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Germplasm characterization is now possible and more reliable using improved molecular markers and genomic tools. Previously citrus cultivars were primarily described according to their morphological or horticultural traits, but trueness-to-type can now be confirmed using molecular markers, thereby limiting inadvertent cultivar misidentification. Following routine testing the reported parentage of two mandarin hybrids is now questioned. ‘Orri’ mandarin is derived from ‘Orah’ mandarin by induced mutation, and was reportedly bred by crossing ‘Temple’ tangor and ‘Dancy’ mandarin. ‘Orri’ has excellent organoleptic qualities, and other favorable traits. With ‘Dancy’ as the pollen parent, at least some degree of susceptibility of ‘Orri’ to Alternaria brown spot (ABS) might be expected, but it is more likely to have inherited a high degree of susceptibility; yet ‘Orri’ appears to be immune to ABS. SSR analysis provided evidence that excludes ‘Dancy’ as the pollen parent of ‘Orah’. Further testing revealed the likely pollen parent candidate as ‘Kinnow’ mandarin. ‘Fortune’ mandarin was a popular late-maturing mandarin cultivar until the high incidence of ABS rendered the cultivar uneconomical to produce in certain citrus production regions. This exceptionally late, high quality, attractive cultivar is reported to have originated from a ‘Clementine’ mandarin A— ‘Dancy’ cross. However, two independent molecular marker studies revealed that the pollen parent of ‘Fortune’ is possibly ‘Orlando’ tangelo and not ‘Dancy’. In both cases, the pollen parent of ‘Orri’ and ‘Fortune’ mandarin hybrids appears not to be ‘Dancy’ as published. This information will assist geneticists and breeders to re-interpret heritability studies on ABS susceptibility of mandarins and their hybrids.

The availability of a saturated genetic map of Clementine was identified by the International Citrus Genome Consortium as an essential prerequisite to assist the assembly of the reference whole genome sequence based on a Clementine derived haploid. The primary goals of the present study were to establish a Clementine reference map, and to perform comparative mapping with pummelo and sweet orange. Five parental genetic maps were established with SNPs, SSRs and InDels. A medium density reference map (961 markers for 1084.1 cM) of Clementine was established and used by the ICGC to facilitate the chromosome assembly of the haploid genome sequence. Comparative mapping with pummelo and sweet orange revealed that the linear order of markers was highly conserved. Reasonable inferences of most citrus genomes should be obtained by mapping next-generation sequencing data against the haploid reference genome sequence. Skewed segregations were frequent and higher in the male than female Clementine potentially leading to false interpretation of the genetic determinism of phenotypic traits. The mapping data confirmed that Clementine arose from hybridization between 'Mediterranean' mandarin and sweet orange and identified nine recombination break points for the sweet orange gamete that contributed to the Clementine genome. Introgression of pummelo genome fragments were identified in heterozygosity in each chromosome. Moreover, it appeared that the genome of the haploid Clementine used to establish the citrus reference genome sequence was inherited primarily from the 'Mediterranean' mandarin. The usefulness of this genetic map, anchored in the reference whole genome sequence, is discussed. Citrus Research and Development Foundation 108O568 Ministerio de Ciencia e Innovación: AGL2008-00596-MCI, 2008/121, IPT-010000-2010-43, PSE-060000-2009-8, AGL2007-65437-C04-01/AGR European Commission Citrus Research and Development Foundation itl-bio-03-10122 015453 This work was principally funded by the French ANR CITRUSSEQ project. The European Commission, under the FP6-2003-INCO-DEV-2 project CIBEWU (n°015453), the Spanish Ministerio de Ciencia e Innovación grants, AGL2007-65437-C04-01/AGR and AGL2008-00596-MCI, the Spanish PSE-060000-2009-8 and IPT-010000-2010-43 projects, the Prometeo project 2008/121 Generalidad Valenciana, the Turkish TUBITAK Project No: 108O568; the California Citrus Research Board and UC Discovery grant itl-bio-03-10122 and the Florida Citrus Research and Development Foundation (CRDF), grants #67 and 71 also contributed to the work.

The `Flying Dragon' cultivar of Poncirus trifoliata L. Raf. is a strongly dwarfing rootstock for Citrus cultivars, reducing canopy volume of 9 year-old `Valencia' orange trees to 1/3 that of trees on standard rootstocks Open-pollinated seed of `Flying Dragon' was screened with isozyme markers to distinguish zygotic from nucellar (apomictic) seedlings. All zygotics had genotypes consistent with an origin by self-pollination. Zygotic seedlings were budded with `Valencia' orange scion and planted in the field. Of 46 progeny evaluated as rootstocks, 35 produced small trees similar to those on nucellar `Flying Dragon' and 11 produced large trees. This ratio is consistent with the 3:1 segregation expected for a single dominant gene. The dwarfing gene was closely linked, or pleiotropic with a gene causing curved thorns and stems. Several RAPD markers close to the dwarfing gene were identified with bulked segregant analysis. `Flying Dragon' apparently originated as a mutation because it had au identical genotype to non-dwarfing strains of trifoliate orange at all 38 isozyme and RFLP markers tested

To assess genetic diversity in the UC Riverside Citrus Variety Collection, all accessions of pummelo (59), citron (24), and trifoliate orange (48) were studied for RFLP variation using 11-18 cDNA probes that had previously been shown to reveal polymorphism in a broad range of citrus germplasm. Inheritance studies have shown that these probes hybridize to at least 20 loci. The taxa studied are believed to represent biological species rather than hybrids. Citrons were nearly monomorphic and most appeared homozygous at all of the loci studied. Pummelos were very polymorphic and highly heterozygous. Trifoliate orange, an important source of disease resistance in rootstock breeding, was nearly monomorphic but moderately heterozygous (17% of loci). Most accessions of trifoliate orange have evidently differentiated only by mutation. One multilocus probe separated trifoliate orange accessions into 3 groups. Two new trifoliate orange accessions had novel alleles at some loci. The use of genetic markers to recognize hybrid accessions classified as members of species will be discussed.

Citron (Citrus medica L.) is one of the three basic species of the genus Citrus L. that have contributed to the development of cultivated citrus. We analyzed the genetic diversity of 47 citrons (32 from Yunnan Province, China; and 15 of Mediterranean origin) to understand their diversity and relationships within the species. Genetic analysis was conducted using data from microsatellite markers, single nucleotide polymorphisms generated from sequences of a nuclear malate dehydrogenase gene and a chloroplast gene, rps16. Neighbor joining and maximum parsimony analyses were conducted. All three approaches found citron to be monophyletic. Population structure analysis clustered the 47 citrons into three distinct groups. The first group consisted of wild, non-fingered citrons generally having locules, juice sacs and seeds within the fruit. The second cluster consisted mostly of fingered citrons that lacked locules, juice sacs or seeds, and some non-fingered types with smaller locules and vestigial juice sacs, but with seeds. All accessions that clustered in groups I and II originated in China. The third cluster consisted of citrons cultivated in the Mediterranean region. Genetic distance between the clusters from population structure analysis indicated considerable diversity within the species. A citron-specific microsatellite marker was identified and characterized. We observed considerable heterozygosity in certain citrons, contrary to previous reports.