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Journal of Integrative Agriculture
Journal of Integrative Agriculture  2025, Vol. 24 Issue (7): 2589-2600    DOI: 10.1016/j.jia.2024.11.004
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Identification and molecular marker development for peel color gene in melon (Cucumis melo L.)

Jian Ma1*#, Guoliang Yuan1*, Xinyang Xu2, Haijun Zhang1, Yanhong Qiu1, Congcong Li3#, Huijun Zhang4#

1 Key Laboratory of Vegetable Biobreeding/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture and Rural Affairs, Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
2 Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
3 Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
4 School of Life Science, Huaibei Normal University, Huaibei 235000, China
 Highlights 
● The dark green peel trait at maturity of the near-isogenic line NIL-G derived from B8 (Yangjiaocui) and B15 (Yiwohou) was controlled by a single dominant gene.  
● The alternative splicing of the CmAPRR2 gene in B15 caused by the SNP.G614331A variation may be the critical factor leading to the loss of function of this gene and ultimately resulting in changes in melon peel color from dark green to white.
● Based on the SNP.G614331A locus, a KASP marker termed APRR2-G/A was developed and can be utilized for molecular marker-assisted breeding of melon peel colors.
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摘要  
果皮颜色是甜瓜的重要外观品质，会极大地影响着消费者的喜好。本研究中，我们利用灰绿色果皮甜瓜材料B8和白色果皮材料B15构建了一个深绿色果皮近等基因系NIL-G，随后以NIL-G和B15为亲本重新构建了次级F2群体来研究果皮颜色的遗传模式，并进一步采用混池分离群体分析测序方法确定目标基因所在的物理位置。遗传分析表明：甜瓜成熟时的深绿色果皮性状由单显性基因控制。利用混池分离群体测序和分子标记将目的基因所在区间定位到4号染色体顶端263.7 kb区间内，该区间包含已报道的CmAPRR2基因。此外，进一步对NIL-G和B15中的CmAPRR2基因序列分析发现两者存在四个SNP变异，其中SNP.G614331A为G到A的突变，位于第6外显子和第6内含子的交界处，该突变导致B15中CmAPRR2基因转录本发生可变剪接，产生两个翻译提前终止的转录本CmAPRR2-A 和 CmAPRR2-B。我们也基于该SNP变异位点开发了一个KASP标记APRR2-G/A，该标记与构建的F2群体中的果皮颜色表型共分离。另外，NIL-G中CmAPRR2的表达水平在果实各个生长阶段都高于B15。因此，我们推测CmAPRR2可能是控制甜瓜果实颜色的关键目的基因。总之，本研究鉴定到一个CmAPRR2的新等位基因，该等位变异导致甜瓜成熟时形成白色果皮。本研究为进一步研究甜瓜果皮颜色调控机制奠定了理论基础，并将来利用分子标记辅助选择改良甜瓜的果皮颜色提供了技术支撑。


Abstract  


Peel color is an important appearance quality of melons that significantly affects consumer preferences.  In this study, a near-isogenic line NIL-G (dark green peel) was generated from B8 (grey-green peel) and B15 (white peel).  The F2 population constructed by crossing NIL-G and B15 was used to study the inheritance pattern of peel color, and bulked-segregant analysis sequencing (BSA-seq) was employed to identify the interval in which the target gene was located.  Genetic analysis showed that a dominant gene controls the dark green peel trait at maturity.  BSA-seq and molecular markers were used to localize the candidate gene in a 263.7 kb interval of chromosome 4, which contained the CmAPRR2 gene with known functions.  Moreover, allelic sequence analysis revealed four SNP variations of the CmAPRR2 gene in B15, of which SNP.G614331A was located at the junction of the 6th exon and 6th intron.  The G-to-A mutation caused alternative splicing of the transcript of CmAPRR2 in B15, generating two transcripts (CmAPRR2-A and CmAPRR2-B) with premature termination codons.  Furthermore, the Kompetitive Allele Specific PCR (KASP) marker, APRR2-G/A, was developed based on this SNP and shown to co-segregate with the peel color phenotype in the F2 population.  Compared to white-peel B15, the expression level of CmAPRR2 in dark green peel NIL-G was higher at each growth stage.  Therefore, CmAPRR2 may be the key gene controlling the fruit color of melons.  This study identified a novel allelic variant of CmAPRR2 that leads to white peel formation in mature melons.  We also provides a theoretical basis for further research on the gene regulatory mechanism of melon peel colors, which promotes using molecular marker-assisted selection to modify melon peel colors in the future.


Keywords:  melon       BSA-seq        mapping        CmAPRR2        peel color        KASP marker  
Received: 22 February 2024   Online: 04 November 2024   Accepted: 27 September 2024
Fund: 

This work was supported by the Innovation and Development Program of Beijing Vegetable Research Center, China (KYCX202301), the Construction of Cucurbits Collaboration and Innovation Center, China (XTCX202301), the Youth Research Fund of Beijing Academy of Agriculture and Forestry Sciences, China (QNJJ202426), the National Natural Science Foundation of China (U21A20229 and 32102397), the Scientific Research Foundation of the Higher Education Institutions for Distinguished Young Scholars in Anhui Province, China (2022AH020037) and the Key Research and Development Projects of Anhui Province, China (2023z04020019). 

About author:  Jian Ma, E-mail: majian@nercv.org; Guoliang Yuan, E-mail: yuanguoliang@nercv.org #Correspondence Jian Ma, E-mail: majian@nercv.org; Congcong Li, E-mail: licongcong01@caas.cn; Huijun Zhang, E-mail: zhhuijun@126.com * These authors contributed equally to this study.
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Jian Ma, Guoliang Yuan, Xinyang Xu, Haijun Zhang, Yanhong Qiu, Congcong Li, Huijun Zhang. 2025. Identification and molecular marker development for peel color gene in melon (Cucumis melo L.). Journal of Integrative Agriculture, 24(7): 2589-2600.

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