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The large genome size of easter lily [ Lilium longiflorum  (77.1 pg/2C nucleus)], coupled with repetitive DNA sequences, makes it difficult to use molecular techniques to identify or fingerprint lily ( Lilium ) species, hybrids, and clones. Previous research demonstrated that amplified fragment length polymorphisms could not be optimized for consistency and repeatability to obtain reliable genetic variation assessments of lily species and clones. The objective of this research was to analyze the effectiveness and stringency of intersimple sequence repeats (ISSRs) to determine genetic differences between  L. longiflorum  ‘Nellie White’ clonal ramet populations from bulb growers over years. DNA from closely related clones of  L. longiflorum  ‘Nellie White’ included 2002 (n = 11 bulb lots) and 2003 (n = 12 bulb lots). Comparison cultivars and species were also included. Five University of British Columbia (UBC) primers (P808, P810, P811, P814, and P818) that were used produced 56 polymorphic loci. ISSR banding patterns were consistent among three replications within ‘Nellie White’ clonal genotypes. ‘Nellie White’ clones differed significantly within (82%) and among (18%) growers in 2002 and 2003. ‘Nellie White’ clones are not uniform or part of a single ramet population. Principal clades within years separated at Nei's genetic distances (GDs) of GD = 0.6 (growers 2, 4, and 12) to GD = 0.82 (grower 6) in 2002 and GD = 0.51 (grower 4) to GD = 0.78 (grower 14). The most closely related ‘Nellie White’ clones within growers ranged from GD = 0.8 to 0.95 in 2002 and GD = 0.7 to 0.91 for 2003. Five top-performing growers (1, and 3–6) from previous morphological studies and, particularly growers 3 and 5, were in similar clades, cosegregating with phenotypic traits of stem emergence and flowering dates. The lack of a meiotic sieve (Muller's ratchet) may be responsible for the high level of mutational differences present in the ‘Nellie White’ clones and significantly affects the ability of commercial greenhouse growers to produce a uniform easter lily crop, particularly in years when the Easter holiday is early.

Intersimple Sequence Repeats Distinguish Genetic Differences in Easter Lily ‘Nellie White’ Clonal Ramets within and among Bulb Growers over Years