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Registro Completo |
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Biblioteca(s): |
Embrapa Café. |
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Data corrente: |
15/10/2020 |
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Data da última atualização: |
15/10/2020 |
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Tipo da produção científica: |
Artigo em Periódico Indexado |
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Autoria: |
SOUSA, I. C. de; NASCIMENTO, M.; SILVA, G. N.; NASCIMENTO, A. C. C.; CRUZ, C. D.; SILVA, F. F. e; ALMEIDA, D. P. de; PESTANA, K. N.; AZEVEDO, C. F.; ZAMBOLIM, L.; CAIXETA, E. T. |
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Afiliação: |
Ithalo Coelho de Sousa, Universidade Federal de Viçosa; Moysés Nascimento, Universidade Federal de Viçosa; Gabi Nunes Silva, Universidade Federal de Rondônia; Ana Carolina Campana Nascimento, Universidade Federal de Viçosa; Cosme Damião Cruz, Universidade Federal de Viçosa; Fabyano Fonseca e Silva, Universidade Federal de Viçosa; Dênia Pires de Almeida, Universidade Federal de Viçosa; Kátia Nogueira Pestana, Embrapa Mandioca e Fruticultura; Camila Ferreira Azevedo, Universidade Federal de Viçosa; Laércio Zambolim, Universidade Federal de Viçosa; EVELINE TEIXEIRA CAIXETA MOURA, CNPCa. |
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Título: |
Genomic prediction of leaf rust resistance to Arabica coffee using machine learning algorithms. |
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Ano de publicação: |
2021 |
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Fonte/Imprenta: |
Scientia Agricola, v. 78, n. 4, e20200021, 2021. |
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DOI: |
http://dx.doi.org/10.1590/1678-992X-2020-0021 |
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Idioma: |
Inglês |
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Conteúdo: |
Genomic selection (GS) emphasizes the simultaneous prediction of the genetic effects of thousands of scattered markers over the genome. Several statistical methodologies have been used in GS for the prediction of genetic merit. In general, such methodologies require certain assumptions about the data, such as the normality of the distribution of phenotypic values. To circumvent the non-normality of phenotypic values, the literature suggests the use of Bayesian Generalized Linear Regression (GBLASSO). Another alternative is the models based on machine learning, represented by methodologies such as Artificial Neural Networks (ANN), Decision Trees (DT) and related possible refinements such as Bagging, Random Forest and Boosting. This study aimed to use DT and its refinements for predicting resistance to orange rust in Arabica coffee. Additionally, DT and its refinements were used to identify the importance of markers related to the characteristic of interest. The results were compared with those from GBLASSO and ANN. Data on coffee rust resistance of 245 Arabica coffee plants genotyped for 137 markers were used. The DT refinements presented equal or inferior values of Apparent Error Rate compared to those obtained by DT, GBLASSO, and ANN. Moreover, DT refinements were able to identify important markers for the characteristic of interest. Out of 14 of the most important markers analyzed in each methodology, 9.3 markers on average were in regions of quantitative trait loci (QTLs) related to resistance to disease listed in the literature. MenosGenomic selection (GS) emphasizes the simultaneous prediction of the genetic effects of thousands of scattered markers over the genome. Several statistical methodologies have been used in GS for the prediction of genetic merit. In general, such methodologies require certain assumptions about the data, such as the normality of the distribution of phenotypic values. To circumvent the non-normality of phenotypic values, the literature suggests the use of Bayesian Generalized Linear Regression (GBLASSO). Another alternative is the models based on machine learning, represented by methodologies such as Artificial Neural Networks (ANN), Decision Trees (DT) and related possible refinements such as Bagging, Random Forest and Boosting. This study aimed to use DT and its refinements for predicting resistance to orange rust in Arabica coffee. Additionally, DT and its refinements were used to identify the importance of markers related to the characteristic of interest. The results were compared with those from GBLASSO and ANN. Data on coffee rust resistance of 245 Arabica coffee plants genotyped for 137 markers were used. The DT refinements presented equal or inferior values of Apparent Error Rate compared to those obtained by DT, GBLASSO, and ANN. Moreover, DT refinements were able to identify important markers for the characteristic of interest. Out of 14 of the most important markers analyzed in each methodology, 9.3 markers on average were in regions of quantitative trait loci (QTLs)... Mostrar Tudo |
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Palavras-Chave: |
Statistical learning. |
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Thesagro: |
Hemileia Vastatrix. |
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Thesaurus Nal: |
Artificial intelligence; Plant breeding. |
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Categoria do assunto: |
-- |
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URL: |
https://ainfo.cnptia.embrapa.br/digital/bitstream/item/216675/1/Sousa-et-al-2020.pdf
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Marc: |
LEADER 02472naa a2200301 a 4500
001 2125524
005 2020-10-15
008 2021 bl uuuu u00u1 u #d
024 7 $ahttp://dx.doi.org/10.1590/1678-992X-2020-0021$2DOI
100 1 $aSOUSA, I. C. de
245 $aGenomic prediction of leaf rust resistance to Arabica coffee using machine learning algorithms.$h[electronic resource]
260 $c2021
520 $aGenomic selection (GS) emphasizes the simultaneous prediction of the genetic effects of thousands of scattered markers over the genome. Several statistical methodologies have been used in GS for the prediction of genetic merit. In general, such methodologies require certain assumptions about the data, such as the normality of the distribution of phenotypic values. To circumvent the non-normality of phenotypic values, the literature suggests the use of Bayesian Generalized Linear Regression (GBLASSO). Another alternative is the models based on machine learning, represented by methodologies such as Artificial Neural Networks (ANN), Decision Trees (DT) and related possible refinements such as Bagging, Random Forest and Boosting. This study aimed to use DT and its refinements for predicting resistance to orange rust in Arabica coffee. Additionally, DT and its refinements were used to identify the importance of markers related to the characteristic of interest. The results were compared with those from GBLASSO and ANN. Data on coffee rust resistance of 245 Arabica coffee plants genotyped for 137 markers were used. The DT refinements presented equal or inferior values of Apparent Error Rate compared to those obtained by DT, GBLASSO, and ANN. Moreover, DT refinements were able to identify important markers for the characteristic of interest. Out of 14 of the most important markers analyzed in each methodology, 9.3 markers on average were in regions of quantitative trait loci (QTLs) related to resistance to disease listed in the literature.
650 $aArtificial intelligence
650 $aPlant breeding
650 $aHemileia Vastatrix
653 $aStatistical learning
700 1 $aNASCIMENTO, M.
700 1 $aSILVA, G. N.
700 1 $aNASCIMENTO, A. C. C.
700 1 $aCRUZ, C. D.
700 1 $aSILVA, F. F. e
700 1 $aALMEIDA, D. P. de
700 1 $aPESTANA, K. N.
700 1 $aAZEVEDO, C. F.
700 1 $aZAMBOLIM, L.
700 1 $aCAIXETA, E. T.
773 $tScientia Agricola$gv. 78, n. 4, e20200021, 2021.
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Registro original: |
Embrapa Café (CNPCa) |
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Biblioteca |
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Registro Completo
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Biblioteca(s): |
Embrapa Gado de Leite; Embrapa Recursos Genéticos e Biotecnologia. |
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Data corrente: |
09/05/2022 |
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Data da última atualização: |
09/05/2022 |
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Tipo da produção científica: |
Artigo em Periódico Indexado |
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Circulação/Nível: |
A - 1 |
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Autoria: |
AMARAL, T. F.; GRAZIA, J. G. V. de; MARTINHAO, L A. G.; DE COL, F.; SIQUEIRA, L. G. B.; VIANA, J. H. M.; HANSEN, P. J. |
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Afiliação: |
THIAGO F. AMARAL, University of Florida; JOAO GABRIEL VIANA DE GRAZIA, FIVX Apoyar Biotech Ltda; LUANY ALVES GALVAO MARTINHAO, FIVX Apoyar Biotech Ltda; FELIPE DE COL, FIVX Apoyar Biotech Ltda; LUIZ GUSTAVO BRUNO SIQUEIRA, CNPGL; JOAO HENRIQUE MOREIRA VIANA, Cenargen; PETER J. HANSEN, University of Florida. |
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Título: |
Actions of CSF2 and DKK1 on bovine embryo development and pregnancy outcomes are affected by composition of embryo culture medium. |
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Ano de publicação: |
2022 |
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Fonte/Imprenta: |
Scientific Reports, v. 12, 7503, 2022. |
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DOI: |
https://doi.org/10.1038/s41598-022-11447-7 |
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Idioma: |
Inglês |
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Conteúdo: |
Procedures for in vitro embryo production in cattle have not been optimized. In the current experiment, we utilized a 3 × 3 factorial design to test whether the proportion of embryos becoming blastocysts in culture and the pregnancy rate after embryo transfer are afected by type of serum in the medium [no serum; 3% (v/v) KnockOut Serum Replacement (SR); 3% (v/v) fetal bovine serum (FBS)] and addition of specifc embryokines [vehicle; 10 ng/mL colony stimulating factor 2 (CSF2); 100 ng/mL dickkopf related protein 1 (DKK1)] at day 5 of culture. Embryos were produced using abattoir-derived ovaries and Y-sorted semen from two Angus sires. The percent of putative zygotes and cleaved embryos becoming blastocysts was improved by SR and FBS. Pregnancy rate at day 30 was determined for 1426 Nelore recipients and calving rate for 266 recipients. In the absence of CSF2 or DKK1, pregnancy rates were lower for embryos cultured with SR or FBS. CSF2 and DKK1 reduced pregnancy rate for embryos cultured without serum but had no detrimental efect in the SR or FBS groups. Indeed, CSF2 blocked the negative efect of FBS on pregnancy rate. Data on birth weights were available for 67 bull calves. There were no efects of treatment. The sire used to produce embryos had signifcant and large efects on development to the blastocyst stage, pregnancy rate at day 30, calving rate and pregnancy loss between day 30 and calving. Results indicate that (1) SR and FBS can improve embryonic development in vitro while also compromising competence of embryos to survive after transfer, (2) actions of CSF2 and DKK1 depend upon other characteristics of the embryo production system, and (3) sire can have a large efect on embryonic development before and after transfer. MenosProcedures for in vitro embryo production in cattle have not been optimized. In the current experiment, we utilized a 3 × 3 factorial design to test whether the proportion of embryos becoming blastocysts in culture and the pregnancy rate after embryo transfer are afected by type of serum in the medium [no serum; 3% (v/v) KnockOut Serum Replacement (SR); 3% (v/v) fetal bovine serum (FBS)] and addition of specifc embryokines [vehicle; 10 ng/mL colony stimulating factor 2 (CSF2); 100 ng/mL dickkopf related protein 1 (DKK1)] at day 5 of culture. Embryos were produced using abattoir-derived ovaries and Y-sorted semen from two Angus sires. The percent of putative zygotes and cleaved embryos becoming blastocysts was improved by SR and FBS. Pregnancy rate at day 30 was determined for 1426 Nelore recipients and calving rate for 266 recipients. In the absence of CSF2 or DKK1, pregnancy rates were lower for embryos cultured with SR or FBS. CSF2 and DKK1 reduced pregnancy rate for embryos cultured without serum but had no detrimental efect in the SR or FBS groups. Indeed, CSF2 blocked the negative efect of FBS on pregnancy rate. Data on birth weights were available for 67 bull calves. There were no efects of treatment. The sire used to produce embryos had signifcant and large efects on development to the blastocyst stage, pregnancy rate at day 30, calving rate and pregnancy loss between day 30 and calving. Results indicate that (1) SR and FBS can improve embryonic development in vitro w... Mostrar Tudo |
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Palavras-Chave: |
Fertilização; Produção in vitro. |
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Thesagro: |
Bovino; Embrião; Reprodução Animal. |
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Thesaurus NAL: |
Animal reproduction; Embryo (animal); In vitro fertilization. |
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Categoria do assunto: |
L Ciência Animal e Produtos de Origem Animal |
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URL: |
https://ainfo.cnptia.embrapa.br/digital/bitstream/doc/1142749/1/Actions-of-CSF2.pdf
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Marc: |
LEADER 02687naa a2200301 a 4500
001 2142749
005 2022-05-09
008 2022 bl uuuu u00u1 u #d
024 7 $ahttps://doi.org/10.1038/s41598-022-11447-7$2DOI
100 1 $aAMARAL, T. F.
245 $aActions of CSF2 and DKK1 on bovine embryo development and pregnancy outcomes are affected by composition of embryo culture medium.$h[electronic resource]
260 $c2022
520 $aProcedures for in vitro embryo production in cattle have not been optimized. In the current experiment, we utilized a 3 × 3 factorial design to test whether the proportion of embryos becoming blastocysts in culture and the pregnancy rate after embryo transfer are afected by type of serum in the medium [no serum; 3% (v/v) KnockOut Serum Replacement (SR); 3% (v/v) fetal bovine serum (FBS)] and addition of specifc embryokines [vehicle; 10 ng/mL colony stimulating factor 2 (CSF2); 100 ng/mL dickkopf related protein 1 (DKK1)] at day 5 of culture. Embryos were produced using abattoir-derived ovaries and Y-sorted semen from two Angus sires. The percent of putative zygotes and cleaved embryos becoming blastocysts was improved by SR and FBS. Pregnancy rate at day 30 was determined for 1426 Nelore recipients and calving rate for 266 recipients. In the absence of CSF2 or DKK1, pregnancy rates were lower for embryos cultured with SR or FBS. CSF2 and DKK1 reduced pregnancy rate for embryos cultured without serum but had no detrimental efect in the SR or FBS groups. Indeed, CSF2 blocked the negative efect of FBS on pregnancy rate. Data on birth weights were available for 67 bull calves. There were no efects of treatment. The sire used to produce embryos had signifcant and large efects on development to the blastocyst stage, pregnancy rate at day 30, calving rate and pregnancy loss between day 30 and calving. Results indicate that (1) SR and FBS can improve embryonic development in vitro while also compromising competence of embryos to survive after transfer, (2) actions of CSF2 and DKK1 depend upon other characteristics of the embryo production system, and (3) sire can have a large efect on embryonic development before and after transfer.
650 $aAnimal reproduction
650 $aEmbryo (animal)
650 $aIn vitro fertilization
650 $aBovino
650 $aEmbrião
650 $aReprodução Animal
653 $aFertilização
653 $aProdução in vitro
700 1 $aGRAZIA, J. G. V. de
700 1 $aMARTINHAO, L A. G.
700 1 $aDE COL, F.
700 1 $aSIQUEIRA, L. G. B.
700 1 $aVIANA, J. H. M.
700 1 $aHANSEN, P. J.
773 $tScientific Reports$gv. 12, 7503, 2022.
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Registro original: |
Embrapa Gado de Leite (CNPGL) |
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