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

Abstract

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.

Genetic Diversity Study on Geographical Populations of the Multipurpose Species Elsholtzia stauntonii Using Transferable Microsatellite Markers

“…Genetic variation of a population can be measured by the number of alleles and heterozygosity ( Huang et al, 2020 ; Savić et al, 2021 ). The mean N A (7.000) and N E (1.971) observed in the present study were slightly higher than the values (6.45 and 1.67, respectively) for 12 Plectranthus edulis populations evaluated using 20 SSR markers ( Gadissa et al, 2018 ), but lower than the values reported for Salvia splendens ( N A = 11.829, N E = 3.261) ( Jiao et al, 2020 ) and Juglans nigra ( N A = 9.99, N E = 7.51) ( Schneider et al, 2019 ). Compared with previous studies on Lamiaceae species, E. stauntonii ( H O = 0.360) has higher genetic diversity than Salvia fruticosa ( H O = 0.307) ( Radosavljević et al, 2015 ) and Hedeoma piperita ( H O = 0.3) ( Herrera-Arroyo et al, 2020 ), but a higher level of genetic diversity has been observed in Rosmarinus officinalis ( H O = 0.63) ( Segarra-Moragues et al, 2015 ).…”

“… N A , number of alleles; H O , observed heterozygosity; H E , expected heterozygosity; PIC, polymorphic information content; F is , inbreeding coefficient; HWE, Hardy–Weinberg equilibrium; **p < 0.01; ***p < 0.001. a, b, c, d, e, f , Previously published microsatellite markers ( a : Sa et al, 2018 ; b : Sa et al, 2019 ; c : Jiao et al, 2020 ; d : Sandes et al, 2013 ; e : Sa et al, 2015 ; f : Vining et al, 2019 ). …”

“…Currently, SSR markers have been widely used in assessments of population genetic diversity ( Gadissa et al, 2018 ), cultivar identification ( Pinto et al, 2018 ; Sulu et al, 2020 ), and association mapping ( Yang et al, 2020 ) as effective tools to describe genetic variation in plants. Using available genomic or expressed sequence tag databases ( Vieira et al, 2016 ), a large number of SSR markers have been developed in Lamiaceae species, such as Scutellaria baicalensis ( Zhang et al, 2014 ), Perilla frutescens ( Ha et al, 2021 ), and Salvia splendens ( Jiao et al, 2020 ). However, owing to the lack of genetic information, to date no SSR markers are available for evaluation of the genetic diversity within E. stauntonii , which limits its breeding and commercial development.…”

Genome-wide association mapping identifies Yellow Rust resistance locus in Ethiopian Durum Wheat germplasm

“…Allele frequency model was employed at Length of burnin period: 10000, number of MCMC Reps after burnin: 100000, K runs from 1 - 10 with 5 times replication for each K. The result of the analysis was zipped in to a folder and uploaded on to STRUCTURE HARVESTER [58], an online analysis tool used to generate an estimate of the optimum number of subpopulations (i.e. the value of K) through Evanno method [59]. Kinship matrix was generated through genetic similarity matching using all possible pairwise combination among the panel using the R package Genomic Association and Prediction Integrated Tool (GAPIT) besides performing the PCA [60].…”

Development and Characterization of Microsatellite Markers Based on the Chloroplast Genome of Tree Peony

“…Microsatellite markers, otherwise known as short tandem repeats (STRs) or simple sequence repeats (SSRs), are short units of 1-6 nucleotide tandem repeat sequences widely distributed in eukaryotic and prokaryotic genomes [ 4 , 5 ]. The sequences at both ends of an SSR are often relatively conservative single-copy sequences, which show polymorphism due to the different number or degree of repetitions.…”