Chloroplast DNA polymorphism of Brassica napus using SSR markers

doi:10.19802/j.issn.1007-9084.2021306

Abstract

Abstract:

Chloroplast genome is characterized by its maternal inheritance, haplotype, high conservation, and distinct intraspecific differences. To facilitate germplasm collection and introduction of rapeseed （Brassica napus L.）, chloroplast DNA diversity was investigated using different B. napus varieties. Global collection of 287 B. napus materials was evaluated using specific chloroplast SSR markers. Among the 15 chloroplast specific SSR-specific primer pairs, 5 pairs produced 19 polymorphic bands with the average of 3.8. Using the 19 polymorphic bands, 287 materials were divided into 14 haplotypes. Among them, the more prevalent haplotypes of H01, H02 and H03 occupied 74.91%, 13.59%, and 4.88%, respectively, while the other 11 haplotypes （H04-H14） accounted for 6.62%. Haplotype H02, a unique haplotype to China is cytoplasmic type of Polima or Shaan2A. In the foreign B. napus varieties, those from Russia or Sweden had more abundant haplotypes than those from other countries. Therefore introduction of resources from Russia or Sweden could efficiently broaden the genetic diversity background of Chinese B. napus varieties. Moreover, a rapid identification of Polima and Shaan2A cytoplasmic types was also established through 2 specific bands amplified by MF-4 and ccmp2 primer pairs, which provided methods for identification of Polima and Shaan2A cytoplasmic type.

Key words: Brassica napus L., chloroplast SSR markers, DNA polymorphism, haplotype

CLC Number:

S565.4

Bi-yun CHEN, Pei-jun LYU, Kun XU, Xiao-ming WU. Chloroplast DNA polymorphism of Brassica napus using SSR markers[J]. CHINESE JOURNAL OF OIL CROP SCIENCES, 2023, 45(1): 46-55.

Figures/Tables 7

Table 1

Information and chloroplast haplotype of 287 Brassica napus accessions

种质编号Line No.	种质名称 Line name	来源 Origin	育成年代 Breeding period	类型 Type	单倍型 Haplotype	种质编号 Line No.	种质名称 Line name	来源 Origin	育成年代 Breeding period	类型 Type	单倍型 Haplotype
1	Midas	Canada	1973	OP	H01	145	Su J209	China	2006	OP	H01
2	Oro	Canada	1968	OP	H01	146	Yangza 1	China	2006	Pol F₁	H02
3	Major	France	1971	OP	H01	147	98D-9	China	2006	Pol F₁	H02
4	Primor	France	1973	OP	H01	148	Huyou 18	China	2006	OP	H01
5	Yaojin Rape	Italy	1957	OP	H01	149	Yiza 02-13	China	2006	GMS F₁	H01
6	Marnoo	Australia	1980	OP	H01	150	5688	China	2006	Pol F₁	H02
7	Ujfertadi	Hungary	/	OP	H01	151	H40	China	2006	OP	H01
8	Savaria	Hungary	/	OP	H01	152	Sanbei 98	China	2006	OP	H01
9	Expander	Germany	1974	OP	H01	153	4026	China	2006	GMS F₁	H01
10	Ledos	Germany	/	OP	H01	154	036-21	China	2006		H01
11	H47	Russia	/	OP	H01	155	Hy1	China	2006	Pol F₁	H02
12	H51	Russia	1988	OP	H07	156	Hz03	China	2006	Pol F₁	H02
13	Janpol	Poland	1976-1985	OP	H01	157	H9945	China	2006	Pol F₁	H02
14	Start	Poland	1979-1985	OP	H03	158	Ezy218	China	2006	Pol F₁	H02
15	Mikado	England	1985	OP	H01	159	Za 532	China	2006	GMS F₁	H01
16	P20	England	/	OP	H01	160	Aoyou 501	China	2006		H01
17	Lingot	France	/	OP	H01	161	Heshengyou 868	China	2008	Pol F₁	H02
18	Wipot	Norway	/	OP	H01	162	Ganyouza 3	China	2007	GMS F₁	H03
19	Regent	Canada	1977	OP	H01	163	H0201	China	2008	Pol F₁	H02
20	Tower	Canada	1974	OP	H01	164	You 85	China	2006	GMS F₁	H01
21	Shiralee	Australia	1988	OP	H01	165	Zhong 160	China	2008	Pol F₁	H02
22	Viking	Denmark	1987	OP	H01	166	Cyz0210	China	2008	CH F₁	H01
23	Cobra	Germany	/	OP	H01	167	Anyou 928	China	2008		H01
24	Parter	Germany	/	OP	H01	168	Gaomi 01	China	2008		H01
25	Falcon	Germany	1989	OP	H01	169	H0433	China	2008		H01
26	Nevin	England	After 2000	OP	H01	170	Chuyouza 79	China	2008	GMS F₁	H01
27	Samouran	France	1989	OP	H04	171	601	China	2008	Pol F₁	H02
28	Roman-1	Netherland	/	OP	H01	172	Za 499	China	2008	GMS F₁	H01
29	Tornado	Sweden	1994	OP	H03	173	Qinyou 66	China	2008		H05
30	Legend	Sweden	1988	OP	H01	174	Ab448	Australia	/	OP	H01
31	Grant	Sweden	1989	OP	H01	175	Rv3	Australia	/	OP	H01
32	Celebra	Canada	1988	OP	H07	176	Liraglu	Australia	/	OP	H01
33	Triton	Canada	1984	OP	H01	177	Rv7	Australia	/	OP	H01
34	Profit	Canada	1989	OP	H01	178	Wesbrook	Australia	/	OP	H01
35	Startigh	Sweden	/	OP	H01	179	Yic Kaden	Australia	/	OP	H01
36	Bounty	Sweden	/	OP	H01	180	Poland Rape（2）	Poland	/	OP	H01
37	Garrison	Sweden	/	OP	H01	181	Garant	Poland	/	OP	H01
38	Gcsunder	Germany	/	OP	H01	182	Gorczanski	Poland	/	OP	H01
39	Disamant	Germany	/	OP	H01	183	P6	Poland	/	OP	H01
40	Mar	Poland	/	OP	H01	184	Rongshan Rape	North Korea	/	OP	H01
41	Star	Denmark	/	OP	H01	185	Wille	Denmark	/	OP	H01
42	Shengliqinggeng	China	1963	OP	H01	186	Sedo-10	France	/	OP	H01
43	Jiuer Rape	China	Before 1980	OP	H01	187	Topas-15	France	1981	OP	H01
44	Zaofeng 1	China	1969	OP	H01	188	Line	France	1978	OP	H03
45	Huayou 13	China	1973	OP	H04	189	H25	France	/	OP	H01
46	Aijiazao	China	1961	OP	H01	190	H62	France	/	OP	H01
47	Xinan 302	China	1969	OP	H01	191	Cresor	France	1975	OP	H01
48	Yunyou 49	China	1970	OP	H01	192	Aao	France	/	OP	H01
49	Qingyou 6	China	1964	OP	H01	193	Tantar	France	/	OP	H01
50	Norin 18	Japan	1949	OP	H01	194	P17	France	/	OP	H01
51	F01/J6 1-1	China	2006	RS	H13	195	Sielecki	France	/	OP	H01
52	Ganyou 5	China	1970	OP	H01	196	Hja 82799	Finland	/	OP	H01
53	Zhongyou 821	China	1987	OP	H01	197	Hn-9464	South Korea	/	OP	H01
54	Xiangyou 5	China	1975	OP	H01	198	Koolzaand-2	Netherland	/	OP	H01
55	Dong-Hae23	Japan	/	OP	H01	199	Turret	Canada	/	OP	H01
56	Ganpol	Japan	/	OP	H01	200	Wester Zn6-2836	Canada	1982	OP	H01
57	Norin16	Japan	/	OP	H01	201	Pivot	Canada	1985	OP	H01
58	Zheyouyou 2	China	1992	OP	H01	202	Arabelle	Canada	/	OP	H01
59	Yuyou 2	China	1989	OP	H01	203	Westar	Canada	1982	OP	H01
60	Zhongyoudijie 1	China	1986	OP	H03	204	P11	Czech	/	OP	H01
61	Qingyou 12	China	1993	OP	H01	205	Bok.Wok 13	USA	/	OP	H01
62	Chikuzen	Japan	Before 1980	OP	H01	206	77-33	USA	/	OP	H01
63	Zhongshuang 4	China	1994	OP	H01	207	Velox	South Korea	/	OP	H01
64	Isn-705	India	2005	RS	H08	208	Norin 34	Japan	1988	OP	H06
65	H0302	China	2006	Pol F₁	H02	209	Japan Kw Changjiao	Japan	/	OP	H01
66	May-00	China	2006	Shaan 2A F₁	H02	210	1.7	Japan	/	OP	H01
67	H9944	China	2006		H01	211	Sv.Niklas	Sweden	/	OP	H01
68	05Za V2	China	2005		H08	212	Sv.0321	Sweden	/	OP	H01
69	01 Za 654	China	2006	Pol/Shaan 2A F₁	H02	213	Omega	Sweden	1989	OP	H03
70	Hy8	China	2006	GMS F1	H01	214	Ww1307	Sweden	1989	OP	H12
71	Youyan 10	China	2006	GMS F1	H01	215	Olga	Sweden	1976	OP	H14
72	Qianyou 20	China	2006	GMS F1	H01	216	H53	Sweden	/	OP	H01
73	6766	China	2006	Pol/Shaan 2A F₁	H02	217	Sv.Tyko	Sweden	/	OP	H01
74	H0202	China	2006	Pol/Shaan 2A F₁	H02	218	Sv.02312	Sweden	/	OP	H01
75	Zheyou 5002	China	2006	OP	H01	219	Altex	Sweden	/	OP	H01
76	Zhongyouza 2	China	2006	Shaan 2A F₁	H02	220	P26	Sweden	/	OP	H01
77	Za 839	China	2006	GMS F₁	H01	221	Target	Sweden	1966	OP	H11
78	Hongyou 3	China	2006	GMS F₁	H01	222	Switzerland Rape（1）	Switzerland	/	OP	H01
79	Zashuang 5	China	2006	Pol F₁	H02	223	H43	Russia	/	OP	H01
80	7633	China	2006	IMS F₁	H01	224	H48	Russia	1989	OP	H09
81	Qinyou 7	China	2006	Shaan 2A F₁	H02	225	Liradonne	Germany	/	OP	H01
82	No 23 Rape	China	/	OP	H01	226	Erra	Germany	/	OP	H01
83	Ganyou 4	China	1971	OP	H01	227	Quinta	Germany	1975	OP	H01
84	Huayou 3	China	1965	OP	H01	228	Librador	Germany	/	OP	H01
85	Huayou 8	China	1969	OP	H01	229	Rucabo	Germany	/	OP	H01
86	Chuannongchangjiao	China	1954	OP	H01	230	Liglandor	Germany	/	OP	H01
87	Chuanyou 7	China	1954	OP	H01	231	Wiama	Germany	/	OP	H01
88	Luzhou 5	China	1958	OP	H01	232	77N	Germany	/	OP	H01
89	Nanyang 41	China	1972	OP	H01	233	H4	Germany	/	OP	H01
90	F11/J2 1-1	China	2006	RS	H03	234	H10	Germany	/	OP	H01
91	You 2501	China	2008		H10	235	H32	Germany	/	OP	H01
92	Zy-1	China	2008	GMS F₁	H05	236	Sollux	Germany	/	OP	H01
93	Shengguang 76	China	2008	Pol F₁	H02	237	P22	Germany	/	OP	H01
94	Jinyou 8	China	2008	GMS F₁	H01	238	7300	Germany	/	OP	H01
95	Mianza 03-33	China	2008		H01	239	7306	Germany	/	OP	H01
96	Dingyouza 3	China	2008	Pol F₁	H02	240	28669	Germany	1994	OP	H04
97	Hm42	China	2008	OP	H01	241	50202	Germany	/	OP	H01
98	You Yl050	China	2008	GMS F₁	H01	242	Diadevu	Germany	/	OP	H01
99	Yangguang 2008	China	2008	OP	H01	243	Score	Germany	/	OP	H01
100	Huyou 21	China	2008	OP	H04	244	Superlati-Velot 601	New Zealand	/	OP	H01
101	Heyou 563	China	2008	GMS F₁	H01	245	Italy Rape	Italy	/	OP	H01
102	Zheza 0603	China	2008	GMS F₁	H01	246	7304	India	/	OP	H01
103	Shengguang 86	China	2008	Pol F₁	H02	247	34406	India	/	OP	H01
104	Qinyou 23	China	2008		H01	248	77-258	England	/	OP	H01
105	Heyou 488	China	2008	GMS F₁	H01	249	Ew-2	England	/	OP	H01
106	H9958	China	2008	Pol F₁	H02	250	Es-1	England	/	OP	H01
107	Yang J6711	China	2008	OP	H01	251	Narc	Pakistan	/	OP	H01
108	Qinyou 99	China	2008		H01	252	Africa Rape	Africa	/	OP	H01
109	Sc76	China	2008	Pol F₁	H02	253	Sel-W	Mexico	/	OP	H01
110	Qinyan 211	China	2008	Shaan 2A F₁	H02	254	Shpat	Russia	/	OP	H01
111	Zy530	China	2008	Shaan 2A F₁	H02	255	Kruglik	Ukraine	/	OP	H01
112	Ningza 11	China	2008	GMS F₁	H01	256	Vniimk-214	Russia	/	OP	H01
113	03Za-14	China	2007		H01	257	Arion	Ukraine	/	OP	H03
114	05V06	China	2007	CH F₁	H01	258	Antej	Byelorussia	/	OP	H01
115	Mianza 01-63	China	2007	GMS F₁	H01	259	Smak	Byelorussia	/	OP	H03
116	07-C-27	China	2007		H01	260	Madrigal	Russia	/	OP	H03
117	02-72	China	2007		H01	261	Rubej	Russia	/	OP	H03
118	507	China	2007	Pol F₁	H02	262	Skriverskij Forrage	Latvia	/	OP	H01
119	Za 0426	China	2007	Pol F₁	H02	263	Snitinskij	Ukraine	/	OP	H01
120	K426	China	2007	Pol F₁	H02	264	Otradnenskij	Russia	/	OP	H01
121	5103	China	2007	Pol F₁	H02	265	Oniks	Russia	/	OP	H03
122	Za 668	China	2007		H01	266	Severianin	Russia	/	OP	H01
123	9158	China	2007	Shaan 2A F₁	H02	267	699	China	2007	OP	H03
124	Heyou 202	China	2007	GMS F₁	H01	268	56602	China	2007	OP	H01
125	Za 0430	China	2007	Pol/Shaan 2A F₁	H02	269	68232	China	2007	OP	H01
126	Huayouza 13	China	2007	Pol F₁	H02	270	99-1055	China	2007	OP	H01
127	Jun-06	China	2007	Pol F₁	H02	271	G-142	China	2007		H01
128	02-16	China	2006		H01	272	P6036-1	China	2007	OP	H01
129	You 1536	China	2006		H01	273	Kt0601	China	2007		H01
130	Shaanyouza 1	China	2006	Shaan 2A F₁	H02	274	N5424	China	2007		H01
131	Mianxinyou 1	China	2006	GMS F₁	H01	275	N6013	China	2008	OP	H03
132	Dh1708*	China	2006	GMS F₁	H01	276	P6036-2	China	2007	OP	H01
133	Su 6106	China	2006	OP	H01	277	Huyou 17	China	2007	OP	H01
134	Xiangnong 03	China	2006	GMS F₁	H01	278	Huyou 19	China	2007	OP	H01
135	Yang 6614	China	2006	OP	H01	279	Shengguang 77	China	2007	OP	H01
136	Zashuang 4	China	2006	Pol F₁	H02	280	Xiwang 106	China	2007	OP	H01
137	Zayou 66	China	2008		H05	281	Yan 6055	China	2008	OP	H06
138	Aoyou 503	China	2006	Pol F₁	H02	282	Yangjian 8	China	2007	OP	H01
139	Sb02	China	2006	Shaan 2A F₁	H02	283	You 88	China	2007	OP	H01
140	Deyou 5668	China	2006		H01	284	Zheyou 17	China	2007	OP	H01
141	Xiangzayou 631	China	2006	GMS F₁	H01	285	Zheyou 6001	China	2007	OP	H01
142	Zheyou 18	China	2006	OP	H01	286	Zhongnongyou 136	China	2008	Pol F₁	H02
143	24729	China	2006		H01	287	Zhongshuang 9	China	2002	OP	H01
144	Zhongshuang 11	China	2006	OP	H01

Table 1

Table 2

Fig. 1

Table 3

Table 4

Table 5

Fig. 2

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引物代号Primer No.	正向序列（5’-3’） Forward sequence	反向序列（5’-3’） Reverse sequence	多态性条带数 Polymorphic bands	多态性信息PIC
均值 Mean			3.8	0.3422
MF-1	TCAATTGCACATTCTAGAATTCTAAG	CAATTCAATATGGTTATATATTAGAG	/	/
MF-2	GGTTCCGTCGTTCCCATCGC	CATAATAATTAGATAAATCTGTTCC	2	0.3607
MF-3	AATGGTATGACTAGCTTATAAGG	CTTAACAATGAGATGAGGCAATC	/	/
MF-4	CGGATCTATTATGACATATCC	GAAATATGAATACACTAGATTAGG	5	0.4009
MF-5	CCTGGCGGTATCAAGATGCCACT	GCCATAATGGTACAGAACTAT	/	/
MF-6	GAAGGAATAGTCGTTTTCAAG	CATAAATAGAGTTCCATTTCGG	/	/
MF-7	CGGCAGGAGTCATTGGTTCAAA	GATTTTGTAACTAGCTGACG	5	0.4076
MF-8	CTTATATTCATAAGCGAAGAAC	AATAACAATAGATGAATAGTCA	/	/
MF-9	GGGCCGTTATGCTCATTACG	TCCTATTCATGGGGATTCCG	/	/
ccmp2	GATCCCGGACGTAATCCTG	ATCGTACCGAGGGTTCGAAT	3	0.1659
ccmp3	CAGACCAAAAGCTGACATAG	GTTTCATTCGGCTCCTTTAT	/	/
ccmp4	AATGCTGAATCGAYGACCTA	CCAAAATATTBGGAGGACTCT	/	/
ccmp6	CGATGCATATGTAGAAAGCC	CATTACGTGCGACTATCTCC	4	0.3759
ccmp7	CAACATATACCACTGTCAAG	ACATCATTATTGTATACTCTTTC	/	/
ccmp10	TTTTTTTTTAGTGAACGTGTCA	TTCGTCGDCGTAGTAAATAG	/	/

品种来源 Origin of accessions		品种数量 Number of varieties	叶绿体单倍型 Chloroplast haplotype
亚洲Asia	中国China	147	H01、H02、H03、H04、H05、H06、H08、H10、H13
	印度India	3	H01、H08
	日本Japan	8	H01、H06
	朝鲜North Korea	1	H01
	巴基斯坦Pakistan	1	H01
	韩国South Korea	2	H01
	小计Subtotal	162	H01、H02、H03、H04、H05、H06、H08、H10、H13
欧洲Europe	白俄罗斯Byelorussia	2	H01、H03
	捷克Czech	1	H01
	丹麦Denmark	3	H01
	英国England	6	H01
	芬兰Finland	1	H01
	法国France	14	H01、H03、H04
	德国Germany	26	H01、H04
	匈牙利Hungary	2	H01
	意大利Italy	2	H01
	拉脱维亚Latvia	1	H01
	荷兰Netherland	2	H01
	挪威Norway	1	H01
	波兰Poland	7	H01、H03
	俄罗斯Russia	11	H01、H03、H11、H12、H14
	瑞典Sweden	17	H01、H03、H07、H09
	瑞士Switzerland	1	H01
	乌克兰Ukraine	3	H01、H03
	小计Subtotal	100	H01、H03、H04、H07、H09、H11、H12、H14
大洋洲Oceania	澳大利亚Australia	8	H01
大洋洲Oceania	新西兰New Zealand	1	H01
美洲America	加拿大Canada	12	H01、H07
	墨西哥Mexico	1	H01
	美国USA	2	H01
非洲Africa	非洲Africa	1	H01
	小计Subtotal	25	H01、H07
合计Total		287	14

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