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Related Concept Videos

DNA Isolation01:24

DNA Isolation

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DNA isolation protocols can be fast and straightforward or complex and time-consuming depending on the type and quality of DNA required for further processing. For example, plasmid DNA extraction is a bit more complicated than genomic DNA extraction because of the need for an appropriate lysis method to separate plasmid DNA from gDNA during isolation. However, for specific applications, such as long-range DNA sequencing that require a good yield of high- quality DNA samples, we need to follow...
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Validating DNA Polymorphisms Using KASP Assay in Prairie Cordgrass (Spartina pectinata Link) Populations in the U.S.

Hannah Graves1, A L Rayburn1, Jose L Gonzalez-Hernandez2

  • 1Department of Crop Science, University of Illinois at Urbana-Champaign Urbana, IL, USA.

Frontiers in Plant Science
|February 3, 2016
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Summary

This study validated single nucleotide polymorphisms (SNPs) in prairie cordgrass, confirming their utility for genetic diversity analysis and marker-assisted breeding programs. These validated SNPs can advance crop improvement strategies.

Keywords:
Prairie cordgrassSNPSpartinamarkerpolymorphismtranscriptome

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Area of Science:

  • Plant Genomics
  • Molecular Biology
  • Population Genetics

Background:

  • Single nucleotide polymorphisms (SNPs) are abundant DNA variants crucial for plant genome and transcriptome comparisons.
  • SNP marker analysis aids in assessing genetic diversity, constructing genetic maps, and implementing marker-assisted selection in crops.
  • Identifying and validating SNPs is a prerequisite for leveraging these advanced genomic technologies.

Purpose of the Study:

  • To validate 121 putative single nucleotide polymorphisms (SNPs) from the nuclear transcriptome of prairie cordgrass (Spartina pectinata Link) using KASP technology.
  • To assess the utility of validated SNPs for analyzing genetic diversity and genomic structure within prairie cordgrass populations.
  • To evaluate the effectiveness of selected SNP markers in assessing the fidelity of breeding crosses.

Main Methods:

  • Development of 121 putative SNPs from prairie cordgrass nuclear transcriptome data.
  • SNP validation using KASP technology on a core collection of 38 natural populations.
  • Phylogenetic tree construction to visualize population relationships.
  • Analysis of polymorphisms across different cytotypes (tetraploid and octoploid).
  • Application of 12 selected SNP markers to evaluate tetraploid crosses and F2 populations.

Main Results:

  • Fifty-nine out of 121 putative SNPs were successfully validated.
  • A phylogenetic tree revealed one main clade, with samples from the same population clustering together.
  • Polymorphisms were detected in 52.6% of the populations, with equal distribution between tetraploid and octoploid cytotypes.
  • Twelve SNP markers effectively distinguished true crosses from self-pollinated individuals in tetraploid prairie cordgrass.

Conclusions:

  • The study successfully validated SNPs in prairie cordgrass, demonstrating their potential for genomic studies.
  • Validated SNPs provide insights into the genomic structure and population dynamics of prairie cordgrass.
  • SNP marker technology holds significant promise for future breeding programs in prairie cordgrass.
  • Further research across diverse cytotypes is recommended for a comprehensive understanding of prairie cordgrass genomics.