Genome-Wide Association Study and Transcriptome Analysis Provide Candidate Genes for Agronomic Traits of Agaricus bisporus

Agaricus bisporus, belonging to the genus Agaricus and the family Agaricaceae, is a popular commercially cultivated mushroom with rich nutritional and medical values. Cultivation of A. bisporus requires superior cultivars. Understanding the differences between wild and cultivated accession at the genetic level is crucial for mining loci and genes associated with cultivation-related traits, informing future breeding directions. Additionally, the identification of loci and genes associated with important agronomic traits (e.g., yield and quality) facilitates mushroom molecular breeding. In this study, we conducted sequencing of 200 strains of A. bisporus and analyzed genomic variations. Population structure and genetic relationships were investigated for 200 strains. Selection signs and genes were also obtained after selection sweep analysis. Thirteen candidate genes in the selective elimination regions had significantly different expression patterns at the fruit body stage. Moreover, six genes were identified for the esterase isozyme type through a combination of GWAS and RNA data. This study provides insight into environmental adaptation at the genetic base, providing valuable genetic resources for button mushroom molecular breeding to improve environmental adaptation, quality, or yield.