Pangenome Analysis Reveals Structural Variations Associated With Citric Acid Accumulation in Prunus mume.

Area of Science:

• Genomics
• Plant Science
• Bioinformatics

Background:

• Pangenomes offer a more complete view of genetic diversity than single reference genomes.
• Understanding genetic variation is crucial for crop improvement.

Purpose of the Study:

• To construct a high-quality pangenome for P. mume.
• To identify genetic variations influencing fruit traits, specifically citric acid content.
• To develop molecular tools for P. mume breeding.

Main Methods:

• Assembly of a telomere-to-telomere genome and 10 chromosome-level genomes for P. mume.
• Construction of a graph pangenome integrating existing and new genome data.
• Pangenome variation detection using P. armeniaca genomes.
• Identification and characterization of structural variations (SVs).
• Development of SV molecular markers.

Main Results:

• The P. mume graph pangenome spans 412.41 Mb, increasing genetic content by 179.60 Mb and including 5918 unique genes.
• Over 51,000 non-redundant SVs were identified, with 60.50% of presence/absence variations attributed to transposons.
• A 376 bp SV insertion in the PmPH4 promoter enhances citric acid accumulation in P. mume fruits.
• SV molecular markers were developed for early screening of high-citric acid germplasm.

Conclusions:

• The constructed P. mume pangenome provides a comprehensive resource for understanding genetic diversity.
• Identified SVs, particularly the PmPH4 promoter insertion, offer targets for improving fruit quality.
• Developed molecular markers facilitate marker-assisted selection for enhanced citric acid content in P. mume breeding programs.