A high-quality Chinese bayberry genome assembly and genome-wide association study highlight the genetic basis of fruit quality

The evergreen Chinese bayberry tree (Myrica rubra or Morella rubra) produces a fruit with a distinctive flavor that yields high value in both nutritional and economic respects. Here, we compiled a high-quality genome assembly for the Chinese bayberry (contig N50 length 25.01 Mb, LTR assembly index 15.89). To explore genomic variation among bayberry plants, we subsequently re-sequenced 173 accessions at an average 36.54-fold coverage depth, which identified 4,469,944 single nucleotide polymorphisms (SNPs). Population structure analyses separated these germplasms into six sub-populations, and gathering germplasms with similar origins revealed a west-to-east trend in cultivated Chinese bayberry domestication. Further phenotyping analyses for 29 fruit quality-related traits were then used to conduct a genome-wide association study that ultimately identified 455 unique SNPs in 215 genes that were significantly associated with 19 traits. Among these loci, the largest proportion were associated with fruit color. A SNP-dense area associated with fruit color was detected on Chr.6:4,660,884-4,880,033 bp, and a novel gene MrChr6G814 encoding an MLP-like protein was identified whose ectopic expression in tobacco leaves facilitated a ten-fold increase in anthocyanin content. Together, these experimental results provide a comprehensive and robust foundation for future efforts to improve bayberry fruit quality and breeding efficiency.