T2T reference genome assembly and genome-wide association study reveal the genetic basis of Chinese bayberry fruit quality

Abstract

Chinese bayberry ( Myrica rubra or Morella rubra ; 2n = 16) produces fruit with a distinctive flavor, high nutritional, and economic value. However, previous versions of the bayberry genome lack sequence continuity. Moreover, to date, no large-scale germplasm resource association analysis has examined the allelic and genetic variations determining fruit quality traits. Therefore, in this study, we assembled a telomere-to-telomere (T2T) gap-free reference genome for the cultivar ‘Zaojia’ using PacBio HiFi long reads. The resulting 292.60 Mb T2T genome, revealed 8 centromeric regions, 15 telomeres, and 28 345 genes. This represents a substantial improvement in the genome continuity and integrity of Chinese bayberry. Subsequently, we re-sequenced 173 accessions, identifying 6 649 674 single nucleotide polymorphisms (SNPs). Further, the phenotypic analyses of 29 fruit quality-related traits enabled a genome-wide association study (GWAS), which identified 1937 SNPs and 1039 genes significantly associated with 28 traits. An SNP cluster pertinent to fruit color was identified on Chr6: 3407532 to 5 153 151 bp region, harboring two MYB genes ( MrChr6G07650 and MrChr6G07660 ), exhibiting differential expression in extreme phenotype transcriptomes, linked to anthocyanin synthesis. An adjacent, closely linked gene, MrChr6G07670 (MLP-like protein), harbored an exonic missense variant and was shown to increase anthocyanin production in tobacco leaves tenfold. This SNP cluster, potentially a quantitative trait locus (QTL), collectively regulates bayberry fruit color. In conclusion, our study presented a complete reference genome, uncovered a suite of allelic variations related to fruit-quality traits, and identified functional genes that could be harnessed to enhance fruit quality and breeding efficiency of bayberries.

Acknowledgements

Financial support for this work was provided by the National Natural Science Foundation of China (No. 32202426), the Special breeding program for new varieties in Zhejiang (2021C02066-2) and the Key R & D in Zhejiang (2023C02031 and 2021C02009) projects. Special thanks to Fan Dai for data analysis.

Author contributions

S.Z., Z.Y., L.S., and S.L. performed the experiments. Z.Y., S.L., X.Z., L.Y., Y.H. and H.R. collected samples. S.Z. and F.X. conducted data analyses. S.Z. and X.Q. writing and editing article.

Data availability

The resequencing and transcriptome data presented in the study are deposited in SRA (http://www.ncbi.nlm.nih.gov/bioproject/936999), and accession number is PRJNA936999; the HiFi and Hi-C data presented in the study are deposited in SRA (http://www.ncbi.nlm.nih.gov/bioproject/937074), and accession number is PRJNA 937074. The genome sequences Zaojia Version 2.0 described in this article were submitted and released to http://cotton.zju.edu.cn/source/Myrica_rubra.zip.

Conflict of interest statement

The authors declare no conflict of interest.

Supplementary Data

Supplementary data is available at Horticulture Research online.

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