Identification of selection signatures and structural variants from next-generation sequencing data in zebu and locally adapted taurine breeds

• Grant number: 16/24084-7
• Support Opportunities: Scholarships in Brazil - Doctorate
• Start date: June 01, 2017
• End date: February 28, 2021
• Field of knowledge: Agronomical Sciences - Animal Husbandry - Genetics and Improvement of Domestic Animals
• Agreement: Coordination of Improvement of Higher Education Personnel (CAPES)
• Principal Investigator: Fernando Sebastián Baldi Rey
• Grantee: Elisa Peripolli
• Host Institution: Faculdade de Ciências Agrárias e Veterinárias (FCAV). Universidade Estadual Paulista (UNESP). Campus de Jaboticabal. Jaboticabal , SP, Brazil
• Associated scholarship(s): 17/27148-9 - Whole genome sequencing of zebu and Brazilian locally adapted taurine breeds for identifying selection signatures, BE.EP.DR

Abstract

Given the drawbacks and the impacts caused by climate change upon livestock production, it is important to characterize at a genome-wide level zebu and locally adapted breeds to elucidate the genetics mechanisms underlying adaptation and selection. The objective of this study is to describe the main effects of selection/adaptation in the bovine genome for zebu and locally adapted cattle breeds through the use of selection signatures and the identification of structural variants (SV) with Next Generation Sequencing (NGS) data. Sequenced data from Sindi (n=12), Caracú Caldeano (n=12), Pantaneiro (n=12), and Crioulo Lageano (n=12) cattle were available from Embrapa Dairy Cattle, Juiz de Fora - MG. Selection signatures will be identified through the standardized extent of haplotype homozygosity score (iHS) and significant SNPs (piHS>4) will be considered to identify candidate genes. CNV regions (CNVRs) will be identified for all 29 bovine autosomes and the X chromosome using the CNV-seq application and putative CNVRs will be used to conduct gene ontology (GO) enrichment analysis using a web-based GO analysis tool kit. ROH will be identified in every individual using PLINK v1.07. The homozygous segments shared by more than 50% of the samples will be chosen as an indication of a possible ROH islands throughout the genome and genes inside these islands will be classified as candidate for selection/adaptation. The results obtained in this study will allow a better characterization of zebu and locally adapted breeds, allow using them more deeply as a genetic reservoir in germplasm bank and as a reservoir of livestock genetic diversity resource upon climate change and adaptation. (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)

STAFUZZA, NEDENIA BONVINO; DE OLIVEIRA SILVA, RAFAEL MEDEIROS; PERIPOLLI, ELISA; FRAMARTINO BEZERRA, LUIZ ANTONIO; LOBO, RAYSILDO BARBOSA; MAGNABOSCO, CLAUDIO DE ULHOA; DI CROCE, FERNANDO A.; OSTERSTOCK, JASON B.; MUNARI, DANISIO PRADO; LINO LOURENCO, DANIELA A.; et al. Genome-wide association study provides insights into genes related with horn development in Nelore beef cattle. PLoS One, v. 13, n. 8, AUG 30 2018. (16/24084-7)

OLIVIERI, BIANCA FERREIRA; BRAZ, CAMILA URBANO; LOPES, FERNANDO BRITO; PERIPOLLI, ELISA; DE OLIVEIRA SILVA, RAFAEL MEDEIROS; PEREIRA DA SILVA CORTE, ROSANA RUEGGER; DE ALBUQUERQUE, LUCIA GALVAO; CRAVO PEREIRA, ANGELICA SIMONE; STAFUZZA, NEDENIA BONVINO; BALDI, FERNANDO. Differentially expressed genes identified through RNA-seq with extreme values of principal components for beef fatty acid in Nelore cattle. JOURNAL OF ANIMAL BREEDING AND GENETICS, v. 138, n. 1, MAY 2020. (17/03221-9, 11/21241-0, 16/24084-7, 19/10438-0)

PERIPOLLI, ELISA; STAFUZZA, NEDENIA BONVINO; MACHADO, MARCO ANTONIO; PANETTO, JOAO CLAUDIO DO CARMO; DO EGITO, ANDREA ALVES; BALDI, FERNANDO; DA SILVA, MARCOS VINICIUS GUALBERTO BARBOSA. Assessment of copy number variants in three Brazilian locally adapted cattle breeds using whole-genome re-sequencing data. ANIMAL GENETICS, v. N/A, p. 17-pg., 2023-02-06. (16/24084-7)

Academic Publications

(References retrieved automatically from State of São Paulo Research Institutions)

PERIPOLLI, Elisa. Identification of structural variants and selection signatures in cattle. 2021. Doctoral Thesis - Universidade Estadual Paulista (Unesp). Faculdade de Ciências Agrárias e Veterinárias. Jaboticabal Jaboticabal.