Tomato breeding in the genomics era: insights from a SNP array

Area of Science:

• Plant genetics
• Molecular biology
• Genomics

Background:

• Limited molecular markers historically hindered genetic and linkage studies in tomato.
• Next-generation sequencing and high-throughput genotyping have revolutionized marker development.
• A set of 6000 single nucleotide polymorphisms (SNPs) was identified, with 5528 used for germplasm evaluation.

Purpose of the Study:

• To develop and utilize a comprehensive set of molecular markers for tomato genetic analysis.
• To evaluate tomato germplasm diversity at species, variety, and population levels.
• To identify markers for distinguishing cultivated tomato from its wild relatives.

Main Methods:

• Identification and selection of 5528 SNPs from 454 and Illumina Solexa sequencing data.
• Genotyping of diverse tomato samples to assess heterozygosity and introgressions.
• Phylogenetic analysis using clustering and neighbor-joining methods.

Main Results:

• Genotyping revealed distinct genetic differences, particularly in cherry tomatoes on specific chromosomes.
• A set of 750 unique SNPs was identified to differentiate *S. lycopersicum* from wild relatives.
• Analysis confirmed *S. pimpinellifolium* as the closest wild relative to commercial tomatoes.

Conclusions:

• SNP markers developed from limited breeding lines are broadly applicable across tomato species and wild relatives.
• Illumina bead array data demonstrated high reproducibility.
• SNPs were categorized into ancestral and domestication-specific types, useful for genotyping, variety identification, and phylogenetic studies.