Whole-genome sequencing provides new insights into genetic mechanisms of tropical adaptation in Nellore (Bos primigenius indicus)

Author(s)

Fernandes Junior, Gerardo Alves ^[1] ; de Oliveira, Henrique Nunes ^[1] ; Carvalheiro, Roberto ^[1] ; Cardoso, Diercles Francisco ^[1] ; Fonseca, Larissa Fernanda Simielli ^[1] ; Ventura, Ricardo Vieira ^[2] ; de Albuquerque, Lucia Galvao ^[1]

Affiliation

^[1] Sao Paulo State Univ UNESP, Sch Agr & Vet Sci, BR-14884900 Jaboticabal, SP - Brazil

^[2] Univ Sao Paulo, Sch Vet Med & Anim Sci, BR-13635900 Pirassununga, SP - Brazil

• Document type: Journal article
• Source: SCIENTIFIC REPORTS; v. 10, n. 1 JUN 10 2020.
• Web of Science Citations: 0

Abstract

Most of the knowledge about genetic variants at the sequence level in cattle is for Bos primigenius taurus populations. Here, we presented a complete genomic characterization of 52 Nellore (Bos primigenius indicus) bulls, revealing specific zebu DNA variants with putative impact in tropical adaptation and productive traits. Single nucleotide polymorphisms (SNPs) and insertion/deletion (INDELs) mutations were identified using the newest bovine reference genome ARS\_UCD1.2, and variant functional consequences were predicted using the Ensembl VEP software. A total of 35,753,707 SNPs and 4,492,636 INDELs were detected and annotated to their functional effects. We identified 400 genes that comprised both, a SNP and an INDEL, of high functional impact on proteins (i.e. variants that cause protein truncation, loss of function or triggering nonsense-mediated decay). Among these, we highlight the following genes: BoLA, associated with cattle immune response to infections and reproduction aspects; HSPA8, DNAJC27, and DNAJC28, involved with thermoregulatory protective mechanisms in mammals; and many olfactory signaling pathway related genes that are important genetic factors in the evolution of mammalian species. All these functional aspects are directly related to cattle adaptability to tropical environments. (AU)

• FAPESP's process: 19/12434-1 - Imputation accuracy to whole genome sequence in Nellore beef cattle
• Grantee: Gerardo Alves Fernandes Júnior
• Support type: Scholarships abroad - Research Internship - Post-doctor
• FAPESP's process: 09/16118-5 - Genomic tools to genetic improvement of direct economic important traits in Nelore cattle
• Grantee: Lucia Galvão de Albuquerque
• Support type: Research Projects - Thematic Grants
• FAPESP's process: 17/10630-2 - Genetic aspects of meat production quality, efficiency and sustainability in Nelore breed animals
• Grantee: Lucia Galvão de Albuquerque
• Support type: Research Projects - Thematic Grants
• FAPESP's process: 18/10109-3 - Identification and analysis of genetic variants obtained from the whole-genome sequencing of Nellore bulls
• Grantee: Gerardo Alves Fernandes Júnior
• Support type: Scholarships in Brazil - Post-Doctorate
• FAPESP's process: 18/20026-8 - Multi-user equipment approved in grant 2017/10630-2: server
• Grantee: Lucia Galvão de Albuquerque
• Support type: Multi-user Equipment Program