Comprehensive Genetic Analysis of Monokaryon and Dikaryon Populations Provides Insight Into Cross-Breeding of Flammulina filiformis

Abstract

Flammulina filiformis, as one of the most popular edible fungi in East Asia, is produced in an industrialized and standardized way. However, its monotonous variety and product convergence have seriously restricted the development of the industry. In this study, 11 cultivated strains and 13 wild strains of F. filiformis were collected from multiple regions of China and Japan and were performed genome sequencing. Together with genome data of six strains previously released, in total 23 dikaryons (formed by two monokaryons mating, can making fruiting body), 35 monokaryons (formed by protoplast-regenerating of dikaryon and isolating) were used for genetic diversity and population structure analysis based on the high-throughput genotyping. Firstly, a set of SNP markers with intrapopulation polymorphism including 849,987 bi-allelic SNPs were developed and basically covered all of 11 chromosomes with a high distribution density of 24.16 SNP markers per kb. The cultivated dikaryotic strains were divided into three subgroups, and their breeding history was made inferences, which is consistent with the available pedigree records. The wild dikaryotic strains were divided into two subgroups and showed varied contributions of genetic components with high genetic diversity. All the investigated dikaryons have a symmetric distribution pattern with their two constituent monokaryons in principal component analysis. Finally, we summarized the pedigree relationship diagram of F. filiformis main strains including six modules, and the genotypes of hybrids can be directly phased by the known parental allele according to it. This study provides a method to distinguish two sets of monokaryon haplotypes, and several valuable genetic resources of wild F. filiformis, and an effective strategy for guiding F. filiformis breeding based on the population structure and pedigree relationship in future.

Variations in Key Aroma Compounds and Aroma Profiles in Yellow and White Cultivars of Flammulina filiformis Based on Gas Chromatography–Mass Spectrometry–Olfactometry, Aroma Recombination, and Omission Experiments Coupled with Odor Threshold Concentrations

“…Flammulina filiformis ( F. filiformis ), or East Asian needle mushroom, falls under the family Physalacriaceae and the order Agaricales [ 1 , 2 ]. F. filiformis is a highly valued edible fungus due to its high nutritional and medicinal value.…”

“…F. filiformis is a highly valued edible fungus due to its high nutritional and medicinal value. Additionally, it is one of the most productive edible types of fungus in industrialized cultivation [ 2 ]. There are two distinct strains of F. filiformis , identified by their stipe color in both yellow and white forms [ 3 ].…”

“…There are two distinct strains of F. filiformis , identified by their stipe color in both yellow and white forms [ 3 ]. Most of the F. filiformis currently consumed in the Asian market consists of the white strains with high yield and the yellow strains with a robust aroma [ 2 ]. Therefore, to generate a strain of F. filiformis that exhibits high yield and a robust aroma, an in-depth analysis of F. filiformis with desirable traits is crucial for breeding.…”

Development of Multiple Nucleotide Polymorphism Molecular Markers for Enoki Mushroom (Flammulina filiformis) Cultivars Identification

“…To understand the genetic background and breeding history of F. velutipes , 124 cultivars and wild strains were tested, and 25 SSR polymorphic markers were developed [ 21 ]. The genome sequencing of F. filiformis [ 22 , 23 , 24 ] aids in the development of large numbers of SSRs to identify F. filiformis strains. However, repetitive SSRs can induce DNA polymerase slippage during polymerase chain reaction, introducing erroneous SSR alleles to analysis [ 25 , 26 ].…”

The AMP-Activated Protein Kinase (AMPK) Positively Regulates Lysine Biosynthesis Induced by Citric Acid in Flammulina filiformis

“…Ge et al P.M. Wang et al) [ 1 ], also known as golden needle mushroom or winter mushroom, is one of the most produced and consumed edible mushroom species in China [ 2 , 3 ]. It is also a species of great interest in macrofungus research today [ 4 , 5 ]. With the gradual application of industrialized large-scale production of F .…”