Li Na, Xing Shilai, Sun Gaofei, Shang Jianli, Yao Jia-Long, Li Nannan, Zhou Dan, Wang Yu, Lu Yuan, Bi Jinpeng, Wang Jiming, Lu Hongfeng, Ma Shuangwu
National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, China.
Zhongyuan Research Center, Chinese Academy of Agricultural Sciences, Xinxiang, 453500, China.
Mol Hortic. 2025 May 14;5(1):46. doi: 10.1186/s43897-025-00166-y.
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 β-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.
西瓜果肉呈现出多种颜色。尽管已经确定了这些颜色变异背后的遗传位点，但其分子机制仍不清楚。在这里，我们组装了一个优良西瓜的染色体级参考基因组，并使用单核苷酸多态性（SNP）和结构变异标记开发了整合遗传图谱。确定了几个与果实形状和果肉颜色相关的关键遗传变异。进一步研究了两个与果肉颜色相关的变异，包括叶绿体覆盖减少2（ClREC2）启动子区域的一个拷贝数变异（CNV，一个1.2 kb DNA的三倍体）和番茄红素β-环化酶（ClLCYB）编码区域的一个SNP。这两个变异共同解释了314份西瓜种质中99.7%的果肉颜色变异。ClLCYB中的SNP与先前报道的相同，破坏了ClLCYB的功能。CNV可以强烈增强ClREC2的表达，从而增加类胡萝卜素生物合成基因的表达、有色体中质体小球的数量以及成熟果肉中类胡萝卜素的水平。最后，我们通过整合两个主要致病位点提出了一个“双开关”遗传模型，该模型可以解释不同西瓜种质中四种主要果肉颜色的形成。这些结果为植物中类胡萝卜素生物合成和颜色形成的调控提供了新的见解。
