High-throughput phenotyping by deep learning to include body shape in the breeding program of pacu (Piaractus mesopotamicus)
Autor(a) principal: | |
---|---|
Data de Publicação: | 2023 |
Outros Autores: | , , , , , , , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Institucional da UNESP |
Texto Completo: | http://dx.doi.org/10.1016/j.aquaculture.2022.738847 http://hdl.handle.net/11449/247644 |
Resumo: | Deep learning (DL) is a cutting-edge technology that enables high-throughput phenotyping in aquaculture. The routine application of DL offers new opportunities for the genetic selection of appearance traits, especially those related to body shape. The criteria currently used for the trait selection of commercial interest, such as rapid growth and weight gain, can directly influence the animal's appearance, which is a criterion for sales and profit. Different morphotypes of the pacu Piaractus mesopotamicus (elliptical and rounded) have been described previously and may represent different commercial trends. Therefore, this study aimed to 1) develop a computer vision system (CVS) through deep learning that targets the prediction of morphometric measurements and body shape (morphotypes) in pacu, 2) analyze whether morphotypes vary according to the environment, sex, and/or age, and 3) estimate genetic parameters for body shape, using the condition factor (K) and ellipticity (E) as criteria. Data from 1380 individuals corresponding to 48 full-sib families were evaluated in two distinct environments (breeding nucleus: env1; commercial fish farm: env2). The animals were evaluated based on their weight and morphometric measurements at 15 and 28 months of age (growth stage). We used the mask R-CNN model as a deep-learning algorithm, which was optimized for a ResNet architecture with only 18 layers. This resulted in a faster training period (8GB NVIDIA 2060 RTX in less than a day), which requires less computational effort. The pacu CVS was effectively developed to account for the segmentation of several fish body regions (head, body, fins, and pelvis), as corroborated by the high correlations of measurements predicted manually and automatically. We detected K and E variation at different growth stages and environments, in which fish tend to have rounded shapes in env2 and at 28 months old. The body shape heritability indicates that this trait is under moderate genetic control and should respond to selection. In conclusion, this study established an efficient CVS for pacu that is resilient to field conditions, allowing high-throughput phenotyping for the routine assessment of body shape in breeding programs for this species. |
id |
UNSP_7c59467f7e0cd2fc46b100a8d84ab5fc |
---|---|
oai_identifier_str |
oai:repositorio.unesp.br:11449/247644 |
network_acronym_str |
UNSP |
network_name_str |
Repositório Institucional da UNESP |
repository_id_str |
2946 |
spelling |
High-throughput phenotyping by deep learning to include body shape in the breeding program of pacu (Piaractus mesopotamicus)Artificial intelligenceGenetic selectionPhenomicsDeep learning (DL) is a cutting-edge technology that enables high-throughput phenotyping in aquaculture. The routine application of DL offers new opportunities for the genetic selection of appearance traits, especially those related to body shape. The criteria currently used for the trait selection of commercial interest, such as rapid growth and weight gain, can directly influence the animal's appearance, which is a criterion for sales and profit. Different morphotypes of the pacu Piaractus mesopotamicus (elliptical and rounded) have been described previously and may represent different commercial trends. Therefore, this study aimed to 1) develop a computer vision system (CVS) through deep learning that targets the prediction of morphometric measurements and body shape (morphotypes) in pacu, 2) analyze whether morphotypes vary according to the environment, sex, and/or age, and 3) estimate genetic parameters for body shape, using the condition factor (K) and ellipticity (E) as criteria. Data from 1380 individuals corresponding to 48 full-sib families were evaluated in two distinct environments (breeding nucleus: env1; commercial fish farm: env2). The animals were evaluated based on their weight and morphometric measurements at 15 and 28 months of age (growth stage). We used the mask R-CNN model as a deep-learning algorithm, which was optimized for a ResNet architecture with only 18 layers. This resulted in a faster training period (8GB NVIDIA 2060 RTX in less than a day), which requires less computational effort. The pacu CVS was effectively developed to account for the segmentation of several fish body regions (head, body, fins, and pelvis), as corroborated by the high correlations of measurements predicted manually and automatically. We detected K and E variation at different growth stages and environments, in which fish tend to have rounded shapes in env2 and at 28 months old. The body shape heritability indicates that this trait is under moderate genetic control and should respond to selection. In conclusion, this study established an efficient CVS for pacu that is resilient to field conditions, allowing high-throughput phenotyping for the routine assessment of body shape in breeding programs for this species.Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)São Paulo State University (Unesp) Aquaculture Center of Unesp, SPSão Paulo State University (Unesp) School of Sciences, SPSão Paulo State University (Unesp) Center for Scientific Computing, SPSão Paulo State University (Unesp) Aquaculture Center of Unesp, SPSão Paulo State University (Unesp) School of Sciences, SPSão Paulo State University (Unesp) Center for Scientific Computing, SPCAPES: 001FAPESP: 2016/21011-9CNPq: 311559/2018-2Universidade Estadual Paulista (UNESP)Freitas, Milena V. [UNESP]Lemos, Celma G. [UNESP]Ariede, Raquel B. [UNESP]Agudelo, John F.G. [UNESP]Neto, Rubens R.O. [UNESP]Borges, Carolina H.S. [UNESP]Mastrochirico-Filho, Vito A. [UNESP]Porto-Foresti, Fábio [UNESP]Iope, Rogério L. [UNESP]Batista, Fabrício M. [UNESP]Brega, José R.F. [UNESP]Hashimoto, Diogo T. [UNESP]2023-07-29T13:21:55Z2023-07-29T13:21:55Z2023-01-15info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articlehttp://dx.doi.org/10.1016/j.aquaculture.2022.738847Aquaculture, v. 562.0044-8486http://hdl.handle.net/11449/24764410.1016/j.aquaculture.2022.7388472-s2.0-85138488940Scopusreponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengAquacultureinfo:eu-repo/semantics/openAccess2024-04-09T15:10:55Zoai:repositorio.unesp.br:11449/247644Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestopendoar:29462024-04-09T15:10:55Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false |
dc.title.none.fl_str_mv |
High-throughput phenotyping by deep learning to include body shape in the breeding program of pacu (Piaractus mesopotamicus) |
title |
High-throughput phenotyping by deep learning to include body shape in the breeding program of pacu (Piaractus mesopotamicus) |
spellingShingle |
High-throughput phenotyping by deep learning to include body shape in the breeding program of pacu (Piaractus mesopotamicus) Freitas, Milena V. [UNESP] Artificial intelligence Genetic selection Phenomics |
title_short |
High-throughput phenotyping by deep learning to include body shape in the breeding program of pacu (Piaractus mesopotamicus) |
title_full |
High-throughput phenotyping by deep learning to include body shape in the breeding program of pacu (Piaractus mesopotamicus) |
title_fullStr |
High-throughput phenotyping by deep learning to include body shape in the breeding program of pacu (Piaractus mesopotamicus) |
title_full_unstemmed |
High-throughput phenotyping by deep learning to include body shape in the breeding program of pacu (Piaractus mesopotamicus) |
title_sort |
High-throughput phenotyping by deep learning to include body shape in the breeding program of pacu (Piaractus mesopotamicus) |
author |
Freitas, Milena V. [UNESP] |
author_facet |
Freitas, Milena V. [UNESP] Lemos, Celma G. [UNESP] Ariede, Raquel B. [UNESP] Agudelo, John F.G. [UNESP] Neto, Rubens R.O. [UNESP] Borges, Carolina H.S. [UNESP] Mastrochirico-Filho, Vito A. [UNESP] Porto-Foresti, Fábio [UNESP] Iope, Rogério L. [UNESP] Batista, Fabrício M. [UNESP] Brega, José R.F. [UNESP] Hashimoto, Diogo T. [UNESP] |
author_role |
author |
author2 |
Lemos, Celma G. [UNESP] Ariede, Raquel B. [UNESP] Agudelo, John F.G. [UNESP] Neto, Rubens R.O. [UNESP] Borges, Carolina H.S. [UNESP] Mastrochirico-Filho, Vito A. [UNESP] Porto-Foresti, Fábio [UNESP] Iope, Rogério L. [UNESP] Batista, Fabrício M. [UNESP] Brega, José R.F. [UNESP] Hashimoto, Diogo T. [UNESP] |
author2_role |
author author author author author author author author author author author |
dc.contributor.none.fl_str_mv |
Universidade Estadual Paulista (UNESP) |
dc.contributor.author.fl_str_mv |
Freitas, Milena V. [UNESP] Lemos, Celma G. [UNESP] Ariede, Raquel B. [UNESP] Agudelo, John F.G. [UNESP] Neto, Rubens R.O. [UNESP] Borges, Carolina H.S. [UNESP] Mastrochirico-Filho, Vito A. [UNESP] Porto-Foresti, Fábio [UNESP] Iope, Rogério L. [UNESP] Batista, Fabrício M. [UNESP] Brega, José R.F. [UNESP] Hashimoto, Diogo T. [UNESP] |
dc.subject.por.fl_str_mv |
Artificial intelligence Genetic selection Phenomics |
topic |
Artificial intelligence Genetic selection Phenomics |
description |
Deep learning (DL) is a cutting-edge technology that enables high-throughput phenotyping in aquaculture. The routine application of DL offers new opportunities for the genetic selection of appearance traits, especially those related to body shape. The criteria currently used for the trait selection of commercial interest, such as rapid growth and weight gain, can directly influence the animal's appearance, which is a criterion for sales and profit. Different morphotypes of the pacu Piaractus mesopotamicus (elliptical and rounded) have been described previously and may represent different commercial trends. Therefore, this study aimed to 1) develop a computer vision system (CVS) through deep learning that targets the prediction of morphometric measurements and body shape (morphotypes) in pacu, 2) analyze whether morphotypes vary according to the environment, sex, and/or age, and 3) estimate genetic parameters for body shape, using the condition factor (K) and ellipticity (E) as criteria. Data from 1380 individuals corresponding to 48 full-sib families were evaluated in two distinct environments (breeding nucleus: env1; commercial fish farm: env2). The animals were evaluated based on their weight and morphometric measurements at 15 and 28 months of age (growth stage). We used the mask R-CNN model as a deep-learning algorithm, which was optimized for a ResNet architecture with only 18 layers. This resulted in a faster training period (8GB NVIDIA 2060 RTX in less than a day), which requires less computational effort. The pacu CVS was effectively developed to account for the segmentation of several fish body regions (head, body, fins, and pelvis), as corroborated by the high correlations of measurements predicted manually and automatically. We detected K and E variation at different growth stages and environments, in which fish tend to have rounded shapes in env2 and at 28 months old. The body shape heritability indicates that this trait is under moderate genetic control and should respond to selection. In conclusion, this study established an efficient CVS for pacu that is resilient to field conditions, allowing high-throughput phenotyping for the routine assessment of body shape in breeding programs for this species. |
publishDate |
2023 |
dc.date.none.fl_str_mv |
2023-07-29T13:21:55Z 2023-07-29T13:21:55Z 2023-01-15 |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
http://dx.doi.org/10.1016/j.aquaculture.2022.738847 Aquaculture, v. 562. 0044-8486 http://hdl.handle.net/11449/247644 10.1016/j.aquaculture.2022.738847 2-s2.0-85138488940 |
url |
http://dx.doi.org/10.1016/j.aquaculture.2022.738847 http://hdl.handle.net/11449/247644 |
identifier_str_mv |
Aquaculture, v. 562. 0044-8486 10.1016/j.aquaculture.2022.738847 2-s2.0-85138488940 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
Aquaculture |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.source.none.fl_str_mv |
Scopus reponame:Repositório Institucional da UNESP instname:Universidade Estadual Paulista (UNESP) instacron:UNESP |
instname_str |
Universidade Estadual Paulista (UNESP) |
instacron_str |
UNESP |
institution |
UNESP |
reponame_str |
Repositório Institucional da UNESP |
collection |
Repositório Institucional da UNESP |
repository.name.fl_str_mv |
Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP) |
repository.mail.fl_str_mv |
|
_version_ |
1803046245655117824 |