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Identification of loci of interest for poultry production

Grant number: 14/08704-0
Support type:Research Projects - Thematic Grants
Duration: August 01, 2014 - March 31, 2018
Field of knowledge:Agronomical Sciences - Animal Husbandry
Principal Investigator:Luiz Lehmann Coutinho
Grantee:Luiz Lehmann Coutinho
Home Institution: Escola Superior de Agricultura Luiz de Queiroz (ESALQ). Universidade de São Paulo (USP). Piracicaba , SP, Brazil
Assoc. researchers:Ana Silvia Alves Meira Tavares Moura ; Clarissa Boschiero ; Gabriel Rodrigues Alves Margarido
Associated grant(s):14/24604-5 - Multi-User Equipment approved in grant 2014/08704-0: Robot Beckman Biomek FXp target PrEP express, AP.EMU
Associated scholarship(s):17/25119-1 - Evaluation of gene associated with muscular development by gene edition (CRISPR/Cas9), BP.DR
16/20440-3 - Epigenetic analysis of methylation profile of chickens submitted to different stress conditions in the livestock production environment, BP.PD
16/13589-0 - Validation and association of non tolerated SNPs with muscle growth and fat deposition traits in chickens, BP.MS
+ associated scholarships 15/10111-0 - Detection and characterization of SNPs in the LEPR gene by next generation in chickens, BP.IC
15/00616-7 - Identification and characterization of CNVs in chicken genome and association with development of breast muscle, BP.DR
14/21380-9 - Genome wide association studies for fat deposition and carcass yield in chickens, BP.DR - associated scholarships

Abstract

The domestic chicken is important for food production with high quality protein for the human consumption population. Technological improvements have allowed the identification of polymorphisms quickly and at relatively low cost. Dense single-nucleotide polymorphism (SNP) chips have emerged as a valuable resource for genetic studies, such as genomic selection and the detection of quantitative trait loci (QTL). Moreover, with the use of thousands of SNPs/insertions and deletions (INDELs) with appropriate statistical methodologies it is possible to identify regions that are under positive selection. The objective of this project is the identification of genomic regions in the chicken that control important economical traits. For this purpose we will perform genome wide association study of 1,000 broilers of one Brazilian experimental population with a dense SNP chip (600K); re-sequencing of the entire genome of four distinct experimental lines slaughtered in 1999 and 2013 by Illumina technology (broiler, white egg layer with and without selection, brown egg layer, with a total of 72 chickens); identification, annotation and validation of genetic variations by bioinformatics tools; identification of selective sweeps, and the construction of a catalog of genetic variations for the Brazilian experimental lines which will be compared with other chicken databases. The results will provide important additional information to the QTL mapping studies already conducted by our group, a better understanding of the genetic mechanisms involved in the biological processes of chicken growth; and also contribute to the development of tools for the genetic selection of superior animals and will allow training of students in the area of genomics and bioinformatics. (AU)

Articles published in Agência FAPESP about the research grant
Healthier chickens with more meat and less fat 

Scientific publications (9)
(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)
COSTA ALMEIDA, OCTAVIO AUGUSTO; MONTEIRO MOREIRA, GABRIEL COSTA; REZENDE, FERNANDA MARCONDES; BOSCHIERO, CLARISSA; PEIXOTO, JANE DE OLIVEIRA; GUARATINI IBELLI, ADRIANA MERCIA; LEDUR, MONICA CORREA; DE NOVAIS, FRANCISCO JOSE; COUTINHO, LUIZ LEHMANN. Identification of selection signatures involved in performance traits in a paternal broiler line. BMC Genomics, v. 20, JUN 3 2019. Web of Science Citations: 0.
PERTILLE, FABIO; DA SILVA, VINICIUS H.; JOHANSSON, ANNA M.; LINDSTROM, TOM; WRIGHT, DOMINIC; COUTINHO, LUIZ L.; JENSEN, PER; GUERRERO-BOSAGNA, CARLOS. Mutation dynamics of CpG dinucleotides during a recent event of vertebrate diversification. Epigenetics, MAY 2019. Web of Science Citations: 0.
MOREIRA, GABRIEL COSTA MONTEIRO; BOSCHIERO, CLARISSA; MELLO CESAR, ALINE SILVA; REECY, JAMES M.; GODOY, THAIS FERNANDA; PERTILLE, FABIO; LEDUR, MONICA CORREA; MEIRA TAVARES MOURA, ANA SILVIA ALVES; GARRICK, DORIAN J.; COUTINHO, LUIZ LEHMANN. Integration of genome wide association studies and whole genome sequencing provides novel insights into fat deposition in chicken. SCIENTIFIC REPORTS, v. 8, NOV 1 2018. Web of Science Citations: 0.
MARCHESI, J. A. P.; BUZANSKAS, M. E.; CANTAO, M. E.; IBELLI, A. M. G.; PEIXOTO, J. O.; JOAQUIM, L. B.; MOREIRA, G. C. M.; GODOY, T. F.; SBARDELLA, A. P.; FIGUEIREDO, E. A. P.; COUTINHO, L. L.; MUNARI, D. P.; LEDUR, M. C. Relationship of runs of homozygosity with adaptive and production traits in a paternal broiler line. ANIMAL, v. 12, n. 6, p. 1126-1134, JUN 2018. Web of Science Citations: 1.
MONTEIRO MOREIRA, GABRIEL COSTA; BOSCHIERO, CLARISSA; MELLO CESAR, ALINE SILVA; REECY, JAMES M.; GODOY, THAIS FERNANDA; TREVISOLI, PRISCILA ANCHIETA; CANTAO, MAURICIO E.; LEDUR, MONICA CORREA; GUARATINI IBELLI, ADRIANA MERCIA; PEIXOTO, JANE DE OLIVEIRA; MEIRA TAVARES MOURA, ANA SILVIA ALVES; GARRICK, DORIAN; COUTINHO, LUIZ LEHMANN. A genome-wide association study reveals novel genomic regions and positional candidate genes for fat deposition in broiler chickens. BMC Genomics, v. 19, MAY 21 2018. Web of Science Citations: 2.
BOSCHIERO, CLARISSA; MONTEIRO MOREIRA, GABRIEL COSTA; GHEYAS, ALMAS ARA; GODOY, THAIS FERNANDA; GASPARIN, GUSTAVO; SAMPAIO CORREA MARIANI, PILAR DRUMMOND; PADUAN, MARCELA; MELLO CESAR, ALINE SILVA; LEDUR, MONICA CORREA; COUTINHO, LUIZ LEHMANN. Genome-wide characterization of genetic variants and putative regions under selection in meat and egg-type chicken lines. BMC Genomics, v. 19, JAN 25 2018. Web of Science Citations: 3.
PERTILLE, FABIO; BRANTSAETER, MARGRETHE; NORDGREEN, JANICKE; COUTINHO, LUIZ LEHMANN; JANCZAK, ANDREW M.; JENSEN, PER; GUERRERO-BOSAGNA, CARLOS. DNA methylation profiles in red blood cells of adult hens correlate with their rearing conditions. Journal of Experimental Biology, v. 220, n. 19, p. 3579-3587, OCT 1 2017. Web of Science Citations: 4.
PERTILLE, FABIO; MONTEIRO MOREIRA, GABRIEL COSTA; ZANELLA, RICARDO; DA SILVA NUNES, JOSE DE RIBAMAR; BOSCHIERO, CLARISSA; ROVADOSCKI, GREGORI ALBERTO; MOURAO, GERSON BARRETO; LEDUR, MONICA CORREA; COUTINHO, LUIZ LEHMANN. Genome-wide association study for performance traits in chickens using genotype by sequencing approach. SCIENTIFIC REPORTS, v. 7, FEB 9 2017. Web of Science Citations: 4.
PERTILLE, FABIO; GUERRERO-BOSAGNA, CARLOS; DA SILVA, VINICIUS HENRIQUE; BOSCHIERO, CLARISSA; DA SILVA NUNES, JOSE DE RIBAMAR; LEDUR, MONICA CORREA; JENSEN, PER; COUTINHO, LUIZ LEHMANN. High-throughput and Cost-effective Chicken Genotyping Using Next-Generation Sequencing. SCIENTIFIC REPORTS, v. 6, MAY 25 2016. Web of Science Citations: 11.

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