Recently, the fruit tree developmental biology team of the College of horticulture, Northwest University of agriculture and forestry science and technology published an online publication entitled”the East Asian wild apples, Malus baccata (L.) Borkh and Malus hupehensis (pamp.) Rehder., are additional coContributors to the genes of cultivated European and Chinese variations”. This paper reveals the genetic contribution of wild relatives of East Asian apples to European Apple Rootstocks and Chinese cultivated apples. This study is of great significance for understanding the complex domestication history of perennial fruit trees such as apples, guiding the utilization of apple germplasm resources and breeding practice.
The domestication process of perennial fruit trees is different from that of annual crops. The gene flow between perennial fruit trees and related wild species in the domestication process shapes the significant differences in the evolutionary mode and speed between them. Apple is a landmark species of perennial fruit trees in the world and one of the major fruit crops in the world. Its complex domestication process and the in-depth analysis of the genetic composition and contribution of wild relatives to the cultivated apple genome are of great significance to guide Apple genetic improvement. At present, there are relatively clear studies on the domestication history of European cultivated apples, but the understanding of the domestication history of apple rootstocks and Chinese cultivated apples is very limited.
The team of Professor Zhang Dong from the College of horticulture and the French National Research Center completed the resequencing of 71 individuals in the genus Malus, and integrated the second-generation sequencing data of apples published by predecessors. A total of 168 individuals were analyzed. Among them, there are 7 individuals of native cultivated species in China, 30 individuals of modern apple cultivated species, 25 individuals of Rootstock Varieties, 4 individuals of ornamental varieties, 43 individuals of wild apple (M. sieversii), 18 individuals of wild apple (M. baccata), 11 individuals of forest apple (M. sylvestris), and 30 individuals of other apple species, The contribution of wild apple species in East Asia to rootstocks and apple genomes in Europe and China and the gene flow of wild and cultivated apples were explored by using the method of population genomics.
The analysis of population genetic structure based on SNP data shows that M. baccata and M. hupehensis in East Asia form a single pan population, while European cultivated apples and rootstocks belong to the same gene pool, while Chinese cultivated apples and rootstocks are mixed populations of three wild apple gene pools, and there is gene exchange between each population (Fig. 1). The analysis of approximate Bayesian random forest model based on ancestor tracing theory shows that European wild apple M. sylvestris has gene exchange with European cultivated apple in the process of spreading westward. European Apple Rootstocks and wild apples in East Asia have gene introgression at the same time. The analysis of the data of Chinese cultivated apples and rootstocks found that the evolutionary history of Chinese apples was different from that of European apples. Gene flow was detected between M. baccata in East Asia, M. hupehensis in Hubei and Chinese cultivated apples and rootstocks, indicating that the domestication process of apples involved gene flow from multiple wild relatives of apples from multiple geographical regions (Fig. 2).
Professor Zhang Dong of the College of horticulture is the corresponding author of the paper, and doctoral student Chen Xilong and researcher Amandine cornelle of the French National Research Center are the co first authors. This research work was supported by the national key research and development plan, the”Zhongying young scholars” of the Tang Zhongying foundation and the”double first-class” construction project of the school.