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

Abstract

Tambaqui or cachama ( Colossoma macropomum ) is one of the most important neotropical freshwater fish used for aquaculture in South America, and its production is concentrated at low latitudes (close to the Equator, 0°), where the water temperature is warm. Therefore, understanding how selection shapes genetic variations and structure in farmed populations is of paramount importance in evolutionary biology. High‐throughput sequencing to generate genome‐wide data for fish species allows for elucidating the genomic basis of adaptation to local or farmed conditions and uncovering genes that control the phenotypes of interest. The present study aimed to detect genomic selection signatures and analyze the genetic variability in farmed populations of tambaqui in South America using single‐nucleotide polymorphism (SNP) markers obtained with double‐digest restriction site‐associated DNA sequencing. Initially, 199 samples of tambaqui farmed populations from different locations (located in Brazil, Colombia, and Peru), a wild population (Amazon River, Brazil), and the base population of a breeding program (Aquaculture Center, CAUNESP, Jaboticabal, SP, Brazil) were genotyped. Observed and expected heterozygosity was 0.231–0.350 and 0.288–0.360, respectively. Significant genetic differentiation was observed using global F ST analyses of SNP loci ( F ST = 0.064, p < 0.050). Farmed populations from Colombia and Peru that differentiated from the Brazilian populations formed distinct groups. Several regions, particularly those harboring the genes of significance to aquaculture, were identified to be under positive selection, suggesting local adaptation to stress under different farming conditions and management practices. Studies aimed at improving the knowledge of genomics of tambaqui farmed populations are essential for aquaculture to gain deeper insights into the evolutionary history of these fish and provide resources for the establishment of breeding programs.

Whole‐genome re‐sequencing provides key genomic insights in farmed Arctic charr (Salvelinus alpinus) populations of anadromous and landlocked origin from Scandinavia

“…Some individual signals were placed in/or cover genes that indicated a very specific selective process such as the top DCMS hit (interferon‐inducible very large GTPase 1‐like) which might be a result of pressure due to pathogenic agents (Kim et al, 2012 ; Meunier & Broz, 2016 ; Pilla‐Moffett et al, 2016 ). Notably, genomic regions harbouring genes with immunity‐related functions have been recently pinpointed as putative selection signatures through the application of high‐density genotyping technologies in various farmed fish like Atlantic salmon ( Salmo salar ) (Gutierrez et al, 2016 ; López et al, 2019 ), coho salmon ( Oncorhynchus kisutch ) (López et al, 2021 ), rainbow trout ( Oncorhynchus mykiss ) (Cádiz et al, 2021 ), tambaqui ( Colossoma macropomum ) (Agudelo et al, 2022 ) and Nile tilapia ( Oreochromis niloticus ) (Cádiz et al, 2020 ). Such pattern, consistent across several different species, could be influenced by the fact that usually farmed fish are either directly selected for traits associated with disease resistance or due to the exposure to high levels of pathogens, strong selective pressure is applied in those genomic regions (López et al, 2015 ; Zueva et al, 2014 ).…”

Genome‐wide association and genomic selection in aquaculture

“…Finally, tambaqui or cachama ( Colossoma macropomum ), one of the most important neotropical freshwater fish used for aquaculture in South America, was investigated using the ddRAD sequencing approach in farmed populations from Brazil, Colombia and Peru to study the effects of recent artificial selection and domestication. Agudelo et al 232 identified several genomic regions potentially associated with stress tolerance and immunity, suggesting local adaptation to the culture environment.…”

Genomics applied to livestock and aquaculture breeding

“…History of domestication and artificial selection in aquaculture species is much more recent, and in some cases very incipient (López et al, 2015 ). Selection signatures, generated during the early domestication and recent selective breeding, have been assessed at a genome‐wide scale in important farmed fish species, including Atlantic salmon (Gutierrez et al, 2016 ; López, Benestan, et al, 2019 ; López, Linderoth, et al, 2019 ; Naval‐Sanchez et al, 2020 ), rainbow trout (Cádiz et al, 2021 ), coho salmon (López et al, 2021 ), Nile tilapia ( Oreochromis niloticus ; Cádiz et al, 2020 ; Hong Xia et al, 2015 ), channel catfish (Sun et al, 2014 ), common carp ( Cyprinus carpio ; Xu et al, 2019 ), turbot ( Scophthalmus maximus ; Aramburu et al, 2020 ), Australasian snapper ( Chrysophrys auratus ; Baesjou & Wellenreuther, 2021 ), gilthead seabream ( Sparus aurata ; Gkagkavouzis et al, 2021 ) tambaqui ( Colossoma macropomum ; Agudelo et al, 2022 ), as well as in shellfish farmed populations, including bay scallop ( Argopecten irradians ; Wang et al, 2021 ), Yesso scallop ( Mizuhopecten yessoensis ; Lv et al, 2022 ), European flat oyster ( Ostrea edulis ; Vera et al, 2019 ) and Pacific oyster ( Crassostrea gigas ; Hu et al, 2021 ; Jiao et al, 2021 ). These studies have used dense genome‐wide genotypes to identify genomic regions harboring genes affecting important phenotypes in farmed fish and shellfish.…”

“…, common carp (Cyprinus carpio;Xu et al, 2019), turbot (Scophthalmus maximus;Aramburu et al, 2020), Australasian snapper (Chrysophrys auratus;Baesjou & Wellenreuther, 2021), gilthead seabream (Sparus aurata;Gkagkavouzis et al, 2021) tambaqui (Colossoma macropomum;Agudelo et al, 2022), as well as in shellfish farmed populations, including bay scallop (Argopecten irradians;Wang et al, 2021), Yesso scallop (Mizuhopecten yessoensis;Lv et al, 2022), European flat oyster (Ostrea edulis;Vera et al, 2019) and Pacific oyster (Crassostrea gigas;Hu et al, 2021;Jiao et al, 2021).These studies have used dense genome-wide genotypes to identify genomic regions harboring genes affecting important phenotypes in farmed fish and shellfish. In general, studies on genomic footprints of domestication and artificial selection in aquaculture species have identified loci, which are putatively associated to adaptation to different biotic and abiotic conditions imposed by farming and management practices, as well as traits improved by selective breeding.Genes enriched within the loci underlying selection aquaculture populations are generally associated with growth, immune response, behavior and reproduction, indicating that these processes are important during the adaptation to captivity and also favored by recent human-driven selection.…”