Development and application of rose (Rosa chinensis Jacq.) SNP markers based on SLAF-seq technology

Molecular markers are important genetic tools that permit the detection and utilization of genetic variation in germplasm resources. To develop high-density single nucleotide polymorphisms (SNPs) markers for rose, specific length amplified fragment sequencing (SLAF-seq) was performed in 158 rose individuals using the Rosa chinensis Jacq. genome as a reference for enzyme digestion prediction. After high-throughput sequencing, SNP marker development, and evolutionary analysis, the phylogenetic trees of 158 rose individuals were constructed according to the SNPs. A total of 1,703,904 SLAF tags were developed, among which 277,749 were polymorphic SLAF tags. According to the obtained polymorphic SLAF tags, a total of 1,816,980 population SNP markers were obtained, and 17,233 highly consistent SNP markers. The cluster analysis revealed that 158 rose individuals could be grouped into two major clusters. The average observed heterozygosity and polymorphism information content were 0.1802 and 0.2306, respectively. The population structure analysis of 158 rose individuals (K = 12) indicated that most of the populations had different ancestors and showed signs of crossover. The obtained SNPs in the rose genome can aid variety identification and have important implications for the conservation and improvement of varieties.