Genome wide association study to resistance against Aeromonas hydrophila in tambaqui (Colossoma macropomum)

• Grant number: 19/10662-7
• Support Opportunities: Scholarships abroad - Research Internship - Doctorate
• Start date: August 01, 2019
• End date: October 31, 2019
• Field of knowledge: Agronomical Sciences - Fishery Resources and Fishery Engineering - Aquaculture
• Principal Investigator: Diogo Teruo Hashimoto
• Grantee: Raquel Belini Ariede
• Supervisor: Jose Manuel Yanez
• Host Institution: Centro de Aquicultura (CAUNESP). Universidade Estadual Paulista (UNESP). Campus de Jaboticabal. Jaboticabal , SP, Brazil
• Institution abroad: Universidad de Chile, Chile
• Associated to the scholarship: 17/19717-3 - Genome analysis for SNPs association with resistance to Aeromonas hydrophila and fillet yield in tambaqui (Colossoma macropomum), BP.DR

Abstract

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 tambaqui (Colossoma macropomum). This study aims to perform a genome-wide association study for resistance to A. hydrophila in tambaqui. The specific objectives are: 1) to develop a dense linkage map using data from ddRAD-seq (double-digest restriction site associated DNA sequencing) in tambaqui; 2) to characterize genomic regions of QTL (quantitative trait locus) associated with resistance to A. hydrophila in tambaqui. Sequencing/genotyping by ddRAD-seq will be characterized in 18 families of tambaqui challenged with A. hydrophila, which will allow assessing thousands of SNPs (single nucleotide polymorphisms). The traits evaluated for disease resistance will be survival rate and time of death. Initially, a medium density linkage map (~15K SNPs) will be constructed for tambaqui, which will serve for downstream analyses of genomic association. Next, statistical models for SNP/traits association will be applied to perform genome-wide association study and to detect QTL. SNPs that have significant association will be functionally annotated by comparisons with genomes of nearby species. The expected result is to generate a significant advance for breeding studies on native fish, particularly for a better understanding of genomic regions associated with disease resistance traits. The potential impact of this study is to make viable technologies for the production of improved fish for the aquaculture industry.

Scientific publications

(4)

(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)

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)

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)