Abstract
Mei (Prunus mume) is an ornamental woody plant that has been domesticated in East Asia for thousands of years. High diversity in floral traits, along with its recent genome sequence, makes mei an ideal model system for studying the evolution of woody plants. Here, we investigate the genetic architecture of floral traits in mei and its domestication history by sampling and resequencing a total of 351 samples including 348 mei accessions and three other Prunus species at an average sequencing depth of 19.3×. Highly-admixed population structure and introgression from Prunus species are identified in mei accessions. Through a genome-wide association study (GWAS), we identify significant quantitative traits locus (QTLs) and genomic regions where several genes, such as MYB108, are positively associated with petal color, stigma color, calyx color, and bud color. Results from this study shed light on the genetic basis of domestication in flowering plants, particularly woody plants.
Highlights
Mei (Prunus mume) is an ornamental woody plant that has been domesticated in East Asia for thousands of years
Deep sequencing data (~70.1-fold coverage) from eight mei trees from different populations and three other Prunus species were used to establish the pan-genome of P. mume and Prunus genus
Applying the same variation calling method to the sequencing data from the same individual of which the genome had been assembled as ref. 10, we identified 0.28% sites to be homozygous as a different genotype which might be false positive, indicating high accuracy of the variation calling method
Summary
Mei (Prunus mume) is an ornamental woody plant that has been domesticated in East Asia for thousands of years. High diversity in floral traits, along with its recent genome sequence, makes mei an ideal model system for studying the evolution of woody plants. Pennsylvania State University, Hershey, PA 17033, USA These authors contributed : Qixiang Zhang, He Zhang, Lidan Sun, Guangyi Fan. Prunus mume has been domesticated for thousands of years in China because of its favorable ornamental features[1], and its cultivation has further expanded to the entire East Asia. The present study has for the first time elucidated the genetic architecture of floral size, color, and structure, in terms of the number of loci, their genomic distribution and the magnitude and pattern of their effects in a woody plant. By comparing mei with other Prunus species, we can begin to study the evolutionary diversification of the Prunus genome
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