Association Analysis Of Important Agronomic Traits With Markers In Lentinula Edodes Cultivars

Lentinula edodes with abundant nutrition and great taste, is the second largest cultivated edible mushroom inferior to Agaricus bisporus, which plays a significant role in Chinese mushroom industry. Dissecting the genetic architecture of important agronomic traits in L. edodes is the precondition and basis of breeding elite strains. This study aimed at analyzing the genetic architecture of important agronomic traits in L. edodes by association analysis, and detecting the loci or candidate gene controlling mycelia growth rates(MGR), precocity, morphological characteristics of fruiting body and yield-related traits, which would lay the foundation for applying marker-assisted selection in L. edodes breeding program.1. 89 L. edodes cultivars collected from the main production area of China were used as population for association analysis. Through two years’ autumn cultivation experiments in shelf, We determined the MGR, precocity, morphological characteristics of fruiting body and yield-related traits of the tested strains. Results demonstrated that the number of fruit body had the highest variety with the variable coefficient of 102.82%. On the contrary, MGR in the sawdust medium had the least variety with the variable coefficient of 5.15%. Results of correlation analysis indicated that there are significantly simple and partial correlations between pairs of precocity, morphological characteristics of fruiting body and yield-related traits.2. Genetic diversity, population structure, and linkage disequilibrium of the tested strains were evaluated by using 48 SSR and 252 InDel markers. The results showed that a total of 880 alleles were detected in the 89 strains, 82% of which were polymorphic. Each marker has two to seven alleles. Average values of Shannon’s information index(I) and polymorphism information content(PIC) were 0.727 and 0.377, respectively, indicating that the Chinese L. edodes cultivars possess relatively high genetic diversity. Results from population structure displayed that 89 strains were divided into two subgroups(Group A and Group B). GroupA contained twenty-Five strains and GroupB included sixty-four ones. The results of UPGMA clustering and principal coordinates analysis(PCoA) were consistent with those from population structure analysis. There were significant differences between Group A and GroupB in the phenotypes of agronomic traits, including primordium forming period,fruiting bodies precocity, pileus thickness,stipe length,amount of fruiting bodies, fresh yield by T-test. Among the 45000 pairwise comparisons generated by 300 markers, 78.27% of which were in significant linkage disequilibrium(P<0.05).3. The association analysis was performed by mixed linear model(MLM) using twoyears’ phenotypic data. Seventy-seven loci were detected to be significantly associated with precocity, morphological characteristics of fruiting body and yield-related traits. Among the seventy-seven loci, forty-six were identified from the phenotypic data in 2013 and fifty loci from those in 2014. among which 11 marker loci were found to be consistent with previously identified QTLs of L. edodes and 66 were new unreported marker loci. Two locis, S211_ID1 and S469_ID1, were proven to be significantly associated with the weight of single fruiting body from the data in both years, which would be highly reliable and stable loci. In addition, some genes(such as argonaute protein gene, ketopantoate reductase gene, oxalate decarboxylase gene, glycoside hydrolase gene, chitin deacetylase gene, glycosyl transferase gene, beta-1,3-glucanase gene, cytochromes P450 gene, alphaketoglutarate-dependent sulfonate dioxygenase gene, histone deacetylase gene), closely located the traits-associated loci, could participate in the regulation of agronomic characters of L. edodes, which could be used as candidate gene.4. By calculating the allelic variation effect of phenotype and average positive(negative) allele effect in the 77 loci significantly associated with the 13 agronomic traits in L. edodes, we detected 161 excellent allelic variations and their corresponding carrier strains.