Development of a Large Gene-Associated SSR Marker Set and in-Depth Genetic Characterization in Scarlet Sage.

Salvia splendens, scarlet or tropical sage, is a tender perennial herbaceous flowering plant popularly grown in public and private gardens all over the world. In this study, we developed a set of simple sequence repeats (SSRs) from genome-wide sequences to assess the genetic diversity and population structure among 112 cultivars. We obtained 364,379 SSRs by mining scarlet sage's recently published whole genome sequence; 14,545 gene-associated SSR loci were identified in 2 kb gene flanking regions. Among the 768 gene-associated SSR primer sets we screened, 576 loci successfully amplified in DNA pools of 3-4 different cultivars, of which 271 remained polymorphic when tested across eight individual plants. We searched for the related gene functions attributable to these gene-associated SSRs using diverse databases, resulting in 259 Non-redundant matching sequences, 205 individual Gene Ontology (GO) terms, 236 assigned to eukaryotic orthologous groups, and 67 KEGG-annotated (Kyoto Encyclopedia of Genes and Genomes) sequences. We finally selected 41 polymorphic SSR loci to infer genetic diversity and population structure among 112 S. splendens accessions. Based on the developed gene-associated SSRs, clustering analyses consistently revealed two distinct genetic groups within the core collection of S. splendens cultivars. This work developed and characterized an exhaustive set of genome-wide gene-associated SSR markers for scarlet sage. These SSRs can provide species identification, genetic diversity and population structure information for S. splendens, and will therefore be important tools for the management and protection of S. splendens germplasm.

Comparative transcriptomic analysis provides insights into the development of a Salvia splendens Ker-Gawler mutant, SX919M.

Salvia splendens is a perennial, ornamental herbaceous flower that is widely cultivated as a bedding plant in gardens. The development of novel S. splendens cultivars and investigating the relevant molecular mechanisms are of great significance. In this study, RNA-sequencing and real-time PCR methods were used to analyze the possible molecular mechanism of S. splendens mutant, SX919M. From the wild-type S. splendens 919CK, we firstly selected a natural mutant, SX919M, which displayed multiple branches, clustered spheroids, and radial symmetrical inflorescence with higher numbers of calyces, ovules, stamens, and perianth tubes. Further, the RNA-seq was used to identify the differentially expressed genes (DEGs) in the mutant which included a total of 3568 upregulated and 3290 downregulated unigenes. We further observed that the indole alkaloid biosynthesis pathway showed the highest DEG enrichment, which was supported by a significant increase in the IAA content in mutant SX919M. In addition, we validated three DEGs, namely, CL2200.Contig2_All encoding methyl IAA esterase, CL12462.Contig1_All and CL12462.Contig2_All, which encoded strictosidine synthase, upregulated in mutant SX919M. We selected a novel S. splendens germplasm SX919M with a high ornamental value and determined that the upregulation of IAA biogenesis may be associated with its development.

High-quality assembly of the reference genome for scarlet sage, Salvia splendens, an economically important ornamental plant.

Background: Salvia splendens Ker-Gawler, scarlet or tropical sage, is a tender herbaceous perennial widely introduced and seen in public gardens all over the world. With few molecular resources, breeding is still restricted to traditional phenotypic selection, and the genetic mechanisms underlying phenotypic variation remain unknown. Hence, a high-quality reference genome will be very valuable for marker-assisted breeding, genome editing, and molecular genetics. Findings: We generated 66 Gb and 37 Gb of raw DNA sequences, respectively, from whole-genome sequencing of a largely homozygous scarlet sage inbred line using Pacific Biosciences (PacBio) single-molecule real-time and Illumina HiSeq sequencing platforms. The PacBio de novo assembly yielded a final genome with a scaffold N50 size of 3.12 Mb and a total length of 808 Mb. The repetitive sequences identified accounted for 57.52% of the genome sequence, and 54,008 protein-coding genes were predicted collectively with ab initio and homology-based gene prediction from the masked genome. The divergence time between S. splendens and Salvia miltiorrhiza was estimated at 28.21 million years ago (Mya). Moreover, 3,797 species-specific genes and 1,187 expanded gene families were identified for the scarlet sage genome. Conclusions: We provide the first genome sequence and gene annotation for the scarlet sage. The availability of these resources will be of great importance for further breeding strategies, genome editing, and comparative genomics among related species.