Pan-Genomes Provide Insights into the Genetic Basis of Domestication

In order to reveal the genetic variation signals of that have occurred during their domestication and to find potential functional gene families, we constructed a monokaryotic pan-genome of representing four cultivated strains and four wild strains. The pan-genome contained 14,089 gene families, of which 67.56% were core gene families and 31.88% were dispensable gene families. We screened substrate utilization-related genes such as the chitinase gene of the glycoside hydrolase (GH) 18 family and a carbohydrate-binding module (CBM)-related gene from the dispensable families of cultivated populations. The genomic difference in the gene between the wild and cultivated genomes was caused by a 33 kb presence/absence variation (PAV). The detection rate of the gene was 93.75% in the cultivated population, significantly higher than that in the wild population (17.39%), indicating that it has been selected in cultivated strains. Principal component analysis (PCA) of the polymorphic markers in fragments near the gene was enriched in cultivated strains, and this was caused by multiple independent instances of artificial selection. We revealed for the first time the genetic basis of the gene in domestication, thereby providing a foundation for elucidating the potential function of the gene in the breeding of .