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Related Concept Videos

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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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.
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RNA-seq03:21

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RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
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Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease
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RNAseq based variant dataset in a black poplar association panel.

Odile Rogier1, Aurélien Chateigner1, Marie-Claude Lesage-Descauses1

  • 1INRAE, ONF, BioForA, 45075, Orléans, France.

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|October 2, 2023
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Summary

This study identifies over 878,000 genetic variants in black poplar (Populus nigra L.) using RNA sequencing. These findings offer crucial data for understanding black poplar population genomics and enabling future genetic studies.

Keywords:
Bioinformatics pipelineGenotypingPopulus nigraRNA polymorphismsSNV discoveryTranscriptomics

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Area of Science:

  • Plant genomics
  • Ecology
  • Bioinformatics

Background:

  • Black poplar (Populus nigra L.) is an ecologically significant tree species native to Eurasia.
  • It serves as a crucial parent for cultivated poplar hybrids.
  • Understanding its genetic diversity is vital for conservation and breeding.

Purpose of the Study:

  • To detect genetic variants in natural populations of black poplar.
  • To provide a valuable dataset for population structure and genomics studies.
  • To facilitate genome-wide association studies in black poplar.

Main Methods:

  • Generated transcriptomics data from xylem and cambium tissues of 241 P. nigra genotypes.
  • Utilized RNA sequencing (RNAseq) technology for data generation.
  • Developed an in-silico pipeline to identify 878,957 biallelic polymorphisms.

Main Results:

  • Identified 878,957 biallelic polymorphisms from transcriptomics data.
  • Over 99% of detected variants are annotated.
  • 98.8% of variants map to the P. trichocarpa reference genome.
  • Data is publicly available for further research.

Conclusions:

  • The study provides a comprehensive variant dataset for black poplar.
  • This resource is essential for advancing population genomics and genetic studies.
  • Facilitates future research on black poplar adaptation and breeding.