Microsatellites Associated with Growth Performance and Analysis of Resistance to Aeromonas hydrophila in Tambaqui Colossoma macropomum

First neurotranscriptome of adults Tambaquis (Colossoma macropomum) with characterization and differential expression between males and females

The Tambaqui is one of the most representative Amazon fish species, being highly exploited in fisheries, aquaculture and as a research model. Nonetheless, data about functional genome are still required to evaluate reproductive and nutrition parameters as well as resistance to pathogens. The of next-generation sequencing has allows assessing the transcriptional processes in non-model species by providing comprehensive gene collections to be used as a database in further genomic applications and increased performance of captive populations. In this study, we relied on RNAseq approach to generate the first transcriptome of the telencephalon from adult males and females of Colossoma macropomum, resulting in a reference dataset for future functional studies. We retrieved 896,238 transcripts, including the identification of 267,785 contigs and 203,790 genes. From this total, 91 transcripts were differentially expressed, being 63 and 28 of them positively regulated for females and males, respectively. The functional annotation resulted in a library of 40 candidate genes for females and 20 for males. The functional enrichment classes comprised reproductive processes (GO:0,048,609; GO:0,003,006; GO:0,044,703; GO:0,032,504; GO:0,019,953) being related to sex differentiation (e.g., SAFB) and immune response (e.g., SLC2A6, AHNAK, NLRC3, NLRP3 and IgC MHC I alpha3), thus indicating that the genes in the neurotranscriptome of Tambaqui participate in sex differentiation and homeostasis of captive specimens. These data are useful to design the selection of genes related to sex determination and animal welfare in raising systems of Tambaqui.

Computer vision system using deep learning to predict rib and loin yield in the fish Colossoma macropomum

Computer vision system (CVSs) are effective tools that enable large-scale phenotyping with a low-cost and non-invasive method, which avoids animal stress. Economically important traits, such as rib and loin yield, are difficult to measure; therefore, the use of CVS is crucial to accurately predict several measures to allow their inclusion in breeding goals by indirect predictors. Therefore, this study aimed (1) to validate CVS by a deep learning approach and to automatically predict morphometric measurements in tambaqui and (2) to estimate genetic parameters for growth traits and body yield. Data from 365 individuals belonging to 11 full-sib families were evaluated. Seven growth traits were measured. After biometrics, each fish was processed in the following body regions: head, rib, loin, R + L (rib + loin). For deep learning image segmentation, we adopted a method based on the instance segmentation of the Mask R-CNN (Region-based Convolutional Neural Networks) model. Pearson's correlation values between measurements predicted manually and automatically by the CVS were high and positive. Regarding the classification performance, visible differences were detected in only about 3% of the images. Heritability estimates for growth and body yield traits ranged from low to high. The genetic correlations between the percentage of body parts and morphometric characteristics were favorable and highly correlated, except for percentage head, whose correlations were unfavorable. In conclusion, the CVS validated in this image dataset proved to be resilient and can be used for large-scale phenotyping in tambaqui. The weight of the rib and loin are traits under moderate genetic control and should respond to selection. In addition, standard length and pelvis length can be used as an efficient and indirect selection criterion for body yield in this tambaqui population.

Antimicrobial resistance profile of Aeromonas spp. isolated from asymptomatic Colossoma macropomum cultured in the Amazonas State, Brazil

Bacterial diseases are important factors that limit productivity in aquaculture. To reduce negative economic impacts, fish farmers use antimicrobials, often indiscriminately, and this action has led to bacterial resistance to drugs. The objectives of this study were to isolate and identify the main putative pathogenic bacterial species in tambaqui (Colossoma macropomum), establish the profile of resistance to antimicrobials by the methods of disc diffusion, and determine the minimum inhibitory concentration (MIC) values. Two hundred and ninety asymptomatic fish were collected between March and November 2015 from ten fish farms in the Amazonas state (Brazil). Of the total strains recovered from tambaqui, seven were identified as Aeromonas spp. by sequencing the 16S rRNA gene. These seven isolates showed resistance to ampicillin, 28% to erythromycin, and 28% to sulfonamide. Additionally, the seven isolates showed a MIC higher than the range evaluated for amoxicillin, penicillin, novobiocin, tylosin tartrate, and clindamycin, and 85% showed resistance to erythromycin. The results of this study indicate the need to increase the awareness of fish farmers and, most importantly, the government, about the lack of drug regulations for use in aquaculture, and good management practices, so the indiscriminate prophylactic and systemic use of antimicrobials be inhibited.

Molecular characterization and evaluation of virulence traits of Aeromonas spp. isolated from the tambaqui fish (Colossoma macropomum)

The present study was developed to characterize, at the species level, 34 strains of Aeromonas spp., previously isolated from stressed tambaqui fish (Colossoma macropomum), to elucidate virulence factors, as well as their antibiotic resistance profile. Amplification of the gyrB gene identified the strains as A. hydrophila, A. dhakensis, A. caviae, A. veronii and A. jandaei. Bacterial virulence was evaluated by enzymatic assays for phenotypical production of hemolysins, proteases and lipases followed by the search for genes codifying the enzymes β-hemolysin, serine protease and lipase. Phenotypical production of virulence factors was diversified and proteolytic activity demonstrated to be a common expression among the strains. On the other hand, the lip gene encoding extracellular lipase was the most expressed. Furthermore, A. hydrophila was the most prevalent species isolated from tambaqui in our work.