Mining of Regulatory Genes Related to Bolting in Carrot

doi:10.16420/j.issn.0513-353x.2024-0980

Acta Horticulturae Sinica ›› 2025, Vol. 52 ›› Issue (12): 3243-3256.doi: 10.16420/j.issn.0513-353x.2024-0980

• Genetic & Breeding·Germplasm Resources·Molecular Biology • Previous Articles Next Articles

Mining of Regulatory Genes Related to Bolting in Carrot

YAO Xiangcun¹, LIU Xing¹, GUO Caifeng³, ZHAO Zhiwei¹, CHEN Xu¹, ZHUANG Feiyun¹, and OU Chenggang¹^,²^,^*()

¹ State Key Laboratory of Vegetable Biobreeding，Institute of Vegetables and Flowers，Chinese Academy of Agricultural Sciences，Beijing 100081，China
² Chengdu National Agricultural Science and Technology Center，Chengdu 610213，China
³ Fengzhen City Heitutai Town People’s Government，Fengzhen，Inner Mongolia 012111，China

Received:2025-09-26 Revised:2025-10-13 Online:2025-12-25 Published:2025-12-20
Contact: and OU Chenggang

Abstract

Abstract:

Premature bolting seriously affects the commercial value of carrot taproots and production of overwintering and spring cultivation in China. To study regulatory mechanism and identify functional genes related to bolting traits，we compared the transcriptome data of the wild species‘Songzi Wild’with bolting-sensitive and annual habit and the cultivated variety‘Amsterdam Forcing’with bolting-tolerant and biennial habit at three growth stages during bolting. A total of 2 320 differentially expressed genes were detected，which were mainly enriched in cellular processes and metabolic processes of biological processes，and the catalytic and binding activity functions in molecular functions. Finally，32 flowering time genes were identified，which mainly involved in the photoperiod，gibberellin，vernalization pathway and flowering integrator factors. Among them，the expression levels of AP1，AP2，AGL19，TPS1，and four SOC1 genes showed significantly higher differences in all three stages between two species. SOC1s（DCAR_209690，DCAR_209695 and DCAR_414778）were specifically expressed in Ws，which provided a scientific basis to research bolting traits and provided theoretical reference for the selection and breeding of carrot varieties with different bolting habits.

Key words: carrot, bolting, flowering pathway, differentially expressed, SOC1

YAO Xiangcun, LIU Xing, GUO Caifeng, ZHAO Zhiwei, CHEN Xu, ZHUANG Feiyun, and OU Chenggang. Mining of Regulatory Genes Related to Bolting in Carrot[J]. Acta Horticulturae Sinica, 2025, 52(12): 3243-3256.

Figures/Tables 7

References 54

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基因（编号） Gene（ID）	上游引物（5′-3′） Forward primer	下游引物（5′-3′） Reverse primer
AP1（DCAR_313081）	CTACTGAAGAAGGCGAATGG	GGAGTACCGATGTTGACAGA
TPS1（MSTRG.28525）	AGTGGAAGATCAAGGAAGGC	CCCGCATCATTCACCGATAT
AGL19（DCAR_206377）	GAAAAACCGTAGCCGTTGAA	ACTCCCAGGAGCTTTTCTTT
SOC1（DCAR_209690）	CAAGCTCCATGAATTTGCCA	GTTTCATGCTTTAGATGCTGC
SOC1（DCAR_209695）	AGAAGGTTTGGGATCGTGTT	GAAGACCTGCATCTTTCTGG
SOC1（DCAR_414777）	TGCTCTCTTTTGCCTTTCCT	TGACTTCTATATACACACCTTTAGC
SOC1（DCAR_414778）	CTATTGGGAGAAGGTCTGGG	TGCTAGGGTCTTCTCCTTTTC
AP2（DCAR_729588）	GACACACCAAATTATCAAAATCAGT	GCCATGACTTGAGGAGAACT
Tubulin（X16608）	GAATACCAGCAGTACCAAGA	CATTACATATCTTGATGAGCC

基因（编号） Gene（ID）	上游引物（5′-3′） Forward primer	下游引物（5′-3′） Reverse primer
AP1（DCAR_313081）	CTACTGAAGAAGGCGAATGG	GGAGTACCGATGTTGACAGA
TPS1（MSTRG.28525）	AGTGGAAGATCAAGGAAGGC	CCCGCATCATTCACCGATAT
AGL19（DCAR_206377）	GAAAAACCGTAGCCGTTGAA	ACTCCCAGGAGCTTTTCTTT
SOC1（DCAR_209690）	CAAGCTCCATGAATTTGCCA	GTTTCATGCTTTAGATGCTGC
SOC1（DCAR_209695）	AGAAGGTTTGGGATCGTGTT	GAAGACCTGCATCTTTCTGG
SOC1（DCAR_414777）	TGCTCTCTTTTGCCTTTCCT	TGACTTCTATATACACACCTTTAGC
SOC1（DCAR_414778）	CTATTGGGAGAAGGTCTGGG	TGCTAGGGTCTTCTCCTTTTC
AP2（DCAR_729588）	GACACACCAAATTATCAAAATCAGT	GCCATGACTTGAGGAGAACT
Tubulin（X16608）	GAATACCAGCAGTACCAAGA	CATTACATATCTTGATGAGCC

途径 Pathway	基因（编号） Gene （ID）	差异表达时期 Differential expression period	差异表达情况Differential expression
途径 Pathway	基因（编号） Gene （ID）	差异表达时期 Differential expression period	T1	T2	T3
赤霉素途径 Gibberellin pathway	FPF1（DCAR_104965）	T1	下调Down	—	—
	GAI（DCAR_310431）	T1	下调Down	—	—
	GA2ox1（DCAR_520140）	T1	下调Down	—	—
	DCL4（DCAR_522155）	T2	—	上调Up	—
	GA2ox8（DCAR_623631）	T1、T3	下调Down	—	下调Down
	RGA1（DCAR_728880）	T1、T3	下调Down	—	下调Down
光周期途径 Photoperiodism pathway	COL5（DCAR_311184）	T1	下调Down	—	—
	PHYA（DCAR_933742）	T1	上调Up	—	—
	UBP13（DCAR_934132）	T1	上调Up	—	—
	CKB4（DCAR_100522）	T3	—	—	下调Down
	CDF2（DCAR_208082）	T3	—	—	下调Down
	UBP13（DCAR_311381）	T3	—	—	下调Down
	COL2（DCAR_730189）	T3	—	—	下调Down
	PRR73（DCAR_831017）	T3	—	—	下调Down
	ADO3（DCAR_832785）	T3	—	—	上调Up
	CDF2（DCAR_935982）	T3	—	—	下调Down
春化途径 Vernalization pathway	VIL2（DCAR_416202）	T1	下调Down	—	—
	FRL2（DCAR_519007）	T1	上调Up	—	—
	FLC（DCAR_728348）	T1	下调Down	—	—
	AGL19（DCAR_206377）	T1、T2、T3	下调Down	下调Down	下调Down
自主途径	FCA（DCAR_103025）	T3	—	—	下调Down
Autonomous pathway
温敏途径 Ambient temperature pathway	TPL（DCAR_729343）	T1、T3	上调Up	—	上调Up
整合因子 Integrator	SOC1（DCAR_207781）	T3	—	—	上调Up
	SOC1（DCAR_209690）	T1、T2、T3	上调Up	上调Up	上调Up
	SOC1（DCAR_209695）	T1、T2、T3	上调Up	上调Up	上调Up
	SOC1（DCAR_414777）	T1、T2、T3	下调Down	下调Down	下调Down
	SOC1（DCAR_414778）	T1、T2、T3	上调Up	上调Up	上调Up
年龄途径 Aging pathway	JMJ14（MSTRG.31033）	T1	下调Down	—	—
	AP2（DCAR_312348）	T1、T3	下调Down	—	下调Down
	AP1（DCAR_313081）	T1、T2、T3	上调Up	上调Up	上调Up
	AP2（DCAR_729588）	T1、T2、T3	下调Down	下调Down	下调Down
无信息 No pathway information	TPS1（MSTRG.28525）	T1、T2、T3	上调Up	上调Up	上调Up

途径 Pathway	基因（编号） Gene （ID）	差异表达时期 Differential expression period	差异表达情况Differential expression
途径 Pathway	基因（编号） Gene （ID）	差异表达时期 Differential expression period	T1	T2	T3
赤霉素途径 Gibberellin pathway	FPF1（DCAR_104965）	T1	下调Down	—	—
	GAI（DCAR_310431）	T1	下调Down	—	—
	GA2ox1（DCAR_520140）	T1	下调Down	—	—
	DCL4（DCAR_522155）	T2	—	上调Up	—
	GA2ox8（DCAR_623631）	T1、T3	下调Down	—	下调Down
	RGA1（DCAR_728880）	T1、T3	下调Down	—	下调Down
光周期途径 Photoperiodism pathway	COL5（DCAR_311184）	T1	下调Down	—	—
	PHYA（DCAR_933742）	T1	上调Up	—	—
	UBP13（DCAR_934132）	T1	上调Up	—	—
	CKB4（DCAR_100522）	T3	—	—	下调Down
	CDF2（DCAR_208082）	T3	—	—	下调Down
	UBP13（DCAR_311381）	T3	—	—	下调Down
	COL2（DCAR_730189）	T3	—	—	下调Down
	PRR73（DCAR_831017）	T3	—	—	下调Down
	ADO3（DCAR_832785）	T3	—	—	上调Up
	CDF2（DCAR_935982）	T3	—	—	下调Down
春化途径 Vernalization pathway	VIL2（DCAR_416202）	T1	下调Down	—	—
	FRL2（DCAR_519007）	T1	上调Up	—	—
	FLC（DCAR_728348）	T1	下调Down	—	—
	AGL19（DCAR_206377）	T1、T2、T3	下调Down	下调Down	下调Down
自主途径	FCA（DCAR_103025）	T3	—	—	下调Down
Autonomous pathway
温敏途径 Ambient temperature pathway	TPL（DCAR_729343）	T1、T3	上调Up	—	上调Up
整合因子 Integrator	SOC1（DCAR_207781）	T3	—	—	上调Up
	SOC1（DCAR_209690）	T1、T2、T3	上调Up	上调Up	上调Up
	SOC1（DCAR_209695）	T1、T2、T3	上调Up	上调Up	上调Up
	SOC1（DCAR_414777）	T1、T2、T3	下调Down	下调Down	下调Down
	SOC1（DCAR_414778）	T1、T2、T3	上调Up	上调Up	上调Up
年龄途径 Aging pathway	JMJ14（MSTRG.31033）	T1	下调Down	—	—
	AP2（DCAR_312348）	T1、T3	下调Down	—	下调Down
	AP1（DCAR_313081）	T1、T2、T3	上调Up	上调Up	上调Up
	AP2（DCAR_729588）	T1、T2、T3	下调Down	下调Down	下调Down
无信息 No pathway information	TPS1（MSTRG.28525）	T1、T2、T3	上调Up	上调Up	上调Up

Mining of Regulatory Genes Related to Bolting in Carrot

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[1]	HU Yun, WEN Chunhuai, XIONG Xingcheng, YU Benyu, HE Shenghua. A New Cultivar of Low-Temperature Resistant Chinese Cabbage‘Zhuochunbai 1’ [J]. Acta Horticulturae Sinica, 2025, 52(S1): 81-82.
[2]	ZHANG Lei, WANG Qingming, ZHOU Jie, WANG Yue’e, CAI Huaqing, WEI Lijun, LIU Daomin. A New Non-Heading Chinese Cabbage Cultivar‘Wancuibai’ [J]. Acta Horticulturae Sinica, 2025, 52(S1): 89-90.
[3]	WANG Yahui, ZHANG Yuqing, ZHANG Rongrong, LIU Peizhuo, LIANG Yi, ZHOU Jianhua, XIONG Aisheng. Analysis of Promoter Activity and Screening of Interaction Factors of Carrot Lycopene ε-Cyclase Gene DcLCYE [J]. Acta Horticulturae Sinica, 2025, 52(9): 2317-2328.
[4]	YAN Lijuan, OU Chenggang, LIANG Chen, HU Tiankuo, LIU Xing, YANG Jing, LIN Guocang, and ZHUANG Feiyun. Response of Premature Bolting of Carrots Under Different Low Temperature and Day Length [J]. Acta Horticulturae Sinica, 2025, 52(6): 1588-1598.
[5]	ZHANG Meidi, MA Ming, LI Xiaonan, JIANG Mingliang. Research Progress on Bolting Resistance Traits in Chinese Cabbage [J]. Acta Horticulturae Sinica, 2025, 52(5): 1136-1158.
[6]	ZHAO Yulei, LI Shan, LI Chengnan, MA Jinlong, MA Hongyi, YIN Xiao. Proteomics Studies on the Early Stages of Botrytis cinerea Infection in Grapevine Leaves [J]. Acta Horticulturae Sinica, 2025, 52(2): 279-291.
[7]	FAN Amei, JIN Yaxin, HE Longjiao, LI Qi, ZHANG Yanqing, SHAO Qi, SONG Yun, NIU Yanbing, and QIAO Yonggang. Effects of Gibberellin on the Growth and Development of Forsythia suspensa Heterostyly [J]. Acta Horticulturae Sinica, 2025, 52(11): 3016-3030.
[8]	WANG Wen, ZHANG Peng, WANG Zhimin, LIU Genzhong, BAO Zhilong, MA Fangfang. Analysis of Differential Genes in Response to Sucrose Feeding in Disc Florets of Chrysanthemum nankingense [J]. Acta Horticulturae Sinica, 2024, 51(6): 1297-1310.
[9]	ZHANG Hong, WANG Chaonan, FAN Weiqiang, HUANG Zhiyin, LIU Xiaohui, LI Mei, ZHANG Bin. A New Cultivar of Early Mature Miniature Headed Chinese Cabbage‘Jinwawa 560’ [J]. Acta Horticulturae Sinica, 2024, 51(12): 2989-2990.
[10]	LI Renjie , YUAN Lingyun , CHEN Guohu , HOU Jinfeng , HUANG Xingxue , and WANG Chenggang, . [J]. Acta Horticulturae Sinica, 2023, 50(S1): 41-42.
[11]	YU Yangjun, WANG Weihong, SU Tongbing, ZHANG Fenglan, ZHANG Deshuang, ZHAO Xiuyun, YU Shuancang, LI Peirong, XIN Xiaoyun, and WANG Jiao. A New Chinese Cabbage Cultivar‘Jingchun CR3’with Clubroot Resistance and Bolting Tolerance [J]. Acta Horticulturae Sinica, 2022, 49(S2): 87-88.
[12]	JIANG Yueyue, WANG Tiantian, ZHAO Yang, WANG Chenggang, HOU Jinfeng, and YUAN Lingyun. A New Pakchoi Cultivar‘Wanlü 2’ [J]. Acta Horticulturae Sinica, 2022, 49(S1): 71-72.
[13]	WANG Hong, YANG Wangli, LIN Jing, YANG Qingsong, LI Xiaogang, SHENG Baolong, CHANG Youhong. Comparative Metabolic and Transcriptomic Analysis of Ripening Fruit in Pear Cultivars of‘Sucui 1’‘Cuiguan’and‘Huasu’ [J]. Acta Horticulturae Sinica, 2022, 49(3): 493-508.
[14]	XU Hongxia, ZHOU Huifen, LI Xiaoying, JIANG Luhua, CHEN Junwei. Comparative Transcriptome Analysis of Different Developmental Stages of Flowers and Fruits in Loquat Under Low Temperature Stress [J]. Acta Horticulturae Sinica, 2021, 48(9): 1680-1694.
[15]	GAN Caixia, CUI Lei, PANG Wenxing, WANG Aihua, YU Xiaoqing, DENG Xiaohui, SONG Liping, PIAO Zhongyun. QTL Mapping of Bolting and Flowering Traits Based on High Density Genetic Map of Radish [J]. Acta Horticulturae Sinica, 2021, 48(7): 1273-1281.