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Transcript-specific, single-nucleotide polymorphism discovery and linkage analysis in hexaploid bread wheat (Triticum
Alexandra M Allen1, Gary L A Barker, Simon T Berry
1School of Biological Sciences, University of Bristol, Bristol, UK.
Plant Biotechnology Journal
|June 2, 2011
Summary
Developing new molecular markers, like single-nucleotide polymorphisms (SNPs), is key for improving wheat yields. This study details the creation and validation of 1114 SNPs, aiding future crop breeding efforts.
Area of Science:
- Agricultural Science
- Genetics
- Plant Breeding
Background:
- Global food security necessitates increased cereal crop yields.
- Wheat breeding is challenged by genomic complexity and reduced genetic diversity.
- Marker-assisted selection (MAS) requires accessible and affordable molecular markers.
Purpose of the Study:
- To develop and validate a panel of single-nucleotide polymorphism (SNP) markers for hexaploid bread wheat.
- To facilitate marker-assisted selection (MAS) in wheat breeding programs.
- To enable rapid generation of linkage maps for genetic studies.
Main Methods:
- Utilized expressed sequence tags (ESTs) and next-generation sequencing (NGS) of wheat cDNA libraries.
- Employed a novel sequence alignment and assembly approach for SNP discovery.
- Developed and validated 1114 SNPs using competitive allele-specific polymerase chain reaction (KASP) genotyping.
- Genotyped 23 diverse wheat varieties and created a linkage map in a doubled haploid population.
Main Results:
- Successfully developed and validated a panel of 1114 SNPs in hexaploid bread wheat.
- Demonstrated the utility of these SNPs across a broad range of wheat germplasm.
- Generated a linkage map with several hundred SNP markers using KASP technology.
- Showcased the feasibility of rapid SNP marker development and application.
Conclusions:
- The developed SNP panel provides a valuable resource for wheat genetic research and breeding.
- Accessible SNP genotyping technologies can accelerate the application of MAS in wheat improvement.
- This work contributes to enhancing wheat for global food security through advanced breeding techniques.
Related Concept Videos
01:11Genome-wide Association Studies-GWAS
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.
GWAS does not require the identification of the target gene involved in...
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,...
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%...