The genetic architecture of floral traits in the woody plant Prunus mume

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.

Association between blooming time and climatic adaptation in Prunus mume

“…The genetic diversity of cultivated P. mume was estimated to range from 0.096 to 0.134. Zhang et al resequenced 333 representative P. mume landraces and noted that their genetic diversity was 2.01 × 10 −3 (Zhang et al, ), which is lower than that of our data. The main reason for this difference may be that the accessions Zhang et al used were ornamental P. mume , but our accessions were fruiting P. mume .…”

“…All the variant genes were annotated using BLASTx in the nonredundant protein (NR), Swiss‐Prot, Clusters of Orthologous Groups (COG), Gene Ontology (GO) database, and Kyoto Encyclopedia of Genes and Genomes (KEGG), and these annotations were performed according to the method of previous reports (Conesa & Gotz, ). The following population genetic summary statistics were then calculated for each dataset: nucleotide diversity (π; Tajima, ), heterozygosity (Hetobs), the inbreeding coefficient ( F IS ), and differentiation, as given by F ST (Zhang et al, ). Nucleotide diversity is related to expected heterozygosity and is an overall measure of genetic variation.…”

“…Furthermore, Zhang et al constructed the phylogenetic tree of P. mume cultivars by using related species of Prunus armeniaca and Prunus persica as reference. After resequencing and genome assembly with P. armeniaca and P. persica and in conjunction with the published genomes of P. persica and P. mume , GWAS analysis identified multiple quantitative trait locus regions and found that the MYB108 gene was associated with flower color (Zhang et al, ).…”

The complex evolutionary history of apricots: Species divergence, gene flow and multiple domestication events

“…Domestication events in Eastern and/or Central Asia from local wild populations have been documented in other fruit crops, such as peach ( Prunus persica and Prunus ferganensis ; Verde et al, ), apple ( Malus domestica Borkh. ; Cornille et al, ), walnut ( Juglans regia L. and Juglans sigillata Dode; Zhao et al, ), as well as in ornamental trees, such as P. mume (Zhang et al, ). In the current study, we also identified an additional genetic cluster of cultivated apricots compared to previous studies, that is, the purple cluster corresponding to cultivated apricots from Xinjiang near‐Western Chinese province and Central Asia.…”

“…(Ledbetter, ). In addition to apricot domestication for fruit consumption, wild species from the Armeniaca section have been also cultivated for ornamental purposes, such as P. mume that is currently cultivated all over East Asia (Zhang et al, ). Previous studies have established the phylogeny of species within the Armeniaca section (Rehder, ) and their geographic distribution (Bailey & Hough, ).…”