Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

Single Nucleotide Polymorphisms-SNPs

Single Nucleotide Polymorphisms-SNPs

A single nucleotide polymorphism or SNP is a single nucleotide variation at a specific genomic position in a large population. It is the most prevalent type of sequence variation found in the human genome. Point mutations that occur in more than 1% of the population qualify as SNPs. These are present once every 1000 nucleotides on an average in the human genome. Replacement of a purine with another purine (A/G) or a pyrimidine with another pyrimidine (C/T) is known as a transition. In contrast,...

Comparing Copy Number Variations and SNPs

Comparing Copy Number Variations and SNPs

Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...

Genetic Variation

Genetic Variation

Genetic variation is the diversity in DNA sequences found among individuals of the same species. This diversity is crucial for a species' survival because it helps organisms adapt to environmental changes. Genetic variation begins with fertilization, where an egg and sperm cell merge. Each of these cells carries 23 chromosomes, up to 46 in the fertilized egg. Chromosomes are long DNA strands that contain genes, the basic units of heredity.
Genes exist in different versions called alleles,...

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by

Same author

[Suggestions for selection and use of masks for dental medical staff during outbreaks of novel coronavirus pneumonia].

Shanghai kou qiang yi xue = Shanghai journal of stomatology·2020

Same author

Changed epidemiology of anthrax and molecular characteristics of Bacillus anthracis in Inner Mongolia Autonomous Region, China.

Transboundary and emerging diseases·2020

Same author

Theta oscillations in prolactinomas: Neurocognitive deficits in executive controls.

NeuroImage. Clinical·2020

Same author

A global database of plant production and carbon exchange from global change manipulative experiments.

Scientific data·2020

Same author

Infection Prevention and Control Strategies for the Peri-Operative Period of Emergency Surgery during the Coronavirus Disease 2019 Outbreak in a Neurosurgery Department in Wuhan, China.

Surgical infections·2020

Same author

Amelioration of imiquimod-induced psoriasis-like dermatitis in mice by DSW therapy inspired hydrogel.

Bioactive materials·2020

Same journal

Multi-omics analysis identifies loci associated with pyrethroid resistance across sister species in the Anopheles gambiae species complex.

BMC genomics·2026

Same journal

Comparative and population genomics analyses of eared pheasants inhabiting highly varying altitudes.

BMC genomics·2026

Same journal

Identification of differentially expressed lncRNAs in different daily weight gains of Jiangquan black pigs and functional analysis of LOC100518120.

BMC genomics·2026

Same journal

A self-attention-based deep learning model for identifying key genes in insect pupal metamorphosis.

BMC genomics·2026

Same journal

Multiple genomic approaches reveal geographic structure and local selection signals in invasive Anopheles stephensi from the Horn of Africa and Yemen.

BMC genomics·2026

Same journal

Integration of bulk RNA-seq and scRNA-seq reveals cell subsets and gene signatures associated with Glaesserella parasuis infection.

BMC genomics·2026

See all related articles

Search research articles

Related Experiment Video

Updated: Feb 25, 2026

Identifying Mutations by High Resolution Melting in a TILLING Population of Rice

Identifying Mutations by High Resolution Melting in a TILLING Population of Rice

Published on: September 2, 2019

Mining sequence variations in representative polyploid sugarcane germplasm accessions.

Xiping Yang¹, Jian Song¹, Qian You¹

¹Department of Agronomy, University of Florida, Gainesville, FL, 32610, USA.

|August 11, 2017

Summary

This summary is machine-generated.

Genotyping by sequencing (GBS) effectively identified numerous genetic variations, including SNPs and InDels, in complex sugarcane genomes. This method aids in understanding sugarcane

Keywords:

Genotyping by sequencing (GBS)Polyploid Saccharum Complex Sequence divergence Sequence features Sequence variations Sugarcane

More Related Videos

Multipronged Phenotyping Approaches to Characterize Sugarcane Root Systems

Multipronged Phenotyping Approaches to Characterize Sugarcane Root Systems

Published on: August 17, 2022

Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER

Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER

Published on: June 23, 2012

Related Experiment Videos

Last Updated: Feb 25, 2026

Identifying Mutations by High Resolution Melting in a TILLING Population of Rice

Identifying Mutations by High Resolution Melting in a TILLING Population of Rice

Published on: September 2, 2019

Multipronged Phenotyping Approaches to Characterize Sugarcane Root Systems

Multipronged Phenotyping Approaches to Characterize Sugarcane Root Systems

Published on: August 17, 2022

Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER

Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER

Published on: June 23, 2012

Area of Science:

Plant Genomics
Agricultural Biotechnology
Bioinformatics

Background:

Sugarcane (Saccharum spp.) is vital for sugar and biofuel production.
Its complex, polyploid genome poses challenges for studying genetic variations.
Understanding these variations is crucial for improving agronomic traits.

Purpose of the Study:

To establish and evaluate genotyping by sequencing (GBS) analysis pipelines for high-throughput genotyping in sugarcane.
To discover and characterize genomic sequence variations in the Saccharum complex.
To investigate the phylogenetic relationships among Saccharum accessions using discovered variations.

Main Methods:

Genotyping by sequencing (GBS) was employed on 14 representative Saccharum complex accessions.
GBS pipelines were optimized by evaluating alignment methods, variant callers, and sequence depth for SNP filtering.
Next-generation sequencing (NGS) and restriction enzyme-based genome complexity reduction were utilized.

Main Results:

A total of 76,251 non-redundant SNPs, 5642 InDels, 6380 PAVs, and 826 CNVs were detected.
De novo SNP calling identified 34,353 (universal network enabled analysis kit) and 109,043 (Stacks) SNPs.
Phylogenetic analysis revealed divergence times, with Saccharum species separating 0.19–1.65 million years ago.

Conclusions:

Genotyping by sequencing (GBS) is an effective NGS-based method for discovering genomic variations in polyploid species.
Recommended GBS pipelines and parameters are provided for the Saccharum complex and related species.
The study identified substantial genomic variations and elucidated evolutionary divergence within the Saccharum complex.