Origin of dwarf, thornless-type trifoliate orange varieties deduced from genome-wide genotyping anal

Trifoliate orange (Poncirus trifoliata) is commonly used as a rootstock in Japan. Several varieties that are differentfor tree height or tree morphology are recognized. However, origin and phylogenetic relationship among them arenot evaluated. We compared genotypes of three varieties, a thornless type trifoliate orange that lacks thorns atthe leaf axil and two dwarf types, 'Hiryu' ('Flying dragon') and 'Unryu' ('Cloudy dragon'), to a reference accessionof trifoliate orange in our citrus collection. Genotyping analysis with 289 genome wide SSR markers gave 265 validgenotypes. Among them, 'Hiryu' lost five loci but 96.2% of genotypes were matched to those of the reference. Incontrast, the thornless-type lost 4 loci and 78.8% of genotypes were matched to those of the reference, and 'Unryu' lost 6 loci and 81.4% of genotypes were matched to those of wild type. Assignment of SSR marker genotypes toa citrus linkage map revealed that genotypes of 'Hiryu' were well conserved among all linkage groups. However,loss of heterozygosity (LOH) was observed at various regions of linkage groups for the thornless-type and 'Unryu'. Ratios of homozygous loci of the reference, the thornless-type, 'Hiryu' and 'Unryu' were 70.3%, 88.5%, 69.1%, and84.9%, respectively. These observations suggested that 'Hiryu' is a sport of trifoliate orange but the thornless-typeand 'Unryu' resulted from trifoliate orange by self-pollination and mutation at particular loci.