Minimum of SSR Markers for Analyzing Genetic Variation of Oryza sativa L.

doi:10.3969/j.issn.1001G7216.2015.06.003

Abstract

Abstract:

A total of 120 SSR markers were used to determine the minimum of SSR markers for analyzing genetic variation of 69 Oryza sativa L. accessions, which have been clearly classified, based on the genetic diversity and population structure. The results showed that: 1) a total of 1,256 alleles were detected with 120 SSR markers. The number of alleles per locus widely ranged from 2 to 27 with an average of 10.5. Nei's genetic diversity index per locus varied from 0.413 to 0.951 with a mean of 0.760; 2) the minimum of SSR markers for analyzing genetic diversity of rice was 72; 3) the number of SSR markers for analyzing population structure of rice was at least 60.

Key words: Oryza sativa L., simple sequence repeat, genetic diversity, population structure, Mantel correlation test

摘要：

以69份类型明确的亚洲栽培稻品种为材料,选用120对SSR引物,通过评估遗传多样性和群体结构,研究分析其遗传变异对SSR引物数的要求。结果表明:1)120对引物在69份试验材料中共检测到1256个等位变异,每个位点的等位基因数差异较大,变化范围为2~27,平均为10.5;平均Nei基因多样性指数变化范围为0.4058~0.9452,平均为0.7616;2)分析亚洲栽培稻遗传多样性时,至少需要72对SSR引物;3)分析亚洲栽培稻群体结构时所需最少引物数可降低至60对。

关键词: 亚洲栽培稻, SSR标记;, 遗传多样性, 群体结构, 矩阵相关性检测

CLC Number:

Xiao-ping YUAN, Cai-hong WANG, Hong-zhong DENG, Qun XU, Yue FENG, Han-yong YU, Yi-ping WANG, Xing-hua WEI. Minimum of SSR Markers for Analyzing Genetic Variation of Oryza sativa L.[J]. Chinese Journal OF Rice Science, 2015, 29(6): 578-586.

袁筱萍, 王彩红, 邓宏中, 徐群, 冯跃, 余汉勇, 王一平, 魏兴华. 亚洲栽培稻遗传变异分析最少SSR引物数的研究[J]. 中国水稻科学, 2015, 29(6): 578-586.

Figures/Tables 6

References 22

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编号 Serial number	品种名称 Accession name	来源地 Country of origin	类型 Classification	编号 Serial number	品种名称 Accession name	来源地 Country of origin	类型 Classification
ind-01	Jaya	India	indica	aro-01	JC101	India	aromatic
ind-02	IR8	Phillipines	indica	aro-02	Nga Ya Pauk	Myanmar	aromatic
ind-03	Taichung Native 1	Taiwan	indica	aro-03	Kui Sali	Bangladesh	aromatic
ind-04	Khao Dawk Mali 105	Thailand	indica	aro-04	DomSofid	Iran	aromatic
ind-05	Padi Boenor	Indonesia	indica	aro-05	Kalijira	Bangladesh	aromatic
ind-06	JC92	India	indica	aro-06	Gordoi	Bangladesh	aromatic
ind-07	Champa Tong 54	Thailand	indica	aro-07	JC73-4	India	aromatic
ind-08	Lageado	Brazil	indica	aro-08	Shwewa	Myanmar	aromatic
ind-09	Dhola Aman	Bangladesh	indica	aro-09	Kanjari	India	aromatic
ind-10	RTS12	Vietnam	indica	aro-10	Pankhari 203	India	aromatic
ind-11	IR36	Phillipines	indica	aro-11	N12	India	aromatic
ind-12	CO18	India	indica	aro-12	Basmati 1	Pakistan	aromatic
ind-13	Gie 57	Vietnam	indica	trj-01	Dou-Agu	Brazil	tropical japonica
ind-14	Macan Binundok	Philippines	indica	trj-02	Trembese	Indonesia	tropical japonica
ind-15	TD25	Thailand	indica	trj-03	Gundil Kuning	Indonesia	tropical japonica
aus-01	Shor Shori	Bangladesh	aus	trj-04	Honduras	Brazil	tropical japonica
aus-02	Jhona 349	India	aus	trj-05	Kinastano	Philippines	tropical japonica
aus-03	Black Gora (Ncs12)	India	aus	trj-06	Dholi Boro	Bangladesh	tropical japonica
aus-04	Shada Boro	Bangladesh	aus	trj-07	Cuba 65	Cuba	tropical japonica
aus-05	Unnamed	Bangladesh	aus	trj-08	IAC25	Brazil	tropical japonica
aus-06	Badal 89	Bangladesh	aus	trj-09	L-202	America	tropical japonica
aus-07	BJ1	India	aus	tej-01	Koshihikari	Japan	temperate japonica
aus-08	Kalamkati	India	aus	tej-02	Geumobyeo	Korea	temperate japonica
aus-09	Dhala Shaitta	Bangladesh	aus	tej-03	Baghlani Nangarhar	Afghanistan	temperate japonica
aus-10	Lalamon 158	Bangladesh	aus	tej-04	Aedal	Korea	temperate japonica
aus-11	Aswina	Bangladesh	aus	tej-05	TainanIku 487	Taiwan	temperate japonica
aus-12	Bamoia	Bangladesh	aus	tej-06	KotobukiMochi	Japan	temperate japonica
ray-01	Matia Amon	Bangladesh	rayada	tej-07	Taipei 309	Taiwan	temperate japonica
ray-02	Kalamon 77-20	Bangladesh	rayada	tej-08	Chodongji	South Korea	temperate japonica
ray-03	Jatra Motuk	Bangladesh	rayada	tej-09	Beonjo	Korea	temperate japonica
ray-04	Matiamon 53-13	Bangladesh	rayada	tej-10	Mansaku	Japan	temperate japonica
ray-05	Khesail	Bangladesh	rayada	tej-11	Oro	Chile	temperate japonica
ray-06	DalKatra	Bangladesh	rayada	tej-12	Luk Takhar	Afghanistan	temperate japonica
ray-07	Lalamon 594	Bangladesh	rayada	tej-13	NepHoa Vang	Vietnam	temperate japonica
ray-08	Nara Bet	Bangladesh	rayada

编号 Serial number	品种名称 Accession name	来源地 Country of origin	类型 Classification	编号 Serial number	品种名称 Accession name	来源地 Country of origin	类型 Classification
ind-01	Jaya	India	indica	aro-01	JC101	India	aromatic
ind-02	IR8	Phillipines	indica	aro-02	Nga Ya Pauk	Myanmar	aromatic
ind-03	Taichung Native 1	Taiwan	indica	aro-03	Kui Sali	Bangladesh	aromatic
ind-04	Khao Dawk Mali 105	Thailand	indica	aro-04	DomSofid	Iran	aromatic
ind-05	Padi Boenor	Indonesia	indica	aro-05	Kalijira	Bangladesh	aromatic
ind-06	JC92	India	indica	aro-06	Gordoi	Bangladesh	aromatic
ind-07	Champa Tong 54	Thailand	indica	aro-07	JC73-4	India	aromatic
ind-08	Lageado	Brazil	indica	aro-08	Shwewa	Myanmar	aromatic
ind-09	Dhola Aman	Bangladesh	indica	aro-09	Kanjari	India	aromatic
ind-10	RTS12	Vietnam	indica	aro-10	Pankhari 203	India	aromatic
ind-11	IR36	Phillipines	indica	aro-11	N12	India	aromatic
ind-12	CO18	India	indica	aro-12	Basmati 1	Pakistan	aromatic
ind-13	Gie 57	Vietnam	indica	trj-01	Dou-Agu	Brazil	tropical japonica
ind-14	Macan Binundok	Philippines	indica	trj-02	Trembese	Indonesia	tropical japonica
ind-15	TD25	Thailand	indica	trj-03	Gundil Kuning	Indonesia	tropical japonica
aus-01	Shor Shori	Bangladesh	aus	trj-04	Honduras	Brazil	tropical japonica
aus-02	Jhona 349	India	aus	trj-05	Kinastano	Philippines	tropical japonica
aus-03	Black Gora (Ncs12)	India	aus	trj-06	Dholi Boro	Bangladesh	tropical japonica
aus-04	Shada Boro	Bangladesh	aus	trj-07	Cuba 65	Cuba	tropical japonica
aus-05	Unnamed	Bangladesh	aus	trj-08	IAC25	Brazil	tropical japonica
aus-06	Badal 89	Bangladesh	aus	trj-09	L-202	America	tropical japonica
aus-07	BJ1	India	aus	tej-01	Koshihikari	Japan	temperate japonica
aus-08	Kalamkati	India	aus	tej-02	Geumobyeo	Korea	temperate japonica
aus-09	Dhala Shaitta	Bangladesh	aus	tej-03	Baghlani Nangarhar	Afghanistan	temperate japonica
aus-10	Lalamon 158	Bangladesh	aus	tej-04	Aedal	Korea	temperate japonica
aus-11	Aswina	Bangladesh	aus	tej-05	TainanIku 487	Taiwan	temperate japonica
aus-12	Bamoia	Bangladesh	aus	tej-06	KotobukiMochi	Japan	temperate japonica
ray-01	Matia Amon	Bangladesh	rayada	tej-07	Taipei 309	Taiwan	temperate japonica
ray-02	Kalamon 77-20	Bangladesh	rayada	tej-08	Chodongji	South Korea	temperate japonica
ray-03	Jatra Motuk	Bangladesh	rayada	tej-09	Beonjo	Korea	temperate japonica
ray-04	Matiamon 53-13	Bangladesh	rayada	tej-10	Mansaku	Japan	temperate japonica
ray-05	Khesail	Bangladesh	rayada	tej-11	Oro	Chile	temperate japonica
ray-06	DalKatra	Bangladesh	rayada	tej-12	Luk Takhar	Afghanistan	temperate japonica
ray-07	Lalamon 594	Bangladesh	rayada	tej-13	NepHoa Vang	Vietnam	temperate japonica
ray-08	Nara Bet	Bangladesh	rayada

引物 Marker	染色体 Chromosome	位置/(cM) Location /(cM)	样本量 Sample	等位基因数 Allele	Nei基因多样性指数 Nei's genetic diversity index	引物 Marker	染色体 Chromosome	位置/(cM) Location /(cM)	样本量 Sample	等位基因数 Allele	Nei基因多样性指数 Nei's genetic diversity index
RM462	1	2.8	69	8	0.6704	RM30	6	105.1	69	11	0.7146
RM1195	1	30.5	69	11	0.7982	RM340	6	113.1	69	17	0.8973
RM583	1	43.2	69	12	0.8670	RM176	6	120.9	69	4	0.6725
RM490	1	51.0	69	5	0.7015	RM481	7	17.6	69	20	0.9309
RM449	1	73.1	69	9	0.8460	RM180	7	42.2	69	11	0.7587
RM129	1	75.9	69	5	0.7263	RM542	7	49.7	69	13	0.8145
RM488	1	102.3	69	13	0.8922	RM418	7	61.8	69	11	0.8952
RM443	1	121.0	69	4	0.7028	RM432	7	64.7	69	4	0.6608
RM297	1	132.0	69	13	0.8544	RM336	7	77.8	69	19	0.9238
RM212	1	135.8	69	7	0.7104	RM505	7	84.4	69	7	0.5285
RM472	1	146.4	69	14	0.8733	RM234	7	93.9	69	12	0.8326
RM414	1	161.8	69	2	0.4621	RM18	7	94.7	69	7	0.8070
RM485	2	0.0	69	15	0.8759	RM420	7	118.3	69	5	0.7444
RM555	2	20.0	69	4	0.6940	RM337	8	0.5	69	9	0.7129
RM8	2	26.9	69	6	0.5869	RM25	8	35.2	69	6	0.7104
RM423	2	28.7	69	8	0.7746	RM72	8	45.4	69	14	0.8780
RM71	2	40.9	69	16	0.8645	RM331	8	54.3	69	14	0.7708
RM475	2	92.5	69	11	0.8540	RM404	8	55.4	69	15	0.8683
RM263	2	104.9	69	9	0.7834	RM515	8	72.2	69	15	0.8082
RM208	2	154.1	69	15	0.9023	RM210	8	86.7	69	10	0.8326
RM498	2	157.1	69	4	0.6452	RM149	8	101.1	69	10	0.8555
RM132	3	2.5	69	4	0.5264	RM230	8	105.7	69	6	0.7494
RM231	3	11.5	69	8	0.7347	RM477	8	120.4	69	2	0.4537
RM545	3	25.0	69	13	0.8750	RM316	9	0.8	69	10	0.8339
RM232	3	44.3	69	15	0.8948	RM219	9	20.7	69	15	0.8750
RM7	3	44.4	69	6	0.7591	RM321	9	40.1	69	2	0.4915
RM554	3	55.3	69	5	0.7284	RM409	9	49.3	69	4	0.4965
RM411	3	87.1	69	5	0.6137	RM566	9	50.7	69	17	0.8872
RM426	3	122.3	69	23	0.9364	RM257	9	64.1	69	23	0.9065
RM448	3	140.1	69	14	0.8732	RM278	9	74.7	69	14	0.8847
RM293	3	142.3	69	4	0.6734	RM215	9	83.2	69	13	0.8414
RM422	3	151.5	69	13	0.8822	RM205	9	93.5	69	24	0.9296
RM85	3	166.4	69	11	0.7372	RM474	10	3.0	69	19	0.9259
RM551	4	3.1	69	16	0.8952	RM216	10	12.5	69	10	0.8385
RM5414	4	7.9	69	12	0.8532	RM311	10	17.2	69	7	0.7664
RM261	4	17.5	69	3	0.4243	RM467	10	28.2	69	12	0.8691
RM307	4	20.9	69	13	0.8456	RM184	10	41.6	69	6	0.8087
RM185	4	42.8	69	3	0.5268	RM258	10	48.8	69	8	0.7356
RM119	4	62.6	69	4	0.5480	RM147	10	70.0	69	3	0.6011
RM273	4	72.8	69	5	0.6268	RM228	10	78.4	69	11	0.7940
RM303	4	90.8	69	22	0.8960	RM333	10	78.4	69	20	0.9355
RM348	4	112.3	69	3	0.5138	RM286	11	1.4	69	14	0.8876
RM567	4	126.2	69	7	0.8309	RM332	11	13.8	69	6	0.6356
RM507	5	1.5	69	3	0.5150	RM167	11	24.1	69	13	0.7893
RM592	5	23.6	69	27	0.9452	RM536	11	49.1	69	10	0.8465
RM267	5	24.7	69	12	0.8158	RM6091	11	56.2	69	7	0.7801
RM169	5	48.6	69	10	0.6994	RM209	11	69.4	69	15	0.8452
RM5140	5	54.6	69	8	0.6499	RM457	11	78.8	69	3	0.4192
RM164	5	74.5	69	15	0.9044	RM206	11	88.4	69	16	0.8809
RM161	5	80.7	69	7	0.8208	RM224	11	115.1	69	12	0.8687
RM421	5	101.5	69	3	0.4318	RM144	11	116.2	69	12	0.8456
RM274	5	109.0	69	9	0.6906	RM20A	12	9.7	69	16	0.8263
RM334	5	117.2	69	22	0.9162	RM19	12	19.1	69	12	0.7742
RM190	6	8.2	69	10	0.8423	RM247	12	26.7	69	22	0.9032
RM225	6	13.2	69	8	0.8158	RM101	12	48.2	69	17	0.7478
RM253	6	25.2	69	20	0.9095	RM7102	12	51.8	69	8	0.7872
RM527	6	56.3	69	14	0.8851	RM511	12	60.3	69	5	0.5793
RM5745	6	64.9	69	3	0.4814	RM463	12	75.8	69	5	0.6767
RM541	6	68.1	69	13	0.8368	RM270	12	91.3	69	4	0.4058
RM275	6	89.0	69	5	0.5238	RM17	12	107.4	69	10	0.6822

引物 Marker	染色体 Chromosome	位置/(cM) Location /(cM)	样本量 Sample	等位基因数 Allele	Nei基因多样性指数 Nei's genetic diversity index	引物 Marker	染色体 Chromosome	位置/(cM) Location /(cM)	样本量 Sample	等位基因数 Allele	Nei基因多样性指数 Nei's genetic diversity index
RM462	1	2.8	69	8	0.6704	RM30	6	105.1	69	11	0.7146
RM1195	1	30.5	69	11	0.7982	RM340	6	113.1	69	17	0.8973
RM583	1	43.2	69	12	0.8670	RM176	6	120.9	69	4	0.6725
RM490	1	51.0	69	5	0.7015	RM481	7	17.6	69	20	0.9309
RM449	1	73.1	69	9	0.8460	RM180	7	42.2	69	11	0.7587
RM129	1	75.9	69	5	0.7263	RM542	7	49.7	69	13	0.8145
RM488	1	102.3	69	13	0.8922	RM418	7	61.8	69	11	0.8952
RM443	1	121.0	69	4	0.7028	RM432	7	64.7	69	4	0.6608
RM297	1	132.0	69	13	0.8544	RM336	7	77.8	69	19	0.9238
RM212	1	135.8	69	7	0.7104	RM505	7	84.4	69	7	0.5285
RM472	1	146.4	69	14	0.8733	RM234	7	93.9	69	12	0.8326
RM414	1	161.8	69	2	0.4621	RM18	7	94.7	69	7	0.8070
RM485	2	0.0	69	15	0.8759	RM420	7	118.3	69	5	0.7444
RM555	2	20.0	69	4	0.6940	RM337	8	0.5	69	9	0.7129
RM8	2	26.9	69	6	0.5869	RM25	8	35.2	69	6	0.7104
RM423	2	28.7	69	8	0.7746	RM72	8	45.4	69	14	0.8780
RM71	2	40.9	69	16	0.8645	RM331	8	54.3	69	14	0.7708
RM475	2	92.5	69	11	0.8540	RM404	8	55.4	69	15	0.8683
RM263	2	104.9	69	9	0.7834	RM515	8	72.2	69	15	0.8082
RM208	2	154.1	69	15	0.9023	RM210	8	86.7	69	10	0.8326
RM498	2	157.1	69	4	0.6452	RM149	8	101.1	69	10	0.8555
RM132	3	2.5	69	4	0.5264	RM230	8	105.7	69	6	0.7494
RM231	3	11.5	69	8	0.7347	RM477	8	120.4	69	2	0.4537
RM545	3	25.0	69	13	0.8750	RM316	9	0.8	69	10	0.8339
RM232	3	44.3	69	15	0.8948	RM219	9	20.7	69	15	0.8750
RM7	3	44.4	69	6	0.7591	RM321	9	40.1	69	2	0.4915
RM554	3	55.3	69	5	0.7284	RM409	9	49.3	69	4	0.4965
RM411	3	87.1	69	5	0.6137	RM566	9	50.7	69	17	0.8872
RM426	3	122.3	69	23	0.9364	RM257	9	64.1	69	23	0.9065
RM448	3	140.1	69	14	0.8732	RM278	9	74.7	69	14	0.8847
RM293	3	142.3	69	4	0.6734	RM215	9	83.2	69	13	0.8414
RM422	3	151.5	69	13	0.8822	RM205	9	93.5	69	24	0.9296
RM85	3	166.4	69	11	0.7372	RM474	10	3.0	69	19	0.9259
RM551	4	3.1	69	16	0.8952	RM216	10	12.5	69	10	0.8385
RM5414	4	7.9	69	12	0.8532	RM311	10	17.2	69	7	0.7664
RM261	4	17.5	69	3	0.4243	RM467	10	28.2	69	12	0.8691
RM307	4	20.9	69	13	0.8456	RM184	10	41.6	69	6	0.8087
RM185	4	42.8	69	3	0.5268	RM258	10	48.8	69	8	0.7356
RM119	4	62.6	69	4	0.5480	RM147	10	70.0	69	3	0.6011
RM273	4	72.8	69	5	0.6268	RM228	10	78.4	69	11	0.7940
RM303	4	90.8	69	22	0.8960	RM333	10	78.4	69	20	0.9355
RM348	4	112.3	69	3	0.5138	RM286	11	1.4	69	14	0.8876
RM567	4	126.2	69	7	0.8309	RM332	11	13.8	69	6	0.6356
RM507	5	1.5	69	3	0.5150	RM167	11	24.1	69	13	0.7893
RM592	5	23.6	69	27	0.9452	RM536	11	49.1	69	10	0.8465
RM267	5	24.7	69	12	0.8158	RM6091	11	56.2	69	7	0.7801
RM169	5	48.6	69	10	0.6994	RM209	11	69.4	69	15	0.8452
RM5140	5	54.6	69	8	0.6499	RM457	11	78.8	69	3	0.4192
RM164	5	74.5	69	15	0.9044	RM206	11	88.4	69	16	0.8809
RM161	5	80.7	69	7	0.8208	RM224	11	115.1	69	12	0.8687
RM421	5	101.5	69	3	0.4318	RM144	11	116.2	69	12	0.8456
RM274	5	109.0	69	9	0.6906	RM20A	12	9.7	69	16	0.8263
RM334	5	117.2	69	22	0.9162	RM19	12	19.1	69	12	0.7742
RM190	6	8.2	69	10	0.8423	RM247	12	26.7	69	22	0.9032
RM225	6	13.2	69	8	0.8158	RM101	12	48.2	69	17	0.7478
RM253	6	25.2	69	20	0.9095	RM7102	12	51.8	69	8	0.7872
RM527	6	56.3	69	14	0.8851	RM511	12	60.3	69	5	0.5793
RM5745	6	64.9	69	3	0.4814	RM463	12	75.8	69	5	0.6767
RM541	6	68.1	69	13	0.8368	RM270	12	91.3	69	4	0.4058
RM275	6	89.0	69	5	0.5238	RM17	12	107.4	69	10	0.6822

类群 Group	等位基因数 Number of alleles			Nei基因多样性指数 Nei's genetic diversity index
类群 Group	最大 Maximum		平均 Average	最大 Maximum	平均 Average
总样本Total	27	10.5	0.9452		0.7616
indica	9	4.3	0.8533		0.4990
aus	10	4.2	0.8889		0.5418
rayada	8	3.6	0.8750		0.4923
aromatic	10	4.4	0.8889		0.5311
tropical japonica	8	4.1	0.8642		0.5499
temperate japonica	11	4.2	0.8994		0.4851