Integrative analyses revealed the domestication history, genomic targets of breeding and the spatiotemporal expression patterns of fruit traits in Chinese bayberry ( Myrica rubra )

Abstract

he Chinese bayberry (Myrica rubra) is an important fruit crop in southern China with a domestication history longer than 3000 years. It is the only domesticated fruit crop in the family Myricaceae. In this study, we sequenced genomes of more than 200 wild and cultivated individuals and proposed that M. rubra diverged firstly in Northeast Asia before spreading from southwest to southeast China where the primary domestication occurred. Modern varieties like ‘dongkui’ and ‘biqi’ were developed from breeding with stronger selection on fruit traits in Zhejiang and Jiangsu. While genetic polymorphisms for fruit quality traits were identified and shown to be under selection, spatiotemporal expression patterns of candidate genes were also revealed across six developmental stages for nine varieties. Notably, by comparing to the white colored variety ‘shuijing’ we discovered a novel gene expression regulatory mechanism for fruit ripening coloration. It includes an activator (bHLH) and a repressor (IBH1), which form bHLH-IBH1 competitive inhibition mechanism regulating anthocyanin biosynthesis. These new insights into the genetic and regulatory mechanisms of Chinese bayberry will facilitate future fruit crop improvement.