| Lentinula edodes is one of the most important edible fungi,widely distributed in China.Genetic and phenotypic differentiation are evolved among populations during artificial cultivation and environmental adaptation.Weak research basis is still in L.edodes genomics,and the genetic basis of its population differentiation remains to be dissected.In this study,we re-sequenced a L.edodes population to analyze its genetic diversity,population structure and genomic regions under selection.We also investigated eleven phenotypic traits of the L.edodes population.Combining with the phenotypic traits data of our laboratory in 2013and this study,as well as high-density SNP markers,we conducted genome-wide association study for these traits.The main conclusions are as follows:（1）73 wild and cultivated L.edodes strains mainly collected from China were re-sequenced,combined with our previous re-sequencing data of 60 L.edodes strains.We identified a total of 1,602,368 high-quality mutation sites,including 1,593,428 SNP,and8,940 InDel.（2）According to the SNP information,we performed the phylogeny and population structure analysis.Results indicated that the 133 L.edodes strains cluster into three subgroups,two wild subgroups（Wild1 and Wild2）,and a cultivated subgroup（Cultivars）.The strains in Wild1 are mainly from southwestern China,and the strains in Wild2 are mainly from the central and western regions of China.The result of demographic historiy of L.edodes indicated that three subgroups originate independently.Modern L.edodes cultivated strains originated from Japan.The nucleotide diversity（π）values of the Cultivars,Wild1 and Wild2 subgroups were 4.951×10-3,8.181×10-3 and 7.154×10-3,respectively.Analysis of molecular variance showed that the genetic diversity of L.edodes population mainly derives from variations among subgroups（65.2%）,followed by those within individual strains（34.33%）.The population differentiation index between Cultivars and Wild1,between Cultivars and Wild2,between Wild1 and Wild2 were 0.379,0.257 and0.259,respectively,indicating a relatively high differentiation between subgroups.（3）We analyzed the genome regions under selection between Culitvars and Wild1,between Cultivars and Wild2,and between Wild1 and wild2.182,154 and 178 genome regions under selection were respectively identified,containing 455,402 and 485 genes under selection.Genes related to fruiting body development,stress response,and substrate degradation were under selection during the differentiation of L.edodes.（4）Through the cultivation trial of the133 strains,combining with the phenotypic traits data of the same population in 2013,we identified that phenotypes of all the traits differentiated among the three subgroups.Strains in Cultivars subgroup grew fast,fructified early,produced fewest fruit bodies,and had the largest fruit body size,largest single fruit body weight and highest yield.Strains in Wild1 subgroup grew slowly,fructified late,produced more fruit bodies,and had the smallest fruit body size,smallest single fruit body weight,and lowest yield.The phenotypes of Wild2 subgroup were between Wild1 and Wild2 subgroups.（5）A total of 1,799 SNP loci were found significantly associated with 13 agronomic traits using genome-wide association study.In 2013,the SNP loci significantly associated with mycelium growth rate,with precocity-related traits,with fruit body morphological traits and with yield traits were 4,611,214 and 93,respectively.In 2018,the SNP loci significantly associated with precocity-related traits,with fruit body morphological traits and with yield traits were 12,323 and 691,respectively.94 candidate genes were repeatedly detected in two years,and these genes were involved in processes such as stress response,cell adhesion,and substrate degradation.（6）Integrating genes under selection and candidate genes in genome-wide association study,we found a lot of co-localization genes that affected phenotypic differentiation among subgroups,such as thermal adaptation gene Ded1 and HSF-1,light signaling pathway gene velvet factor gene and COP9 signalosome complex gene,substrate degradation gene laccase 7 gene.3 L.edoes subgroups are from areas with significant environmental differences.It can be inferred that adaptive evolution of different subgroups to local temperature and light factors affects fruit body development,and phenotypic differentiation among subgroups of L.edodes. |
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