SNP discovery and development of a high-density genotyping array for sunflower
Eleni Bachlava1, Christopher A Taylor, Shunxue Tang
1Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia, United States of America.
Plos One
|January 13, 2012
Summary
Researchers developed a new SNP genotyping resource for sunflower (Helianthus annuus L.), enabling high-density genetic mapping and advanced breeding strategies. This resource identified numerous polymorphic single-nucleotide polymorphisms (SNPs) with high cross-species transferability.
Area of Science:
- Plant genetics
- Genomics
- Bioinformatics
Background:
- Next-generation sequencing enables high-throughput single-nucleotide polymorphism (SNP) genotyping.
- SNP genotyping platforms facilitate genetic mapping, genome-wide association studies, and molecular breeding.
Purpose of the Study:
- To develop a SNP genotyping resource for sunflower (Helianthus annuus L.).
- To enable high-density genetic mapping and molecular breeding in sunflower.
Main Methods:
- Developed a reference transcriptome assembly for sunflower.
- Discovered thousands of high-quality SNPs from transcriptome re-sequencing data.
- Selected 10,640 SNPs for a genotyping array and screened diverse sunflower accessions and wild relatives.
Main Results:
- High frequency of polymorphic SNPs identified (>95% of successful assays).
- High cross-species transferability of SNP assays (>90% to related wild species).
- Polymorphism data revealed genetic differentiation patterns congruent with sunflower's evolutionary history at finer resolution.
Conclusions:
- The developed SNP resource is valuable for sunflower genetics and breeding.
- High SNP polymorphism and transferability support broad applications in Helianthus species.
- Advanced genetic analysis and molecular breeding are facilitated by this high-density SNP resource.
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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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GWAS does not require the identification of the target gene involved in...
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,...