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

文献类型： 外文期刊

作者： Zhang, Shuwen 1 ; Yu, Zheping 1 ; Sun, Li 1 ; Liang, Senmiao 1 ; Xu, Fei 1 ; Li, Sujuan 1 ; Zheng, Xiliang 1 ; Yan, Lijv 2 ; Huang, Yinghong 3 ; Qi, Xingjiang 1 ; Ren, Haiying 1 ;

作者机构： 1.Zhejiang Acad Agr Sci, Inst Hort, State Key Lab Managing Biot & Chem Threats Qual &, 298 Desheng Rd, Hangzhou 310021, Zhejiang, Peoples R China

2.Linhai Specialty & Technol Extens Stn, 219 Dongfang Ave, Linhai 317000, Zhejiang, Peoples R China

3.Jiangsu Taihu Evergreen Fruit Tree Technol Promot, Suzhou 215107, Jiangsu, Peoples R China

4.Xianghu Lab, 168 Gengwen Rd, Hangzhou 311231, Zhejiang, Peoples R China

期刊名称：HORTICULTURE RESEARCH （ 影响因子：8.7； 五年影响因子：9.0 ）

ISSN： 2662-6810

年卷期： 2024 年 11 卷 3 期

页码：

收录情况： SCI

摘要： 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.

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