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System genetics studies of feedlot traits using super-dense SNP panel

Grant number: 14/14121-7
Support type:Scholarships abroad - Research Internship - Post-doctor
Effective date (Start): September 15, 2014
Effective date (End): September 14, 2015
Field of knowledge:Agronomical Sciences - Animal Husbandry
Principal Investigator:José Bento Sterman Ferraz
Grantee:Miguel Henrique de Almeida Santana
Supervisor abroad: Haja Kadarmideen
Home Institution: Faculdade de Zootecnia e Engenharia de Alimentos (FZEA). Universidade de São Paulo (USP). Pirassununga , SP, Brazil
Local de pesquisa : University of Copenhagen, Denmark  
Associated to the scholarship:13/20571-2 - Functional genomics of feed intake and efficiency in Nellore cattle, BP.PD

Abstract

The beef cattle industry is one of the main highlights of Brazilian agribusiness, and has great importance in the world market, since Brazil has one of the largest herds of cattle in the world, with about 200 million head. This herd is composed predominantly of Bos indicus animals, whose Nellore cattle and its crosses makes up about 90%. Because of the importance, economic interest and increased food production, improvements in efficient production are needed, such as the selection of genetically superior animals and the use of management strategies such as feedlot. Feed intake, feed efficiency, and weight gain are important traits of beef cattle in feedlots. The use of information from single nucleotide polymorphisms (SNP) allows the identification of genes or genomic regions responsible for the phenotypes, such as carcass traits, growth and feed efficiency. This is performed by of association studies of genome wide (GWAS) comparing the hundreds of thousands of SNPs with these traits of interest. However, the panels of markers were designed for Bos taurus, and when they are used in Bos indicus (Nellore) may be less informative, especially for much of the SNPs are not polymorphic or present very low minor allele frequency. A possible strategy to overcome this problem would be to increase the density of the panels to be used in GWAS for Bos indicus cattle. The aim of this project is to perform the GWAS using a super-dense panel with about 1.2 million SNPs, exploring genomic regions, linkage disequilibrium and copy number variations regions (CNVs) for carcass traits, performance, intake and feed efficiency in about 900 Nellore cattle. Additionally, these results will be analyzed from system genetics perspective for feed intake/efficiency and weight gain; and also for carcass traits. (AU)

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 ALMEIDA SANTANA, MIGUEL HENRIQUE; OLIVEIRA JUNIOR, GERSON ANTONIO; MELLO CESAR, ALINE SILVA; FREUA, MATEUS CASTELANI; GOMES, RODRIGO DA COSTA; DA LUZ E SILVA, SAULO; LEME, PAULO ROBERTO; FUKUMASU, HEIDGE; CARVALHO, MINOS ESPERANDIO; VENTURA, RICARDO VIEIRA; COUTINHO, LUIZ LEHMANN; KADARMIDEEN, HAJA N.; STERMAN FERRAZ, JOSE BENTO. Copy number variations and genome-wide associations reveal putative genes and metabolic pathways involved with the feed conversion ratio in beef cattle. JOURNAL OF APPLIED GENETICS, v. 57, n. 4, p. 495-504, NOV 2016. Web of Science Citations: 20.
SANTANA, M. H. A.; FREUA, M. C.; DO, D. N.; VENTURA, R. V.; KADARMIDEEN, H. N.; FERRAZ, J. B. S. Systems genetics and genome-wide association approaches for analysis of feed intake, feed efficiency, and performance in beef cattle. Genetics and Molecular Research, v. 15, n. 4 2016. Web of Science Citations: 3.
SANTANA, M. H. A.; VENTURA, R. V.; UTSUNOMIYA, Y. T.; NEVES, H. H. R.; ALEXANDRE, P. A.; OLIVEIRA JUNIOR, G. A.; GOMES, R. C.; BONIN, M. N.; COUTINHO, L. L.; GARCIA, J. F.; SILVA, S. L.; FUKUMASU, H.; LEME, P. R.; FERRAZ, J. B. S. A genomewide association mapping study using ultrasound-scanned information identifies potential genomic regions and candidate genes affecting carcass traits in Nellore cattle. JOURNAL OF ANIMAL BREEDING AND GENETICS, v. 132, n. 6, p. 420-427, DEC 2015. Web of Science Citations: 9.

Please report errors in scientific publications list by writing to: cdi@fapesp.br.