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Related Concept Videos

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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Comparing Copy Number Variations and SNPs02:26

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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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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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Isolation of Histone from Sorghum Leaf Tissue for Top Down Mass Spectrometry Profiling of Potential Epigenetic Markers
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SorGSD: a sorghum genome SNP database.

Hong Luo1,2, Wenming Zhao3, Yanqing Wang3

  • 1Genomics and Molecular Breeding of Biofuel Crops, Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, 100093 Beijing, China.

Biotechnology for Biofuels
|January 9, 2016
PubMed
Summary
This summary is machine-generated.

A new Sorghum Genome SNP Database (SorGSD) provides extensive genetic variation data for 48 sorghum accessions. This resource supports molecular breeding for improved traits like drought tolerance and biomass production in this vital crop.

Keywords:
Bio-energy plantDatabase curationGenome variationSNPsSorghum

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Area of Science:

  • Plant Genomics
  • Bioinformatics
  • Crop Science

Background:

  • Sorghum (Sorghum bicolor) is a globally significant cereal crop and a key candidate for biofuel production.
  • Understanding genetic variation is crucial for improving traits like drought tolerance, yield, and biomass via molecular breeding.

Purpose of the Study:

  • To develop a comprehensive database of sorghum genome-wide single nucleotide polymorphisms (SNPs).
  • To create a bioinformatics platform supporting genomic selection and molecular breeding in sorghum.

Main Methods:

  • Assembly and annotation of sorghum genome sequences (v2.1).
  • Analysis of re-sequencing data from 48 diverse sorghum accessions.
  • Development of the Sorghum Genome SNP Database (SorGSD) with web-based query and visualization tools.

Main Results:

  • Identification of approximately 62.9 million SNPs across 48 sorghum accessions.
  • Classification of sorghum lines into improved varieties, landraces, wild, and weedy types, plus a wild relative.
  • SorGSD offers detailed SNP annotations, including type, location, and links to external databases, with data freely downloadable.

Conclusions:

  • SorGSD serves as a comprehensive web portal for large-scale genome variation in cultivated and wild sorghum.
  • The database facilitates genomics research and molecular breeding activities for sorghum and other C4 grasses.