Development of EST-SSR Markers for Cultivar Determination and Genetic Diversity Studies of Commercial Chrysanthemums in the Korean Floral Market

Abstract

Chrysanthemum morifolium Ramat. is one of the major flowering crop plants worldwide. However, domestic chrysanthemum markets have recently faced a downturn. To stimulate related industries, breeding technologies and efficient protection systems using molecular markers must be established. However, high cost and intensive efforts are required to develop useful molecular markers for the chrysanthemum as it is a polyploid crop with highly complex genome organization. Thus, the aim of this research was to develop expressed sequence tag-based simple sequence repeat (EST-SSR) markers, which are applicable to the chrysanthemum breeding program and cultivar protection, based on next-generation sequencing technology. From the RNAseq data of the standard chrysanthemum cultivars 'Jungwoon' and 'Seinoisei,' we identified 31,121 SSR loci and further retrieved 1,846 polymorphic SSRs. To test the marker efficiency of the 1,846 SSRs, we first chose 50 of the SSRs and designed primers by using the flanking sequences. It is noted that the nine EST_SSR markers show a single band-like amplicon, which can be exploited in various genetic studies. We proceeded to polymorphism tests for those SSRs with 56 chrysanthemum cultivars, confirming that the average polymorphism index content (PIC) was 0.69±0.058. Among those, we found that six SSRs were sufficient to specify the genetic identities of 55 chrysanthemum cultivars, which may be useful for protections of the related cultivars, as well as breeding programs, in the future.

Assessment of Genetic Diversity in the White-Colored Variants of Spray-Type Chrysanthemum Cultivars Using SSR Markers

“…These six SSR markers generated 2 to 6 alleles with an average of 3.5 alleles per locus. The allele number per SSR locus is comparable with other results reporting an average of 2.7 alleles and 5.6 alleles per locus in 11 and 147 varieties of chrysanthemum tested with 7 and 14 SSR markers, respectively [29,30]. The degree of polymorphism (PIC) for the 57 white chrysanthemum cultivars with respect to six SSR markers was an average of 0.53, which is similar to that related in previous reports for chrysanthemum cultivars.…”

“…Analysis of genetic identity among the varieties is useful for the protection of breeders' intellectual property rights. The standard chrysanthemum varieties Pingpong and White Runner have shown higher degrees of genetic similarity that preclude discrimination [30]. In contrast, Feng et al [41] reported a genetic distance of 0.97, proving the higher genetic diversity of the tested cultivars and confirming the effectiveness of the SSR markers.…”

“…About 11 standard-type chrysanthemum cultivars were discriminated using two SSR markers [29]. Han et al [30] developed the SSR database for chrysanthemum used to discriminate chrysanthemum cultivars. However, considering the vast number of chrysanthemum cultivars, the use of SSR markers to discriminate them has been relatively uncommon.…”