Evaluating genetic diversity and constructing core collections of Chinese Lentinula edodes cultivars using ISSR and SRAP markers

Abstract

Genetic diversity among 89 Chinese Lentinula edodes cultivars was analyzed by inter-simple sequence repeat (ISSR) and sequence-related amplified polymorphism (SRAP) markers. A 123 out of 126 ISSR loci (97.62%) and 108 out of 129 SRAP loci (83.73%) were polymorphic between two or more strains. A dendrogram constructed by cluster analysis based on the ISSR and SRAP markers separated the L. edodes strains into two major groups, of which group B was further divided into five subgroups. Clustering results also showed a positive correlation with the main agronomic traits of the strains, and that strains with similar traits clustered together into the same groups or subgroups in most cases. The average coefficient of pairwise genetic similarity was 0.820 (range: 0.576-0.988). Compared to the wild strains, Chinese L. edodes cultivars indicated a lower level of genetic diversity. Two preliminary core collections of L. edodes, Core1 and Core2, were established based on the ISSR and SRAP data, respectively. Core1 was constructed by the advanced M (maximization) strategy using the PowerCore version 1.0 software and contained 21 strains, whereas Core2 was created by the allele preferred sampling strategy using the cluster method and contained 18 strains. Both core collections were highly representative of the genetic diversity of the original germplasm, as confirmed by the values of Na (observed number of alleles), Ne (effective number of alleles), H (Nei's gene diversity) and I (Shannon's information index), as well as results of principal coordinate analysis. The loci retention ratio of Core1 (99.61%) was higher than that of Core2 (97.65%). Moreover, Core1 contained strains with more types of agronomic traits than those in Core2. This study builds the basis for further effective protection, management and use of L. edodes germplasm resource.

Population genomic analysis uncovers environmental stress-driven selection and adaptation of Lentinula edodes population in China

“…This is consistent with previous clustering analyses which revealed that ZP85 was distinctly different from other cultivars79. This strain was recently developed from a Chinese wild strain by the Guangdong Institute of Microbiology, and this may be the reason why it was not grouped with the other cultivars.…”

“…In our previous study, the 21 cultivars constituted a core collection of Chinese cultivated strains9, while 35 out of the 39 wild strains constituted a core collection of Chinese wild strains. Core collection is a subset of accessions representing the maximum possible genetic diversity contained in the entire collection with minimum repetition16.…”

“…Previously, two major groups were revealed among 89 Chinese L. edodes cultivars by using inter-simple sequence repeat (ISSR) and sequence-related amplified polymorphism (SRAP) markers9. In another study, population structure analysis identified two unambiguous genetic groups among 88 wild strains of Chinese L. edodes , which correspond to two geographic regions from which the samples were collected10.…”

Proteome and Transcriptome Reveal Involvement of Heat Shock Proteins and Indoleacetic Acid Metabolism Process in Lentinula Edodes Thermotolerance

“…Sixty L. edodes strains from wild and cultivation strains [32,33] were used to screen thermotolerance in this study by primarily observing the mycelial recovery. The well-grown mycelial plugs were inoculated into sawdust plates (78 g of hardwood sawdust, 20 g of wheat bran, 2 g of lime and 20 g of agar in 1 L of distilled water).…”

Development of 44 Novel Polymorphic SSR Markers for Determination of Shiitake Mushroom (Lentinula edodes) Cultivars

“…Analysis of the genetic relationship between the relevant strains and the association of DNA markers in mushrooms can effectively increase breeding efficiency [9], because molecular markers save time in the selection process of the strain. During the last few decades, studies on the genetic diversity and population genetics in shiitake mushrooms have been conducted using various types of molecular markers, including restriction fragment length polymorphism (RFLP) [10], random amplified polymorphic DNA (RAPD) [11,12,13], amplified fragment length polymorphism (AFLP) [14], inter-simple sequence repeat (ISSR) [12,15,16], sequence-characterized amplified region (SCAR) [13,17,18], and sequence-related amplified polymorphism (SRAP) [12,16]. In spite of their diverse applications, the use of developed markers for the breeding and classification of shiitake mushrooms has been challengeable due to few available markers and little information regarding effectiveness for determination and specificity.…”