Genome-wide SSR marker development and application in molecular breeding of Hemerocallis

The Hemerocallis genus belongs to the Asphodelaceae family and is a perennial herbaceous plant. To facilitate molecular breeding and industrial development in Hemerocallis, this study developed genome-wide simple sequence repeat (SSR) markers based on the genome of Hemerocallis 'Meng Zi Hua'. Two independent marker sets were applied for germplasm genetic diversity analysis and genetic linkage map construction. A total of 913,004 SSR loci were identified, with dinucleotide and mononucleotide repeats being the dominant types and AT-rich motifs being the main repeat units. From the first set of 48 randomly selected SSRs, 32 demonstrated polymorphism when validated across six germplasm accessions. These 32 polymorphic markers were subsequently employed to analyze a panel of 287 Hemerocallis germplasms. The analysis revealed high polymorphism with an average polymorphic information content (PIC) value of 0.7371. The germplasms were classified into six groups via unweighted pair group method with arithmetic mean (UPGMA) clustering and inferred to comprise two distinct gene pools based on population structure analysis. The second set comprised 156 SSRs, of which 153 produced clear amplification products. Among these, 90 SSRs showed parent-progeny polymorphism and were used to construct a genetic linkage map. This genetic map contained 90 markers distributed across 11 linkage groups with a total map length of 3051.49 cM. Additionally, five quantitative trait loci (QTLs) associated with petal color traits were detected and explained 8.41% to 38.82% of phenotypic variation. These findings enrich molecular marker resources available, and establish a technical foundation for future marker-assisted breeding and genetic improvement for Hemerocallis.