Ultrahigh-density linkage map for cultivated cucumber (Cucumis sativus L.) using a single-nucleotide polymorphism...

Area of Science:

• Plant genetics and genomics
• Molecular biology
• Agricultural science

Background:

• Genetic mapping in cucumbers has historically relied on SSR and SRAP markers.
• Previous genetic maps lacked the resolution for detailed complex trait analysis.
• Advancements in genotyping technologies are crucial for high-throughput genetic studies.

Purpose of the Study:

• To develop the first cucumber genotyping array utilizing single-nucleotide polymorphisms (SNPs).
• To construct an ultrahigh-density genetic map for cucumber using the developed array.
• To demonstrate the array's utility for high-throughput genotyping and genetic studies in cucumbers.

Main Methods:

• Development of a genotyping array with 32,864 SNPs covering the cucumber genome.
• Validation of genotype calls using Fluidigm technology, achieving 96% concordance.
• Construction of a genetic map using 11,156 SNPs from a recombinant inbred line (RIL) population.

Main Results:

• The genotyping array provides markers with a median interval of ~2 Kb.
• An ultrahigh-density genetic map of 598.7 cM was constructed with high marker collinearity (R2 = 0.97).
• The array demonstrated 82% polymorphism in other cucumber variants, indicating broad applicability.

Conclusions:

• The developed cucumber genotyping array is a powerful tool for high-throughput genotyping.
• The array facilitates the construction of ultrahigh-density genetic maps for improved QTL mapping and genome assembly.
• This resource will advance genetic research and breeding in cucumber.