Development and Validation of an Open Access SNP Array for Nile Tilapia (Oreochromis niloticus).

G3 : Genes - Genomes - Genetics
Carolina PeñalozaRoss D Houston

Abstract

Tilapia are among the most important farmed fish species worldwide, and are fundamental for the food security of many developing countries. Several genetically improved Nile tilapia (Oreochromis niloticus) strains exist, such as the iconic Genetically Improved Farmed Tilapia (GIFT), and breeding programs typically follow classical pedigree-based selection. The use of genome-wide single-nucleotide polymorphism (SNP) data can enable an understanding of the genetic architecture of economically important traits and the acceleration of genetic gain via genomic selection. Due to the global importance and diversity of Nile tilapia, an open access SNP array would be beneficial for aquaculture research and production. In the current study, a ∼65K SNP array was designed based on SNPs discovered from whole-genome sequence data from a GIFT breeding nucleus population and the overlap with SNP datasets from wild fish populations and several other farmed Nile tilapia strains. The SNP array was applied to clearly distinguish between different tilapia populations across Asia and Africa, with at least ∼30,000 SNPs segregating in each of the diverse population samples tested. It is anticipated that this SNP array will be an enabling tool for popu...Continue Reading

References

Feb 12, 1998·Nucleic Acids Research·S M Aljanabi, I Martinez
Apr 23, 2002·Nature Reviews. Genetics·Kristin G ArdlieMark Seielstad
Aug 5, 2003·Nature Reviews. Genetics·Jeffrey D Wall, Jonathan K Pritchard
Sep 25, 2003·Annual Review of Plant Biology·Sherry A Flint-GarciaEdward S Buckler
Oct 19, 2006·Nature Reviews. Genetics·Eric Jorgenson, John S Witte
Dec 30, 2006·PLoS Genetics·Nick PattersonDavid Reich
Oct 15, 2008·PloS One·Nathan A BairdEric A Johnson
Feb 5, 2009·Genetics·Melissa M GrayRobert K Wayne
May 19, 2009·Nature Reviews. Genetics·Michael E Goddard, Ben J Hayes
May 20, 2009·Bioinformatics·Heng Li, Richard Durbin
Jun 10, 2009·Bioinformatics·Heng LiUNKNOWN 1000 Genome Project Data Processing Subgroup
Jul 2, 2009·Genetics, Selection, Evolution : GSE·Anna K Sonesson, Theo H E Meuwissen
Sep 20, 2011·Molecular Ecology·Andrew R WhiteleyLouis Bernatchez
Apr 25, 2012·Molecular Ecology Resources·N E M Van BersJ Komen
Jun 1, 1968·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·W G Hill, A Robertson
Jan 23, 2014·Molecular Ecology Resources·S LapègueC Klopp
Mar 13, 2014·BMC Research Notes·Shikai LiuZhanjiang Liu
Apr 4, 2014·Bioinformatics·Anthony M BolgerBjoern Usadel
Feb 28, 2015·GigaScience·Christopher C ChangJames J Lee
Apr 19, 2015·BMC Genomics·Christos PalaiokostasDavid J Penman
Dec 18, 2015·Nucleic Acids Research·Robert D FinnAlex Bateman
Jul 1, 2016·Genetics, Selection, Evolution : GSE·Hsin-Yuan TsaiRoss D Houston
Feb 9, 2018·G3 : Genes - Genomes - Genetics·Diego RobledoRoss D Houston
Sep 18, 2018·Reviews in Aquaculture·Diego RobledoRoss Houston
Mar 20, 2019·PloS One·Girish KumarAndone Estonba
Apr 18, 2020·Nature Reviews. Genetics·Ross D HoustonDiego Robledo

❮ Previous
Next ❯

Datasets Mentioned

BETA
PRJNA520791
PRJEB38548

Methods Mentioned

BETA
genotyping
Illumina sequencing
electrophoresis
PCR
PCA
chip

Software Mentioned

FastQC
Axiom Analysis Suite
SAMtools
WorldFish
Trimmomatic
R package ggplot2
R package LEA
Ma
LDcorSV
NoMinorHom

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.