Table 1 Summary of SNP arrays developed for fish and shellfish species
Sr. No | Species | NGS Platform used | SNP array /Panel | Name of technology used | Purpose of study | Reference |
|---|---|---|---|---|---|---|
1 | Rainbow trout (Oncorhynchus mykiss) | Illumina HiSeq 2000 | 57 K | Affymetrix Axiom genotyping technology | Investigate the genetic basis of economically and ecologically important traits in rainbow trout for use in aquaculture breeding programs. | [26] |
2 | Common carp (Cyprinus carpio) | Illumina | 25 K | Affymetrix Axiom technology | To analyze linkage disequilibrium in various samples, focusing on three domestic C. carpio strains. | [27] |
3 | Catfish species (Ictalurus furcatus, Ameiurus nebulosus, A. catus) | Illumina HiSeq2500 | 250 K | Affymetrix Axiom genotyping technology | To develop a high-density SNP array for catfish to facilitate genome-wide association studies, high-density linkage map construction, fine QTL mapping, haplotype analysis, and whole genome-based selection. | [28] |
4 | Atlantic salmon (Salmo salar) | Illumina | 130 K | Affymetrix Axiom genotyping technology | To use the developed SNP array as a platform for high-resolution genetics research in salmonids and aquaculture breeding programs for traits of evolutionary and economic significance. | [29] |
5 | Pacific oyster (Crassostrea gigas) and European flat oyster (Ostrea edulis) | Illumina Hisequation 2500 | 27 K (C. gigas) and 11 K (O. edulis) | To detect population structure and assess levels of linkage disequilibrium (LD) using an array. | [30] | |
6 | Nile tilapia (Oreochromis niloticus) | Illumina HiSeq 2500 | 58 K | Affymetrix Axiom genotyping technology | To develop a high density integrated genetic and physical linkage map, highlighting sex-specific recombination patterns in LGs. | [31] |
7 | Coho salmon (Oncorhynchus kisutch) | Illumina | 93 K | Affymetrix Axiom technology | To conduct linkage disequilibrium (LD) analysis using the developed array. | [32] |
8 | Arctic charr (Salvelinus alpinus) | Illumina HiSeq2500 | 87 K | Affymetrix Axiom genotyping technology | To investigate genetic diversity, quantitative trait genetics, population structure, pedigree analysis, and evolutionary divergence in wild populations. | [33] |
9 | Chinese tongue sole (Cynoglossus semilaevis) | Illumina HiSeq 2000 platform, | 38 K | Affymetrix Axiom technology | To enhance V. harveyi resistance in C. semilaevis through the use of SNP arrays and genomic selection methods. | [34] |
10 | The European seabass (Dicentrarchus labrax) and the gilt-head seabream (Sparus aurata) | HiSeq X Ten platform | 60 K | Affymetrix Axiom technology | To develop the MedFish array to aid in stock management, population genomics, and genomic selection for selective breeding. | [35] |
11 | Nile tilapia (Oreochromis niloticus) | Illumina HiSeq X platform | 65 K | Axiom platform | To utilize the SNP array for distinguishing tilapia populations in Africa and Asia, aiding population genetics and breeding research for consistent and comparable results. | [36] |
12 | Tambaqui (Colossoma macropomum), pacu (Piaractus mesopotamicus) | Illumina HiSeq 4000 | 60 K | Affymetrix Axiom genotyping technology | To investigate ecological, economic, and evolutionary traits of two Serrasalmidae species using genomics for applications like QTL mapping, phylogenetic analyses, genomic selection, and conservation genetics. | [37] |
13 | Mediterranean trout (Salmo trutta) | Illumina HiSeq X platform | 57 K | Affymetrix Axiom genotyping technology | To identify informative SNPs for fine-scale population genetic research and genetic biodiversity improvement in Mediterranean trout populations using trout 57 K SNP array. | [38] |
14 | Pacific white shrimp (Litopenaeus vannamei) | Illumina | 50 K | Affymetrix Axiom technology | To evaluate linkage disequilibrium and genetic diversity. | [39] |
15 | Sea cucumber (Apostichopus japonicus) | Illumina HiSeq 2500 platform | 24 K | Affymetrix Axiom technology | To develop a powerful tool for high-throughput genotyping in genetics and molecular breeding applications in the sea cucumber using SNPs identified and utilized for DNN-MCP and HaishenSNP24K array. | [40] |
16 | Nile tilapia (Oreochromis niloticus) | Illumina Hiseq X platform | 17 K | whole-genome pooled sequencing (Poolseq) approach, | To utilize SNP array data for population structure analysis and relationship resolution within Nile tilapia populations. | [41] |
17 | Atlantic salmon (Salmo salar) | Illumina NovaSeq | 50 K | Affymetrix Axiom genotyping technology | To implement genomic selection to investigate the biology, evolution, and ecology of a valuable aquaculture species in multiple regions. | [42] |
18 | Japanese flounder (Paralichthys olivaceus) | Illumina HiSeq 2000 | 50 K | Affymetrix Axiom genotyping technology | To facilitate genotyping and selective breeding programs for economically important traits. | [43] |