Development and Assessment of SNP Genotyping Arrays for Citrus and Its Close Relatives

Area of Science:

• Genomics
• Plant Science
• Agricultural Biotechnology

Background:

• Technological advancements enable detailed analysis of fruit crop genomes for understanding genetic diversity and improving breeding.
• Genome-wide single nucleotide polymorphism (SNP) genotyping arrays provide cost-effective, high-throughput genetic analysis.

Purpose of the Study:

• To develop and validate high-density SNP genotyping arrays for Citrus and its close relatives.
• To assess the accuracy, reproducibility, and utility of these arrays for genomic studies and breeding.

Main Methods:

• Development of 1.4M and 58K SNP Axiom® Citrus Genotyping Arrays using a citrus variant discovery panel of 41 diverse accessions.
• Selection of SNPs targeting genic regions for accurate calling across Citrus and related genera.
• Validation of array performance through reproducibility, polymorphism classification (PolyHighResolution), and concordance with sequence data.

Main Results:

• Nearly 100% reproducibility and high accuracy (98% concordance with sequence data) for the developed SNP arrays.
• A large majority of SNPs were classified as PolyHighResolution (PHR), indicating high quality.
• Phylogenetic analyses using array data closely mirrored those from sequence data, demonstrating robustness even with minor genotyping errors (3-5%).

Conclusions:

• The developed Axiom® Citrus HD and 58K SNP arrays are reliable and accurate tools for citrus genomics.
• These publicly available arrays will significantly aid research into citrus genetic diversity, relationships, and breeding programs.
• The arrays provide excellent genome coverage and marker quality for diverse citrus and related species.