Genetic diversity in Sclerotinia sclerotiorum assessed with SRAP markers

doi:10.3724/SP.J.1003.2010.509

Abstract

Abstract:

Assessing the genetic diversity of Sclerotinia sclerotiorum isolates from different eco-geographi- cal regions and host plants is crucially important for understanding the evolution of this fungal pathogen and its control. We detected DNA polymorphism of 76 S. sclerotiorum isolates from different regions and host plants using sequence-related amplified polymorphism (SRAP) markers. A total of 260 scorable fragments were identified with seven SRAP primer combinations; among them 114 were polymorphic loci (43.85%). UPMGA (Unweighted Pair Group Method with Arithmetic Mean) indicated that the dendrogram consisted of four groups, which included 54, 18, 2, and 2 isolates, respectively, when the genetic similarity coefficient was 0.64. Little genetic difference was identified among the isolates from different host species by cluster and principal component analyses. AMOVA (Analysis of Molecular Variance) revealed that the percentage of variation among populations differed by geographical region (24.8%, P<0.001) and by ecological region (18.8%, P<0.001), but variation among populations of different host plants was not different than expected at random (2.4%, P = 0.8673). One of our most significant results was that S. sclerotiorum isolates on rapeseed plants from winter and spring ecological regions can be divided into two clusters, and that genetic diversity in isolates of spring rapeseed ecological regions was higher than that of winter rapeseed ecological regions.

Key words: Sclerotinia sclerotiorum, rape, SRAP markers, genetic variation, genetic differentiation

Biyun Chen, Qiong Hu, Christina Dixelius, Guoqing Li, Xiaoming Wu. Genetic diversity in Sclerotinia sclerotiorum assessed with SRAP markers[J]. Biodiv Sci, 2010, 18(5): 509-515.

Add to citation manager EndNote|Ris|BibTeX

URL: https://www.biodiversity-science.net/EN/10.3724/SP.J.1003.2010.509

https://www.biodiversity-science.net/EN/Y2010/V18/I5/509

Figures/Tables 7

References 19

[1]	Botstein D, White RL, Skolnick M, Davis RW (1980) Construction of a genetic linkage map in man using restriction fragment length polymorphisms. The American Journal of Human Genetics, 32, 314-331. URL PMID
[2]	Chen BY (陈碧云), Wu XM (伍晓明) , Lu GY (陆光远), Gao GZ (高桂珍), Xu K (许鲲), Li XZ (李响枝) (2006) Molecular mapping of the gene(s) controlling petal-loss trait in Brassica napus L. Hereditas (Beijing) (遗传), 28, 707-712. (in Chinese with English abstract)
[3]	Dong YC (董玉琛), Cao YS (曹永生), Zhang XY (张学勇), Liu SC (刘三才), Wang LF (王兰芬), You GX (游光霞), Pang BS (庞斌双), Li LH (李立会), Jia JZ (贾继增) (2003) Establishment of candidate core collections in Chinese common wheat germplasm. Journal of Plant Genetic Resources (植物遗传资源学报), 4, 1-8. (in Chinese with English abstract)
[4]	Excoffier L, Smouse PE, Quattro JM (1992) Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics, 131, 179-191.
[5]	Felsenstein J (1993) PHYLIP (Phylogeny Inference Package), Version 3.6. Department of Genetics, University of Washington, Seattle, USA.
[6]	Fu HT (傅洪拓), Qiao H (乔慧), Yao JH (姚建华), Gong YS (龚永生), Wu Y (吴滟), Jiang SF (蒋速飞), Xiong YW (熊贻伟) (2010) Genetic diversity in five Macrobrachium hainanense populations using SRAP markers. Biodiversity Science (生物多样性), 18, 145-149. (in Chinese with English abstract)
[7]	Li G, Quiros CF (2001) Sequence-related amplified polymorphism (SRAP), a new marker system based on a simple PCR reaction: its application to mapping and gene tagging in Brassica. Theoretical and Applied Genetics, 103, 455-461.
[8]	Li GQ (李国庆) (1996) Study on Diversity of Crop Sclerotinia Disease Pathogeny: Sclerotinia sclerotiorum (作物菌核病病原——核盘菌的多样性研究). PhD dissertation, Huazhong Agricultural University, Wuhan. (in Chinese with English abstract)
[9]	Li GQ (李国庆), Wang DB (王道本), Zhou Q (周启), Huang HZ (黄鸿章) (1997) Study on diversity of Sclerotinia sclerotiorum in sclerotial germinations. Journal of Plant Protection (植物保护学报), 24, 59-64. (in Chinese with English abstract)
[10]	Li GQ (李国庆), Wang DB (王道本), Jiang DH (姜道宏), Huang HZ (黄鸿章), Erickson RS, Yi XH (易先宏), Zhou Q (周启) (2000) RAPD assay of strains of Sclerotinia sclerotiorum and its related species. Acta Phytopathologica Sinica (植物病理学报), 30, 166-170. (in Chinese with English abstract)
[11]	Li J (李佳), Shen BZ (沈斌章), Han JX (韩继祥), Gan L (甘莉) (1994) An effective procedure for extracting total DNA in rape. Journal of Huazhong Agricultural University (华中农业大学学报), 13, 521-523. (in Chinese with English abstract)
[12]	Li LL (李丽丽) (1994) Advances in study of the world rape disease. Chinese Journal of Oil Crop Sciences (中国油料), 16, 79-81. (in Chinese with English abstract)
[13]	Liu XH (刘晓红), Zhou H (周航), Ji HL (姬红丽), Peng LN (彭丽年), Wen CJ (文成敬), Peng YL (彭云良) (2004) Primary studies on population structure of Sclerotinia sclerotiorum on vegetables in Sichuan Province. Southwest China Journal of Agricultural Sciences (西南农业学报), 17, 618-623. (in Chinese with English abstract)
[14]	Lu GY (陆光远), Yang GS (杨光圣), Fu TD (傅廷栋) (2003) An effective SSR detection system in rapeseed. Chinese Journal of Oil Crop Sciences (中国油料作物学报), 25, 79-81. (in Chinese with English abstract)
[15]	Nei M, Li WH (1979) Mathematical model for studying genetic variation in terms of restriction endonucleases. Proceedings of the National Academy of Sciences, USA, 76, 569-573.
[16]	Rolhf FJ (1997) NTSYSpc Version 2.1. Numerical Taxonomy and Multivariate Analysis System. Exeter Software, Setauket, New York.
[17]	Sexton AC, Howlett BJ (2004) Microsatellite markers reveal genetic differentiation among populations of Sclerotinia sclerotiorum from Australian canola fields. Current Genetics, 46, 357-365.
[18]	Sun JM, Witold I, Malgorzata J, Han FX (2005) Analysis of the genetic structure of Sclerotinia sclerotiorum (Lib.) de Bary populations from different regions and host plants by random amplified polymorphic DNA markers. Journal of Integrative Plant Biology, 47, 385-395.
[19]	Wen YC (文雁成), Wang HZ (王汉中), Shen JX (沈金雄), Liu GH (刘贵华), Zhang SF (张书芬) (2006) Analysis of genetic diversity and genetic basis of Chinese rapeseed cultivars (Brassica napus L.) by sequence-related amplified polymorphism markers. Scientia Agricultura Sinica (中国农业科学), 39, 246-256. (in Chinese with English abstract)

编号 No.	菌株名称 Isolate	寄主 Host		来源 Origin	编号 No.		菌株名称 Isolate		寄主 Host	来源 Origin
1	RSC-1	油菜 Rape		陕西勉县 Mianxian, Shaanxi	31		F5-219-S2 clone 39		大豆 Soybean	加拿大 Canada
2	RSC-2	油菜 Rape		陕西咸阳 Xianyang, Shaanxi	32		F5-138-L4 clone 321		大豆 Soybean	加拿大 Canada
3	RSC-3	油菜 Rape		陕西大荔 Dali, Shaanxi	33		LMK211 clone 2		油菜 Rape	加拿大 Canada
4	RSC-4	油菜 Rape		湖北武汉 Wuhan, Hubei	34		CW312 clone 1		大豆 Soybean	加拿大 Canada
5	RSC-5	油菜 Rape		湖北武汉 Wuhan, Hubei	35		CW317 clone 2		大豆 Soybean	加拿大 Canada
6	RSC-6	油菜 Rape		湖北武汉 Wuhan, Hubei	36		SC-13 Sweden		油菜 Rape	瑞典 Sweden
7	RSC-7	油菜 Rape		湖北襄樊 Xiangfan, Hubei	37		IC16		油菜 Rape	挪威 Norway
8	RSC-8	油菜 Rape		河南确山 Queshan, Henan	38		IC6		油菜 Rape	挪威 Norway
9	RSC-9	油菜 Rape		湖南汉寿 Hanshou, Hunan	39		824 clone 1		油菜 Rape	加拿大 Canada
10	RSC-10	油菜 Rape		河南遂平 Suiping, Henan	40		Xbz-4		小白菜 Pakchoi	湖北罗田 Luotian, Hubei
11	RSC-11	油菜 Rape		河南信阳 Xinyang, Henan	41		Xbz-5		小白菜 Pakchoi	湖北十堰 Shiyan, Hubei
12	RSC-12	油菜 Rape		河南郑州 Zhengzhou, Henan	42		Xbz-9		小白菜 Pakchoi	湖北洪湖 Honghu, Hubei
13	RSC-13	油菜 Rape		河南郑州 Zhengzhou, Henan	43		Sb-2		大豆 Soybean	黑龙江 Heilongjiang
14	RSC-14	油菜 Rape		江西宜春 Yichun, Jiangxi	44		Sb-4		大豆 Soybean	美国 USA
15	RSC-15	油菜 Rape		浙江杭州 Hangzhou, Zhejiang	45		Sb-6		大豆 Soybean	加拿大 Canada
16	RSC-16	油菜 Rape		浙江杭州 Hangzhou, Zhejiang	46		Cor-3		芫荽 Coriander	湖北神农架 Shennongjia, Hubei
17	RSC-17	油菜 Rape		贵州思南 Sinan, Guizhou	47		Cor-6		芫荽 Coriander	湖北通城 Tongcheng, Hubei
18	RSC-18	油菜 Rape		湖北罗田 Luotian, Hubei	48		Brb-1		蚕豆 Horsebean	湖北武汉 Wuhan, Hubei
19	RSC-19	油菜 Rape		湖北英山 Yingshan, Hubei	49		Brb-9		蚕豆 Horsebean	湖北通城 Tongcheng, Hubei
20	RSC-20	油菜 Rape		江苏南京 Nanjing, Jiangsu	50		Rap-1		油菜 Rape	湖北云梦 Yunmeng, Hubei
21	RSC-21	油菜 Rape		江苏南京 Nanjing, Jiangsu	51		Rap-2		油菜 Rape	湖北沙市 Shashi, Hubei
22	RSC-22	油菜 Rape		江西南昌 Nanchang, Jiangxi	52		Rap-6		油菜 Rape	四川雅安 Yaan, Sichuan
23	RSC-23	油菜 Rape		四川绵阳 Mianyang, Sichuan	53		Rap-20		油菜 Rape	湖北罗田 Luotian, Hubei
24	RSC-24	油菜 Rape		陕西杨凌 Yangling, Shaanxi	54		Rap-21		油菜 Rape	湖北宣恩 Xuanen, Hubei
25	RSC-25	油菜 Rape		湖北武汉 Wuhan, Hubei	55		Rap-31		油菜 Rape	湖北宜昌 Yichang, Hubei
26	RSC-26	油菜 Rape		黑龙江佳木斯 Jiamusi, Heilongjiang	56		Rap-35		油菜 Rape	湖北五峰 Wufeng, Hubei
27	RSC-27	油菜 Rape		青海西宁 Xining, Qinghai	57		Rap-36		油菜 Rape	英国 Britain
28	RSC-28	油菜 Rape		青海西宁 Xining, Qinghai	58		Rap-37		油菜 Rape	加拿大 Canada
29	RSC-29	油菜 Rape		青海西宁 Xining, Qinghai	59		Hzd-3		小白菜 Pakchoi	湖北仙桃 Xiantao, Hubei
30	RSC-30	油菜 Rape		青海西宁 Xining, Qinghai	60		Hzd-4		小白菜 Pakchoi	湖北黄梅 Huangmei, Hubei
编号 No.	菌株名称 Isolate	寄主 Host	来源 Origin			编号 No.		菌株名称 Isolate	寄主 Host	来源 Origin
61	Nic-1	烟草 Tobacco	湖北咸丰 Xianfeng, Hubei			69		Let-46	莴苣 Lettuce	湖北神农架 Shennongjia, Hubei
62	Zxd-1	红豆 Red bean	内蒙古扎兰屯 Zalanten, Inner Monglia			70		Brb-8	蚕豆 Horsebean	湖北通山 Tongshan, Hubei
63	Rad-1	萝卜 Radish	湖北竹山 Zhushan, Hubei			71		Let-9	莴苣 Lettuce	湖北五峰 Wufeng, Hubei
64	clone-22	油菜 Rape	加拿大 Canada			72		Let-3	莴苣 Lettuce	湖北武汉 Wuhan, Hubei
65	UK-2	不清 Unknown	湖北武汉 Wuhan, Hubei			73		Let-27	莴苣 Lettuce	台湾 Taiwan
66	Can02-6	油菜 Rape	湖北武汉 Wuhan, Hubei			74		Let-11	莴苣 Lettuce	湖北宜昌 Yichang, Hubei
67	Cor-10	芫荽 Coriander	湖北宜昌 Yichang, Hubei			75		Can02-22	油菜 Rape	湖北武汉 Wuhan, Hubei
68	Rad-30-2	萝卜 Radish	湖北神农架 Shennongjia, Hubei			76		Let-26	莴苣 Lettuce	加拿大 Canada

编号 No.	菌株名称 Isolate	寄主 Host		来源 Origin	编号 No.		菌株名称 Isolate		寄主 Host	来源 Origin
1	RSC-1	油菜 Rape		陕西勉县 Mianxian, Shaanxi	31		F5-219-S2 clone 39		大豆 Soybean	加拿大 Canada
2	RSC-2	油菜 Rape		陕西咸阳 Xianyang, Shaanxi	32		F5-138-L4 clone 321		大豆 Soybean	加拿大 Canada
3	RSC-3	油菜 Rape		陕西大荔 Dali, Shaanxi	33		LMK211 clone 2		油菜 Rape	加拿大 Canada
4	RSC-4	油菜 Rape		湖北武汉 Wuhan, Hubei	34		CW312 clone 1		大豆 Soybean	加拿大 Canada
5	RSC-5	油菜 Rape		湖北武汉 Wuhan, Hubei	35		CW317 clone 2		大豆 Soybean	加拿大 Canada
6	RSC-6	油菜 Rape		湖北武汉 Wuhan, Hubei	36		SC-13 Sweden		油菜 Rape	瑞典 Sweden
7	RSC-7	油菜 Rape		湖北襄樊 Xiangfan, Hubei	37		IC16		油菜 Rape	挪威 Norway
8	RSC-8	油菜 Rape		河南确山 Queshan, Henan	38		IC6		油菜 Rape	挪威 Norway
9	RSC-9	油菜 Rape		湖南汉寿 Hanshou, Hunan	39		824 clone 1		油菜 Rape	加拿大 Canada
10	RSC-10	油菜 Rape		河南遂平 Suiping, Henan	40		Xbz-4		小白菜 Pakchoi	湖北罗田 Luotian, Hubei
11	RSC-11	油菜 Rape		河南信阳 Xinyang, Henan	41		Xbz-5		小白菜 Pakchoi	湖北十堰 Shiyan, Hubei
12	RSC-12	油菜 Rape		河南郑州 Zhengzhou, Henan	42		Xbz-9		小白菜 Pakchoi	湖北洪湖 Honghu, Hubei
13	RSC-13	油菜 Rape		河南郑州 Zhengzhou, Henan	43		Sb-2		大豆 Soybean	黑龙江 Heilongjiang
14	RSC-14	油菜 Rape		江西宜春 Yichun, Jiangxi	44		Sb-4		大豆 Soybean	美国 USA
15	RSC-15	油菜 Rape		浙江杭州 Hangzhou, Zhejiang	45		Sb-6		大豆 Soybean	加拿大 Canada
16	RSC-16	油菜 Rape		浙江杭州 Hangzhou, Zhejiang	46		Cor-3		芫荽 Coriander	湖北神农架 Shennongjia, Hubei
17	RSC-17	油菜 Rape		贵州思南 Sinan, Guizhou	47		Cor-6		芫荽 Coriander	湖北通城 Tongcheng, Hubei
18	RSC-18	油菜 Rape		湖北罗田 Luotian, Hubei	48		Brb-1		蚕豆 Horsebean	湖北武汉 Wuhan, Hubei
19	RSC-19	油菜 Rape		湖北英山 Yingshan, Hubei	49		Brb-9		蚕豆 Horsebean	湖北通城 Tongcheng, Hubei
20	RSC-20	油菜 Rape		江苏南京 Nanjing, Jiangsu	50		Rap-1		油菜 Rape	湖北云梦 Yunmeng, Hubei
21	RSC-21	油菜 Rape		江苏南京 Nanjing, Jiangsu	51		Rap-2		油菜 Rape	湖北沙市 Shashi, Hubei
22	RSC-22	油菜 Rape		江西南昌 Nanchang, Jiangxi	52		Rap-6		油菜 Rape	四川雅安 Yaan, Sichuan
23	RSC-23	油菜 Rape		四川绵阳 Mianyang, Sichuan	53		Rap-20		油菜 Rape	湖北罗田 Luotian, Hubei
24	RSC-24	油菜 Rape		陕西杨凌 Yangling, Shaanxi	54		Rap-21		油菜 Rape	湖北宣恩 Xuanen, Hubei
25	RSC-25	油菜 Rape		湖北武汉 Wuhan, Hubei	55		Rap-31		油菜 Rape	湖北宜昌 Yichang, Hubei
26	RSC-26	油菜 Rape		黑龙江佳木斯 Jiamusi, Heilongjiang	56		Rap-35		油菜 Rape	湖北五峰 Wufeng, Hubei
27	RSC-27	油菜 Rape		青海西宁 Xining, Qinghai	57		Rap-36		油菜 Rape	英国 Britain
28	RSC-28	油菜 Rape		青海西宁 Xining, Qinghai	58		Rap-37		油菜 Rape	加拿大 Canada
29	RSC-29	油菜 Rape		青海西宁 Xining, Qinghai	59		Hzd-3		小白菜 Pakchoi	湖北仙桃 Xiantao, Hubei
30	RSC-30	油菜 Rape		青海西宁 Xining, Qinghai	60		Hzd-4		小白菜 Pakchoi	湖北黄梅 Huangmei, Hubei
编号 No.	菌株名称 Isolate	寄主 Host	来源 Origin			编号 No.		菌株名称 Isolate	寄主 Host	来源 Origin
61	Nic-1	烟草 Tobacco	湖北咸丰 Xianfeng, Hubei			69		Let-46	莴苣 Lettuce	湖北神农架 Shennongjia, Hubei
62	Zxd-1	红豆 Red bean	内蒙古扎兰屯 Zalanten, Inner Monglia			70		Brb-8	蚕豆 Horsebean	湖北通山 Tongshan, Hubei
63	Rad-1	萝卜 Radish	湖北竹山 Zhushan, Hubei			71		Let-9	莴苣 Lettuce	湖北五峰 Wufeng, Hubei
64	clone-22	油菜 Rape	加拿大 Canada			72		Let-3	莴苣 Lettuce	湖北武汉 Wuhan, Hubei
65	UK-2	不清 Unknown	湖北武汉 Wuhan, Hubei			73		Let-27	莴苣 Lettuce	台湾 Taiwan
66	Can02-6	油菜 Rape	湖北武汉 Wuhan, Hubei			74		Let-11	莴苣 Lettuce	湖北宜昌 Yichang, Hubei
67	Cor-10	芫荽 Coriander	湖北宜昌 Yichang, Hubei			75		Can02-22	油菜 Rape	湖北武汉 Wuhan, Hubei
68	Rad-30-2	萝卜 Radish	湖北神农架 Shennongjia, Hubei			76		Let-26	莴苣 Lettuce	加拿大 Canada

上游引物 Forward primers		下游引物 Reverse primers
em1	5′-GACTGCGTACGAATTAAT-3′	me1	5′-TGAGTCCAAACCGGATA-3′
em2	5′-GACTGCGTACGAATTTGC-3′	me2	5′-TGAGTCCAAACCGGAGC-3′
em3	5′-GACTGCGTACGAATTGAC-3′	me3	5′-TGAGTCCAAACCGGAAT-3′
em4	5′-GACTGCGTACGAATTTGA-3′	me4	5′-TGAGTCCAAACCGGACC-3′
em5	5′-GACTGCGTACGAATTAAC-3′	me5	5′-TGAGTCCAAACCGGAAG-3′
em6	5′-GACTGCGTACGAATTGCA-3′

上游引物 Forward primers		下游引物 Reverse primers
em1	5′-GACTGCGTACGAATTAAT-3′	me1	5′-TGAGTCCAAACCGGATA-3′
em2	5′-GACTGCGTACGAATTTGC-3′	me2	5′-TGAGTCCAAACCGGAGC-3′
em3	5′-GACTGCGTACGAATTGAC-3′	me3	5′-TGAGTCCAAACCGGAAT-3′
em4	5′-GACTGCGTACGAATTTGA-3′	me4	5′-TGAGTCCAAACCGGACC-3′
em5	5′-GACTGCGTACGAATTAAC-3′	me5	5′-TGAGTCCAAACCGGAAG-3′
em6	5′-GACTGCGTACGAATTGCA-3′

引物组合 Primer combination	位点总数 Total fragments	多态位点数 Number of polymorphic loci	多态位点比例 Percentage of polymorphic loci (%)
em1-me3	43	16	37.21
em2-me2	35	12	34.29
em2-me3	38	14	36.84
em1-me4	51	26	50.98
em6-me5	32	18	56.25
em4-me1	28	15	53.57
em1-me2	33	13	39.39
总计 Total	260	114	43.85
平均 Mean	37.1	16.3	43.85