Molecular Identification and Genetic Variation Analysis of Chilli Veinal Mottle Virus Infecting Taro

doi:10.16420/j.issn.0513-353x.2024-0797

Acta Horticulturae Sinica ›› 2025, Vol. 52 ›› Issue (10): 2787-2798.doi: 10.16420/j.issn.0513-353x.2024-0797

• Plant Protection • Previous Articles Next Articles

Molecular Identification and Genetic Variation Analysis of Chilli Veinal Mottle Virus Infecting Taro

CHEN Yue¹^,²^,³, ZHENG Xue¹, DONG Kun⁴, WU Kuo¹, XIAO Xiangli⁵, LI Yu¹, ZHANG Jie¹^,^**()

¹ Yunnan Province Key Laboratory of Agricultural Biotechnology，Key Lab of the Southwestern Crop Gene Resources and Germplasm Innovation，Ministry of Agriculture and Rural Affairs，Institute of Biotechnology and Germplasm Resources，Yunnan Academy of Agricultural Sciences，Kunming 650205，China
² School of Life Sciences，Yunnan Normal University，Kunming 650500，China
³ Southwest United Graduate School，Kunming 650092，China
⁴ Fuyuan Konjac Institute，Yunnan Academy of Agricultural Sciences，Qujing，Yunnan 655500，China
⁵ School of Biological and Chemical Science，Pu’er University，Pu’er，Yunan 665000，China

Received:2024-11-22 Revised:2025-06-04 Online:2025-10-25 Published:2025-10-28
Contact: ZHANG Jie

Abstract

Abstract:

To clarify the types of viral pathogens infecting taro[Colocasia esculenta（L.）Schott] samples in Yunnan Province，virus testing was conducted on taro samples collected from Fuyuan County，Yunnan Province that exhibited suspected symptoms of viral disease. The research results provide a theoretical basis for virus screening and effective prevention and control of taro plants in the future. PCR and RT-PCR detection of Yunnan taro samples were conducted using universal primers for virus genera such as Begomovirus，Potyvirus，Orthosporovirus and Tobamovirus，as well as specific primers for chilli vein mottle virus. The CP gene sequence of the ChiVMV isolate from Yunnan taro was obtained through cloning and sequencing. By combined the CP genes of other ChiVMV isolates which were published in GenBank，genetic variation and population genetic structure analysis were conducted using bioinformatics software. The ChiVMV CP gene conservation high conservation during the evolutionary process. The identity of nucleotide and amino acid sequences of the CP gene between the Yunnan taro isolate obtained in this study and 29 ChiVMV isolates was 85.13%-99.65% and 90.59%-99.65%，respectively. Phylogenetic analysis and trait association analysis shows that there was a signification between the genetic differentiation of ChiVMV and the geographical origin of its isolates to a certain extent，but not significantly correlated with the species of host plants. Analysis of genetic diversity and population genetic structure indicates that，influenced by geographical factors，all four geographical populations of ChiVMV isolates display high levels of genetic diversity. Genetic drift and gene flow were significant means of genetic variation in ChiVMV populations. This study represents the first report on the natural invasion of ChiVMV into the Araceae plant，taro. The research results enrich the host range and population genetic information of ChiVMV，which is of great significance for monitoring the spread of ChiVMV in China.

Key words: Colocasia esculenta（L.）Schott, chilli veinal mottle virus, CP gene, genetic variation, population genetic structure

CHEN Yue, ZHENG Xue, DONG Kun, WU Kuo, XIAO Xiangli, LI Yu, ZHANG Jie. Molecular Identification and Genetic Variation Analysis of Chilli Veinal Mottle Virus Infecting Taro[J]. Acta Horticulturae Sinica, 2025, 52(10): 2787-2798.

Figures/Tables 11

References 33

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病毒 Viruses	引物 Primers	序列（5′-3′） Sequence	长度/bp Length
Begomovirus	PA	TAATATTACGKGWKGVCCSC	530
	PB	TGGACYTTRCAWJJBCCGCACA	530
	PCRc1	CATATTTACRARWATGCCA	650
	PBL1v2040	CARTGRTCKATCTTCATACA	650
Potyvirus	CIFor	GGI VVI GTI GGI WSI GGI AAR TCI AC	680
Potyvirus	CIRev	ACI CCR TTY TCD ATD ATR TTI GTI GC	680
Orthotospovirus	dTospo-F2	GATCAATCNAARTGGTCDGCWTC	312
Orthotospovirus	dTospo-R2	CATDGCACAAGARTGRTAVACWGA	312
Tobamovirus	TobamodF	TKGAYGGNGTBCCNGGNTGYGG	880
Tobamovirus	TobamodR	TTAGCCTGGAGGATGGGACA	880
ChiVMV	ChiVMV-CP-F	TATCTGAAGGCACTCATTGA	1 030
ChiVMV	ChiVMV-CP-R	GGAACCACACTGAGGAATA	1 030

病毒 Viruses	引物 Primers	序列（5′-3′） Sequence	长度/bp Length
Begomovirus	PA	TAATATTACGKGWKGVCCSC	530
	PB	TGGACYTTRCAWJJBCCGCACA	530
	PCRc1	CATATTTACRARWATGCCA	650
	PBL1v2040	CARTGRTCKATCTTCATACA	650
Potyvirus	CIFor	GGI VVI GTI GGI WSI GGI AAR TCI AC	680
Potyvirus	CIRev	ACI CCR TTY TCD ATD ATR TTI GTI GC	680
Orthotospovirus	dTospo-F2	GATCAATCNAARTGGTCDGCWTC	312
Orthotospovirus	dTospo-R2	CATDGCACAAGARTGRTAVACWGA	312
Tobamovirus	TobamodF	TKGAYGGNGTBCCNGGNTGYGG	880
Tobamovirus	TobamodR	TTAGCCTGGAGGATGGGACA	880
ChiVMV	ChiVMV-CP-F	TATCTGAAGGCACTCATTGA	1 030
ChiVMV	ChiVMV-CP-R	GGAACCACACTGAGGAATA	1 030

分离物 Isolate	来源 Origin	寄主 Host	GenBank登录号 Accession No.	一致性/% Identity
分离物 Isolate	来源 Origin	寄主 Host	GenBank登录号 Accession No.	核苷酸 Nucleotide sequences	氨基酸 Amino acid sequences
74PAV	意大利 Italy	辣椒 Pepper	KX889918	91.52	97.56
AABC2PK	巴基斯坦 Pakistan	辣椒 Pepper	KX236451	89.78	94.43
AH	安徽 Anhui	辣椒 Pepper	PP582383	85.71	90.59
ATIPK	巴基斯坦 Pakistan	辣椒 Pepper	KJ472764	86.41	92.33
CHM19	印度 India	辣椒 Pepper	EF213689	85.13	90.94
Chi Mv Uravakonda	印度 India	辣椒 Pepper	MN508960	85.95	91.29
ChiVMV-LS	四川 Sichuan	烟草 Tobacco	PP871400	89.90	96.52
ChiVMV-PK	巴基斯坦 Pakistan	辣椒 Pepper	MN207122	87.11	91.29
ChiVMV-YuN Yuxi4	云南 Yunnan	龙葵Nightshade	ON838425	89.66	96.52
ChiVMV-YuN Yuxi5	云南 Yunnan	辣椒 Pepper	ON838424	85.71	91.99
D10	印度 India	辣椒 Pepper	EF221615	85.25	91.64
GD	广东 Guangdong	辣椒 Pepper	KU987835	86.30	90.94
GX	广西 Guangxi	辣椒 Pepper	MT782116	86.76	91.99
GZ-tobacco	贵州 Guizhou	烟草 Tobacco	OP378160	89.43	96.17
GZ109	贵州 Guizhou	南瓜 Pumpkin	OR734212	98.61	99.30
GZ111	贵州 Guizhou	鱼腥草Houttuynia cordata	OR734224	98.72	99.30
GZ84	贵州 Guizhou	莴苣 Lettuce	OR727862	89.78	96.17
GZ91	贵州 Guizhou	苋 Amaranth	OR727863	90.59	95.82
LJ	四川 Sichuan	番茄 Tomato	KF738253	98.95	98.61
LNSY-LKC	辽宁 Liaoning	龙葵Nightshade	MG674072	94.19	99.30
MBDS	印度 India	辣椒 Pepper	OR820901	93.96	98.95
Sichuan Luzhou	四川 Sichuan	烟草 Tobacco	MK405594	99.30	99.65
To	印度 India	番茄 Tomato	OR347840	85.37	91.29
Tomato_Thirumalapura	印度 India	番茄 Tomato	MK165662	85.13	90.59
Wenchang	海南 Hainan	辣椒 Pepper	GQ981316	85.71	91.64
YN	云南 Yunnan	辣椒 Pepper	MT974520	91.41	97.21
YN-tobacco	云南 Yunnan	烟草 Tobacco	JX088636	89.66	96.52
Zunyi	贵州 Guizhou	烟草 Tobacco	PQ126526	99.65	99.66
02ChiVMV	云南 Yunnan	人参果 Ginseng fruit	OM829894	94.31	99.30

分离物 Isolate	来源 Origin	寄主 Host	GenBank登录号 Accession No.	一致性/% Identity
分离物 Isolate	来源 Origin	寄主 Host	GenBank登录号 Accession No.	核苷酸 Nucleotide sequences	氨基酸 Amino acid sequences
74PAV	意大利 Italy	辣椒 Pepper	KX889918	91.52	97.56
AABC2PK	巴基斯坦 Pakistan	辣椒 Pepper	KX236451	89.78	94.43
AH	安徽 Anhui	辣椒 Pepper	PP582383	85.71	90.59
ATIPK	巴基斯坦 Pakistan	辣椒 Pepper	KJ472764	86.41	92.33
CHM19	印度 India	辣椒 Pepper	EF213689	85.13	90.94
Chi Mv Uravakonda	印度 India	辣椒 Pepper	MN508960	85.95	91.29
ChiVMV-LS	四川 Sichuan	烟草 Tobacco	PP871400	89.90	96.52
ChiVMV-PK	巴基斯坦 Pakistan	辣椒 Pepper	MN207122	87.11	91.29
ChiVMV-YuN Yuxi4	云南 Yunnan	龙葵Nightshade	ON838425	89.66	96.52
ChiVMV-YuN Yuxi5	云南 Yunnan	辣椒 Pepper	ON838424	85.71	91.99
D10	印度 India	辣椒 Pepper	EF221615	85.25	91.64
GD	广东 Guangdong	辣椒 Pepper	KU987835	86.30	90.94
GX	广西 Guangxi	辣椒 Pepper	MT782116	86.76	91.99
GZ-tobacco	贵州 Guizhou	烟草 Tobacco	OP378160	89.43	96.17
GZ109	贵州 Guizhou	南瓜 Pumpkin	OR734212	98.61	99.30
GZ111	贵州 Guizhou	鱼腥草Houttuynia cordata	OR734224	98.72	99.30
GZ84	贵州 Guizhou	莴苣 Lettuce	OR727862	89.78	96.17
GZ91	贵州 Guizhou	苋 Amaranth	OR727863	90.59	95.82
LJ	四川 Sichuan	番茄 Tomato	KF738253	98.95	98.61
LNSY-LKC	辽宁 Liaoning	龙葵Nightshade	MG674072	94.19	99.30
MBDS	印度 India	辣椒 Pepper	OR820901	93.96	98.95
Sichuan Luzhou	四川 Sichuan	烟草 Tobacco	MK405594	99.30	99.65
To	印度 India	番茄 Tomato	OR347840	85.37	91.29
Tomato_Thirumalapura	印度 India	番茄 Tomato	MK165662	85.13	90.59
Wenchang	海南 Hainan	辣椒 Pepper	GQ981316	85.71	91.64
YN	云南 Yunnan	辣椒 Pepper	MT974520	91.41	97.21
YN-tobacco	云南 Yunnan	烟草 Tobacco	JX088636	89.66	96.52
Zunyi	贵州 Guizhou	烟草 Tobacco	PQ126526	99.65	99.66
02ChiVMV	云南 Yunnan	人参果 Ginseng fruit	OM829894	94.31	99.30

统计 Statistic	BaTS检验 BaTS estimate（95% ^*HPD CIs）	P值 P-value
AI	0.76（0.60，0.88）	0.030
PS	6.00（6.00，6.00）	0.000
MC（中国） MC（China）	7.00（7.00，7.00）	0.030
MC（印度） MC（India）	2.11（2.00，3.00）	0.080
MC（巴基斯坦） MC（Pakistan）	1.00（1.00，1.00）	1.000

Molecular Identification and Genetic Variation Analysis of Chilli Veinal Mottle Virus Infecting Taro

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统计 Statistic	BaTS检验 BaTS estimate（95% ^*HPD CIs）	P值 P-value
AI	1.76（1.51，2.01）	0.070
PS	12.00（12.00，12.00）	0.000
MC（辣椒） MC（Pepper）	4.35（3.00，5.00）	0.060
MC（烟草） MC（Tobacco）	2.23（2.00，3.00）	0.080
MC（番茄） MC（Tomato）	1.00（1.00，1.00）	1.000

群体 Population	序列数 Sequence	Pi 核苷酸多样性 Nucleotide diversity	H_d 单倍型多样性 Haplotype diversity analysis	k 核酸差异数 Average number of nucleotide differences	Eta 突变位点总数 Total number of mutations	S 多态性位点数 Total number of polymorphic sites
中国西南地区种群 Southwest China	15	0.080 ± 0.086	1.000 ± 0.006	68.990	226	203
印度种群 India	6	0.090 ± 0.097	1.000 ± 0.009	77.333	199	186
中国沿海地区种群 Coastal areas of China	5	0.090 ± 0.098	1.000 ± 0.016	77.700	173	166
其他国家种群 Other	4	0.129 ± 0.141	1.000 ± 0.031	110.667	211	198

变异来源 Source of variation	自由度 Degree of freedom	平方和 Sum of squares	变量组分 Variation component	变异百分比/% Percentage of variation
不同种群间Among populations	3	385.267	13.553 Va	26.10
种群内Within populations	26	997.667	38.372 Vb	73.90
总计Total	29	1 382.933	51.925	—

种群 Population	Tajima’s D	P值 P-value	Fu’s F_S	P值 P-value
中国西南地区 Southwest China	0.465	0.735	-1.150	0.197
印度 India	-0.329	0.447	1.567	0.525
中国沿海地区 Coastal areas of China	-0.190	0.544	2.005	0.485
其他 Other	0.260	0.720	2.898	0.571

群体Population	群体Population	K_S	K_ST	K_S，K_ST P-value	Z	Z P-value	S_nn	S_nnP-value	F_ST	N_m
中国西南地区 Southwest China	印度 India	71.374	0.192	0.000^***	76.508	0.000^***	0.857	0.008^**	0.359^**	0.446
	中国沿海地区 Coastal areas of China	71.168	0.164	0.002^**	73.738	0.001^**	0.800	0.055	0.337^***	0.492
	其他 Other	77.765	0.058	0.058	75.601	0.007^**	0.763	0.181	0.188^*	1.083
印度India	中国沿海地区 Coastal areas of China	77.500	0.058	0.128	22.738	0.032^*	0.727	0.032^*	0.102	2.203
印度India	其他 Other	90.667	0.055	0.147	19.533	0.120	0.400	0.687	0.113	1.964
中国沿海地区 Coastal areas of China	其他 Other	92.352	0.050	0.148	16.307	0.200	0.444	0.200	0.096	2.352

[1]	XU Qiang, MA Quanhui, YAN Fenfen, WU Cuiyun, WANG Jiurui, and LIU Mengjun. Genetic Variation and Analysis of Important Traits of Dried Fruits in F₁ Hybrid Jujube [J]. Acta Horticulturae Sinica, 2025, 52(6): 1427-1440.
[2]	JIANG Fengchao, YANG Li, ZHANG Junhuan, ZHANG Meiling, YU Wenjian, SUN Haoyuan. QTL Mapping and Identification of Major Genes Regulating Organic Acid Accumulation in Apricot Fruits [J]. Acta Horticulturae Sinica, 2025, 52(4): 846-856.
[3]	HOU Binghao, GAO Ting, WEI Yuede, GAO Shuilian, CAI Yinbi, CHEN Zhiming, JIN Shan, ZHANG Xingtan, WANG Pengjie, YE Naixing. Studies on Genetic Variation of‘Tieguanyin’Tea Trees Asexual Reproduction Based on High-depth Genome Resequencing [J]. Acta Horticulturae Sinica, 2023, 50(7): 1505-1517.
[4]	CHEN Jianxin, WEI Yuqian, TANG Jie, ZHU Yongjin, MA Huancheng, WU Jianrong. Molecular Detection and Sequence Analysis of ORSV and CymMV in Cultivated Cymbidium goeringii in Dali,Yunnan [J]. Acta Horticulturae Sinica, 2022, 49(3): 655-662.
[5]	XU Guochun, LUO Wenbin, LI Huawei, XU Yongqing, JI Rongchang, ZHANG Hong, QIU Sixin, TANG Hao. Screening for Genetic Variation in Photosynthesis and High Photosynthetic Efficiency Germplasm in Potato [J]. Acta Horticulturae Sinica, 2021, 48(11): 2239-2250.
[6]	GONG Mingxia, WANG Meng, ZHAO Hu, WU Xing, ZHAO Zengjing, HE Zhi, HUANG Jinmei, and WANG Risheng, . Research Progress on Chilli Veinal Mottle Virus Disease [J]. Acta Horticulturae Sinica, 2020, 47(9): 1741-1751.
[7]	YE Dan，LU Zhaowen，SU Jiangshuo，GUAN Zhiyong，FANG Weimin，CHEN Fadi，and ZHANG Fei**. Association Analysis and QTL Mapping for Vase Life of Cut Chrysanthemum [J]. ACTA HORTICULTURAE SINICA, 2020, 47(4): 717-724.
[8]	FU Xiao，SU Jiangshuo，LI Yuanyuan，ZHANG Fei，FANG Weimin，CHEN Sumei，CHEN Fadi，and GUAN Zhiyong*. Genetic Variation and QTL Mapping for Aphid Resistance in an F1 Population of Chrysanthemum [J]. ACTA HORTICULTURAE SINICA, 2019, 46(7): 1351-1358.
[9]	JIANG Xibing1，ZHANG Pingsheng1，YANG Long2，WU Qiang2，WU Conglian2，WU Xiaoyun2，GONG Bangchu1,*，and LAI Junsheng2. Genetic Variation of Leaf Phenotypic Traits in F1 Progeny of Interspecific Cross Between Castanea mollissima and C. henryi [J]. ACTA HORTICULTURAE SINICA, 2019, 46(11): 2129-2142.
[10]	DU Xiaoyun1，SONG Laiqing1，ZHAO Lingling1,3，LIU Meiying1，TANG Yan1，SUN Yanxia1，JIANG Zhongwu1,3,，and SHU Huairui1,2,. DNA Methylation in Red Fuji Apple Bud Sports Lines [J]. ACTA HORTICULTURAE SINICA, 2019, 46(1): 107-120.
[11]	MA Jie，XU Tingting，SU Jiangshuo，YANG Xincheng，FANG Weimin，CHEN Fadi，and ZHANG Fei*. Genetic Variation and QTL Mapping for Cold Tolerance of Ray Florets in an F1 Population of Chrysanthemum morifolium [J]. ACTA HORTICULTURAE SINICA, 2018, 45(4): 717-724.
[12]	TANG Yafei1,2，PEI Fan1，YU Lin1，HE Zifu1,2,*，SHE Xiaoman1，LAN Guobing1，and DENG Mingguang1. Molecular Characterization of Chilli veinal mottle virus Infecting Pepper in Guangdong Province [J]. ACTA HORTICULTURAE SINICA, 2018, 45(11): 2209-2216.
[13]	PAN Ya-nan1,2,，HAN Jian1,2,，WU Hai-bo3，JI Yan-ling4，WANG Chun-li5，LIU Fang5，LUO Ming1,2,**，and ZHANG Xiang-lin6. Detection of Viruses Infecting Hami Melon and Their Molecular Identification in Xinjiang [J]. ACTA HORTICULTURAE SINICA, 2016, 43(6): 1107-1116.
[14]	LIU Xi-yan，ZHENG Zheng，DENG Xue-bin，FENG Jing-jing，BAI Jin-rui，SONG Yan，LIU Lei，and LI Jun-ming*. Analysis the Genetic Diversity of Processing Tomato in China [J]. ACTA HORTICULTURAE SINICA, 2016, 43(3): 485-495.
[15]	ZHAO Qin1,*，XIE Da-sen1，HE Xiao-ming1，LI Hua-ping2，YOU Yi3，LUO Shao-bo1，and PENG Qing-wu1. Detection of Zucchini yellow mosaic virus Infecting Wax Gourd in Guangdong Province and Genetic Variation of Its Coat Protein Gene [J]. ACTA HORTICULTURAE SINICA, 2016, 43(1): 151-160.