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Genomic homology between cattle and buffaloes and comparison of different machine learning methods for genotype imputation in buffalo genome

Grant number: 17/00462-5
Support type:Scholarships abroad - Research Internship - Post-doctor
Effective date (Start): May 28, 2017
Effective date (End): May 27, 2018
Field of knowledge:Agronomical Sciences - Animal Husbandry - Genetics and Improvement of Domestic Animals
Principal researcher:Humberto Tonhati
Grantee:Daniel Jordan de Abreu Santos
Supervisor abroad: Li Ma
Home Institution: Faculdade de Ciências Agrárias e Veterinárias (FCAV). Universidade Estadual Paulista (UNESP). Campus de Jaboticabal. Jaboticabal , SP, Brazil
Research place: University of Maryland, College Park, United States  
Associated to the scholarship:15/12396-1 - IMPUTATION OF MARKER GENOTYPES IN BUFFALO GENOME AND ITS IMPACT ON GENOMIC EVALUATION OF MILK YIELD AND CONTENT, BP.PD

Abstract

The homology between the buffalo and bovine species is especially important because it may enable transferring of developed genomic technologies between the two species. The homology principle may be applied to cover the lack of a reference genome for buffaloes because the bovine reference genome has been widely studied. Thus, this project aim at determining existing homologies among bovine species to propose a rearrangement of the buffalo genome. A panel of bovine SNPs will be used for principal component analysis (PCA) and admixture cluster analyses with genomic data of others bovids. Other aim of this project is to assess the genotype imputation in buffalo using machine learning methods (LM). Considering the imputations methods depend on the ordering of the markers in some genomic region, methods based on artificial intelligence can be a good alternative for genotype imputations in buffalo genome. Thus, we will also compare the traditional methods for imputation that needs the order of the SNPs with alternative methods based on machine learning (LM). The LM methods do not require any priori information about the relationship between the predictions and the original data set, and they can to learn this relationship by the own data according to the LM algorithm used. For this study, we will use Support Vector Machines and Random Forest algorithms that represent the supervised learning and unsupervised learning algorithm, respectively. Different scenarios with few numbers of markers and reference populations will be used in this study. The traditional methods can to show litter better results than ML methods, but for the cases with markers with unknown position, as for species without genome reference assembled, the accuracy of genotype imputation could be lower than ML. Thus, considering the absence of imputation studies and the specific genome reference for buffaloes, the genotype imputation using ML methods can be viable alternative. (AU)

News published in Agência FAPESP Newsletter about the scholarship:
Novo método aumenta eficiência na seleção de gado 
Un nuevo método aumenta la eficiencia en la selección de ganado  
New dairy cattle breeding method increases genetic selection efficiency 
Articles published in other media outlets (56 total):
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The Dairy Site (EUA): New Dairy Breeding Method Increases Genetic Selection Efficiency (09/Oct/2019)
The Cattle Site (Reino Unido): New Dairy Breeding Method Increases Genetic Selection Efficiency (09/Oct/2019)
The Beef Site (Reino Unido): New Dairy Breeding Method Increases Genetic Selection Efficiency (09/Oct/2019)
Paulo Cabral: Pouca massa muscular pode indicar risco de morte para idosos (17/Sep/2019)
UK Sires (Reino Unido): New dairy cattle breeding method increases genetic selection efficiency (11/Jul/2019)
Belted Galloway Cattle: New dairy cattle breeding method increases genetic selection efficiency (11/Jul/2019)
Agrolink: Novo método aumenta eficiência na seleção de animais (10/Jul/2019)
A Notícia Agora: Pouca massa muscular pode indicar risco de morte para idosos (10/Jul/2019)
Jornal Agroin Agronegócios online: Novo método aumenta eficiência na seleção de animais (10/Jul/2019)
Sucesso no Campo: Novo método aumenta eficiência na seleção de animais (10/Jul/2019)
AgroAlimentando: Un nuevo método aumenta la eficiencia en la selección de ganado (10/Jul/2019)
Green Area (Líbano): Un nuevo método aumenta la eficiencia en la selección de ganado (10/Jul/2019)
EresViral (República Dominicana): Un nuevo método aumenta la eficiencia en la selección de ganado (10/Jul/2019)
Portal CN1: Pouca massa muscular pode indicar risco de morte para idosos (10/Jul/2019)
Brasil CT&I: Pouca massa muscular pode indicar risco de morte para idosos (10/Jul/2019)
SintapiCUT - Sindicato dos Aposentados, Pensionistas e Idosos: Pouca massa muscular pode indicar risco de morte para idosos (10/Jul/2019)
Mundo Agropecuario (Venezuela): Um novo método aumenta a eficiência da seleção de gado (09/Jul/2019)
Blog do Evando Moreira: Pouca massa muscular pode indicar risco de morte para idosos (09/Jul/2019)
Silva Jardim: Pouca massa muscular pode indicar risco de morte para idosos (09/Jul/2019)
NCYT Amazings (Espanha): Un nuevo método aumenta la eficiencia en la selección de ganado (08/Jul/2019)
The Bullvine (Canadá): New dairy cattle breeding method increases genetic selection efficiency (08/Jul/2019)
Lab Manager (Canadá): New Dairy Cattle Breeding Method Increases Genetic Selection Efficiency (08/Jul/2019)
Ag Daily (EUA): New dairy cattle breeding method increases genetic selection efficiency (08/Jul/2019)
Folha News Goiás: Pouca massa muscular pode indicar risco de morte para idosos (08/Jul/2019)
TechaPeek: New dairy cattle breeding method increases genetic selection efficiency (06/Jul/2019)
Phys.Org (Reino Unido): New dairy cattle breeding method increases genetic selection efficiency (05/Jul/2019)
Long Room (EUA): New dairy cattle breeding method increases genetic selection efficiency (05/Jul/2019)
The Beef Site (Reino Unido): New Dairy Cattle Breeding Method Increases Genetic Selection Efficiency (05/Jul/2019)
Feedstuffs (EUA): Novel Dairy Cattle Breeding Method Increases Genetic Selection Efficiency (05/Jul/2019)
Live Daily Times (EUA): Novel Dairy Cattle Breeding Method Increases Genetic Selection Efficiency (05/Jul/2019)
BibLeo News Network (EUA): New dairy cattle breeding method increases genetic selection efficiency (05/Jul/2019)
MondialNews: New Dairy Cattle Breeding Method Increases Genetic Selection Efficiency (05/Jul/2019)
DairyBusiness (EUA): Novel Dairy Cattle Breeding Method Increases Genetic Selection Efficiency (05/Jul/2019)
Agrolatam: Un método que aumenta la eficiencia en la selección de ganado (05/Jul/2019)
Newsllive.com: New dairy cattle breeding method increases genetic selection efficiency (05/Jul/2019)
Suitax: New dairy cattle breeding method increases genetic selection efficiency (05/Jul/2019)
The Dairy Site (EUA): New dairy cattle breeding method increases genetic selection efficiency (04/Jul/2019)
Portal CanaMix : Novo método aumenta eficiência na seleção de gado (04/Jul/2019)
The Cattle Site (Reino Unido): New dairy cattle breeding method increases genetic selection efficiency (04/Jul/2019)
Perulactea (Peru): Un nuevo método aumenta la eficiencia en la selección de ganado (04/Jul/2019)
Jornal Joseense News: Novo método aumenta eficiência na seleção de gado (04/Jul/2019)
Agrovista Profits (Índia): New dairy cattle breeding method increases genetic selection efficiency (04/Jul/2019)
Deuxieme (Holanda): New dairy cattle breeding method increases genetic selection efficiency (04/Jul/2019)
Environmental News Network (EUA): New Dairy Cattle Breeding Method Increases Genetic Selection Efficiency (03/Jul/2019)
Bioengineer (Reino Unido): New dairy cattle breeding method increases genetic selection efficiency (03/Jul/2019)
Health Medicine Network (EUA): New dairy cattle breeding method increases genetic selection efficiency (03/Jul/2019)
Science Codex: New dairy cattle breeding method increases genetic selection efficiency (03/Jul/2019)
Scienmag Science Magazine (Reino Unido): New dairy cattle breeding method increases genetic selection efficiency (03/Jul/2019)
Brightsurf: New dairy cattle breeding method increases genetic selection efficiency (03/Jul/2019)
Career Biotech: New dairy cattle breeding method increases genetic selection efficiency (03/Jul/2019)
AgroTV News: Unesp elabora método que aumenta eficiência na seleção de gado (03/Jul/2019)
Daily Science (Tokelau): New dairy cattle breeding method increases genetic selection efficiency (03/Jul/2019)
Inforex: Unesp elabora método que aumenta eficiência na seleção de gado (02/Jul/2019)
Compre Rural: Revolução: Método prediz se animal transmitirá características (01/Jul/2019)
Camisa 10: Pouca massa muscular pode indicar risco de morte para idosos (18/Jan/2019)
Felipe Vieira: Pouca massa muscular pode indicar risco de morte para idosos (09/Jul/2019)

Scientific publications
(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)
DE ABREU SANTOS, DANIEL JORDAN; FERREIRA DE CAMARGO, GREGORIO MIGUEL; CARDOSO, DIERCLES FRANCISCO; BUZANSKAS, MARCOS ELI; ASPILCUETA-BORQUIS, RUSBEL RAUL; HURTADO-LUGO, NAUDIN ALEJANDRO; DE ARAUJO NETO, FRANCISCO RIBEIRO; DE ALBUQUERQUE, LUCIA GALVAO; MA, LI; TONHATI, HUMBERTO. Linkage Disequilibrium-Based Inference of Genome Homology and Chromosomal Rearrangements Between Species. G3-GENES, GENOMES, GENETICS, v. 10, n. 7, p. 2327-2343, JUL 2020. Web of Science Citations: 0.
SANTOS, D. J. A.; COLE, J. B.; LAWLOR JR, T. J.; VANRADEN, P. M.; TONHATI, H.; MA, L. Variance of gametic diversity and its application in selection programs. JOURNAL OF DAIRY SCIENCE, v. 102, n. 6, p. 5279-5294, JUN 2019. Web of Science Citations: 1.
SANTOS, D. J. A.; COLE, J. B.; NULL, D. J.; BYREM, T. M.; MA, L. Genetic and nongenetic profiling of milk pregnancy-associated glycoproteins in Holstein cattle. JOURNAL OF DAIRY SCIENCE, v. 101, n. 11, p. 9987-10000, NOV 2018. Web of Science Citations: 0.

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