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Related Concept Videos

Genomic DNA in Eukaryotes00:58

Genomic DNA in Eukaryotes

Eukaryotes have large genomes compared to prokaryotes. To fit their genomes into a cell, eukaryotic DNA is packaged extraordinarily tightly inside the nucleus. To achieve this, DNA is tightly wound around proteins called histones, which are packaged into nucleosomes that are joined by linker DNA and coil into chromatin fibers. Additional fibrous proteins further compact the chromatin, which is recognizable as chromosomes during certain phases of cell division.
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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,...

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Rapid gene-based SNP and haplotype marker development in non-model eukaryotes using 3'UTR sequencing.

Tyson Koepke1, Scott Schaeffer, Vandhana Krishnan

  • 1Department of Horticulture, Washington State University, Pullman, WA, USA.

BMC Genomics
|January 14, 2012
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Summary

This study rapidly generated gene-linked single nucleotide polymorphism (SNP) and haplotype markers for sweet cherry using RNA-seq. These markers will enhance genomic resources and facilitate efficient Gene Assisted Breeding (GAB) in this non-model crop.

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Area of Science:

  • Plant genomics
  • Molecular breeding
  • Bioinformatics

Background:

  • Sweet cherry (Prunus avium L.) has limited genetic and genomic information compared to other Rosaceae species.
  • Developing molecular markers like single nucleotide polymorphisms (SNPs) is crucial for breeding non-model crops.
  • RNA-sequencing (RNA-seq) offers a rapid method for identifying gene-based SNPs.

Purpose of the Study:

  • To rapidly identify gene-linked single nucleotide polymorphism (SNP) and haplotype markers in sweet cherry.
  • To establish a cost-effective method for SNP discovery in non-model plants.
  • To improve genomic resources for sweet cherry breeding.

Main Methods:

  • RNA-sequencing (RNA-seq) was performed on two sweet cherry cultivars (Bing and Rainier) using a 3' untranslated region (UTR) sequencing method.
  • Contigs were screened for high-quality SNPs, and primer pairs were designed for amplification.
  • High-resolution melting (HRM) analysis was conducted on parental cultivars and their offspring to identify polymorphic markers.

Main Results:

  • RNA-seq yielded 43,396 assembled contigs, with 207 contigs identified containing high-quality SNPs.
  • Out of 223 primer sets tested, 84 (38.7%) demonstrated variation among the germplasm.
  • Further analysis identified 2243 putative SNPs and 685 putative haplotypes, significantly enhancing genomic resources.

Conclusions:

  • The RNA-seq approach enabled rapid generation of gene-linked SNP and haplotype markers for sweet cherry.
  • This methodology is applicable to other non-model eukaryotes for identifying gene-linked polymorphisms.
  • The identified markers are expected to significantly improve genomic resources and facilitate efficient Gene Assisted Breeding (GAB) in sweet cherry.