Loss of Heterozygosity Analysis in Citrus Using a High Density SNP Array

Loss of Heterozygosity (LOH) is a powerful molecular genetic approach for high resolution screening to detect heterozygous deletions or gene conversions.Hybridization to single nucleotide polymorphism (SNP) arrays is an efficient method to identify LOH regions within the genome. In this study, the Affymetrix^® Axiom^® Citrus15 array containing 1.5M SNPs was used to identify LOH of chromosomal regions among cultivars that have diverged by mutation. In several cultivar groups, such as sweet oranges, LOH events were found on certain chromosomes extending from one to several megabases in some varieties compared with others. For example, Valencia Late and Olinda Valencia showed several LOH regions on chromosomes 1 (17-19Mb) & 9 (7-8Mb) compared with Pineapple Sweet Orange. The LOH affected parts of the chromosomes which are large enough to encompass multiple genes. CNV (Copy number variation) analysis confirms that these events are deletions rather than gene conversions. Other examples of cultivars showing LOH include Delta Valencia, acidless orange, Star Ruby grapefruit, and Oroval Clementine. Many Citrus varieties have originated through careful selection of spontaneous somatic mutations, so these LOH events may have played an important role in the origin of new varieties by altering fruit traits and other horticultural characters. A high-density SNP array thus can be used effectively to detect small and large deletion events and provide more information regarding the boundaries of deleted regions.