Transcriptome sequencing to produce SNP-based genetic maps of onion

Area of Science:

• Plant Genomics
• Molecular Genetics
• Bioinformatics

Background:

• Developing molecular markers is crucial for advancing crop genetics and breeding.
• Onion (Allium cepa) genetics has lagged due to its complex genome and long breeding cycles.

Purpose of the Study:

• To identify and map single nucleotide polymorphisms (SNPs) in expressed regions of the onion genome.
• To develop a valuable resource for genetic analysis and marker-assisted breeding in onion.

Main Methods:

• Sequencing normalized cDNA libraries from two onion inbred lines (OH1 and 5225) using Roche-454 technology.
• Assembling cDNA contigs and identifying single nucleotide polymorphisms (SNPs) between the inbred lines.
• Constructing a genetic map using a gynogenic haploid population derived from an OH1 x 5225 cross.

Main Results:

• Assembled 27,065 and 33,254 cDNA contigs from OH1 and 5225, respectively.
• Identified 3,364 well-supported SNPs on 1,716 cDNA contigs.
• Constructed a genetic map with ten linkage groups comprising 597 segregating SNPs.

Conclusions:

• The identified SNPs are located in expressed genomic regions and are common across onion germplasms.
• These SNPs provide a powerful tool for genetic mapping, gene tagging, and marker-aided selection in onion breeding.
• The developed SNP resource will aid in cultivar fingerprinting and quality control of onion seed lots.