An SSR-Base Linkage Map Reveals QTLs for Floral-Related Traits in Nightlily (Hemerocallis citrina)

Nightlily (Hemerocallis citrina Baroni) is mainly cultivated for bud consumption with medicinal, nutritional, and economic value. Enhancing nightlily yield is one of the most significant breeding goals of modern agriculture of H. citrina breeding objective, but it also faces great challenges. In this study, an intraspecific hybridization population crossed between two varieties, ‘Liuyuehua’ and ‘Datong Huanghua’ of Hemerocallis, was used to establish 715 F1 individuals. Phenotypic data for eight floral traits, including scape number, bud number, scape length, scape diameter, bud length, bud diameter, fresh flower bud weight, and dry flower bud weight, were collected from 715 F1 individuals over a three-year period (2022, 2023, and 2024). The Simple Repeat Sequence (SSR) markers were validated to genotype the 116 random F1 individuals and to construct a linkage map. The intraspecific hybridization map contained 11 linkage groups. A total of 169 SSR markers were used to construct a linkage map, spanning a total map length of 1605.3 cM, with an average marker interval of 9.50 cM. The linkage map revealed 11 floral QTLs from 7.21% to 24.29% of phenotypic variation. Through collinearity analysis, it was found that 122 markers could be aligned to the published genome sequence of H. citrina. A total of five candidate genes for floral traits were predicted. The linkage map is essential for mapping and marker-assisted progeny selection that will accelerate the pace of nightlily breeding.