Development and Evaluation of a High-Throughput Single-Nucleotide Polymorphism Array for Large Yellow Croaker (Larimichthys crocea )

Frontiers in Genetics
Tao ZhouPeng Xu

Abstract

High-density single-nucleotide polymorphism (SNP) genotyping array is an essential tool for genetic analyses of animals and plants. Large yellow croaker (Larimichthys crocea) is one of the most commercially important marine fish species in China. Although plenty of SNPs have been identified in large yellow croaker, no high-throughput genotyping array is available. In this study, a high-throughput SNP array named NingXin-I with 600K SNPs was developed and evaluated. A set of 82 large yellow croakers were collected from different locations of China and re-sequenced. A total of 9.34M SNPs were identified by mapping sequence reads to the large yellow croaker reference genome. About 1.98M candidate SNPs were selected for further analyses by using criteria such as SNP quality score and conversion performance in the final array. Finally, 579.5K SNPs evenly distributed across the large yellow croaker genome with an average spacing of 1.19 kb were proceeded to array production. The performance of NingXin-I array was evaluated in 96 large yellow croaker individuals from five populations, and 83.38% SNPs on the array were polymorphic sites. A further test of the NingXin-I array in five closely related species in Sciaenidae identified 26.6...Continue Reading

References

May 20, 2009·Bioinformatics·Heng Li, Richard Durbin
Jul 2, 2009·Genetics, Selection, Evolution : GSE·Anna K Sonesson, Theo H E Meuwissen
Jun 10, 2011·Bioinformatics·Petr DanecekUNKNOWN 1000 Genomes Project Analysis Group
Jan 30, 2013·BMC Genomics·Andreas KranisDavid W Burt
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
Nov 6, 2015·International Journal of Molecular Sciences·Jingqun AoXinhua Chen
Jan 18, 2017·Bioinformatics·Daniel E Cook, Erik C Andersen
Feb 22, 2017·BMC Genomics·UNKNOWN Aquaculture Genomics, Genetics and Breeding WorkshopTao Zhou
Sep 18, 2018·Reviews in Aquaculture·Diego RobledoRoss Houston
May 24, 2019·BMC Genomics·Ranran LiuJie Wen
Dec 13, 2019·G3 : Genes - Genomes - Genetics·Smaragda TsairidouRoss D Houston
Jun 14, 2020·G3 : Genes - Genomes - Genetics·Carolina PeñalozaRoss D Houston

❮ Previous
Next ❯

Datasets Mentioned

BETA
PRJNA629649

Methods Mentioned

BETA
genotyping
electrophoresis

Software Mentioned

GATK
VCF
kit
R package “ ggmap
Trimmomatic
PLINK
BWA
vcftools
Axion

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.