Development and application of a multiple nucleotide polymorphism (MNP)-based molecular identification system for...

Area of Science:

• Genetics
• Horticulture
• Agricultural Science

Background:

• Pear (Pyrus species) exhibits high cultivar diversity and interspecies gene flow due to self-incompatibility and lack of reproductive barriers.
• Accurate pear cultivar identification is crucial for production, innovation, and industry development.
• Multiple Nucleotide Polymorphism (MNP) technology combines multiplex PCR and high-throughput sequencing for efficient and accurate genetic analysis.

Purpose of the Study:

• To develop and validate Multiple Nucleotide Polymorphism (MNP) markers for pear cultivar identification.
• To assess the utility of MNP markers for pear population structure analysis.

Main Methods:

• Genomic resequencing data from 143 pear accessions were used to develop 558 marker loci, refined to 310 core MNP markers.
• The 310 MNP markers were validated on 76 representative pear cultivars for reproducibility and accuracy.
• Population structure analysis was performed using the developed MNP markers.

Main Results:

• The 310 MNP markers demonstrated high polymorphism (avg. 18.14 alleles/locus, PIC 0.57-0.99) and achieved >99% accuracy in cultivar identification.
• Analysis revealed high genetic differentiation among cultivars (avg. 90.89%).
• MNP markers effectively distinguished between European and Asian pear groups, reflecting their classification relationships.

Conclusions:

• Developed pear MNP markers exhibit high polymorphism, stability, and discrimination capability.
• These markers show significant potential for future applications in pear cultivar identification.
• The MNP markers are promising tools for pear population genetic research and breeding programs.