Development of single nucleotide polymorphism (SNP) markers and construction of DNA fingerprinting of Alcea rosea L. based on specific-locus amplified fragment sequencing (SLAF-seq) technology

Abstract

Alcea rosea L. are herbaceous plants with several cultivars and a wide range of flower types and colors. They are commonly grown for their ornamental value and are widely cultivated worldwide. However, the lack of genetic diversity and effective molecular markers has hindered efforts to improve and identify A. rosea cultivars. In this study, specific-locus amplified fragment sequencing (SLAF-seq) was employed to develop markers for 38 samples of A. rosea (17 samples from Chengdu Botanical Garden, 19 samples from Flower Valley, and 2 samples from wild species) using the Hibiscus syriacus L. genome as a reference for enzyme digestion prediction. A total of 1,345,364 SLAF tags were obtained by high-throughput sequencing, with an average sequencing depth of 31.80X. There were 162,476 polymorphic SLAF tags and a total of 425,098 single nucleotide polymorphism (SNP) markers were discovered and used for phylogenetic tree, population structure, principal component, and genetic diversity analyses. The results showed that relatedness among samples was generally correlated with plant type, flower type, and flower color. At the same time, the population genetic structure and phylogenetic relationships of high-stem A. rosea in the Flower Valley were more complex. Besides, the genetic diversity of the wild species was higher than cultivated species. At last, 26 variant loci were also screened and identified as core markers for DNA fingerprinting for A. rosea identification. The development of SNP markers and the construction of DNA fingerprints in this study provide references for future analyses in A. rosea cultivar identification, genetic diversity, and molecular breeding.