| Lentinula edodes is considered as a medicinal and edible white-rot fungus.It has a wide range of cultivation and is one of the important pillars of edible mushroom industry in China.Lentinual edodes has a small genome size with 41.8M,making its population genetics to be an affordable sequencing project.Recently,with the rapid development of molecular biotechnology,molecular marker-assisted breeding has increasingly become the preferred breeding method for breeders.Genomic-wide association analysis was used to efficiently discover genetic loci associated with agronomic traits,providing more choices and excellent germplasm resources for molecular-assisted breeding.This study mainly measured the traits of fruiting bodies of Lentinula edodes,of which contain cap diameter,stipe length,stipe diameter and single mushroom weight.Only 37 strain fruiting during the plant process.The wild strain L0285 had a larger stem diameter and length than most of the wild type,but the diameter of the cap was not much different.There are also some wild strains that the fruit bodies are extremely dense on the rod,but their caps are thin and small and the stems are fine and short,such as L0259.The strain L0255 has a hemispherical cap,which has a tendency to bend down and a short stipe.In addition to,there are obvious differences in the color of some cap.The color of the cap of strain L0274 is light yellow,whereas the L0026 strain is dark brown.In the process of population structure and evolution analysis,in addition to using the second-generation high-throughput sequencing technology to complete the whole genome sequencing of the 59 strains of Lentinula edodes we collected,we have also collected 61 re-sequencing data of Lentinula.edodes from NCBI database.Based on the re-sequencing data of 120 strains,a genome-wide genetic map of shiitake mushrooms was constructed with 3.66 million sites.On this basis,a detailed analysis of the population structure and the initial exploration of artificial domestication of mushrooms were analysed.We found that the mushroom population can be divided into three subgroups,of which the Group III subgroup has a distinct regionality,both from Yunnan and Sichuan.The Group I,which contains most of the cultivars,is widely distributed.The wild strain contained in Group I may not be wild-type,and may be a marker error caused by human activities spreading the cultivated species to the wild.The results showed a large difference that comparison of nucleotide diversity between two subgroups Group I and Group II,Group I and Group III.The average Fst between two subgroups of Group I and Group II,Group I and Group III is 0.212 and 0.204.Combining the above two results,there are two obvious domestication characteristics of genetic differentiation and nucleotide polymorphism reduction in the population.We speculate that there may be artificial selection in the evolution process of Lentinus edodes.For further analysis,a total of 152 potential artificial selection sites were obtained.With the development of genomics,people gradually realized that the structural variation of the genome was more common than that of the SNP,and had a very important impact on the apparent characteristics of the individual.Therefore,we have performed a preliminary study on the structural variation of the shiitake mushroom.Through structural variation analysis,it was found that 1957 structural variations in the population of Lentinula edodes might be located in the coding region,followed by functional annotation and Pathway enrichment analysis of these coding regions.Of these 1957 genes,the number of genes that are functionally enriched to participate in metabolism is the highest,and that Pathway enriched has accumulated to participate in the cell cycle pathway is the most. |
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