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Multi-omics analyses unveil dual genetic loci governing four distinct watermelon flesh color phenotypes

文献类型： 外文期刊

作者： Li, Na 1 ; Xing, Shilai 3 ; Sun, Gaofei 4 ; Shang, Jianli 1 ; Yao, Jia-Long 1 ; Li, Nannan 1 ; Zhou, Dan 1 ; Wang, Yu 1 ; Lu, Yuan 1 ; Bi, Jinpeng 3 ; Wang, Jiming 1 ; Lu, Hongfeng 3 ; Ma, Shuangwu 1 ;

作者机构： 1.Chinese Acad Agr Sci, Zhengzhou Fruit Res Inst, Natl Key Lab Germplasm Innovat & Utilizat Hort Cro, Zhengzhou 450009, Peoples R China

2.Chinese Acad Agr Sci, Zhongyuan Res Ctr, Xinxiang 453500, Peoples R China

3.Berry Genom Corp, Beijing 100015, Peoples R China

4.Anyang Inst Technol, Sch Comp Sci & Informat Engn, Anyang 455000, Peoples R China

5.New Zealand Inst Plant & Food Res Ltd, Auckland 1025, New Zealand

关键词： Fruit flesh color; Carotenoid biosynthesis; Gene structural variation; Chromoplast development; Marker-assisted breeding; Citrullus lanatus (watermelon)

期刊名称：MOLECULAR HORTICULTURE （ 影响因子：8.1； 五年影响因子：11.0 ）

ISSN： 2730-9401

年卷期： 2025 年 5 卷 1 期

页码：

收录情况： SCI

摘要： Watermelon fruit flesh displays various colors. Although genetic loci underlying these variations are identified, the molecular mechanism remains elusive. Here, we assembled a chromosome-scale reference genome of an elite watermelon and developed integrated genetic maps using single nucleotide polymorphism (SNP) and structural variation markers. Several key genetic varients for fruit shape and flesh color were identified. Two variants associated with flesh color were further studied, including one copy number variant (CNV, a triplicate of 1.2 kb DNA) in the promoter region of REDUCED CHLOROPLAST COVERAGE 2 (ClREC2) and one SNP in Lycopene beta-Cyclase (ClLCYB) coding region. These two variants together explained 99.7% of the flesh color variations in 314 watermelon accessions. The SNP in ClLCYB was the same as previously reported, disrupting ClLCYB function. The CNV could strongly enhance ClREC2 expression, consequently increasing the expression of carotenoid biosynthesis genes, the number of plastoglobules within chromoplasts, and carotenoid level in mature fruit flesh. Finally, we proposed a "two-switch" genetic model by integrating two major causative loci, which can explain the formation of the four main flesh colors in different watermelon accessions. These results provide new insights into the regulation of carotenoid biosynthesis and color formation in plants.

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