Genotyping-by-sequencing application on diploid rose and a resulting high-density SNP-based consensus map

Area of Science:

• Plant genetics
• Genomics
• Horticulture

Background:

• Roses are globally significant ornamental crops with limited genetic resources due to interspecific hybridization and high heterozygosity.
• Identifying markers for quantitative trait loci (QTL) controlling traits like disease resistance requires abundant genomic markers and precise phenotyping.

Purpose of the Study:

• To construct the first high-density integrated consensus genetic map for diploid roses.
• To facilitate marker-trait association studies for improved rose breeding programs.

Main Methods:

• Genotyping by sequencing (GBS) was employed to generate thousands of single nucleotide polymorphism (SNP) markers.
• These SNPs, along with existing simple sequence repeat (SSR) markers, were integrated into individual maps for three rose populations.
• An integrated consensus map was built using data from multiple populations, referencing the strawberry (Fragaria vesca) genome.

Main Results:

• A high-density diploid rose consensus map was created, comprising seven linkage groups (LGs) spanning 892.2 cM with 3527 markers.
• The consensus map achieved an average marker distance of 0.25 cM, improving marker density and order reliability.
• Significant synteny was observed between the rose and strawberry genomes, indicating conserved genomic structure.

Conclusions:

• The developed consensus map is a valuable tool for marker-trait association discovery in rose breeding.
• The high genomic conservation with strawberry supports comparative genomics within the Rosaceae family.
• This map can aid in identifying candidate genes underlying important agronomic traits in roses.