Local-Level Genetic Diversity and Structure of Matsutake Mushroom (Tricholoma matsutake) Populations in Nagano Prefecture, Japan, Revealed by 15 Microsatellite Markers

Abstract

The annual yield of matsutake mushrooms (Tricholoma matsutake) has consistently decreased in Japan over the past few decades. We used 15 polymorphic and codominant simple sequence repeat (SSR) markers, developed using next-generation sequencing, to carry out genetic analyses of 10 populations in Nagano, Japan. Using the SSRs, we identified 223 genotypes, none of which was observed in more than one population. The mean expected heterozygosity and standardized allelic richness values were 0.67 and 4.05, respectively. Many alleles appeared in only one of the 10 populations; 34 of these private alleles were detected with a mean number per population of 3.4. The fixation index (FST) and standardized genetic differentiation (G′ST) values were 0.019 and 0.028, respectively. Analysis of molecular variance (AMOVA) showed that the contribution of among population, among genets within a population, and within genets variation to the total variation was 2.91%, 11.62%, and 85.47%, respectively, with genetic differentiation being detected for all sources. Twenty-eight of 45 pairwise FST values were significantly larger than zero, and no pattern of isolation by distance was detected among the 10 populations. Bayesian-based clustering did not show clear differences among populations. These results suggest that reestablishment of a colony would be best accomplished by transplantation within a field; if this is not possible, then transplantation from within several dozen kilometers will cause little damage to the original population genetic structure.

Telomere-to-telomere genome assembly of matsutake (Tricholoma matsutake)

“…Two sporocarps, which were probably ramets derived from a single shiro (radius > 2 m) that has been generating sporocarps for more than 20 years 11 , were collected from Ina, Nagano, Japan. The sporocarps were flash-frozen in liquid nitrogen, dried under vacuum, and then stored at room temperature until needed for DNA extraction.…”

Telomere-to-telomere genome assembly of matsutake (Tricholoma matsutake)

“…Two sporocarps, which were probably ramets derived from a single shiro (radius > 2 m) that has been generating sporocarps for more than 20 years, 10 were collected from Ina, Nagano, Japan. The sporocarps were flash-frozen in liquid nitrogen, dried under vacuum, and then stored at room temperature until needed for DNA extraction.…”

Molecular Characterization of 170 New gDNA-SSR Markers for Genetic Diversity in Button Mushroom (Agaricus bisporus)

“…To date, SSR markers have been developed from various biological resources including plants, such as rice and peas, and fungi [11,[18][19][20]. SSR markers have previously been developed for the mushrooms L. edodes [21,22], Tricholoma matsutake [23,24], and A. bisporus [25][26][27][28]. However, the majority of existing SSR markers are based on enriched sequencing [26,27], and further development of markers based on the entire A. bisporus genome is necessary.…”