Development of novel chloroplast microsatellite markers for Ginkgo biloba

Abstract

ABSTRACT. Ginkgo biloba is considered to be a living fossil that can be used to understand the ancient evolutionary history of gymnosperms, but little attention has been given to the study of its population genetics, molecular phylogeography, and genetic resources assessment. Chloroplast simple sequence repeat (cpSSR) markers are powerful tools for genetic studies of plants. In this study, a total of 30 perfect cpSSRs of Ginkgo were identified and characterized, including di-, tri, tetra-, penta-, and hexanucleotide repeats. Fifteen of 21 designed primer pairs were successfully amplified to yield specific polymerase chain reaction products from 16 Ginkgo cultivars. Polymorphic cpSSRs were further applied to determine the genetic variation of 116 individuals in 5 populations of G. biloba. The results showed that 24 and 76% genetic variation existed within and among populations of this species, respectively. These polymorphic and monomorphic cpSSR markers can be used to trace the origin and evolutionary history of Ginkgo.

Development of Chloroplast Microsatellite Markers and Evaluation of Genetic Diversity and Population Structure of Cutleaf Groundcherry (Physalis angulata L.) in China

“…Mononucleotides (68.24% of the total) were the most common SSR loci detected in our study, followed by tetranucleotides (12.28% of the total). These proportions are similar to those of cpSSR marker types found in many plants [33][34][35]. Polymorphism is an important index for evaluating the application value of molecular markers in the study of plant genetic diversity [18,30,36].…”

Sequencing and Analysis of Strobilanthes cusia (Nees) Kuntze Chloroplast Genome Revealed the Rare Simultaneous Contraction and Expansion of the Inverted Repeat Region in Angiosperm

“…The cp genomes offer numerous applications. First, the cp genome is rich with molecular markers that can be used to distinguish different species ( Song et al, 2015 ; Yang et al, 2016 ; Xu et al, 2017 ); different varieties from the same species ( Xu et al, 2015 ; Pervaiz et al, 2016 ), and possibly different individuals within the same species ( Lei et al, 2016 ). Owing to the acquisition of the first complete genome of S. cusia , sequencing of additional plastid genomes from other Strobilanthes species and varieties of S. cusia becomes increasingly easy, consequently providing the basis for the identification of molecular markers that can be used for identity determination at various levels.…”

Cultural Extension of Ginkgo biloba L. in Slovakia

“…On the importance of recognizing genetic diversity of Ginkgo biloba populations pointed out several studies focused on applying different molecular markers as genomic microsatellites (Yan et al, 2006;Yan et al, 2009;Li et al, 2009;Xie et al, 2013), RAPD (Fan et al, 2004;Li et al, 2013;Mei et al, 2014), ISSR (Mei et al, 2014), RFLP (Shen et al, 2005) and microsatellites (Xu et al, 2015) markers based on chloroplast DNA and microRNA-based markers (Ražná et al, 2020).…”