‐seq) in comparison to SSRs. That SSRs are not dead is reflected in the development of new analytical tools, for example, for the automatic inference of SSR genotypes (Zhan et al, ), and in a variety of publications that employed NGS for obtaining SSR sequence data directly from PCR amplicons (Bradbury et al, ; De Barba et al, ; Vartia et al, ). While these studies used animals as study systems, similar approaches have not yet been applied to plants.…”

“…In order to tackle the homoplasy problem and assess FR variation, some authors combined cloning or single‐strand conformation polymorphism and sequencing (e.g., Germain‐Aubrey et al, ; Lia, Bracco, Gottlieb, Poggio, & Confalonieri, ; Ortí, Pearse, & Avise, ; Šarhanová et al, ), but these methods are costly, time‐consuming, and not easily applicable for polyploids. There are first forays among animals (Bradbury et al, ; De Barba et al, ; Vartia et al, ), but comparisons between traditionally scored fragment length data and the information obtained from sequencing are still missing.…”

“…There are first forays among animals (Bradbury et al, 2018;De Barba et al, 2017;Vartia et al, 2016), but comparisons between traditionally scored fragment length data and the information obtained from sequencing are still missing.…”

The future is now: Amplicon sequencing and sequence capture usher in the conservation genomics era

“…When microsatellites are the preferred marker due to high polymorphism or existing datasets, amplicon sequencing methods can also be applied to transition from capillary sequencing to a next‐generation sequencing based approach (Zhan et al, ). Bradbury et al () highlight this approach by identifying 101 microsatellite loci from the available Atlantic salmon genome and genotyping 1,558 individuals via amplicon sequencing. The results of this study identified previously undescribed fine‐scale population structure in Atlantic salmon.…”

“…) Bradbury et al (2018). highlight this approach by identifying 101 microsatellite loci from the available Atlantic salmon genome and genotyping 1,558 individuals via amplicon sequencing.…”