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Comparing Copy Number Variations and SNPs

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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.
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Updated: May 30, 2026

Array Comparative Genomic Hybridization (Array CGH) for Detection of Genomic Copy Number Variants

Array Comparative Genomic Hybridization (Array CGH) for Detection of Genomic Copy Number Variants

Published on: February 21, 2015

Detection of copy number variations in rice using array-based comparative genomic hybridization.

Ping Yu¹, Caihong Wang, Qun Xu

¹State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China.

|July 21, 2011

Summary

Copy number variations (CNVs) are significant sources of genetic diversity in rice. This study mapped 641 CNVs, revealing their impact on gene content and potential role in rice varietal differences.

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Technical Demonstration of Whole Genome Array Comparative Genomic Hybridization

Technical Demonstration of Whole Genome Array Comparative Genomic Hybridization

Published on: August 5, 2008

Area of Science:

Genomics
Plant Science
Molecular Biology

Background:

Copy number variations (CNVs) are major drivers of genetic diversity, influencing gene dosage, structure, and expression.
While CNVs contribute significantly to variation in many organisms, their role in rice genetics remains largely unexplored.

Purpose of the Study:

To investigate the contribution of CNVs to genetic variation in rice.
To create a high-resolution map of CNVs in the rice genome.

Main Methods:

Utilized NimbleGen whole-genome comparative genomic hybridization arrays with 718,256 oligonucleotide probes.
Analyzed CNVs between two rice cultivars: 'Nipponbare' (O. sativa ssp. japonica) and 'Guang-lu-ai 4' (O. sativa ssp. indica).

Main Results:

Identified 641 CNVs across the rice genome, ranging from 1.1 kb to 180.7 kb, totaling approximately 7.6 Mb.
Detected 85 DNA segments, including genic sequences, with contracted genes significantly outnumbering duplicated genes.
Observed that contracted genes were often functionally related or involved in similar biological processes, including disease and defense.

Conclusions:

Array-based comparative genomic hybridization successfully detected CNVs in rice, many containing known genes.
CNVs are linked to variations among rice varieties and likely contribute to distinct subspecific characteristics.
Further research into rice CNVs is crucial for understanding crop diversity and improvement.