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

Abstract

Elsholtzia stauntonii Benth. (Lamiaceae) is an economically important ornamental, medicinal and aromatic plant species. To meet the increasing market demand for E. stauntonii, it is necessary to assess genetic diversity within the species to accelerate the process of genetic improvement. Analysis of the transferability of simple sequence repeat (SSR) markers from related species or genera is a fast and economical method to evaluate diversity, and can ensure the availability of molecular markers in crops with limited genomic resources. In this study, the cross-genera transferability of 497 SSR markers selected from other members of the Lamiaceae (Salvia L., Perilla L., Mentha L., Hyptis Jacq., Leonurus L., Pogostemon Desf., Rosmarinus L., and Scutella L.) to E. stauntonii was 9.05% (45 primers). Among the 45 transferable markers, 10 markers revealed relatively high polymorphism in E. stauntonii. The genetic variation among 825 individuals from 18 natural populations of E. stauntonii in Hebei Province of China was analyzed using the 10 polymorphic SSR markers. On the basis of the SSR data, the average number of alleles (NA), expected heterozygosity (HE), and Shannon’s information index (I) of the 10 primers pairs were 7.000, 0.478, and 0.688, respectively. Lower gene flow (Nm = 1.252) and high genetic differentiation (Fst = 0.181) were detected in the populations. Analysis of molecular variance (AMOVA) revealed that most of the variation (81.47%) was within the populations. Integrating the results of STRUCTURE, UPGMA (Unweighted Pair Group Method with Arithmetic Mean) clustering, and principal coordinate analysis, the 825 samples were grouped into two clusters associated with geographical provenance (southwestern and northeastern regions), which was consistent with the results of a Mantel test (r = 0.56, p < 0.001). Overall, SSR markers developed in related genera were effective to study the genetic structure and genetic diversity in geographical populations of E. stauntonii. The results provide a theoretical basis for conservation of genetic resources, genetic improvement, and construction of a core collection for E. stauntonii.

Analysis of the Genetic Relationship and Inbreeding Coefficient of the Hetian Qing Donkey through a Simplified Genome Sequencing Technology

“…There are many methods of studying the population genetics of species, such as using morphological, cellular, biochemical, and molecular markers. These latter three are vulnerable to environmental and other aspects compared with morphological markers [24]. Previous studies have shown that the limited number of SNPs is the main bottleneck limiting the accuracy of kinship estimation [25].…”

Analysis of genetic relationship and inbreeding coefficient of Hetian Qing donkey based on simplified genome sequencing

“…There are many ways to study population genetics of species, such as morphological, cellular, biochemical, and molecular markers. Compared with morphological markers, they are vulnerable to environmental and other factors [20]. Cell markers are relatively time-consuming and laborious; biochemical markers are prone to tissue differences; and molecular markers have certain advantages [21].…”

Cross-Species Transferability of Specific SSR Markers from Carex curvula (Cyperaceae) to Other Carex Species

“…Consequently, it is anticipated that phylogenetically related taxa will exhibit a greater likelihood of success in achieving amplification due to their closer genetic relationships and more similar genomic structures [8,9]. Heterologous amplification has been extensively applied across a broad spectrum of plant species, at intergeneric (e.g., [10][11][12][13][14]) and infrageneric levels (e.g., [15][16][17]). As expected, the greatest success in terms of using cross-amplification was found when applying this approach at the infrageneric level (success rate of about 60% [8]).…”