A high-density integrated map for grapevine based on three mapping populations genotyped by the Vitis18K SNP chip

Area of Science:

• Plant genomics
• Molecular genetics
• Biotechnology

Background:

• Grapevine improvement relies on understanding the genetic basis of traits.
• High-density genetic maps are crucial for genome assembly refinement and marker-trait association studies.
• Existing grapevine maps often lack density and order conservation.

Purpose of the Study:

• To construct the densest integrated genetic map for grapevine to date.
• To evaluate the Vitis18K SNP chip for high-density linkage mapping.
• To refine the grapevine genome assembly and anchor unanchored scaffolds.

Main Methods:

• Development of three high-density population maps using the Vitis18K SNP chip.
• Integration of population maps into a comprehensive map.
• Comparison of the integrated map with the reference grapevine genome assembly.

Main Results:

• Construction of an integrated grapevine map with 6697 molecular markers and a 0.60 cM inter-locus gap.
• High correlation (0.9974) between the integrated map and the reference assembly.
• Anchoring of 104 unanchored scaffolds to the grapevine genome assembly.
• Identification of 88 markers with discrepancies across maps.

Conclusions:

• The Vitis18K SNP chip is effective for high-density grapevine linkage mapping.
• The developed integrated map significantly enhances grapevine genome understanding.
• This high-density map serves as a valuable tool for future grapevine characterization and trait dissection.