Single nucleotide polymorphism markers with applications in aquaculture and assessment of its impact on natural populations

Abstract

-An increase in aquatic animal production can be achieved by extending aquaculture areas geographically, utilizing new species for culture, and using new technologies. Among new technologies useful for the increase of aquaculture production is the application of genetics and genomics. New molecular tools that benefit aquaculture have been developed. There has been a large number of experimental and review papers published concerning molecular markers and the range of their applications, including aquaculture and food product analyses. Analysis of single nucleotide polymorphisms (SNPs) has emerged as genotyping technology with wide and significant applications in aquaculture. SNPs can be used for construction of genetic linkage maps, finding quantitative trait loci (QTL) for useful traits like growth, body weight, grilsing, thermal and low oxygen tolerance, resistance to stress and diseases, mapping sex determination loci and identification of progeny in selection and chromosome manipulation experiments, assessment of genomic selectionand marker assisted selection in aquaculture. Genome-wide association studies (GWAS) facilitate the finding associations between SNPs and a trait in related or unrelated specimens. However, many traits are complex and can be controlled by number of QTL. Genotyping by genome reduction complexity sequencing emerged as an efficient and applicable technology in genomic selection. Identification of genes, sequences and nucleotides (substitutions) directly influencing phenotypic variations opens the possibility of marker-assisted selection for desirable characters in culture. SNP and QTL associations can be enhanced using genome editing technology. Examples of successful applications of SNPs in aquaculture of fish, crustacean and mollusk species, representing most geographic areas, and ecological risks assessment are reviewed.

Analysis of 16S mitochondrial ribosomal DNA sequence variations and phylogenetic relations among some Serranidae fishes

“…Calculation of SNPs revealed from molecular marker analysis would allow for accurate identification of biological taxa, including plants (Gao et al, 2016), and aquatic animal species (Saad & El-Sebaie 2017;Wenne, 2018). These DNA markers were developed to investigate the evolutionary variations within and among fish taxa (Wenne, 2018). The author calculated and explored the genetic distance values within and among the fish genera.…”

Hsp70 function and polymorphism, its implications for mollusk aquaculture: a review

“…Genetic polymer-phism refers, therefore, to changes in the nucleotide sequence of a gene coding for a particular protein type and has a significant frequency along the population (King, 2000). In species of interest for aquaculture, many single nucleotide polymorphisms (SNPs) have been detected that are associated with important traits such as linkage maps, growth, morphological characters, sex determination, resistance to pathogens, responses to thermal stress and low oxygen tolerance, and traceability (Wenne, 2018).…”

Single-Nucleotide Polymorphisms (SNP) Mining and Their Effect on the Tridimensional Protein Structure Prediction in a Set of Immunity-Related Expressed Sequence Tags (EST) in Atlantic Salmon (Salmo salar)

“…However, several efforts have been made to provide information regarding the consequences of genetic alterations in immune responserelated genes and may influence susceptibility to diseases in fish (Kongchum et al, 2011). In this context, SNP variations were found on il-1b of Cyprinus pellegrini and C. carpio that can be helpful in understanding differential resistance to koi herpesvirus (KHV) and Aeromonas hydrophila, respectively (Jia et al, 2015;Wenne, 2018). On the other hand, three SNPs were identified in the leukocyte cell-derived chemotaxin-2 (lect2) gene to be associated with resistance to the big belly disease on Latis calcarifer (Fu et al, 2014a;Wenne, 2018).…”

“…In this context, SNP variations were found on il-1b of Cyprinus pellegrini and C. carpio that can be helpful in understanding differential resistance to koi herpesvirus (KHV) and Aeromonas hydrophila, respectively (Jia et al, 2015;Wenne, 2018). On the other hand, three SNPs were identified in the leukocyte cell-derived chemotaxin-2 (lect2) gene to be associated with resistance to the big belly disease on Latis calcarifer (Fu et al, 2014a;Wenne, 2018). Three SNPs in the mast cell protease 8 (mcp-8) gene were also significantly associated with resistance of tilapia to Streptococcus agalactiae (Fu et al, 2014b;Wenne, 2018).…”

“…On the other hand, three SNPs were identified in the leukocyte cell-derived chemotaxin-2 (lect2) gene to be associated with resistance to the big belly disease on Latis calcarifer (Fu et al, 2014a;Wenne, 2018). Three SNPs in the mast cell protease 8 (mcp-8) gene were also significantly associated with resistance of tilapia to Streptococcus agalactiae (Fu et al, 2014b;Wenne, 2018).…”