Development Core SNP Markers for Tobacco Germplasm Genotyping

doi:10.13560/j.cnki.biotech.bull.1985.2022-0810

Abstract

Abstract:

Based on kompetitive allele specific PCR（KASP）technology platform, the tobacco SNP（single nucleotide polymorphism）markers and corresponding primers were developed and validated，which could assist tobacco germplasm evaluation, genetic diversity analysis, and core germplasm screening. Using Python and Perl tools, 1 179 154 SNPs covering tobacco genome were designed and screened for KASP primers, and their accuracy and applicability were verified by experiment. As results, 217 621 SNPs were enough for designing corresponding KASP primers. Then 1 378 SNPs were selected for experimental validation, and 732 were approved for SNP marker. Further 48 SNP markers, with an average PIC of 0.36 and an average MAF of 0.39, were finally identified as core markers, and they were evenly distributed on 24 chromosomes of the tobacco genome. The various germplasm, especially the genotypes of current major tobacco cultivars could be distinguished by the 48 core SNPs, and the marking is of extremely high reliability.

Key words: tobacco, germplasm, single nucleotide polymorphism, kompetitive allele specific PCR

YU Shi-zhou, CAO Ling-gai, WANG Shi-ze, LIU Yong, BIAN Wen-jie, REN Xue-liang. Development Core SNP Markers for Tobacco Germplasm Genotyping[J]. Biotechnology Bulletin, 2023, 39(3): 89-100.

Figures/Tables 4

References 31

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序号 No.	种质库编号 GenBank number	种质名称 Accession name	调制类型 Curing status	序号 No.	资源库编号 GenBank number	种质名称 Accession name	调制类型 Curing status
1	FD002	独山软杆Dushanruangan	烤烟 Flue-cured	76	XZ018	PX5	烤烟 Flue-cured
2	FD011	福泉团叶摺烟 Fuquan tanyezheyan	烤烟Flue-cured	77	XZ019	PX6	烤烟 Flue-cured
3	FD032	麻将大红花 Majiangdahonghua	烤烟Flue-cured	78	XZ020	PX7	烤烟 Flue-cured
4	FD041	黔江一号Qianjiangyihao	烤烟Flue-cured	79	XZ021	PX8	烤烟 Flue-cured
5	FD047	瓮安中坪烤烟 Wenganzhongpingkaoyan	烤烟 Flue-cured	80	XZ022	PX9	烤烟 Flue-cured
6	FS054	柳叶尖0695 Liuyejian 0695	烤烟 Flue-cured	81	XZ023	PX10	烤烟 Flue-cured
7	FS070	胎里富1011 Tailifu 1011	烤烟 Flue-cured	82	XZ024	PX11	烤烟 Flue-cured
8	FS071	歪把子Waibazi	烤烟 Flue-cured	83	XZ025	PX12	烤烟 Flue-cured
9	FY064	哲伍毛烟Zhewumaoyan	烤烟 Flue-cured	84	XZ026	PX13	烤烟 Flue-cured
10	FY061	片片黄Pianpianhuang	烤烟 Flue-cured	85	XZ027	PX14	烤烟 Flue-cured
11	FG015	Coker86	烤烟 Flue-cured	86	XZ028	PX15	烤烟 Flue-cured
12	FG018	Dixie Bright 101	烤烟 Flue-cured	87	XZ029	PX17	烤烟 Flue-cured
13	FG024	Hicks	烤烟 Flue-cured	88	XZ030	PX19	烤烟 Flue-cured
14	FG027	K149	烤烟 Flue-cured	89	SG003	安龙护耳大柳叶 Anlonghuerdaliuye	晒烟 Sun-cured
15	FG029	K346	烤烟 Flue-cured	90	SG009	安顺二吊枝 Anshunerdiaozhi	晒烟 Sun-cured
16	FG028	K326	烤烟 Flue-cured	91	SG048	大方大红花 Dafangdahonghua	晒烟 Sun-cured
17	FG047	NC567	烤烟 Flue-cured	92	SG052	大柳叶节骨密 Daliuyegumi	晒烟 Sun-cured
18	FG049	NC729	烤烟 Flue-cured	93	SG069	德江中花烟（2） Dejiangzhonghuayan（2）	晒烟 Sun-cured
19	FG052	NC82	烤烟 Flue-cured	94	SG079	光柄柳叶（罗） Guangbingliuye（luo）	晒烟 Sun-cured
20	FG053	NC89	烤烟 Flue-cured	95	SG080	光柄柳叶（木） Guangbingliuye（mu）	晒烟 Sun-cured
21	FG054	NC95	烤烟 Flue-cured	96	SG094	花溪大青杆 Huaxidaqinggan	晒烟 Sun-cured
22	FG061	牛津26 Oxford 26	烤烟 Flue-cured	97	SG102	惠水三都大白花 Huishuisandudabaihua	晒烟 Sun-cured
23	FG077	RG11	烤烟 Flue-cured	98	SG112	凯里枇杷烟 Kailipipayan	晒烟 Sun-cured
24	FG079	RG17	烤烟 Flue-cured	99	SG134	马耳烟Maeryan	晒烟 Sun-cured
25	FG080	RG8	烤烟 Flue-cured	100	SG156	盘县大柳叶Panxiandaliuye	晒烟 Sun-cured
26	FG089	Special 400	烤烟 Flue-cured	101	SG169	平塘中坝晒烟 Pingtangzhongbashaiyan	晒烟 Sun-cured
27	FG090	Special 401	烤烟 Flue-cured	102	SG170	普安寸骨烟 Puancunguyan	晒烟 Sun-cured
28	FG094	SpeightG-164	烤烟 Flue-cured	103	SG178	黔西红花吊把 Qianxihonghuadiaoba	晒烟 Sun-cured
29	FG095	Speight G-28	烤烟 Flue-cured	104	SG248	贞丰柳叶烟 Zhenfengliuyeyan	晒烟 Sun-cured
30	FG099	Speight G-80	烤烟 Flue-cured	105	SG258	镇远莲花烟（周） Zhenyuanlianhuayan（zhou）	晒烟 Sun-cured
31	FG100	SPTG-172	烤烟 Flue-cured	106	SS006	81—26	晒烟 Sun-cured
32	FG105	Ti448A	烤烟 Flue-cured	107	SS012	Va309	晒烟 Sun-cured
33	FG118	Vesta 47	烤烟 Flue-cured	108	SS021	矮株一号Aizhuyihao	晒烟 Sun-cured
34	FG120	佛光Foguang	烤烟 Flue-cured	109	SS027	把柄烟Babingyan	晒烟 Sun-cured
35	FG122	Yellow mammoth	烤烟 Flue-cured	110	SS045	大瓦垅Dawalong	晒烟 Sun-cured
36	FG071	PVH06	烤烟 Flue-cured	111	SS053	风林一号Fenglinyihao	晒烟 Sun-cured
37	XZ001	CV87	烤烟 Flue-cured	112	SS066	贺县公会晒烟 Hexiangonghuishaiyan	晒烟 Sun-cured
38	XZ002	Cash	烤烟 Flue-cured	113	SS075	护脖香1368 Huboxiang 1368	晒烟 Sun-cured
39	XZ003	Coker139	烤烟 Flue-cured	114	SS087	老山烟Laoshanyan	晒烟 Sun-cured
40	XZ004	Gold doller	烤烟 Flue-cured	115	SS091	马里村晒烟（二） Malicunshaiyan（2）	晒烟 Sun-cured
41	XZ005	Mcnair 30	烤烟 Flue-cured	116	SS097	勐板晒烟 Mengbanshaiyan	晒烟 Sun-cured
42	XZ006	Orinoco	烤烟 Flue-cured	117	SS113	千层塔Qiancengta	晒烟 Sun-cured
43	XZ007	Mammoth gold	烤烟 Flue-cured	118	SS132	腾冲大柳叶 Tengchongdaliuye	晒烟 Sun-cured
44	XZ008	Golden wilf	烤烟 Flue-cured	119	SS142	小叶尖Xiaoyejian	晒烟 Sun-cured
45	XZ009	CV91	烤烟 Flue-cured	120	SS146	一朵花Yiduohua	晒烟 Sun-cured
46	XZ010	云烟315Yunyan 315	烤烟 Flue-cured	121	SS164	大枇杷烟Dapipayan	晒烟 Sun-cured
47	FS027	大黄金5210 Dahuangjin 5210	烤烟 Flue-cured	122	SS169	金山乡旱烟 Jinshanxianghanyan	晒烟 Sun-cured
48	FS029	单育2号Danyu No.2	烤烟 Flue-cured	123	XZ031	K17	晒烟 Sun-cured
49	FS037	广黄55 Guanghuang 55	烤烟 Flue-cured	124	XZ032	寸三皮Cunsanpi	晒烟 Sun-cured
50	FS044	红星一号Hongxingyihao	烤烟 Flue-cured	125	XZ033	九月寒Jiuyuehan	晒烟 Sun-cured
51	FS045	金星6007 Jinxing 6007	烤烟 Flue-cured	126	XZ034	三生烟Sanshengyan	晒烟 Sun-cured
52	FS050	净叶黄Jingyehuang	烤烟 Flue-cured	127	BG012	W.B68	白肋烟 Burley
53	FS061	潘园黄Panyuanhuang	烤烟 Flue-cured	128	BG018	ky41A	白肋烟Burley
54	FS077	许金2号Xujin No. 2	烤烟 Flue-cured	129	BG023	半铁泡Bantiepao	白肋烟Burley
55	FS084	云烟87 Yunyan 87	烤烟 Flue-cured	130	BG029	BY21	白肋烟Burley
56	FS085	云烟2号Yunyan No.2	烤烟 Flue-cured	131	BG032	KY10	白肋烟Burley
57	FS089	中烟90 Zhongyan 90	烤烟 Flue-cured	132	BG033	KY14	白肋烟Burley
58	FY017	春雷三号 Chunlei No.3	烤烟 Flue-cured	133	AG002	从江塘洞烟 Congjiangtangdongyan	晾烟Air-cured
59	FY030	湄潭黑团壳 Meitanheituanke	烤烟 Flue-cured	134	AG018	台江小柳叶 Taijiangxiaoliuye	晾烟Air-cured
60	FS083	云烟85 Yunyan 85	烤烟 Flue-cured	135	AG006	剑河乡洞土烟 Jianhexiangdongtuyan	晾烟Air-cured
61	XZ011	云烟97 Yunyan 97	烤烟 Flue-cured	136	GG001	Ambale-ma	雪茄烟 Cigar
62	FY048	兴烟一号Xingyanyihao	烤烟 Flue-cured	137	GG002	Beinhart1000-1	雪茄烟 Cigar
63	FT011	南江3号Nanjiang No.3	烤烟 Flue-cured	138	GG004	Florida301	雪茄烟Cigar
64	FY068	遵烟6号Zunyan No.6	烤烟 Flue-cured	139	GG005	Pennbel 69	雪茄烟Cigar
65	XZ012	中烟100 Zhongyan 100	烤烟 Flue-cured	140	XZ035	包皮Baopi	雪茄烟Cigar
66	FS032	贵烟3号Guiyan No.3	烤烟 Flue-cured	141	XZ036	坦桑尼亚烟 Tansangniyayan	香料烟 Oriental
67	FS087	中烟14 Zhongyan 14	烤烟 Flue-cured	142	TG002	Adcook	香料烟Oriental
68	FS032	革新3号Gexin No.3	烤烟 Flue-cured	143	TG004	Basma536	香料烟Oriental
69	PG142	K326LF	烤烟 Flue-cured	144	TG006	Cekpka	香料烟Oriental
70	FY094	Q6	烤烟 Flue-cured	145	TG011	xanthi-nc	香料烟Oriental
71	XZ013	瓮安2号Wengan No.2	烤烟 Flue-cured	146	XZ037	YY1	药烟 Medicinal
72	XZ014	2010A4	烤烟 Flue-cured	147	XZ038	YY2	药烟Medicinal
73	XZ015	兴烟2号Xingyan No.2	烤烟 Flue-cured	148	XZ039	YY4	药烟Medicinal
74	XZ016	99215-1	烤烟 Flue-cured	149	XZ040	YY11	药烟Medicinal
75	XZ017	PX2	烤烟 Flue-cured	150	XZ041	YY15	药烟Medicinal

序号 No.	种质库编号 GenBank number	种质名称 Accession name	调制类型 Curing status	序号 No.	资源库编号 GenBank number	种质名称 Accession name	调制类型 Curing status
1	FD002	独山软杆Dushanruangan	烤烟 Flue-cured	76	XZ018	PX5	烤烟 Flue-cured
2	FD011	福泉团叶摺烟 Fuquan tanyezheyan	烤烟Flue-cured	77	XZ019	PX6	烤烟 Flue-cured
3	FD032	麻将大红花 Majiangdahonghua	烤烟Flue-cured	78	XZ020	PX7	烤烟 Flue-cured
4	FD041	黔江一号Qianjiangyihao	烤烟Flue-cured	79	XZ021	PX8	烤烟 Flue-cured
5	FD047	瓮安中坪烤烟 Wenganzhongpingkaoyan	烤烟 Flue-cured	80	XZ022	PX9	烤烟 Flue-cured
6	FS054	柳叶尖0695 Liuyejian 0695	烤烟 Flue-cured	81	XZ023	PX10	烤烟 Flue-cured
7	FS070	胎里富1011 Tailifu 1011	烤烟 Flue-cured	82	XZ024	PX11	烤烟 Flue-cured
8	FS071	歪把子Waibazi	烤烟 Flue-cured	83	XZ025	PX12	烤烟 Flue-cured
9	FY064	哲伍毛烟Zhewumaoyan	烤烟 Flue-cured	84	XZ026	PX13	烤烟 Flue-cured
10	FY061	片片黄Pianpianhuang	烤烟 Flue-cured	85	XZ027	PX14	烤烟 Flue-cured
11	FG015	Coker86	烤烟 Flue-cured	86	XZ028	PX15	烤烟 Flue-cured
12	FG018	Dixie Bright 101	烤烟 Flue-cured	87	XZ029	PX17	烤烟 Flue-cured
13	FG024	Hicks	烤烟 Flue-cured	88	XZ030	PX19	烤烟 Flue-cured
14	FG027	K149	烤烟 Flue-cured	89	SG003	安龙护耳大柳叶 Anlonghuerdaliuye	晒烟 Sun-cured
15	FG029	K346	烤烟 Flue-cured	90	SG009	安顺二吊枝 Anshunerdiaozhi	晒烟 Sun-cured
16	FG028	K326	烤烟 Flue-cured	91	SG048	大方大红花 Dafangdahonghua	晒烟 Sun-cured
17	FG047	NC567	烤烟 Flue-cured	92	SG052	大柳叶节骨密 Daliuyegumi	晒烟 Sun-cured
18	FG049	NC729	烤烟 Flue-cured	93	SG069	德江中花烟（2） Dejiangzhonghuayan（2）	晒烟 Sun-cured
19	FG052	NC82	烤烟 Flue-cured	94	SG079	光柄柳叶（罗） Guangbingliuye（luo）	晒烟 Sun-cured
20	FG053	NC89	烤烟 Flue-cured	95	SG080	光柄柳叶（木） Guangbingliuye（mu）	晒烟 Sun-cured
21	FG054	NC95	烤烟 Flue-cured	96	SG094	花溪大青杆 Huaxidaqinggan	晒烟 Sun-cured
22	FG061	牛津26 Oxford 26	烤烟 Flue-cured	97	SG102	惠水三都大白花 Huishuisandudabaihua	晒烟 Sun-cured
23	FG077	RG11	烤烟 Flue-cured	98	SG112	凯里枇杷烟 Kailipipayan	晒烟 Sun-cured
24	FG079	RG17	烤烟 Flue-cured	99	SG134	马耳烟Maeryan	晒烟 Sun-cured
25	FG080	RG8	烤烟 Flue-cured	100	SG156	盘县大柳叶Panxiandaliuye	晒烟 Sun-cured
26	FG089	Special 400	烤烟 Flue-cured	101	SG169	平塘中坝晒烟 Pingtangzhongbashaiyan	晒烟 Sun-cured
27	FG090	Special 401	烤烟 Flue-cured	102	SG170	普安寸骨烟 Puancunguyan	晒烟 Sun-cured
28	FG094	SpeightG-164	烤烟 Flue-cured	103	SG178	黔西红花吊把 Qianxihonghuadiaoba	晒烟 Sun-cured
29	FG095	Speight G-28	烤烟 Flue-cured	104	SG248	贞丰柳叶烟 Zhenfengliuyeyan	晒烟 Sun-cured
30	FG099	Speight G-80	烤烟 Flue-cured	105	SG258	镇远莲花烟（周） Zhenyuanlianhuayan（zhou）	晒烟 Sun-cured
31	FG100	SPTG-172	烤烟 Flue-cured	106	SS006	81—26	晒烟 Sun-cured
32	FG105	Ti448A	烤烟 Flue-cured	107	SS012	Va309	晒烟 Sun-cured
33	FG118	Vesta 47	烤烟 Flue-cured	108	SS021	矮株一号Aizhuyihao	晒烟 Sun-cured
34	FG120	佛光Foguang	烤烟 Flue-cured	109	SS027	把柄烟Babingyan	晒烟 Sun-cured
35	FG122	Yellow mammoth	烤烟 Flue-cured	110	SS045	大瓦垅Dawalong	晒烟 Sun-cured
36	FG071	PVH06	烤烟 Flue-cured	111	SS053	风林一号Fenglinyihao	晒烟 Sun-cured
37	XZ001	CV87	烤烟 Flue-cured	112	SS066	贺县公会晒烟 Hexiangonghuishaiyan	晒烟 Sun-cured
38	XZ002	Cash	烤烟 Flue-cured	113	SS075	护脖香1368 Huboxiang 1368	晒烟 Sun-cured
39	XZ003	Coker139	烤烟 Flue-cured	114	SS087	老山烟Laoshanyan	晒烟 Sun-cured
40	XZ004	Gold doller	烤烟 Flue-cured	115	SS091	马里村晒烟（二） Malicunshaiyan（2）	晒烟 Sun-cured
41	XZ005	Mcnair 30	烤烟 Flue-cured	116	SS097	勐板晒烟 Mengbanshaiyan	晒烟 Sun-cured
42	XZ006	Orinoco	烤烟 Flue-cured	117	SS113	千层塔Qiancengta	晒烟 Sun-cured
43	XZ007	Mammoth gold	烤烟 Flue-cured	118	SS132	腾冲大柳叶 Tengchongdaliuye	晒烟 Sun-cured
44	XZ008	Golden wilf	烤烟 Flue-cured	119	SS142	小叶尖Xiaoyejian	晒烟 Sun-cured
45	XZ009	CV91	烤烟 Flue-cured	120	SS146	一朵花Yiduohua	晒烟 Sun-cured
46	XZ010	云烟315Yunyan 315	烤烟 Flue-cured	121	SS164	大枇杷烟Dapipayan	晒烟 Sun-cured
47	FS027	大黄金5210 Dahuangjin 5210	烤烟 Flue-cured	122	SS169	金山乡旱烟 Jinshanxianghanyan	晒烟 Sun-cured
48	FS029	单育2号Danyu No.2	烤烟 Flue-cured	123	XZ031	K17	晒烟 Sun-cured
49	FS037	广黄55 Guanghuang 55	烤烟 Flue-cured	124	XZ032	寸三皮Cunsanpi	晒烟 Sun-cured
50	FS044	红星一号Hongxingyihao	烤烟 Flue-cured	125	XZ033	九月寒Jiuyuehan	晒烟 Sun-cured
51	FS045	金星6007 Jinxing 6007	烤烟 Flue-cured	126	XZ034	三生烟Sanshengyan	晒烟 Sun-cured
52	FS050	净叶黄Jingyehuang	烤烟 Flue-cured	127	BG012	W.B68	白肋烟 Burley
53	FS061	潘园黄Panyuanhuang	烤烟 Flue-cured	128	BG018	ky41A	白肋烟Burley
54	FS077	许金2号Xujin No. 2	烤烟 Flue-cured	129	BG023	半铁泡Bantiepao	白肋烟Burley
55	FS084	云烟87 Yunyan 87	烤烟 Flue-cured	130	BG029	BY21	白肋烟Burley
56	FS085	云烟2号Yunyan No.2	烤烟 Flue-cured	131	BG032	KY10	白肋烟Burley
57	FS089	中烟90 Zhongyan 90	烤烟 Flue-cured	132	BG033	KY14	白肋烟Burley
58	FY017	春雷三号 Chunlei No.3	烤烟 Flue-cured	133	AG002	从江塘洞烟 Congjiangtangdongyan	晾烟Air-cured
59	FY030	湄潭黑团壳 Meitanheituanke	烤烟 Flue-cured	134	AG018	台江小柳叶 Taijiangxiaoliuye	晾烟Air-cured
60	FS083	云烟85 Yunyan 85	烤烟 Flue-cured	135	AG006	剑河乡洞土烟 Jianhexiangdongtuyan	晾烟Air-cured
61	XZ011	云烟97 Yunyan 97	烤烟 Flue-cured	136	GG001	Ambale-ma	雪茄烟 Cigar
62	FY048	兴烟一号Xingyanyihao	烤烟 Flue-cured	137	GG002	Beinhart1000-1	雪茄烟 Cigar
63	FT011	南江3号Nanjiang No.3	烤烟 Flue-cured	138	GG004	Florida301	雪茄烟Cigar
64	FY068	遵烟6号Zunyan No.6	烤烟 Flue-cured	139	GG005	Pennbel 69	雪茄烟Cigar
65	XZ012	中烟100 Zhongyan 100	烤烟 Flue-cured	140	XZ035	包皮Baopi	雪茄烟Cigar
66	FS032	贵烟3号Guiyan No.3	烤烟 Flue-cured	141	XZ036	坦桑尼亚烟 Tansangniyayan	香料烟 Oriental
67	FS087	中烟14 Zhongyan 14	烤烟 Flue-cured	142	TG002	Adcook	香料烟Oriental
68	FS032	革新3号Gexin No.3	烤烟 Flue-cured	143	TG004	Basma536	香料烟Oriental
69	PG142	K326LF	烤烟 Flue-cured	144	TG006	Cekpka	香料烟Oriental
70	FY094	Q6	烤烟 Flue-cured	145	TG011	xanthi-nc	香料烟Oriental
71	XZ013	瓮安2号Wengan No.2	烤烟 Flue-cured	146	XZ037	YY1	药烟 Medicinal
72	XZ014	2010A4	烤烟 Flue-cured	147	XZ038	YY2	药烟Medicinal
73	XZ015	兴烟2号Xingyan No.2	烤烟 Flue-cured	148	XZ039	YY4	药烟Medicinal
74	XZ016	99215-1	烤烟 Flue-cured	149	XZ040	YY11	药烟Medicinal
75	XZ017	PX2	烤烟 Flue-cured	150	XZ041	YY15	药烟Medicinal