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Currently, research on regional genetic diversity and population genetic structure of Hericium erinaceus remains relatively scarce. Additionally, the analysis of the genetic background of germplasm resources has largely relied on fragmented molecular markers, lacking a comprehensive landscape of genome-wide variations, and thereby hindering the progress of genetic improvement. In this study, whole-genome resequencing of 35 H. erinaceus germplasm resources from Jilin Province was performed. Based on variation data such as single nucleotide polymorphisms (SNPs) and small insertions/deletions (InDels), their genetic structure, evolutionary relationships, and diversity characteristics were systematically analyzed. Population genetic structure analysis revealed that the optimal number of clusters was K=2, with significant genetic isolation between the cultivated strains and wild populations (Fst=0.079 8-0.090 4), indicating that artificial selection has led to a significant deviation in the genomic genetic background of the cultivated populations from wild populations. Genetic distance and linkage disequilibrium (LD) analyses showed low genetic differentiation among wild populations (Fst=0.022 5- 0.030 5) with an LD decay distance of 6-15 kb (r2<0.3), reflecting a coexistence pattern of geographical isolation and gene flow. Gene flow simulation confirmed weak gene flow to the cultivated strains only from the wild populations of Songshan Town and Changbai Mountain, with no genetic contribution from the wild populations of Huangsongdian Town and Manjiang Town. Principal component analysis (PCA) validated the geographical clustering of strains (the first three principal components explained 6.81%, 3.35%, and 3.31% of the genetic variation, respectively) and simultaneously revealed that artificial selection had led to abnormal genomic genetic characteristics in the cultivated strains. This study provides crucial genomic data support for the precise conservation and targeted genetic improvement of H. erinaceus germplasm resources. By deciphering genetic patterns, it aids in broadening the genetic basis of cultivated populations and promotes sustainable industrial development.
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| 科 Family | 属数 Number of genus | 种数 Number of species | 占总种数比例 Percentage of total species (%) | 属 Genus | 种数 Number of species | 占总种数比例 Percentage of total species (%) |
|---|---|---|---|---|---|---|
| 鹅膏菌科Amanitaceae | 2 | 11 | 5.26 | 鹅膏菌属 Amanita | 10 | 4.78 |
| 小菇科 Mycenaceae | 2 | 12 | 5.74 | 丝盖伞属 Inocybe | 5 | 2.39 |
| 多孔菌科 Polyporaceae | 8 | 14 | 6.70 | 蜡蘑属 Laccaria | 5 | 2.39 |
| 红菇科 Russulaceae | 3 | 23 | 11.00 | 小皮伞属 Marasmius | 6 | 2.87 |
| 小菇属 Mycena | 11 | 5.26 | ||||
| 光柄菇属 Pluteus | 5 | 2.39 | ||||
| 红菇属 Russula | 17 | 8.13 | ||||
| 栓菌属 Trametes | 5 | 2.39 |
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