Low-cost genome-wide association study and genomic predictions for resistance to Aeromonas hydrophila in pacu (Piaractus mesopotamicus)

• Grant number: 18/08416-5
• Support Opportunities: Regular Research Grants
• Duration: May 01, 2019 - April 30, 2022
• Field of knowledge: Agronomical Sciences - Fishery Resources and Fishery Engineering - Aquaculture
• Convênio/Acordo: Comisión Nacional de Investigación Científica y Tecnológica (CONICYT)
• Principal Investigator: Diogo Teruo Hashimoto
• Grantee: Diogo Teruo Hashimoto
• Principal researcher abroad: Jose Manuel Yanez
• Institution abroad: Universidad de Chile, Chile
• Host Institution: Centro de Aquicultura (CAUNESP). Universidade Estadual Paulista (UNESP). Campus de Jaboticabal. Jaboticabal , SP, Brazil
• Associated 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 SPRINT
• Associated scholarship(s): 21/02592-9 - Genomic analysis of pacu (Piaractus mesopotamicus) resistant against Aeromonas hydrophila by dense SNP panel using ddRAD-seq, BP.TT; 20/04436-1 - Genomic analysis of pacu (Piaractus mesopotamicus) resistant against Aeromonas hydrophila by dense SNP panel using ddRAD-Seq, BP.TT

Abstract

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)

Scientific publications

(5)

(References retrieved automatically from Web of Science and SciELO through information on FAPESP grants and their corresponding numbers as mentioned in the publications by the authors)

ARIEDE, RAQUEL B.; FREITAS, MILENA, V; LIRA, LIESCHEN V. G.; AGUDELO, JOHN F. G.; BORGES, CAROLINA H. S.; MASTROCHIRICO-FILHO, VITO A.; CACERES, PABLO; YANEZ, JOSE M.; HASHIMOTO, DIOGO T.. Linkage map for chromosome-level genome anchoring and genome-wide association study for resistance to Aeromonas hydrophila in Colossoma macropomum. Aquaculture, v. 560, p. 11-pg., 2022-06-11. (17/19717-3, 19/10662-7, 18/08416-5)

MASTROCHIRICO-FILHO, VITO A.; BORGES, CAROLINA H. S.; FREITAS, MILENA V.; ARIEDE, RAQUEL B.; PILARSKI, FABIANA; UTSUNOMIA, RICARDO; CARVALHEIRO, ROBERTO; GUTIERREZ, ALEJANDRO P.; PENALOZA, CAROLINA; YANEZ, JOSE M.; et al. Development of a SNP linkage map and genome-wide association study for resistance to Aeromonas hydrophila in pacu (Piaractus mesopotamicus). BMC Genomics, v. 21, n. 1, SEP 29 2020. (18/08416-5, 16/21011-9, 17/26900-9, 16/18294-9)

ARIEDE, RAQUEL B.; LEMOS, CELMA G.; BATISTA, FABRICIO M.; OLIVEIRA, RUBENS R.; AGUDELO, JOHN F. G.; BORGES, CAROLINA H. S.; IOPE, ROGERIO L.; ALMEIDA, FERNANDA L. O.; BREGA, JOSE R. F.; HASHIMOTO, DIOGO T.. Computer vision system using deep learning to predict rib and loin yield in the fish Colossoma macropomum. ANIMAL GENETICS, v. 54, n. 3, p. 14-pg., 2023-02-09. (17/19717-3, 18/08416-5, 19/10662-7)

ARIEDE, RAQUEL B.; FREITAS, V, MILENA; AGUDELO, JOHN F. G.; BORGES, CAROLINA H. S.; LIRA, LIESCHEN V. G.; YOSHIDA, GRAZYELLA M.; PILARSKI, FABIANA; YANEZ, JOSE M.; HASHIMOTO, DIOGO T.. Genetic (co)variation between resistance to Aeromonas hydrophila and growth in tambaqui (Colossoma macropomum). Aquaculture, v. 523, JUN 30 2020. (18/08416-5, 17/19717-3, 19/10662-7)

MASTROCHIRICO-FILHO, VITO A.; ARIEDE, RAQUEL B.; FREITAS, V, MILENA; BORGES, CAROLINA H. S.; LIRA, LIESCHEN V. G.; MENDES, NATALIA J.; AGUDELO, JOHN F. G.; CACERES, PABLO; BERROCAL, MILTHON H. M.; SUCERQUIA, GUSTAVO A. L.; et al. Development of a multi-species SNP array for serrasalmid fish Colossoma macropomum and Piaractus mesopotamicus. SCIENTIFIC REPORTS, v. 11, n. 1, SEP 29 2021. (16/21011-9, 17/26900-9, 20/11049-4, 16/18294-9, 18/08416-5, 17/19717-3, 19/10662-7, 19/08972-8)