Analysis of genetic diversity in Ganoderma population with a novel molecular marker SRAP

Abstract

Genetic marker technology designed to detect naturally occurring polymorphisms at the DNA level had become an invaluable and revolutionizing tool for both applied and basic studies of fungi. To eliminate the confusion on the taxonomy of Ganoderma strains, in this study, a collection of 31 accessions representative of morphotypes and some unclassified types was used for analyzing molecular diversity using a novel molecular marker sequence-related amplified polymorphism (SRAP). This collection included commercial cultivars and wild varieties that represented the great diversification of types from different countries and regions. The experimental results showed that 50 out of 95 combinations of primers turned out to be polymorphic, and 85 polymorphism bands were obtained using six combinations. Based on the appearances of markers, the genetic similarity coefficients were calculated, and genetic variations were observed (0 approximately 1) among the 31 different Ganoderma strains. The group of Ganoderma lucidum showed significant differences from the group of Ganoderma sinense. Moreover, G. lucidum in China was also different from G. lucidum in Yugoslavia. At the same time, cluster analysis successfully categorized these 31 Ganoderma strains into five groups. These results revealed the genetic diversity of Ganoderma strains and their correlation with geographic environments. It also suggested SRAP marker could be used in the taxonomic analysis of fungi. To our knowledge, this is the first application of SRAP marker on the systematics of Ganoderma strains within basidiomycetes.

Species Clarification of the Widely Cultivated Ganoderma in China Based on rDNA and FIP Gene Sequence Analysis

“…The 5.8S gene that located between the ITS I and II regions was very well conserved (158 bp in length). The 5.8S rDNA sequences of the basidiomycetes fungi were identical, which was a result agreeing with our findings (Sun et al, 2006). Nucleotide sequence in the FIPs gene varied in length from 333 bp to 336 bp, with 100% consensus positions and 77.1% identity positions (Fig.…”

“…Now, a variety of sequence-based DNA fingerprinting techniques have been used to the identification of cultivation of Ganoderma, such as internal transcribed spacer (ITS) 25S ribosomal DNA sequencing PCR amplification (Moncalvo et al, 1995;Gottlieb et al, 2000;Hong and Jung, 2004;Sun et al, 2006), PCR-RFLP (Zhou et al, 2008;Park et al, 2012), sequence characterized amplified region (Xu et al, 2008) and sequence-related amplified polymorphism molecular marker system (Sun et al, 2006). The use of these techniques is dependent on the ribosomal RNA sequences.…”

“…DNA markers that those could be obtained by sequencing methods, are reliable for informative genetic polymorphisms. There are various mature molecular marker techniques that had been widely applied in the classification of Ganoderma strains, such as the encoding regions of the 18S, 5.8S, 28S and ITS regions of nucleotide sequences of the rDNA (Moncalvo et al, 1995;Gottlieb et al, 2000;Smith and Sivasithamparam, 2003;Lee et al, 2006;Sun et al, 2006;Zheng et al, 2009) and mt SSU rDNA (mitochondrial small subunit rDNA) (Hong et al, 2002;Hong and Jung, 2004), etc.…”

Genetic Diversity and Population Structure of Toona Ciliata Roem. Based on Sequence-Related Amplified Polymorphism (SRAP) Markers

“…Of the various molecular marker techniques available, sequence-related amplified polymorphism (SRAP) is a novel third-generation technique. The SRAP protocol is a polymerase chain reaction (PCR) based marker system designed to amplify open reading frames (ORFs) [12,13]. The protocol is simple, efficient, and has a high production rate.…”

Development of RAPD-SCAR markers for different Ganoderma species authentication by improved RAPD amplification and molecular cloning

“…For example, G. lucidum HG is typically grown in Northern and North-Eastern China in cold environments, while G. tropicum is grown in tropical forests. A sequence-related amplified polymorphism analysis by Sun et al (2006) revealed significant genetic variation between G. lucidum and G. sinense. Zhao et al (2003) showed 80-100% polymorphism in genetic materials in different Ganoderma species, and Mei et al (2014b) showed high levels of genetic distance between G. gibbosum, G. tropicum, G. sinense, and G. lucidum.…”