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Journal of Integrative Agriculture  2021, Vol. 20 Issue (8): 2100-2111    DOI: 10.1016/S2095-3119(20)63487-6
Special Issue: 园艺-分子生物合辑Horticulture — Genetics · Breeding
Horticulture Advanced Online Publication | Current Issue | Archive | Adv Search |
Mapping and predicting a candidate gene for flesh color in watermelon
WANG Chao-nan1, LUAN Fei-shi1, LIU Hong-yu1, Angela R. DAVIS2, ZHANG Qi-an3, DAI Zu-yun4, LIU Shi
1 Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs/Horticulture and Landscape Architecture College, Northeast Agricultural University, Harbin 150030, P.R.China
2 South Central Agricultural Research Laboratory, Agricultural Research Service, U.S. Department of Agriculture, Washington, D.C. 94710, USA
3 Horticulture Institute, Anhui Academy of Agricultural Science, Hefei 230031, P.R.China
4 Anhui Jianghuai Horticulture Technology Co., Ltd., Hefei 230031, P.R.China
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西瓜果肉颜色是由一系列类胡萝卜素类物质决定的一种重要性状。本文通过浅黄色果肉西瓜COS和白色果肉西PI 186490作为亲本配制F2代分离群体进行BSA-seq分析。BSA-seq结果分析发现在西瓜的6号染色体2.45 Mb区间内存在一个与果肉颜色性状形成的相关区段,该区域初步定位在382 kb范围内。然后利用1260株F2代精细定位群体进行精细定位,将定位区间缩短至66.8 kb。该区间内共包含9个候选基因,其中仅有Cla007528(叶绿素酶基因)在双亲中发生差异表达,并存在非同义突变位点。同时基于RNA-seq数据和qRT-PCR验证我们对类胡萝卜素代谢中的关键基因表达模式进行分析发现,叶黄素循环中的三个基因(ClCHYBClNCED-1ClNCED-7)在双亲果实不同成熟阶段发生差异表达。随着类胡萝卜的不断积累,ClPSY1ClPDSClZDSClCHXEClCRTISOClLCYB也表现出显著差异的表达模式。

The color of watermelon flesh is an important trait determined by a series of carotenoids.  Herein, we used Cream of Saskatchewan (pale yellow flesh) and PI 186490 (white flesh) as parental materials for an F2 segregation and initial mapping using the bulked segregant analysis sequencing (BSA-seq) strategy.  The BSA results revealed a flesh color-related QTL  that spans approximately 2.45 Mb on chromosome 6.  This region was preliminarily positioned in a 382-kb segment, and then narrowed down into a 66.8-kb segment with 1 260 F2 individuals.  A total of nine candidate genes were in the fine mapping interval, but only Cla007528 (encoding chlorophyllase) had non-synonymous mutations and was significantly expressed between the parental materials throughout flesh development.  We also checked the expression patterns of the carotenoid metabolic pathway genes based on RNA-seq data and qRT-PCR validation.  Three genes in the xanthophyll cycle (ClCHYB, ClNCED-1 and ClNCED-7) exhibited differential expression patterns between the two parental lines at different flesh color formation stages.  ClPSY1, ClPDS, ClZDS, ClCHXE, ClCRTISO and ClLCYB also exhibited clearly different expression patterns accompanied by carotenoid accumulation.
Keywords:  watermelon        fine mapping        flesh color        QTL        transcriptome  
Received: 08 May 2020   Accepted:
Fund: This work was supported by the National Natural Science Foundation of China (31601775), the Project of China Postdoctoral Science Foundation (2017M611345), the earmarked fund for China Agriculture Research System of MOF and MARA (CARS-25), and the Natural Science Foundation of Heilongjiang Province, China (C2017034).
Corresponding Authors:  Correspondence LIU Shi, E-mail:   
About author:  WANG Chao-nan, E-mail:;

Cite this article: 

WANG Chao-nan, LUAN Fei-shi, LIU Hong-yu, Angela R. DAVIS, ZHANG Qi-an, DAI Zu-yun, LIU Shi. 2021. Mapping and predicting a candidate gene for flesh color in watermelon. Journal of Integrative Agriculture, 20(8): 2100-2111.

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