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

Scientific Reports
Gerardo Alves Fernandes JúniorLucia Galvão de Albuquerque

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 aspec...Continue Reading

References

Jun 25, 1998·Revue Scientifique Et Technique·M AmillsH A Lewin
Aug 9, 2007·PloS One·Yoshihito Niimura, Masatoshi Nei
Jul 30, 2008·Cell Stress & Chaperones·Harm H KampingaLawrence E Hightower
Dec 3, 2008·Genetics and Molecular Research : GMR·M A C DaniS U Dani
Apr 25, 2009·Science·UNKNOWN Bovine Genome Sequencing and Analysis ConsortiumFeng-Qi Zhao
May 20, 2009·Bioinformatics·Heng Li, Richard Durbin
Jun 10, 2009·Bioinformatics·Heng LiUNKNOWN 1000 Genome Project Data Processing Subgroup
May 19, 2010·Animal Genetics·E K F ChanA Reverter
Jul 21, 2010·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Caitriona MurrayDaniel G Bradley
Dec 25, 2010·Tropical Animal Health and Production·Concepta McManusPatricia Spoto Corrêa
Jun 28, 2011·Veterinary Parasitology·Laercio R Porto NetoWilliam Barendse
May 9, 2012·Animal : an International Journal of Animal Bioscience·H M Burrow
Jul 13, 2012·The Journal of Reproduction and Development·Lei ShuKechun Zhang
Feb 19, 2013·The International Journal of Developmental Biology·Ferdinand DiedrichsJames Adjaye
Dec 18, 2013·BMC Genomics·Laercio R Porto-NetoCurtis P Van Tassell
Apr 4, 2014·Bioinformatics·Anthony M BolgerBjoern Usadel
Nov 25, 2014·PloS One·Laercio R Porto-NetoWilliam Barendse
May 1, 2015·Genetics, Selection, Evolution : GSE·Ana M Perez O'BrienJohann Sölkner
Nov 8, 2015·The Journal of Immunology : Official Journal of the American Association of Immunologists·Pablo EngelGeorgina Clark
Jun 9, 2016·Genome Biology·William McLarenFiona Cunningham
Mar 23, 2017·PloS One·Nedenia Bonvino StafuzzaMarcos Vinicius Gualberto Barbosa da Silva
Mar 14, 2018·Journal of Animal Science·Erin E ConnorGeorge E Liu
May 4, 2018·Genetics, Selection, Evolution : GSE·Diercles F CardosoHumberto Tonhati
Dec 7, 2018·Annual Review of Animal Biosciences·Ben J Hayes, Hans D Daetwyler
Jan 10, 2019·Evolutionary Applications·Daniel PittPablo Orozco-terWengel

❮ Previous
Next ❯

Citations

Mar 14, 2021·Genetics, Selection, Evolution : GSE·Gerardo A Fernandes JúniorLucia G de Albuquerque

❮ Previous
Next ❯

Methods Mentioned

BETA
genotyping
PCR

Software Mentioned

Ensembl VEP
SAMtools
GATK
MEM
Cytoscape
Ensembl
Trimmomatic
FastQC
ClueGO
HaplotypeCaller

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.