Lilii Bulbus (Lilium spp., Liliaceae) is a plant with rich nutrition and good ornamental value (Zhang, Wang, Zhang, Peng, Zhan, & Yang, 2019). There are about 110 species in the world, which are widely distributed in the temperate regions of the Northern Hemisphere, such as Eastern Asia, Europe and North America (Chung, López-Pujol, Chung, Kim, Park, & Chung, 2015; Munafo, Ramanathan, Jimenez, & Gianfagna, 2010; Yan, Sun, & Sun, 2020). China is also one of the important distribution centers of lilies. Lily mainly contains bioactive substances such as polysaccharides, saponins, flavonoids, polyphenols, and also contains fatty acids, vitamins, essential amino acids and trace elements (Iguchi, Yokosuka, Kuroda, Takeya, Hagiya, & Mimaki, 2020; Kan, Hui, Xie, Chen, Liu, & Jin, 2021; F. Wang, Wang, Niu, Huang, & Zhang, 2018). Studies have shown that Lilii Bulbus extracts can be effectively applied to the therapy of anti-bacteria, anti-depression, anti-tumor, anti-oxidation, and lowering blood glucose (Jia et al., 2020; Sim et al., 2020; P. Wang et al., 2019). Lily is widely planted in Shandong, Hunan, Hubei, Gansu, Anhui, Jiangsu, Henan and other places because of its high economic value, which has greatly promoted the local economic development. The research shows that different varieties have great influence on their quality. At present, researches on Lilii Bulbus mainly focuses on edible methods, cultivation techniques, quality evaluation and extraction of organic compounds (Zhou, An, & Huang, 2021), while the research on identification of germplasm resources is less. Identification and selection of suitable lily varieties have become an urgent problem to be solved, and breeding high-quality lily varieties is of great significance.
Nowadays, numerous methods have been used for genetic breeding. For example, PCR-based molecular marker techniques include Simple Sequence Repeats (Tikendra, Amom, & Nongdam, 2019), Random Amplified Polymorphic DNA (Nasim et al., 2020), and Amplified Fragment Length Polymorphism(Amom et al., 2020). Specific Length Amplified Fragment sequencing (SLAF-seq) can perform sequencing to a deeper degree, which is suitable for large-scale genotypic (Sun et al., 2013), and has the advantages of high flux, effective reading length, high accuracy, good repeatability, and relatively low cost (Rehman & Gong, 2020). With the advantages of high density, stable inheritance, strong representation, and easy automation (Arbelaez et al., 2019), Single nucleotide polymorphism(SNPs) have been widely used in human genetics (Ruan, Yang, Long, & Sun, 2018; Ustiugova, Korneev, Kuprash, & Afanasyeva, 2019; Yahya et al., 2020), and assisted breeding (Choi et al., 2020; Liao & Lee, 2010; Niciura et al., 2018; Perez-Enriquez, Robledo, Houston, & Llera-Herrera, 2018), serving as a genetic marker of important research significance.
The SLAF-seq technology utilizes bioinformatics to find the most suitable enzyme to perform enzyme digestion on the genome, and constructs a library of insertion fragments with a certain size, performs high-throughput sequencing and quickly identifies high-accuracy mutation marker information in the whole genome range for population evolution, and has been applied to species such as soybeans (Sui et al., 2020), peanuts (S. Zhang et al., 2019) and cucumber(Qingzhen et al., 2014). However, researches on the development of molecular markers and analysis of the genetic relationship between different germplasm using SLAF sequence technology for Lilii Bulbus are quite rare. Therefore, new genetic markers of 29 Lilii Bulbus individuals were developed and analyzed within the whole genome range. It provided a robust basis for studying genetic relationships, the construction of genetic linkage map and the correlation analysis of essential characters in Lilii Bulbus in the future.