Population Genetic Structure of Xanthomonas citri pv. citri in Guangdong Province Based on the STR Locus

doi:10.16420/j.issn.0513-353x.2021-0297

Acta Horticulturae Sinica ›› 2022, Vol. 49 ›› Issue (6): 1233-1246.doi: 10.16420/j.issn.0513-353x.2021-0297

• Research Papers • Previous Articles Next Articles

Population Genetic Structure of Xanthomonas citri pv. citri in Guangdong Province Based on the STR Locus

LI Wenting, LI Cuixiao, LIN Xiaoqing, ZHENG Yongqin, ZHENG Zheng(), DENG Xiaoling()

College of Plant Protection,South China Agricultural University,Guangzhou 510642,China

Received:2021-05-10 Revised:2022-01-24 Online:2022-06-25 Published:2022-07-04
Contact: ZHENG Zheng,DENG Xiaoling E-mail:zzheng@scau.edu.cn;xldeng@scau.edu.cn

Abstract

Abstract:

Citrus canker is one of the most serious diseases in citrus production,which is caused by Xanthomonas citri pv. citri（Xcc）. In order to systematically and comprehensively learn the genetic structure of citrus canker strains in Guangdong Province,six highly variable locus were selected by comparing and analyzing the short tandem repeat loci of the whole genome sequence of eight Chinese strains,and the genetic diversity of 352 strains of 14 varieties from 15 cities（counties）in Guangdong Province was analyzed. The results showed that based on the genetic diversity and genetic distance of Guangdong Province in different parts of the citrus canker strains identified six groups：Ⅰgroup（Chaozhou and Shanwei）,Ⅱ group（Meizhou and Heyuan）,Ⅲ group（Zhaoqing,Guangzhou,Jiangmen,Foshan and Huizhou）,Ⅳ group（Yangjiang,Maoming and Zhanjiang）Ⅴ group（Yunfu）,Ⅵ group（Shaoguan and Qingyuan）. Based on the genetic diversity and genetic distance on the different varieties of citrus canker in Guangdong strains identified five groups：Ⅰgroup（Wogan,Gonggan,Zhushaju,Shatamhju,Chazhigan,Hongjiangcheng and Mashuiju）,Ⅱ group（Qicheng and Ningmeng）,Ⅲ group（Jiaogan,Maogugan and Chuntianju）,Ⅳ group（Shatianyou）. The results can provide a theoretical basis for the epidemic regularity of citrus canker disease in Guangdong province.

Key words: citrus, Xanthomonas citri pv. citri, short tandem repeat, genetic diversity

CLC Number:

S666

LI Wenting, LI Cuixiao, LIN Xiaoqing, ZHENG Yongqin, ZHENG Zheng, DENG Xiaoling. Population Genetic Structure of Xanthomonas citri pv. citri in Guangdong Province Based on the STR Locus[J]. Acta Horticulturae Sinica, 2022, 49(6): 1233-1246.

Figures/Tables 12

References 30

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地理来源 Geographical region	数量 Number	柑橘品种 Citrus varieties
茂名 Maioming	29	橘红,沃柑,贡柑 Juhong,Orah,Gonggan
梅州 Meizhou	28	沙田柚,柠檬,脐橙 Shatian pomelo,Lemon,Sweet organge
江门 Jiangmen	26	茶枝柑,沃柑 Chazhigan,Orah
阳江 Yangjiang	26	马水橘,贡柑 Mashuiju,Gonggan
云浮 Yunfu	26	沃柑,砂糖橘 Orah,Shatangju
湛江 Zhanjiang	25	红江橙,沃柑,茂谷柑 Hongjiangcheng,Orah,Maogugan
肇庆 Zhaoqing	24	砂糖橘,贡柑 Shatangju,Gonggan
惠州 Huizhou	24	砂糖橘,春甜橘,沃柑,沙田柚 Shatangju,Chuntianju,Orah,Shatian pomelo
汕尾 Shanwei	24	贡柑,脐橙 Gonggan,Qicheng
佛山 Foshan	23	脐橙,朱砂橘 Qicheng,Zhushaju
韶关 Shaoguan	21	贡柑,沃柑 Gonggan,Orah
广州 Guangzhou	21	沃柑,贡柑,茂谷柑,砂糖橘 Orah,Gonggan,Maogugan,Shatangju
清远 Qingyuan	20	砂糖橘,沃柑 Shatang,Orah
潮州 Chaozhou	18	沃柑,蕉柑 Orah,Jiaogan
河源 Heyuan	17	贡柑,马水橘,砂糖橘 Gonggan,Mashuiju,Shatangju

地理来源 Geographical region	数量 Number	柑橘品种 Citrus varieties
茂名 Maioming	29	橘红,沃柑,贡柑 Juhong,Orah,Gonggan
梅州 Meizhou	28	沙田柚,柠檬,脐橙 Shatian pomelo,Lemon,Sweet organge
江门 Jiangmen	26	茶枝柑,沃柑 Chazhigan,Orah
阳江 Yangjiang	26	马水橘,贡柑 Mashuiju,Gonggan
云浮 Yunfu	26	沃柑,砂糖橘 Orah,Shatangju
湛江 Zhanjiang	25	红江橙,沃柑,茂谷柑 Hongjiangcheng,Orah,Maogugan
肇庆 Zhaoqing	24	砂糖橘,贡柑 Shatangju,Gonggan
惠州 Huizhou	24	砂糖橘,春甜橘,沃柑,沙田柚 Shatangju,Chuntianju,Orah,Shatian pomelo
汕尾 Shanwei	24	贡柑,脐橙 Gonggan,Qicheng
佛山 Foshan	23	脐橙,朱砂橘 Qicheng,Zhushaju
韶关 Shaoguan	21	贡柑,沃柑 Gonggan,Orah
广州 Guangzhou	21	沃柑,贡柑,茂谷柑,砂糖橘 Orah,Gonggan,Maogugan,Shatangju
清远 Qingyuan	20	砂糖橘,沃柑 Shatang,Orah
潮州 Chaozhou	18	沃柑,蕉柑 Orah,Jiaogan
河源 Heyuan	17	贡柑,马水橘,砂糖橘 Gonggan,Mashuiju,Shatangju

引物名称 Primer name	引物（5′-3′） Sequence	退火温度/℃ Annealing temperature
GT1-F	TTGCCACGGGCCAGGGTCGC	64
GT1-R	GCCCAGATGCTCGATCAAGG
GT2-F	CTGTGGTGTTGCGAAGTCAT	55
GT2-R	GTTCGCTTGCTTGAGACTGA
GT3-F	TCGGCGAGTTCGATCGGGTGCT	60
GT3-R	CTGGCGTGCTGCAGGATGTT
GT4-F	ATCGAAACTGTGCAGGCAAT	55
GT4-R	TGGAACAGCATGAGCAGAAC
GT5-F	GGACATCGTCTCCCAGCAACCG	58
GT5-R	GCCTGCCACGCTTTTCCGATT
GT6-F	GCTCGGCGACTTCTTGATAG	55
GT6-R	AAGGTAAAATCGGGCGACTC

引物名称 Primer name	引物（5′-3′） Sequence	退火温度/℃ Annealing temperature
GT1-F	TTGCCACGGGCCAGGGTCGC	64
GT1-R	GCCCAGATGCTCGATCAAGG
GT2-F	CTGTGGTGTTGCGAAGTCAT	55
GT2-R	GTTCGCTTGCTTGAGACTGA
GT3-F	TCGGCGAGTTCGATCGGGTGCT	60
GT3-R	CTGGCGTGCTGCAGGATGTT
GT4-F	ATCGAAACTGTGCAGGCAAT	55
GT4-R	TGGAACAGCATGAGCAGAAC
GT5-F	GGACATCGTCTCCCAGCAACCG	58
GT5-R	GCCTGCCACGCTTTTCCGATT
GT6-F	GCTCGGCGACTTCTTGATAG	55
GT6-R	AAGGTAAAATCGGGCGACTC

位点名称 Loci Name	位置 Position	长度 Period size	重复数量 Copy number
GT1	241859 ~ 241926	7	9.7
GT2	1065817 ~ 1065895	7	11.3
GT3	1441963 ~ 1442079	7	16.7
GT4	1884560 ~ 1884621	7	8.9
GT5	565742 ~ 565790	7	7
GT6	4367068 ~ 4367102	7	5

Population Genetic Structure of Xanthomonas citri pv. citri in Guangdong Province Based on the STR Locus

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样品来源 Sample origin	样品数量 Sample number	多样性指数 H Nei’s genetic diversity	标准误 St. dev
韶关 Shaoguan	21	0.7989	0.0582
肇庆 Zhaoqing	24	0.7825	0.0933
梅州 Meizhou	27	0.7795	0.0473
江门 Jiangmen	26	0.7766	0.0547
阳江 Yangjiang	26	0.7665	0.0662
云浮 Yunfu	26	0.7593	0.0567
广州 Guangzhou	21	0.7535	0.1677
湛江 Zhanjiang	25	0.7506	0.0438
惠州 Huizhou	24	0.7092	0.1013
茂名 Maoming	29	0.6672	0.1011
河源 Heyuan	18	0.6629	0.0983
佛山 Foshan	23	0.6337	0.1026
清远 Qingyuan	20	0.5957	0.1342
潮州 Chaozhou	18	0.5710	0.2362
汕尾 Shanwei	24	0.4925	0.1854
合计 Total	352	0.7000	0.1031

地理来源 Geographical region	遗传相似性（左上）和遗传距离（右下）Nei’s genetic identity（above diagonal）and genetic distance（below diagonal）
地理来源 Geographical region	潮州 Chaozhou	汕尾 Shanwei	广州 Guangzhou	佛山 Foshan	河源 Heyuan	惠州 Huizhou	江门 Jiangmen	肇庆 Zhaoqing
潮州Chaozhou		0.8748	0.6895	0.6089	0.5849	0.5715	0.5265	0.5229
汕尾Shanwei	0.1337		0.6742	0.6631	0.5351	0.5638	0.6244	0.4674
广州Guangzhou	0.3717	0.3943		0.2793	0.3686	0.7228	0.2328	0.2480
佛山Foshan	0.4962	0.4108	0.7563		0.3796	0.8141	0.1643	0.2785
河源Heyuan	0.5363	0.6252	0.6917	0.6841		0.6195	0.6511	0.6915
惠州 Huizhou	0.5595	0.5731	0.3246	0.2057	0.4789		0.3791	0.2624
江门Jiangmen	0.6415	0.4709	0.7923	0.8485	0.4290	0.6845		0.3002
肇庆Zhaoqing	0.6484	0.7605	0.7804	0.7569	0.3689	0.7692	0.7407
梅州 Meizhou	0.7301	0.7215	0.6483	0.5979	0.7453	0.5789	0.5709	0.6067
清远Qingyuan	0.7925	0.8092	0.5564	0.5464	0.6369	0.6862	0.5366	0.5220
湛江Zhanjiang	0.8030	0.8967	0.3130	0.3334	0.3595	0.4773	0.2414	0.2817
云浮Yunfu	0.8947	0.5997	0.7549	0.3845	0.8932	0.5531	0.4025	0.7441
茂名Maoming	0.9018	1.0651	0.5764	0.5628	0.5187	0.9064	0.5991	0.4877
阳江Yangjiang	1.0114	1.1057	0.5873	0.5456	0.4440	0.7583	0.4630	0.4007
韶关Shaoguan	1.5174	1.4725	0.3136	0.4148	1.0068	0.4163	0.4614	0.3375
地理来源 Geographical region	遗传相似性（左上）和遗传距离（右下）Nei’s genetic identity（above diagonal）and genetic distance（below diagonal）
地理来源 Geographical region	梅州 Meizhou	清远 Qingyuan	湛江 Zhanjiang	云浮 Yunfu	茂名 Maoming	阳江 Yangjiang	韶关 Shaoguan
潮州Chaozhou	0.4819	0.4527	0.4480	0.4087	0.4058	0.3637	0.2193
汕尾Shanwei	0.4860	0.4452	0.4079	0.5490	0.3447	0.3310	0.2293
广州Guangzhou	0.4334	0.5862	0.7312	0.2812	0.5619	0.5558	1.1596
佛山Foshan	0.5143	0.6044	0.7165	0.6808	0.5696	0.5795	0.8800
河源Heyuan	0.2939	0.5289	0.6980	0.4094	0.5953	0.6415	0.3654
惠州 Huizhou	0.5467	0.3767	0.6205	0.5921	0.4040	0.4684	0.8763
江门Jiangmen	0.5605	0.6225	0.7855	0.6686	0.5493	0.6294	0.7734
肇庆Zhaoqing	0.4997	0.6502	0.7545	0.4751	0.6140	0.6699	1.0861
梅州 Meizhou		0.4600	0.6639	0.4230	0.6422	0.5105	0.3876
清远Qingyuan	0.7766		0.4559	0.3526	0.3238	0.2931	0.4094
湛江Zhanjiang	0.4096	0.7854		0.7504	0.1739	0.2695	1.0007
云浮Yunfu	0.8604	1.0423	0.4722		0.3760	0.3472	1.4062
茂名Maoming	0.4428	1.1275	0.8403	0.9781		0.1963	1.0493
阳江Yangjiang	0.6723	1.2273	0.7638	1.0578	0.8217		1.4630
韶关Shaoguan	0.9478	0.6640	0.3676	0.2451	0.3502	0.2315

柑橘品种 Citrus varieties	样品数量 Sample number	多样性指数 H Nei’s genetic diversity	标准误 St. dev
沃柑 Wogan	140	0.7884	0.0567
砂糖橘 Shatangju	10	0.7767	0.0999
脐橙 Qicheng	23	0.7707	0.0584
茶枝柑 Chazhigan	40	0.7669	0.0539
橘红 Juhong	25	0.7656	0.0761
朱砂橘 Zhushaju	13	0.7624	0.0493
春甜橘 Chuntianju	22	0.7513	0.0730
红江橙 Hongjiangcheng	16	0.7440	0.1205
蕉柑 Jiaogan	9	0.7370	0.0520
茂谷柑 Maogugan	21	0.6955	0.0929
贡柑 Gonggan	16	0.6133	0.1204
马水橘 Mashuiju	6	0.6095	0.0888
柠檬 Ningmeng	6	0.5185	0.1477
沙田柚 Shatianyou	5	0.4440	0.1361
合计 Total	352	0.6960	0.0876

柑橘品种 Citrus varieties	遗传相似性（左上）和遗传距离（右下） Nei’s genetic identity（above diagonal）and genetic distance（below diagonal）
柑橘品种 Citrus varieties	沃柑 Wogan	贡柑 Gonggan	砂糖橘 Shatangju	朱砂橘 Zhushaju	茶枝柑 Chazhigan	红江橙 Hongjiangcheng	马水橘 Mashuiju
沃柑 Wogan		0.8995	0.8734	0.8686	0.8109	0.7912	0.7479
贡柑 Gonggan	0.1059		0.2483	0.7721	0.7873	0.3055	0.6970
砂糖橘 Shatangju	0.1354	0.7801		0.8099	0.6818	0.2119	0.7394
朱砂橘 Zhushaju	0.1409	0.2586	0.2109		0.6129	0.3873	0.4127
茶枝柑 Chazhigan	0.2096	0.2392	0.3830	0.4895		0.3135	0.6870
红江橙 Hongjiangcheng	0.2342	0.7367	0.8090	0.6789	0.7309		0.6895
马水橘 Mashuiju	0.2904	0.3609	0.3019	0.6619	0.5031	0.3718
脐橙Qicheng	0.3915	0.4629	0.4680	0.7709	0.6201	0.5974	0.5077
春甜橘 Chuntianju	0.4194	0.4457	0.6764	0.4337	0.8294	0.8799	0.4491
茂谷柑 Maogugan	0.4527	0.4910	0.5379	0.4302	0.8954	0.6263	0.7093
蕉柑 Jiaogan	0.4897	0.5114	0.4224	0.3992	1.0025	0.6673	0.5378
橘红 Juhong	0.5988	0.6003	0.7078	0.5759	0.7029	0.3832	0.9555
柠檬 Lemon	0.8011	0.7167	0.6146	0.5366	0.8371	0.5258	0.7028
沙田柚 Shatianyou	0.9087	0.9306	1.0036	1.1194	1.1683	0.8756	1.1206
柑橘品种 Citrus varieties	遗传相似性（左上）和遗传距离（右下） Nei’s genetic identity（above diagonal）and genetic distance（below diagonal）
柑橘品种 Citrus varieties	脐橙 Qicheng	春甜橘 Chuntianju	茂谷柑 Maogugan	蕉柑 Jiaogan	橘红 Juhong	柠檬 Lemon	沙田柚 Shatianyou
沃柑 Wogan	0.6760	0.6574	0.6359	0.6128	0.5495	0.4489	0.4030
贡柑 Gonggan	0.6294	0.6404	0.6120	0.5997	0.5487	0.4884	0.3943
砂糖橘 Shatangju	0.6263	0.5085	0.5839	0.6555	0.4927	0.5409	0.3666
朱砂橘 Zhushaju	0.2602	0.6481	0.6504	0.6708	0.5622	0.5848	0.3265
茶枝柑 Chazhigan	0.4779	0.4363	0.4084	0.3670	0.4952	0.4330	0.3109
红江橙 Hongjiangcheng	0.5502	0.4148	0.5346	0.5131	0.6817	0.5911	0.4166
马水橘 Mashuiju	0.6778	0.6382	0.4920	0.5840	0.3846	0.4952	0.3261
脐橙Qicheng		0.3900	0.3817	0.3710	0.4154	0.6468	0.3868
春甜橘 Chuntianju	0.9417		0.7339	0.5151	1.0140	0.8044	0.9511
茂谷柑 Maogugan	0.9631	0.4800		0.0623	1.2180	1.6044	1.7646
蕉柑 Jiaogan	0.9914	0.5975	0.9396		1.1878	1.0596	1.7944
橘红 Juhong	0.8786	0.3628	0.2958	0.3049		1.1395	0.9599
柠檬 Lemon	0.4357	0.4474	0.2010	0.3466	0.3200		0.2116
沙田柚 Shatianyou	0.9498	0.3863	0.1712	0.1662	0.3829	1.5529

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