Domestication History Of Cultivated Morella Rubra And Genetic Basis Of Related Traits

Morella rubra Lour.is a subtropical evergreen fruit tree belonging to the family Myricaceae of the order Fagaceae.M.rubra is the only domesticated species in Myricaceae and is originated in China.The fruit of M.rubra,or the red bayberry,has various attractive colors,delicate texture,rich taste and high nutritional value.China has a long history of the red bayberry cultivation and consumption,and barbors the richest germplasm resources that nowdays approximate 300 landraces and varieties are cultivated in Southern China.However,the evolutionary history of M.rubra,especially the domestication process has not been clarified and the genetic mechanisms of the selection on domestication related traits,e.g.fruit size and taste,remains unknown.Therefore,we peformed population genetic analyses using RAD-seq（restriction-site associated DNA sequencing）and whole genome resequencing to infer the domestication history of the red bayberry and to further identify candidate genes under artificial selection of domestication.Meanwhile,genome-wide association analyses were carried out based on whole genome genetic polymorphisms and two important agronomic traits.Our main results are as follows:（1）The genetic diversity and genetic structuresBased on RAD-seq sequencing of 78 Morella individuals and whole-genome resequencing of237 Morella individuals,we classified the wild red bayberry populations into three major groups:Yunnan Group,Chinese Taiwan,Korea and Japan Group,and the remaining in mainland China Group according to the combined results of phylogenetic relationship,population genetic structures and the clustering analysis of PCA.Meanwhile the cultivated populations can be divided into four lineages:PL（Fujian）,FH（Jiangsu and Zhejiang）,BQ（Zhejiang）,and DK（Zhejiang）.The genetic diversity of cultivated populations was 30%less than that of the wild populations.（2）The domestication and demographic historyThe demographic history inference based on Fastsimcoal2 showed that the divergence of the three wild bayberry groups took place approximately 24,000～26,000 years ago,which could be driven by climatic cooling during the Last Glacial Maximum.The domestication of the red bayberry occurred about 3,300～5,600 years ago,and the main improvement evennts began from approximately 1,800 years ago and are still going on,which could be caused by artificial cultivation and grafting.The divergence of the two main lineages BQ and DK occurred between 100 and 820years ago.（3）Artificial selection and the genetic mechanism of agronomic traits in the domestication of bayberryIn total,76 genomic regions were identified under selection using genetic diversity ratio（Pi-ratio）and F_ST by comparing the wild and cultived populations,of which 112 genes were blasted to100 homologous genes of Arabidopsis thaliana.The results of GO enrichment show that these genes are mainly related to organic substance metabolic process and primary metabolic process,which may affect the flavor of the fruits.The selective sweep analysis performed in two improved lineages BQ and DK also identified candidate genes related to fruit size and flavor.The genome-wide association analysis also identified candidate genes with similar functions related for fruit size and fruit sweetness.