SNP discovery and linkage map construction in cultivated tomato
Kenta Shirasawa1, Sachiko Isobe, Hideki Hirakawa
1Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan. shirasaw@kazusa.or.jp
Summary
This study developed new single nucleotide polymorphism (SNP) markers to create genetic linkage maps for cultivated tomato. These maps are crucial for advancing molecular breeding in tomato varieties.
Area of Science:
- Plant Genomics
- Molecular Genetics
- Crop Science
Background:
- Intraspecific genetic linkage maps for cultivated tomato (Solanum lycopersicum) are scarce due to limited genetic diversity.
- Single nucleotide polymorphisms (SNPs) offer a promising approach for constructing linkage maps in closely related lines.
Purpose of the Study:
- To develop SNP markers from expressed sequence tags for creating intraspecific genetic linkage maps in tomato.
- To assess the utility of these SNP markers for molecular breeding in cultivated tomato.
Main Methods:
- In silico analysis identified 5607 SNP positions, with 1536 selected for high-throughput genotyping.
- Two mapping populations were generated from crosses involving 'Micro-Tom'.
- A total of 1137 markers, including 793 SNPs, were mapped onto two linkage maps.
Main Results:
- Two linkage maps were constructed, spanning 1467.8 cM and 1422.7 cM.
- The developed SNP markers demonstrated transferability across various cultivated tomato lines.
- The study provides a valuable resource for tomato genomics and breeding.
Conclusions:
- The developed SNP markers and linkage maps are a significant advancement for cultivated tomato genomics.
- This work represents a foundational step towards implementing molecular breeding strategies in tomato.
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,...
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...