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Single Nucleotide Polymorphisms-SNPs01:05

Single Nucleotide Polymorphisms-SNPs

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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,...
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Genome-wide Association Studies-GWAS01:11

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Genome-wide association studies or GWAS are used to identify whether common SNPs are associated with certain diseases. Suppose specific SNPs are more frequently observed in individuals with a particular disease than those without the disease. In that case, those SNPs are said to be associated with the disease. Chi-square analysis is performed to check the probability of the allele likely to be associated with the disease.
GWAS does not require the identification of the target gene involved in...
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Genomics02:02

Genomics

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Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...
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Comparing Copy Number Variations and SNPs02:26

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.
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%...
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Genetic Variation01:25

Genetic Variation

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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,...
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Related Experiment Video

Updated: Jul 12, 2025

Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER
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Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER

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10k-level integrated rice database shows power for exploiting rare variants.

Hong Yu1,2, Liquan Kou1, Jiayang Li1,2,3

  • 1State Key Laboratory of Plant Genomics, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.

Journal of Integrative Plant Biology
|October 25, 2023
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Summary

Researchers analyzed genomic data from over 10,000 rice varieties worldwide. This created a massive dataset of genetic variations in Asian cultivated rice (Oryza sativa) and its wild relatives (Oryza rufipogon).

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Area of Science:

  • Genomics
  • Plant Science
  • Bioinformatics

Background:

  • Understanding genetic diversity is crucial for crop improvement.
  • Previous studies have cataloged rice genetic variations, but a comprehensive dataset is needed.

Purpose of the Study:

  • To create a super-large genomic variation dataset for rice.
  • To re-analyze existing resequencing data for Asian cultivated rice (Oryza sativa) and wild rice (Oryza rufipogon).

Main Methods:

  • Re-analysis of published resequencing data.
  • Inclusion of 10,548 accessions from 98 countries.
  • Focus on Asian cultivated rice and wild rice species.

Main Results:

  • Generation of a comprehensive rice genomic variation dataset.
  • The dataset covers a wide geographical distribution and diverse rice accessions.

Conclusions:

  • The generated dataset provides a valuable resource for rice genetic research.
  • Facilitates future studies on rice evolution, breeding, and conservation.