Identification of loci of interest for poultry production

• Grant number: 14/08704-0
• Support Opportunities: Research Projects - Thematic Grants
• Start date: August 01, 2014
• End date: March 31, 2018
• Field of knowledge: Agronomical Sciences - Animal Husbandry - Genetics and Improvement of Domestic Animals
• Principal Investigator: Luiz Lehmann Coutinho
• Grantee: Luiz Lehmann Coutinho
• Host Institution: Escola Superior de Agricultura Luiz de Queiroz (ESALQ). Universidade de São Paulo (USP). Piracicaba , SP, Brazil
• Associated researchers: Ana Silvia Alves Meira Tavares Moura ; Clarissa Boschiero ; Gabriel Rodrigues Alves Margarido
• Associated research 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)

Scientific publications

(16)

(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)

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; et al. 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. (14/21380-9, 15/00616-7, 16/00569-1, 14/08704-0)

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. (16/20440-3, 14/08704-0)

PERTILLE, FABIO; IBELLI, ADRIANA MERCIA GUARATINI; SHARIF, MAJ EL; POLETI, MIRELE DAIANA; FROHLICH, ANNA SOPHIE; REZAEI, SHIVA; LEDUR, MONICA CORREA; JENSEN, PER; GUERRERO-BOSAGNA, CARLOS; COUTINHO, LUIZ LEHMANN. Putative Epigenetic Biomarkers of Stress in Red Blood Cells of Chickens Reared Across Different Biomes. FRONTIERS IN GENETICS, v. 11, NOV 2 2020. (16/20440-3, 18/13600-0, 14/08704-0)

MONTEIRO MOREIRA, GABRIEL COSTA; SALVIAN, MAYARA; BOSCHIERO, CLARISSA; MELLO CESAR, ALINE SILVA; REECY, JAMES M.; GODOY, THAIS FERNANDA; LEDUR, MONICA CORREA; GARRICK, DORIAN; MOURAO, GERSON BARRETO; COUTINHO, LUIZ L.. Genome-wide association scan for QTL and their positional candidate genes associated with internal organ traits in chickens. BMC Genomics, v. 20, n. 1, AUG 22 2019. (14/21380-9, 16/00569-1, 14/08704-0)

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, v. 14, n. 7, MAY 2019. (16/20440-3, 14/08704-0, 18/13600-0)

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.; et al. 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. (14/08704-0)

PETROLI MARCHESI, JORGE AUGUSTO; ONO, RAFAEL KEITH; CANTAO, MAURICIO EGIDIO; GUARATINI IBELLI, ADRIANA MERCIA; PEIXOTO, JANE DE OLIVEIRA; MONTEIRO MOREIRA, GABRIEL COSTA; GODOY, THAIS FERNANDA; COUTINHO, LUIZ LEHMANN; MUNARI, DANISIO PRADO; LEDUR, MONICA CORREA. Exploring the genetic architecture of feed efficiency traits in chickens. SCIENTIFIC REPORTS, v. 11, n. 1, FEB 25 2021. (14/08704-0)

FERNANDES, ANNA CAROLINA; DA SILVA, VINICIUS HENRIQUE; GOES, CAROLINA PURCELL; MONTEIRO MOREIRA, GABRIEL COSTA; GODOY, THAIS FERNANDA; GUARATINI IBELLI, ADRIANA MERCIA; PEIXOTO, JANE DE OLIVEIRA; CANTAO, MAURICIO EGIDIO; LEDUR, MONICA CORREA; DE REZENDE, FERNANDA MARCONDES; et al. Genome-wide detection of CNVs and their association with performance traits in broilers. BMC Genomics, v. 22, n. 1, MAY 17 2021. (14/08704-0)

PETRY, BRUNA; MOREIRA, GABRIEL COSTA MONTEIRO; COPOLA, ALINE GONCALVES LIO; DE SOUZA, MARCELA MARIA; DA VEIGA, FERNANDA CRISTINA; JORGE, ERIKA CRISTINA; DE OLIVEIRA PEIXOTO, JANE; LEDUR, MONICA CORREA; KOLTES, JAMES E.; COUTINHO, LUIZ LEHMANN. SAP30 Gene Is a Probable Regulator of Muscle Hypertrophy in Chickens. FRONTIERS IN GENETICS, v. 12, SEP 27 2021. (14/08704-0)

MONTEIRO MOREIRA, GABRIEL COSTA; POLETI, MIRELE DAIANA; PERTILLE, FABIO; BOSCHIERO, CLARISSA; MELLO CESAR, ALINE SILVA; GODOY, THAIS FERNANDA; LEDUR, MONICA CORREA; REECY, JAMES M.; GARRICK, DORIAN J.; COUTINHO, LUIZ LEHMANN. Unraveling genomic associations with feed efficiency and body weight traits in chickens through an integrative approach. BMC GENETICS, v. 20, n. 1, NOV 6 2019. (14/21380-9, 16/20440-3, 16/00569-1, 14/08704-0, 15/00616-7)

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. (15/00616-7, 14/08704-0, 14/21380-9, 16/20440-3, 16/00569-1)

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. (14/21380-9, 16/00569-1, 14/08704-0)

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. (14/08704-0)

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. (14/21380-9, 15/00616-7, 14/08704-0)

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. (14/08704-0)

SALVIAN, MAYARA; MONTEIRO MOREIRA, GABRIEL COSTA; FREITAS SILVEIRA, ROBSON MATEUS; REIS, ANDREA PLOTZKI; D'AURIA, BRAYAN DIAS; PILONETTO, FABRICIO; GERVASIO, IZALLY CARVALHO; LEDUR, MONICA CORRE; COUTINHO, LUIZ LEHMANN; SPANGLER, MATTHEW LEE; et al. Estimation of breeding values using different densities of SNP to inform kinship in broiler chickens. LIVESTOCK SCIENCE, v. 267, p. 8-pg., 2022-11-29. (14/08704-0, 14/21380-9, 16/00569-1)