Development of a multi-species SNP array for serrasalmid fish Colossoma macropomum and Piaractus mesopotamicus

Abstract

Scarce genomic resources have limited the development of breeding programs for serrasalmid fish Colossoma macropomum (tambaqui) and Piaractus mesopotamicus (pacu), the key native freshwater fish species produced in South America. The main objectives of this study were to design a dense SNP array for this fish group and to validate its performance on farmed populations from several locations in South America. Using multiple approaches based on different populations of tambaqui and pacu, a final list of 29,575 and 29,612 putative SNPs was selected, respectively, to print an Axiom AFFYMETRIX (THERMOFISHER) SerraSNP array. After validation, 74.17% (n = 21,963) and 71.25% (n = 21,072) of SNPs were classified as polymorphic variants in pacu and tambaqui, respectively. Most of the SNPs segregated within each population ranging from 14,199 to 19,856 in pacu; and from 15,075 to 20,380 in tambaqui. Our results indicate high levels of genetic diversity and clustered samples according to their hatchery origin. The developed SerraSNP array represents a valuable genomic tool approaching in-depth genetic studies for these species.

A multiplexed plant-animal SNP array for selective breeding and species conservation applications

“…When looking at the numbers of high-quality SNPs (PHR and NMH), this array had conversion rates of 58%, 56%, 61% and 58% for each genus, respectively (S8 Table). These proportions are similar or higher than those of other plant Axiom SNP arrays designed [15,47–50], and similar or slightly lower than for other aquaculture species [16,23]. The new SNP array developed in this study is a necessary genotyping tool for these increasingly important species, for which so far researchers have had to rely on limited genetic resources.…”

“…A small number of Japanese red seabream (n = 39) and yellowtail kingfish (n = 23) DNA samples were screened over the array. The objective was to evaluate the performance of snapper and silver trevally SNPs on two closely related species within the same family, as it has been performed successfully in other taxa [16,17,22,23]. Almost all red seabream samples were successfully genotyped with snapper SNPs (S3 Table).…”

“…In some cases, researchers have exploited the known synteny among genomes of sister or closely related species and developed SNP arrays that combine markers from different genera. Key examples are the apple ( Malus domestica ) and pear ( Pyrus communis ) Illumina Infinium II 9K SNP array [22], the Pacific ( Crassostrea gigas ) and European oysters ( Ostrea edulis ) Axiom™ 60K SNP array [23], the “MedFish” Axiom™ 60K SNP array for European seabass ( Dicentrarchus labrax ) and gilthead seabream ( Sparus aurata ) [17], and the Axiom™ SerraSNP array with ∼30K SNPs each for the South American fresh water fishes pacu ( Piaractus mesopotamicus ) and tambaqui ( Colossoma macropomum ) [16]. However, multi-species SNP arrays designed for different and completely unrelated taxa with the purpose of pooling DNA from two (or more) samples have not been explored thus far.…”

The farming and husbandry ofColossoma macropomum: From Amazonian waters to sustainable production

“…A high‐quality genome assembly and annotation for tambaqui was assembled with PacBio reads and scaffolded with the high‐density genetic map, 224 yielding a highly contiguous assembly; it then was submitted to NCBI for annotation, where it passed all quality checks and subsequently was made available in a genome data viewer for this species 247 . Added to this was the development of a multispecies SNP array, the Affymetrix SerraSNP array, for two serrasalmid species ( Piaractus mesopotamicus and Colossoma macropomum ) with validation of 74.17% ( n = 21,963) and 71.25% ( n = 21,072) of polymorphic SNP variants for the respective species 248 …”

Genomic selection signatures in farmed Colossoma macropomum from tropical and subtropical regions in South America

“…Genomic breeding programs for tambaqui were initiated in the first decade of the 21 st century, with emphasis on improving the growth performance and disease resistance of these fish (Ariede et al, 2020 ; De Mello et al, 2015 ; Lira et al, 2020 ; Perazza et al, 2019 ). Although the assessment of genetic diversity is a fundamental step in the introduction of genomic breeding programs (Mastrochirico‐Filho et al, 2019 ), there have been few large‐scale population genetic studies of farmed populations (Mastrochirico‐Filho et al, 2021 ; Nunes et al, 2017 , 2020 ). Furthermore, no study has focus on the efficient breeding management of tambaqui, as opposed to a closely related serrasalmid species, pacu ( Piaractus mesopotamicus ) (Freitas et al, 2021 ).…”