- Background: Pacu (Piaractus mesopotamicus) is one of the most important Neotropical aquaculture species from South America. - Disease outbreaks caused by Aeromonas hydrophila infection have been considered significant contributors to the declining levels of pacu production. - An experimental challenge was performed to gain access to the levels of genetic variation for resistance against the bacteria using the following trait definitions: binary test survival (TS) and time of death (TD).. - The length of the LGs varied from 79.95 (LG14) to 137.01 (LG1) cM, with a total map length of 2755.60 cM. - 1% of the additive genetic variance (AGV) for the trait. - Conclusion: This study describes the development of the first medium density linkage map for pacu, which will be used as a framework to study relevant traits to the production of this species. - hydrophila was found to be moderately heritable but with a polygenic architecture suggesting that genomic selection, instead of marker assisted selection, might be useful for efficiently improving resistance to one of the most problematic diseases that affects the South American aquaculture.. - To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.. - The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.. - Paulo Donato Castellane, s/n, Jaboticabal, SP Brazil Full list of author information is available at the end of the article Mastrochirico-Filho et al. - BMC Genomics https://doi.org/10.1186/s z. - hydrophila infection is responsible for total mortalities ranging between 20 to 30% of the annual production [6].. - hydrophila were iden- tified, containing candidate genes related to the immune responses.. - hydrophila when bin- ary survival status and time of death were used as trait definitions, which have demonstrated the potential of the genetic improvement for Aeromonas resistance in this species [6]. - Based on this pro- posal, restriction site-associated DNA sequencing (RAD- Seq) represents an affordable and viable technique for the discovery and genotyping of several sets of SNPs, through a reduced representation of the genome belong- ing to multiplexed libraries of samples [22–24], particu- larly for non-model species without reference genome, such as pacu.. - No symptoms associated with infection were reported in individuals belonging to the unchallenged control group. - Considering the 381 challenged indi- viduals, the total cumulative mortality rate at the end of the test period was individuals) across all the families. - The cumulative mortality rate of the most sus- ceptible family to A. - was similar to the pedigree-based results (data not shown).. - From the total, 795,613 low quality reads were excluded of the analysis. - Additionally, genomic synteny was not conclu- sive for two LGs (LG19 and LG27), showing a poor syn- teny relationship with any chromosome of the blind cave tetra species (Fig. - Additionally, 38 immune system genes were located close to the iden- tified QTLs (Table 2).. - The major contribution of this study was to generate and apply genomic tools to improve the un- derstanding of the genomic architecture of resistance against A. - Recently, dense SNP arrays have facilitated researchers assessing the association between genome-wide markers and utilizing them for optimization of the disease resistance through genetic improvement in aquaculture . - The linkage map was comprised of 27 linkage groups that correspond to the number of chromosomes of pacu, ar- ranging 10,220 loci (Fig. - Our results were structurally similar to the linkage map constructed for tambaqui (C. - Here, we prefer to use the genome of the blind cave tetra (A.. - Some of these genes were already reported in several studies involv- ing the functioning of immune system mechanisms of fish in face of bacterial infections [40], corrobor- ating the results of the present study and suggesting similar mechanisms for bacterial resistance in differ- ent fish species. - Genes related to the immune system. - 11 GBLUP 1.10 1.05 rps6ka5, ccr3, cyp2k1. - of these predicted genes as important components in the role of the genetic variation for resistance against A. - Thus, genomic selection might be suitable to in- corporate molecular information to aim for the improve- ment of resistance to one of the most problematic diseases that affects the South American aquaculture.. - The names of the fish farms were kept confidential. - Briefly, a le- thal dose in 50% of the individuals (LD50) was tested in 60 randomly selected fish from the same pacu fam- ilies. - The mean weight of the individuals prior to the bacteria inoculation time was 23.0 g (SD. - When the individuals reached the dormant state, intraperitoneal inoculation of the predefined LD 50 of A. - Individuals of the control tank were injected by intraperitoneal inoculation of phosphate- buffered-saline solution (PBS). - Fish mortality events were registered all the time in the initial 3 days, and in 8-h intervals in the remaining days of the challenge experiment. - At the end of the challenge period, surviving fish were checked externally for detection of clinical signs of the disease, and posteriorly euthanized using benzocaine.. - Resistance was assessed as survival to the challenge test using the trait definitions of Mastrochirico et al. - [6], such as Test survival (TS), which was analysed using a binary threshold (probit) model (THR) to account for the binary nature of the trait. - μ was the fixed effect of the overall mean. - t i was the fixed effect of the tank i. - Barcode adapters were ligated to the end of the DNA fragments following digestion with Sbfl, using the T4 DNA ligase (New England Biolabs). - Size selection (300–500 bp) was carried out using excision of the appropriate band from gel electrophoresis. - Purification was then carried out by the MinElute Gel Extraction kit, following the recom- mendations of the manufacturer. - In relation of the main parameters that control locus formation by Stacks 2.0 software [50], the minimum depth of coverage (m) to create a putative allele (stack) was 3. - The orphan markers were assigned to existing linkage groups (op- timized LOD score = 6.7) using JoinSingles2 to maximize the map-abilities of the total input of markers, and ordered the binned markers within link- age groups using OrderMarkers2. - The animal models applied to the test was the same used for estimation of genetic parameters (above), but with addition of the genotype data. - u 2 jðiÞ was considered the square of the jth SNP marker effect in the ith individual, and p j expressed the observed allele frequency for the second allele of the jth marker. - SNP windows that explained more than 1% of the AGV for the traits were defined as suggestive QTL asso- ciated with A. - We thanks to The Roslin Institute (College of Medicine and Veterinary Medicine, University of Edinburgh), where the laboratorial infrastructure supported the preparation of the RAD-Seq libraries.. - All scripts are available upon request to the corresponding author.. - This study was conducted in strict accordance with the recommendations of the National Council for Control of Animal Experimentation (CONCEA) (Brazilian Ministry for Science, Technology and Innovation) and was approved by the Ethics Committee on Animal Use (CEUA number of Faculdade de Ciências Agrárias e Veterinárias, UNESP, Campus Jaboticabal, SP, Brazil. - Technical Proceedings of the Conference on Aquaculture in the Third Millennium. - 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