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Low-cost Genome-Wide Association Study and genomic predictions for resistance to Aeromonas hydrophila in pacu (Piaractus mesopotamicus)

Grant number: 18/08416-5
Support type:Regular Research Grants
Duration: May 01, 2019 - April 30, 2022
Field of knowledge:Agronomical Sciences - Fishery Resources and Fishery Engineering
Cooperation agreement: Comisión Nacional de Investigación Científica y Tecnológica (CONICYT)
Principal Investigator:Diogo Teruo Hashimoto
Grantee:Diogo Teruo Hashimoto
Principal investigator abroad: Jose Manuel Yanez
Institution abroad: Universidad de Chile, Chile
Home Institution: Centro de Aquicultura (CAUNESP). Universidade Estadual Paulista (UNESP). Campus de Jaboticabal. Jaboticabal , SP, Brazil
Assoc. researchers:Rafael Vilhena Reis Neto
Associated grant(s):19/08972-8 - Evaluation of the genetic diversity in Colossoma macropomum for pre-breeding programs in Brazil and Peru, AP.R


The species Piaractus mesopotamicus (pacu) occurs in the watersheds of the Paraná-Paraguay River and corresponds to one of the freshwater fish most produced in the South America aquaculture. Therefore, pacu represents one of the main candidate fish to be improved by means of selective breeding, especially due to its market acceptance (national and international). Aeromonas hydrophila is a gram-negative bacterium considered a harmful pathogen to human health and to fish from freshwater environments. In Brazil, aeromoniosis causes high mortality rates in several fish species, including pacu. Nowadays, the application of commercial antimicrobial is the main treatment used by producers, such as oxytetracycline and florfenicol. However, the use of these substances in fish farming can contaminate the aquatic environment, result in meat residue, contribute to the emergence of resistant pathogens, impact on other species and/or the entire food chain and, consequently, on the consumers health. Therefore, the selection of superior genotypes for disease resistance is a fundamental approach to maximize production in the context of environmental sustainability and food safety. The objectives of this project are: i) to perform a genome-wide association study for resistance to Aeromonas hydrophila in pacu and ii) to evaluate genomic prediction approaches using a low-cost strategy based on combining genotyping-by-sequencing (GBS), low-density single nucleotide polymorphisms (SNPs) and genotype imputation. Fifty families of pacu from the breeding program of Caunesp will be used as biological material. This breeding population was established in 2017 (project FAPESP 2016/21011-9). The traits evaluated for disease resistance will be survival rate and time of death. In relation to the genomic analysis, we intend to obtain the parental genotypes using a high-density panel (~10K SNPs) by GBS approaches and, then, perform the genotypes imputation in the progeny using a low-density panel (~0.5K SNPs) and pedigree-based imputation approaches, which will provide a cost-effective strategy for the application of genome-wide association studies and incorporation of genomic selection in pacu. The expected result of the project is to assist in the selection of pacu superior genotypes to increase the productivity, which will directly contribute to the food safety of South America by providing quality fish meat economically affordable to the population, together with the sustainable development of the activity. Moreover, the results of this project will assist in the reduction of the uncontrolled use of antibiotics and to decrease the occurrence of A. hydrohila outbreaks in aquaculture facilities, since it is a bacterium of special concern to human health. (AU)