利用SSRseq分子标记的大蒜种质资源遗传多样性研究

doi:10.16420/j.issn.0513-353x.2021-0203

园艺学报 ›› 2021, Vol. 48 ›› Issue (7): 1397-1408.doi: 10.16420/j.issn.0513-353x.2021-0203

利用SSRseq分子标记的大蒜种质资源遗传多样性研究

赵青, 都真真, 李锡香, 宋江萍, 张晓辉, 阳文龙, 贾会霞, 王海平^*()

中国农业科学院蔬菜花卉研究所,农业农村部园艺作物生物学与种质创制重点实验室,北京 100081

收稿日期:2021-02-23 修回日期:2021-04-07 出版日期:2021-07-25 发布日期:2021-08-10
通讯作者: 王海平 E-mail:wanghaiping@caas.cn
基金资助:
国家自然科学基金项目(31872946);国家重点研发计划项目(2016YFD0100204);国家现代农业产业技术体系建设专项资金项目(CARS-24-A-01);中国农业科学院创新工程项目(CAAS-ASTIP-2017-IVFCAAS);中央级公益性科研院所基本科研业务费专项(IVF-BRF2018001);农业农村部作物种质资源保护项目;农业农村部作物种质资源安全保存项目;国家园艺种质北京蔬菜分库运行服务项目(NHGRC2021-NH01);国家作物种质资源数据中心观测监测任务项目(ZX01NK-03)

Genetic Diversity of Garlic Germplasm Resources Based on SSRseq Molecular Markers

ZHAO Qing, DU Zhenzhen, LI Xixiang, SONG Jiangping, ZHANG Xiaohui, YANG Wenlong, JIA Huixia, WANG Haiping^*()

Institute of Vegetables and Flowers,Chinese Academy of Agricultural Sciences/Key Laboratory of Horticultural Crop Biology and Germplasm Creation in the Ministry of Agriculture and Rural Affairs,Beijing 100081,China

Received:2021-02-23 Revised:2021-04-07 Online:2021-07-25 Published:2021-08-10
Contact: WANG Haiping E-mail:wanghaiping@caas.cn

摘要/Abstract

摘要：

利用筛选出的24对SSRseq引物对来自世界各地的676份大蒜种质进行遗传多样性、主坐标和群体遗传结构分析。结果表明：24对SSRseq标记在676份种质中共检测到124个多态性位点,平均等位位点数为5.17个,Nei’s多样性指数平均为1.77,Shannon’s 信息指数平均为0.62,平均观测杂合度和期望杂合度分别为0.33和0.34。用邻近法将676份资源划分为4类,其中第Ⅰ类包括以来源于亚洲中高纬度为主的186份种质,第Ⅱ类包括以来源于欧洲、中亚和北美洲为主的205份种质,第Ⅲ类包括以亚洲半抽薹类型的资源为主的132份种质,第Ⅳ类包括以来源于亚洲低纬度为主的153份种质。主坐标分析表明,亚洲低纬度地区的种质聚集在第Ⅰ类与第Ⅲ类,亚洲中高纬地区、欧洲、北美洲地区的种质聚集在第Ⅱ类。群体遗传结构分析将种质资源划分为4类,与邻近法聚类分析相似,以来自欧洲、中亚、北美洲为主的种质资源群体基因多样性和Shannon’s多样性信息指数最大,分别为0.3213与0.5933。用邻近法聚类分析与群体遗传结构分析均将382份中国资源划分为4类,分别以华北、华南、蒙新、西南地区种质为主。主坐标分析表明,中国华北、华南地区的种质分布在PC1的两端,表现出较远的亲缘关系。研究结果将为后期大蒜资源的深入评价和品种选育提供重要参考。

关键词: 大蒜, SSRseq, 群体结构, 遗传多样性

Abstract:

In this study,we revealed the genetic diversity,principal coordinate analysis and population structure analysis of 676 garlic accessions from all over the word by using 24 pairs of selected primers. The results indicate that a total of 124 polymorphic sites were detected,with an average of 5.17 alleles,an average of 1.77 for Nei's diversity index and 0.62 for Shannon information index. The mean values of observed and expected heterozygosity were 0.33 and 0.34,respectively. The method of neighbor-joining clustered all the accessions into four groups,group Ⅰ included 186 accessions,most of which were derived from middle and high latitudes of Asia,group Ⅱ included 205 accessions,most of which were derived from Europe,Central Asia and North America,group Ⅲ included 132 accessions,most of which were half-bolting types from Asia,group Ⅳ included 153 accessions,most of which were derived from lower latitudes of Asia. The garlic population was divided into three groups by principal coordinate analysis,accessions from lower latitude of Asia gathered in group Ⅰ and group,accessions from middle and high latitudes of Asia,Europe,North America area gathered in group Ⅱ. Population structure analysis divided the germplasm into four groups,which were similar to cluster analysis,there was gene exchange among different garlic groups. The genetic diversity and Shannon's diversity information index of germplasm resources from Europe,Central Asia and North America were the highest,which were 0.3213 and 0.5933,respectively,indicating that this population had rich genetic diversity. The method of neighbor-joining cluster analysis and population genetic structure analysis divided 382 Chinese resources into four groups,mainly from North China,South China,Mongol Xinjiang and Southwest China,respectively. The germplasm of North and South China was distributed at both ends of PC1 by principal coordinate analysis,showing a distant phylogenetic relationship. The results can provide scientific basis for the identification and evaluation of garlic germplasm and the breeding of superior garlic varieties.

Key words: garlic, SSRseq, population structure, genetic diversity

中图分类号:

S633.4

赵青, 都真真, 李锡香, 宋江萍, 张晓辉, 阳文龙, 贾会霞, 王海平. 利用SSRseq分子标记的大蒜种质资源遗传多样性研究[J]. 园艺学报, 2021, 48(7): 1397-1408.

ZHAO Qing, DU Zhenzhen, LI Xixiang, SONG Jiangping, ZHANG Xiaohui, YANG Wenlong, JIA Huixia, WANG Haiping. Genetic Diversity of Garlic Germplasm Resources Based on SSRseq Molecular Markers[J]. Acta Horticulturae Sinica, 2021, 48(7): 1397-1408.

图/表 12

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编号 Number	正向引物（5′-3′） Primer F	反向引物（5′-3′） Primer R	测序片段长度/bp Target length	重复类型Motif
0627E_1	GCTCATCTTGCCCTGTTCTC	CGCAAAGACAAAGACCTTTCA	270	GA
0627E_2	GCCGTATCCAAAGCTATCTATCA	AAAGAAGATCTCCCTGCCGT	228	CTT
0627E_3	ATCCGCTAGTTTGGCGACTA	CAAACTCTCCCGCCATTTTA	269	CTT
0627E_4	ATTTGATGCGGAGCAGATTT	TTCATCTTCACTTTCGCCCT	244	AGA
0627E_5	GATCAGCTGCGAAGAAGGAG	TTGAGCAATGGATTTCAGCA	114	GAA
0627E_6	AACTCTCCGTACCAACACCG	CTTGATCGAATTGAGCGTGA	196	CCT
0627E_7	CTGAGAGCGTGATGCCTGTA	TAGGTGGATTGTGCGAATGA	124	GAA
0627E_8	GACAATGATGGGGGACTTTG	CAACTCCATCACCTCCACCT	184	AGG
0627E_9	TGCTGGAAAGGAGTGTTTGA	CACTGCATAATCATGTCGGAA	214	GAA
0627E_10	GCCCTACTTGCAGAACCAAA	TAGGTCACGATTCACACGGA	267	GCA
0627E_11	GTGCAAGCTCAACTTCGTGA	AAAAGTGGAGCTGGGTTCCT	237	CAG
0627E_12	CTGCACTGAAAGCGATTGTG	AGGACTGTGGGGAAGGAGAT	174	ATC
0627E_13	CTTAAAACTCAGTTCGGCGG	AACCTTCAGCAAGCTTTGGA	194	AGA
0627E_14	GCTTGCTTCAGAAATACCCG	ATGGTACAATGCTGATGCCA	245	ACC
0627E_15	CTTGTCCGGTATGCAGGTTT	ACATTTCCAGTGCCTTCGAC	229	CTT
0627E_16	AAGCCAAGTCCTCTTAGCCC	CATGGGAATGACCGGATACT	269	TG
0627E_17	ACGTTTCGCCTTCTTCTTCA	CCGGTGAACTCTTGAACCAT	148	TCC
0627E_18	CCAGGAGTGAAGTTTGCCAT	AGCAAAGCCGCAAGAAATAA	180	CGG
0627E_19	GCAAAGCCTCAAATGTACCC	TGTGTCTGAGCCGCTAGATG	259	CAC
0627E_20	ATTCCTGGTAGACACGCACA	GTCCACCCCAAAATATGCAG	119	CA
0627E_21	CCACGAACAACATCACGATT	AGGTTGGTCATTTCGTCGTC	110	CGC
0627E_22	AAACGCAGATTCCAAAGTAATGA	CCAGCAAATTTGGTTGAAAAA	257	TG
0627E_23	GCTTCAGAGCCACCATTAGC	ACGTTTCGAACGGAGGAGTA	190	TAC
0627E_24	GGTCAATCGCAGGGTACCTA	AAGCAATATCAGTCATCGTCACA	242	CTT

编号 Number	正向引物（5′-3′） Primer F	反向引物（5′-3′） Primer R	测序片段长度/bp Target length	重复类型Motif
0627E_1	GCTCATCTTGCCCTGTTCTC	CGCAAAGACAAAGACCTTTCA	270	GA
0627E_2	GCCGTATCCAAAGCTATCTATCA	AAAGAAGATCTCCCTGCCGT	228	CTT
0627E_3	ATCCGCTAGTTTGGCGACTA	CAAACTCTCCCGCCATTTTA	269	CTT
0627E_4	ATTTGATGCGGAGCAGATTT	TTCATCTTCACTTTCGCCCT	244	AGA
0627E_5	GATCAGCTGCGAAGAAGGAG	TTGAGCAATGGATTTCAGCA	114	GAA
0627E_6	AACTCTCCGTACCAACACCG	CTTGATCGAATTGAGCGTGA	196	CCT
0627E_7	CTGAGAGCGTGATGCCTGTA	TAGGTGGATTGTGCGAATGA	124	GAA
0627E_8	GACAATGATGGGGGACTTTG	CAACTCCATCACCTCCACCT	184	AGG
0627E_9	TGCTGGAAAGGAGTGTTTGA	CACTGCATAATCATGTCGGAA	214	GAA
0627E_10	GCCCTACTTGCAGAACCAAA	TAGGTCACGATTCACACGGA	267	GCA
0627E_11	GTGCAAGCTCAACTTCGTGA	AAAAGTGGAGCTGGGTTCCT	237	CAG
0627E_12	CTGCACTGAAAGCGATTGTG	AGGACTGTGGGGAAGGAGAT	174	ATC
0627E_13	CTTAAAACTCAGTTCGGCGG	AACCTTCAGCAAGCTTTGGA	194	AGA
0627E_14	GCTTGCTTCAGAAATACCCG	ATGGTACAATGCTGATGCCA	245	ACC
0627E_15	CTTGTCCGGTATGCAGGTTT	ACATTTCCAGTGCCTTCGAC	229	CTT
0627E_16	AAGCCAAGTCCTCTTAGCCC	CATGGGAATGACCGGATACT	269	TG
0627E_17	ACGTTTCGCCTTCTTCTTCA	CCGGTGAACTCTTGAACCAT	148	TCC
0627E_18	CCAGGAGTGAAGTTTGCCAT	AGCAAAGCCGCAAGAAATAA	180	CGG
0627E_19	GCAAAGCCTCAAATGTACCC	TGTGTCTGAGCCGCTAGATG	259	CAC
0627E_20	ATTCCTGGTAGACACGCACA	GTCCACCCCAAAATATGCAG	119	CA
0627E_21	CCACGAACAACATCACGATT	AGGTTGGTCATTTCGTCGTC	110	CGC
0627E_22	AAACGCAGATTCCAAAGTAATGA	CCAGCAAATTTGGTTGAAAAA	257	TG
0627E_23	GCTTCAGAGCCACCATTAGC	ACGTTTCGAACGGAGGAGTA	190	TAC
0627E_24	GGTCAATCGCAGGGTACCTA	AAGCAATATCAGTCATCGTCACA	242	CTT

标记 Marker	等位基因数 N_a	有效等位基因数N_e	Shannon's指数 I	观测杂合度 H_o	期望杂合度 H_e	基因流 N_m
0627E_1	7	3.58	1.38	0.77	0.72	2.89
0627E_2	7	3.82	1.48	0.70	0.74	4.39
0627E_3	4	2.39	1.06	0.53	0.58	14.33
0627E_4	6	1.47	0.65	0.37	0.32	6.83
0627E_5	3	1.00	0.02	0.00	0.00	7.08
0627E_6	4	1.03	0.08	0.01	0.03	5.92
0627E_7	4	1.70	0.65	0.25	0.41	1.39
0627E_8	4	1.03	0.08	0.01	0.03	5.07
0627E_9	4	2.14	0.88	0.34	0.53	1.83
0627E_10	6	1.57	0.60	0.45	0.36	3.90
0627E_11	6	1.87	0.71	0.54	0.47	1.66
0627E_12	5	1.56	0.64	0.44	0.36	0.15
0627E_13	2	1.02	0.04	0.00	0.01	3.43
0627E_14	5	1.30	0.47	0.25	0.23	6.58
0627E_15	6	2.04	0.80	0.12	0.51	4.08
0627E_16	5	1.74	0.69	0.54	0.43	2.32
0627E_17	5	2.56	1.07	0.97	0.61	20.86
0627E_18	7	1.93	0.88	0.43	0.48	3.85
0627E_19	5	1.15	0.32	0.14	0.13	3.05
0627E_20	5	1.18	0.32	0.15	0.15	3.28
0627E_21	7	1.36	0.57	0.19	0.27	5.89
0627E_22	4	1.04	0.11	0.02	0.04	4.36
0627E_23	9	2.98	1.32	0.71	0.66	9.79
0627E_24	4	1.02	0.06	0.00	0.02	3.21
总计Total	124	42.48	14.88	7.93	8.09	126.14
平均值Average	5.17	1.77	0.62	0.33	0.34	5.26
标准差St. Dev	1.55	0.80	0.44	0.28	0.24	4.46

标记 Marker	等位基因数 N_a	有效等位基因数N_e	Shannon's指数 I	观测杂合度 H_o	期望杂合度 H_e	基因流 N_m
0627E_1	7	3.58	1.38	0.77	0.72	2.89
0627E_2	7	3.82	1.48	0.70	0.74	4.39
0627E_3	4	2.39	1.06	0.53	0.58	14.33
0627E_4	6	1.47	0.65	0.37	0.32	6.83
0627E_5	3	1.00	0.02	0.00	0.00	7.08
0627E_6	4	1.03	0.08	0.01	0.03	5.92
0627E_7	4	1.70	0.65	0.25	0.41	1.39
0627E_8	4	1.03	0.08	0.01	0.03	5.07
0627E_9	4	2.14	0.88	0.34	0.53	1.83
0627E_10	6	1.57	0.60	0.45	0.36	3.90
0627E_11	6	1.87	0.71	0.54	0.47	1.66
0627E_12	5	1.56	0.64	0.44	0.36	0.15
0627E_13	2	1.02	0.04	0.00	0.01	3.43
0627E_14	5	1.30	0.47	0.25	0.23	6.58
0627E_15	6	2.04	0.80	0.12	0.51	4.08
0627E_16	5	1.74	0.69	0.54	0.43	2.32
0627E_17	5	2.56	1.07	0.97	0.61	20.86
0627E_18	7	1.93	0.88	0.43	0.48	3.85
0627E_19	5	1.15	0.32	0.14	0.13	3.05
0627E_20	5	1.18	0.32	0.15	0.15	3.28
0627E_21	7	1.36	0.57	0.19	0.27	5.89
0627E_22	4	1.04	0.11	0.02	0.04	4.36
0627E_23	9	2.98	1.32	0.71	0.66	9.79
0627E_24	4	1.02	0.06	0.00	0.02	3.21
总计Total	124	42.48	14.88	7.93	8.09	126.14
平均值Average	5.17	1.77	0.62	0.33	0.34	5.26
标准差St. Dev	1.55	0.80	0.44	0.28	0.24	4.46

群体 Subpopulation	样品大小 Samples number	基因多样性 Gene diversity	Shannon’s 多样性指数 Shannon’s index
G1	215	0.3213	0.5933
G2	150	0.2243	0.3390
G3	186	0.1276	0.1802
G4	125	0.2383	0.4030

利用SSRseq分子标记的大蒜种质资源遗传多样性研究

Genetic Diversity of Garlic Germplasm Resources Based on SSRseq Molecular Markers

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群体Subpopulation	G1	G2	G3	G4
G1		0.221	0.095	0.186
G2	0.148		0.245	0.288
G3	0.094	0.249		0.275
G4	0.124	0.185	0.207

群体 Subpopulation	样品大小 Samples number	基因多样性 Gene diversity	Shannon’s 多样性指数 Shannon’s index
G1	143	0.1350	0.2005
G2	125	0.2170	0.3186
G3	19	0.4345	0.7895
G4	95	0.1553	0.2256

群体Subpopulation	G1	G2	G3	G4
G1		0.2525	0.1779	0.3377
G2	0.2550		0.2495	0.3297
G3	0.1580	0.1720		0.2390
G4	0.3660	0.3020	0.1820

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利用SSRseq分子标记的大蒜种质资源遗传多样性研究

Genetic Diversity of Garlic Germplasm Resources Based on SSRseq Molecular Markers

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