Related Experiment Video
Updated: May 14, 2026
14:06
Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER
Published on: June 23, 2012
Switchgrass genomic diversity, ploidy, and evolution: novel insights from a network-based SNP discovery protocol
Fei Lu1, Alexander E Lipka, Jeff Glaubitz
1Institute for Genomic Diversity, Cornell University, Ithaca, New York, USA.
Plos Genetics
|January 26, 2013
Summary
Switchgrass breeding is accelerated by new genomic tools. Researchers discovered millions of single nucleotide polymorphisms (SNPs) and mapped the switchgrass genome, revealing its evolutionary history and population structure.
Area of Science:
- Plant genomics
- Bioenergy crops
- Population genetics
Background:
- Switchgrass (Panicum virgatum L.) is a key biofuel crop in the USA.
- Developing genomic resources for switchgrass is crucial for breeding programs.
- High heterozygosity and polyploidy in switchgrass pose challenges for genetic analysis.
Purpose of the Study:
- To develop novel methods for single nucleotide polymorphism (SNP) discovery in switchgrass.
- To construct high-density genetic maps for switchgrass.
- To investigate the population structure, phylogeny, and evolutionary dynamics of switchgrass.
Main Methods:
- Developed the Universal Network-Enabled Analysis Kit (UNEAK) for SNP discovery.
- Genotyped 840 switchgrass individuals using genotyping by sequencing (GBS).
- Constructed synteny-based, ultra high-density linkage maps using foxtail millet as a reference.
Main Results:
- Discovered 1.2 million putative SNPs in switchgrass.
- Revealed the diploid nature of tetraploid switchgrass.
- Established linkage maps with 88,217 SNPs and identified patterns of isolation-by-distance and ploidy.
- Phylogenetic analysis indicated a south-to-north migration and suggested tetraploid origin from octoploid.
Conclusions:
- The UNEAK pipeline effectively addresses SNP discovery challenges in complex polyploids like switchgrass.
- This study provides comprehensive genomic insights into switchgrass diversity, evolution, and population structure.
- The developed resources will significantly advance switchgrass breeding for biofuel applications.
Related Concept Videos
01:05Single 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,...
02:26Comparing Copy Number Variations and SNPs
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%...
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%...
01:25Genetic Variation
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, which...
Genes exist in different versions called alleles, which...
02:54Evolutionary Relationships through Genome Comparisons
Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
02:37Gene Duplication and Divergence
The seminal work of Ohno in 1970 popularized the idea of gene duplication and divergence. DNA sequence comparison studies reveal that a large portion of the genes in bacteria, archaebacteria, and eukaryotes was generated by gene duplication and divergence, indicating its critical role in evolution.
The duplicated copies of the gene are called Paralogs. Paralogs with similar sequences and functions form a gene family. Across several species, a large number of gene families are characterized.
The duplicated copies of the gene are called Paralogs. Paralogs with similar sequences and functions form a gene family. Across several species, a large number of gene families are characterized.
01:09Mutation, Gene Flow, and Genetic Drift
In a population that is not at Hardy-Weinberg equilibrium, the frequency of alleles changes over time. Therefore, any deviations from the five conditions of Hardy-Weinberg equilibrium can alter the genetic variation of a given population. Conditions that change the genetic variability of a population include mutations, natural selection, non-random mating, gene flow, and genetic drift (small population size).