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. 2022 Feb 24;15(4):679-693.
doi: 10.1111/eva.13351. eCollection 2022 Apr.

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

John Fredy Gómez Agudelo  1 , Vito Antonio Mastrochirico-Filho  1 , Carolina Heloisa de Souza Borges  1 , Raquel Belini Ariede  1 , Lieschen Valeria Guerra Lira  1 , Rubens Ricardo de Oliveira Neto  1 , Milena Vieira de Freitas  1 , Gustavo Adolfo Lenis Sucerquia  2 , Manuel Vera  3 , Milthon Honorio Muñoz Berrocal  4 , Diogo Teruo Hashimoto  1
Affiliations

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

John Fredy Gómez Agudelo et al. Evol Appl. .

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 FST analyses of SNP loci (FST = 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.

Keywords: South American Aquaculture; genetic structure; neotropical fish; serrasalmidae; signatures of selection; stress in aquaculture.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

FIGURE 1
FIGURE 1
Heatmap showing differentiation between tambaqui stocks from South America based on F ST
FIGURE 2
FIGURE 2
Population genetic analysis of tambaqui stocks from South America. Multidimensional scaling (MDS) analysis resulted from 199 individuals. Individuals were plotted according to their coordinates on the first two components (C1 and C2)
FIGURE 3
FIGURE 3
Plot of discriminant analysis of principal components (DAPC) showing relationship of 199 individual fish color coded by sample site, representing the structure between tambaqui stocks from South America. Twenty five PCs were retained using a‐score optimization
FIGURE 4
FIGURE 4
Analysis of genetic structure of tambaqui stocks from South America. Genetic structure was analyzed approaching K = 2 according to Delta K statistics. Each vertical bar represents an individual. Populations are separated by vertical white bars. The color proportions of each bar correspond to the estimated fractions of association of the individuals in each of the clusters
See this image and copyright information in PMC

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