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Article|30 Jan 2024|OPEN
T2T reference genome assembly and genome-wide association study reveal the genetic basis of Chinese bayberry fruit quality
Shuwen Zhang1 , , Zheping Yu1 , Li Sun1 , Senmiao Liang1 , Fei Xu1 , Sujuan Li1 , Xiliang Zheng1 , Lijv Yan2 , Yinghong Huang3 , , Xingjiang Qi1,4 , Haiying Ren,1
1State Key Laboratory for Managing Biotic and Chemical Threats to Quality and Safety of Agro-products, Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, 298 Desheng Road, Shangcheng District, Hangzhou 310021, Zhejiang, China
2Linhai Specialty and Technology Extension Station, 219 Dongfang Avenue, Linhai 317000, Zhejiang, China
3Jiangsu Taihu Evergreen Fruit Tree Technology Promotion Center, Dongshan Town, Wuzhong District, Suzhou 215107, Jiangsu, China
4Xianghu Laboratory, 168 Gengwen Road, Xiaoshan District, Hangzhou 311231, Zhejiang, China
*Corresponding author. E-mail: hizhangshuwen@163.com,qixj@zaas.ac.cn

Horticulture Research 11,
Article number: uhae033 (2024)
doi: https://doi.org/10.1093/hr/uhae033
Views: 951

Received: 05 Nov 2023
Accepted: 23 Jan 2024
Published online: 30 Jan 2024

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.