IMPUTATION OF MARKER GENOTYPES IN BUFFALO GENOME AND ITS IMPACT ON GENOMIC EVALUATION OF MILK YIELD AND CONTENT

• Grant number: 15/12396-1
• Support Opportunities: Scholarships in Brazil - Post-Doctoral
• Effective date (Start): October 01, 2015
• Effective date (End): May 31, 2018
• Field of knowledge: Agronomical Sciences - Animal Husbandry - Genetics and Improvement of Domestic Animals
• Principal Investigator: Humberto Tonhati
• Grantee: Daniel Jordan de Abreu Santos
• Host Institution: Faculdade de Ciências Agrárias e Veterinárias (FCAV). Universidade Estadual Paulista (UNESP). Campus de Jaboticabal. Jaboticabal , SP, Brazil
• Associated scholarship(s): 17/00462-5 - Genomic homology between cattle and buffaloes and comparison of different machine learning methods for genotype imputation in buffalo genome, BE.EP.PD

Abstract

The Buffalo River has aptitude for meat and milk production. The buffalo milk is rich in content, which enables the production of dairy products such as butter and cheese, especially the "mozzarella". Among the breeds of buffalo brought to Brazil, the Murrah breed, due to milk production, has important economic participation in Brazilian cities, mainly in São Paulo State. Thus, the genetic improvement for the milk yield and content is desired and an important step for this is to apply methods for accurate identification of top genotypes in short term. The latest technology called genomic selection (GS) may be useful for genetic evaluations of buffaloes, because the reliability of genomic breeding values for young sires may be higher than those obtained with traditional evaluation. However, the cost reduction of genotyping is a important point for the viability of this technology. The use of panels with smaller number of SNPs with an imputation process in the genetic evaluation is an economic alternative. Therefore, the aim of this project is to study the imputation of genotypes of the markers present on the Illumina® panel for cattle "BovineHD BeadChip" and on the "Axiom® Buffalo Genotyping" from Affymetrix panel for buffalo, comparing different scenarios with fewer markers, and to evaluate the impact of genomic predictions of milk yield and content in the Murrah breed from these imputed data.

Scientific publications

(7)

(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. (10/20887-1, 17/00462-5, 15/12396-1)

FREITAS, ANA C.; STAFUZZA, NEDENIA B.; BARBERO, MARINA M. D.; SANTOS, DANIEL J. A.; FORTES, MARINA R. S.; TONHATI, HUMBERTO. Polymorphisms in major histocompatibility complex genes and its associations with milk quality in Murrah buffaloes. TROPICAL ANIMAL HEALTH AND PRODUCTION, v. 52, n. 1, p. 415-423, JAN 2020. (15/12396-1, 14/25309-7)

BUZANSKAS, MARCOS ELI; VENTURA, RICARDO VIEIRA; SELEGUIM CHUD, TATIANE CRISTINA; BERNARDES, PRISCILA ARRIGUCCI; DE ABREU SANTOS, DANIEL JORDAN; DE ALMEIDA REGITANO, LUCIANA CORREIA; DE ALENCAR, MAURICIO MELLO; MUDADU, MAURICIO DE ALVARENGA; ZANELLA, RICARDO; GUALBERTO BARBOSA DA SILVA, MARCOS VINICIUS; et al. Study on the introgression of beef breeds in Canchim cattle using single nucleotide polymorphism markers. PLoS One, v. 12, n. 2, FEB 9 2017. (12/23638-8, 15/12396-1, 15/08939-0, 13/19335-2, 15/25096-6)

OLIVEIRA JUNIOR, GERSON A.; SANTOS, DANIEL J. A.; CESAR, ALINE S. M.; BOISON, SOLOMON A.; VENTURA, RICARDO V.; PEREZ, BRUNO C.; GARCIA, JOSE F.; FERRAZ, JOSE BENTO S.; GARRICK, DORIAN J.. Fine mapping of genomic regions associated with female fertility in Nellore beef cattle based on sequence variants from segregating sires. JOURNAL OF ANIMAL SCIENCE AND BIOTECHNOLOGY, v. 10, n. 1, p. 13-pg., 2019-12-16. (12/50533-2, 14/07566-2, 15/12396-1, 13/12097-9)

OLIVEIRA JUNIOR, GERSON A.; SANTOS, DANIEL J. A.; CESAR, ALINE S. M.; BOISON, SOLOMON A.; VENTURA, RICARDO V.; PEREZ, BRUNO C.; GARCIA, JOSE F.; FERRAZ, JOSE BENTO S.; GARRICK, DORIAN J.. Fine mapping of genomic regions associated with female fertility in Nellore beef cattle based on sequence variants from segregating sires. JOURNAL OF ANIMAL SCIENCE AND BIOTECHNOLOGY, v. 10, n. 1, DEC 16 2019. (13/12097-9, 12/50533-2, 15/12396-1, 14/07566-2)

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. (15/12396-1, 17/00462-5)

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. (17/00462-5, 15/12396-1)