Genetic Diversity and Principal Component Analysis of 125 Potato Germplasm Resources

doi:10.13560/j.cnki.biotech.bull.1985.2024-1285

Abstract

Abstract:

Objective To clarify the genetic relationship between potato germplasm resources, and to provide a research basis for the creation of new germplasm. Method In this paper, 125 potato varieties (lines) were used as research materials. Morphological markers and SSR molecular markers were used to analyze the differences among germplasm resources, and principal component analysis was used to evaluate the genetic diversity. Result The coefficient of variation of the eight phenotypic traits ranged from 19.40% to 63.90%, and the diversity index ranged from 0.990 7 to 1.001 0. According to phenotypic traits, the tested materials could be divided into four categories, most of which were clustered according to phenotypic index characteristics. Twenty-seven pairs of polymorphic SSR primers were screened, and 910 alleles and 832 polymorphic sites were amplified, with a polymorphism site ratio of 90.93%. The average Nei’s genetic diversity (H) and Shannon’s index (I) were 0.228 6 and 0.362 1, respectively. According to SSR test results, the test materials were clustered into five categories. Most of the varieties were clustered according to their geographical origin, and the new strains were clustered according to their parents. PCA analysis of SSR marker clusters showed that the coordinated distribution results of each group were basically consistent with the clustering results, and the two analysis results supported each other. Conclusion There are differences in the classification of groups between phenotypic traits and SSR marker clustering results, but some potato materials show consistent in the two clustering methods, and the materials from the same geographical origin are clustered into one group. Phenotypic traits are affected by environmental conditions and human factors, and cannot reflect all genomic information, but molecular markers directly detect molecular differences in the genome. The combination of the two methods should be used in the analysis and evaluation of genetic diversity of potato germplasm resources, which may provide reference for potato germplasm innovation and genetic improvement.

Key words: potato, germplasm resources, phenotypic traits, SSR marker, genetic diversity

DUAN Yong-hong, YANG Xin, YU Guan-qun, XIA Jun-jun, SONG Lu-shuai, BAI Xiao-dong, PENG Suo-tang. Genetic Diversity and Principal Component Analysis of 125 Potato Germplasm Resources[J]. Biotechnology Bulletin, 2025, 41(6): 130-143.

Figures/Tables 10

References 34

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编号 Code	材料名称 Accession	编号 Code	材料名称 Accession	编号 Code	新品系 New strain	编号 Code	新品系 New strain
1	陇薯7号 Longshu No.7	32	克新27号 Kexin No.27	63	L10HJG-6	94	H14HJG-8
2	陇薯10号 Longshu No.10	33	克新30号 Kexin No3.0	64	L10HJG-7	95	H14HJG-9
3	陇薯14号 Longshu No.14	34	克新33号 Kexin No.33	65	L10HJG-8	96	H14HJG-10
4	陇薯20号 Longshu No.20	35	克新34号 Kexin No.34	66	L10HJG-9	97	L6HJG-2
5	青薯9号 Qingshu No.9	36	华颂7号 Huasong No.7	67	L10HJG-11	98	L6HJG-3
6	青薯10号 Qingshu No.10	37	华颂34 Huasong No.34	68	L10476-5	99	L6HJG-4
7	石薯1号 shishu No.1	38	东农312号 Dongnong No.312	69	L10476-6	100	L6HJG-6
8	石薯3号 shishu No.3	39	东农321号 Dongnong No.321	70	L10476-12	101	Z9476-1
9	京张薯1号 Jingzhangshu No.1	40	东农322号 Dongnong No.322	71	E3ZMG-2	102	Z9476-2
10	京张薯2号 Jingzhangshu No.2	41	丽薯6号 Lishu No.6	72	E3ZMG-3	103	Z9476-5
11	京张薯3号 Jingzhangshu No.3	42	丽薯14号 Lishu No.14	73	E3ZMG-4	104	E3476-2
12	天薯11号 Tianshu No.11	43	希森6号 Xishen No.6	74	L6H14-7	105	E3476-3
13	天薯12号 Tianshu No.12	44	荷兰14号 Holland No.14	75	L6H14-11	106	E3476-6
14	天薯17号 Tianshu No.17	45	夏波帝 shepody	76	L10H14-1	107	MFHL14-1
15	晋薯15号 Jingshu No.15	46	麦肯1号 innovator	77	L10H14-4	108	MFHL14-2
16	晋薯16号 Jingshu No.16	47	大西洋 Atlantic	78	H14ZMG-5	109	Z306K25-2
17	中薯9号 Zhongshu No.9	48	延薯9号 Yanshu No.9	79	H14ZMG-9	110	Z306K25-3
18	中薯10号 Zhongshu No.10	49	辽薯6号 Liaoshu No.6	80	H14ZMG-10	111	L14K23-1
19	中薯17号 Zhongshu No.17	50	定薯6号 Dingshu No.6	81	H14ZMG-11	112	J15476-1
20	中薯18号 Zhongshu No.18	51	云薯401 Yunshu No.401	82	MFH476-1	113	J15476-3
21	中薯19号 Zhongshu No.19	52	垦薯1号 Kengshu No.1	83	MFH476-2	114	J15476-4
22	中薯21号 Zhongshu No.21	53	费乌瑞它 FAVORITA	84	MFH476-4	115	L17L16-7
23	中薯306 Zhongshu No.306	54	华晟7号 Huasheng No.7	85	MFH476-5	116	L17L16-8
24	中加2号 Zhongjia No.2	55	冀张薯8号 Jizhangshu No.8	86	MFH476-8	117	MFH476-6
25	中加7号 Zhongjia No.7	56	延薯13号 Yanshu No.13	87	MFH476-9	118	MFH476-10
26	鄂薯3号 Eshu No.3	57	北方016 Beifang No.016	88	MFH476-11	119	E3ZMG-6
27	鄂薯13号 Eshu No.13	58	EV	89	MFH476-12	120	E3ZMG-9
28	鄂薯14号 Eshu No.14	59	黑金刚 Black king kong	90	K13H14-6	121	H14HJG-2
29	克新13号 Kexin No.13	60	476	91	K13H14-10	122	H14HJG-7
30	克新23号 Kexin No.23	61	民丰红 Mingfenghong	92	K13H14-12	123	L6HJG-5
31	克新25号 Kexin No.25	62	紫玫瑰 Zimeigui	93	H14HJG-6	124	L10476-4
						125	L10HJG-3

编号 Code	材料名称 Accession	编号 Code	材料名称 Accession	编号 Code	新品系 New strain	编号 Code	新品系 New strain
1	陇薯7号 Longshu No.7	32	克新27号 Kexin No.27	63	L10HJG-6	94	H14HJG-8
2	陇薯10号 Longshu No.10	33	克新30号 Kexin No3.0	64	L10HJG-7	95	H14HJG-9
3	陇薯14号 Longshu No.14	34	克新33号 Kexin No.33	65	L10HJG-8	96	H14HJG-10
4	陇薯20号 Longshu No.20	35	克新34号 Kexin No.34	66	L10HJG-9	97	L6HJG-2
5	青薯9号 Qingshu No.9	36	华颂7号 Huasong No.7	67	L10HJG-11	98	L6HJG-3
6	青薯10号 Qingshu No.10	37	华颂34 Huasong No.34	68	L10476-5	99	L6HJG-4
7	石薯1号 shishu No.1	38	东农312号 Dongnong No.312	69	L10476-6	100	L6HJG-6
8	石薯3号 shishu No.3	39	东农321号 Dongnong No.321	70	L10476-12	101	Z9476-1
9	京张薯1号 Jingzhangshu No.1	40	东农322号 Dongnong No.322	71	E3ZMG-2	102	Z9476-2
10	京张薯2号 Jingzhangshu No.2	41	丽薯6号 Lishu No.6	72	E3ZMG-3	103	Z9476-5
11	京张薯3号 Jingzhangshu No.3	42	丽薯14号 Lishu No.14	73	E3ZMG-4	104	E3476-2
12	天薯11号 Tianshu No.11	43	希森6号 Xishen No.6	74	L6H14-7	105	E3476-3
13	天薯12号 Tianshu No.12	44	荷兰14号 Holland No.14	75	L6H14-11	106	E3476-6
14	天薯17号 Tianshu No.17	45	夏波帝 shepody	76	L10H14-1	107	MFHL14-1
15	晋薯15号 Jingshu No.15	46	麦肯1号 innovator	77	L10H14-4	108	MFHL14-2
16	晋薯16号 Jingshu No.16	47	大西洋 Atlantic	78	H14ZMG-5	109	Z306K25-2
17	中薯9号 Zhongshu No.9	48	延薯9号 Yanshu No.9	79	H14ZMG-9	110	Z306K25-3
18	中薯10号 Zhongshu No.10	49	辽薯6号 Liaoshu No.6	80	H14ZMG-10	111	L14K23-1
19	中薯17号 Zhongshu No.17	50	定薯6号 Dingshu No.6	81	H14ZMG-11	112	J15476-1
20	中薯18号 Zhongshu No.18	51	云薯401 Yunshu No.401	82	MFH476-1	113	J15476-3
21	中薯19号 Zhongshu No.19	52	垦薯1号 Kengshu No.1	83	MFH476-2	114	J15476-4
22	中薯21号 Zhongshu No.21	53	费乌瑞它 FAVORITA	84	MFH476-4	115	L17L16-7
23	中薯306 Zhongshu No.306	54	华晟7号 Huasheng No.7	85	MFH476-5	116	L17L16-8
24	中加2号 Zhongjia No.2	55	冀张薯8号 Jizhangshu No.8	86	MFH476-8	117	MFH476-6
25	中加7号 Zhongjia No.7	56	延薯13号 Yanshu No.13	87	MFH476-9	118	MFH476-10
26	鄂薯3号 Eshu No.3	57	北方016 Beifang No.016	88	MFH476-11	119	E3ZMG-6
27	鄂薯13号 Eshu No.13	58	EV	89	MFH476-12	120	E3ZMG-9
28	鄂薯14号 Eshu No.14	59	黑金刚 Black king kong	90	K13H14-6	121	H14HJG-2
29	克新13号 Kexin No.13	60	476	91	K13H14-10	122	H14HJG-7
30	克新23号 Kexin No.23	61	民丰红 Mingfenghong	92	K13H14-12	123	L6HJG-5
31	克新25号 Kexin No.25	62	紫玫瑰 Zimeigui	93	H14HJG-6	124	L10476-4
						125	L10HJG-3

序号 Code	引物名称 Primer name	正向引物 Forward primer （5′-3′）	反向引物 Reverse primer （5′-3′）	重复基元类型 Repeat motif type	染色体 Chromosome	退火温度 Annealing temperature （℃）
1	C33	TCCCCTTACCCCTCTTCAAAT	AACCCGTGTCAACTTCYGCT	（CAG）n	III	48.3
2	C59	TCATCACAACGTGACCCCA	GGGCTTGAATGATGTGAAGCTC	（CAG）n	II	55.1
3	S25	AGAGATCGATGTAAAACACGT	GTGGCATTTTGATGGATT	（TCA）n	V	48.5
4	S151	GCTGCTAAACACTCAAGCAGAA	CAACTACAAGATTCCATCCACAC	（TCA）n	VI	54.7
5	STM-2022	GCGTCAGCGATTTCAGTACTA	TTCAGTCAACTCCTGTTGCG	（CAA）n…（CAA）n	II	48.5
6	STM0030	AGAGATCGATGTAAAACACGT	GTGGCATTTTGATGGATT	（GT/GC）（GT）n	III	57.7
7	SSI	TCTCTTGACACGTGTCACTGAAAC	TCACCGATTACAGTAGGCAAGAGA	（CA）n	VIII	53.4
8	Patatin	CAACCAACAAGGTAAATGGTACC	TGGTCTGGTGCATTAGAAAAAA	（TCT）n	VIII	54.0
9	S189	CCTTGTAGTACAGCAGTGGTC	TCCGCCAAGACIGATGCA	（AC）n	VI	56.7
10	C42	AGGCAAACCCCGTAAATCTT	TCTTCCTCACTCGTCCCCCACT	（GAA）n	II	53.1
11	STM1052	CAATTTCGTTTTTTCATGTGACAC	ATGGCGTAATTTGATTTAATACGTAA	（AT）n GT （AT）n （GT）n	IX	54.5
12	S25-2	GCGAATGACAGGACAAGAGG	TGCCACTGCTACCATAACCA	（CGG）n	X	52.7
13	S174	TGAGGGTTTTCAGAAAGGGA	CATCCTTGCAACAACCTCCT	（GA）n（AT）n（AC）n	VII	52.8
14	S153	TATGTTCCACGCCATTTCAG	ACGGAAACTCATCGTGCATT	（GAT）n（GCA）n	XII	48.5
15	S118	AGAGATCGATGTAAAACACGT	GTGGCATTTTGATGGATT	（ATT）n	VIII	51.7
16	S170	CGCAAATCTTCATCCGATTC	TCCGGCGGATAATACTTGTT	（GAC）n	VIII	53.0
17	C54	TGGCTGCAGAAATCAAGATG	TGAAACCACTGGGAGGACTT	（AT）n	VI	51.4
18	STM0019a	AATAGGTGTACTGACTCTCAATG	TTGAAGTAAAAGTCCTAGTATGTG	（AT）n（GT）n（AT）n（GT）n（GC）n（GT）n	VI	53.0
19	STL003	ACCATCCACCATGTCAATGC	CTCATGGATGGTGTCATTGG	（CAG）n	VIII	54.1
20	S7	GACTGGCTGACCCTGAACTC	GACAAAATTACAGGAACTGCAAA	（CGA）n（GAA）n（TCT）n	II	55.6
21	STM1014	AGAAACTGAGTTGTGTGTTGGGA	TCAACAGTCTCAGAAACCCTCT	（TCT）n	III	54.6
22	C58	GCTGCTAAACACTCAAGCAGAA	CAACTACAAGATTCCATCCACAG	（TCA）n	VI	55.1
23	S184	TCATCACAACGTGACCCCA	GGGCTTGAATGATGTGAAGCTC	（TG）n（AT）n	II	53.3
24	S192	ACTTCTGCATCTGGTGAAGC	GGTCTGGATTCCCAGGTTG	（ATA）n	III	54.9
25	SSR59	TTCGTTGAAGAAGATGATGGTC	CAAAGAGGGCAAGCATCCAAGA	（AAG）n（ATA）n（TCT）n	VIII	54.7
26	STM3023	AAGCTGTTACTTGATTGCTGCA	GTTCTGGCATTTCCATCTAGAGA	（GA）9 （GA）8 （GA）4	IV	52.5
27	C3	CCGGGAGAATTAGACGATGA	TTTATGGGGAGCAGTTGAGG	（GAT）n	XI	55.5
28	STM1104	TGATTCTCTTGCCTACTGTAATCG	GAAAGTGGTGTGAAGCTGTGA	（TCT）n	VIII	54.8
29	STI049	TCATCACAACGTGACCCC	CGGGCTTGAATGATGTGAAGCT	（TG）n（AT）n	II	54.8
30	SSR0707	AGAAATTGGCAGAGCATTTAGCTG	GGATTAGACAAACCTTCTTTTCCACA	（TA）n（AC）n	III	56.6
31	S180	ACTGCTGTGGTTGGCGTC	ACGGCATAGATTTGGAAGCATC	（TAA）n	VIII	55.5
32	PM0936	AGTTGTGTCTCAATCCTTTCACGA	TGCTTAAAAATCTGACTTTGGTGTTC	（GA）n	XII	56.4
33	SSR0675	GCTGTGTTTTCAATTTCTTCAGCA	GTCTCGTTGTTCATCAAA	（AC）n	VI	50.6
34	STM0037	AATTTAACTTAGAAGATTAGTCTC	ATTTGGTTGGGTATGATA	（TC）n（AC）nAA（AC）n（AT）n	VI	44.6
35	STI0012	GAAGCGACTTCCAAAATCAGA	AAAGGGAGGATTAGAAACCAAAA	（ATT）n	IV	52.4
36	STM1106	TCCAGCTGATTGGTTAGGTTG	ATGCGAATCTACTCGTCATGG	（ATT）n	X	53.9
37	STG0016	AGCTGCTCAGCATCAAGAGA	ACCACCTCAGGCACTTCATC	（AGA）n	I	55.0

序号 Code	引物名称 Primer name	正向引物 Forward primer （5′-3′）	反向引物 Reverse primer （5′-3′）	重复基元类型 Repeat motif type	染色体 Chromosome	退火温度 Annealing temperature （℃）
1	C33	TCCCCTTACCCCTCTTCAAAT	AACCCGTGTCAACTTCYGCT	（CAG）n	III	48.3
2	C59	TCATCACAACGTGACCCCA	GGGCTTGAATGATGTGAAGCTC	（CAG）n	II	55.1
3	S25	AGAGATCGATGTAAAACACGT	GTGGCATTTTGATGGATT	（TCA）n	V	48.5
4	S151	GCTGCTAAACACTCAAGCAGAA	CAACTACAAGATTCCATCCACAC	（TCA）n	VI	54.7
5	STM-2022	GCGTCAGCGATTTCAGTACTA	TTCAGTCAACTCCTGTTGCG	（CAA）n…（CAA）n	II	48.5
6	STM0030	AGAGATCGATGTAAAACACGT	GTGGCATTTTGATGGATT	（GT/GC）（GT）n	III	57.7
7	SSI	TCTCTTGACACGTGTCACTGAAAC	TCACCGATTACAGTAGGCAAGAGA	（CA）n	VIII	53.4
8	Patatin	CAACCAACAAGGTAAATGGTACC	TGGTCTGGTGCATTAGAAAAAA	（TCT）n	VIII	54.0
9	S189	CCTTGTAGTACAGCAGTGGTC	TCCGCCAAGACIGATGCA	（AC）n	VI	56.7
10	C42	AGGCAAACCCCGTAAATCTT	TCTTCCTCACTCGTCCCCCACT	（GAA）n	II	53.1
11	STM1052	CAATTTCGTTTTTTCATGTGACAC	ATGGCGTAATTTGATTTAATACGTAA	（AT）n GT （AT）n （GT）n	IX	54.5
12	S25-2	GCGAATGACAGGACAAGAGG	TGCCACTGCTACCATAACCA	（CGG）n	X	52.7
13	S174	TGAGGGTTTTCAGAAAGGGA	CATCCTTGCAACAACCTCCT	（GA）n（AT）n（AC）n	VII	52.8
14	S153	TATGTTCCACGCCATTTCAG	ACGGAAACTCATCGTGCATT	（GAT）n（GCA）n	XII	48.5
15	S118	AGAGATCGATGTAAAACACGT	GTGGCATTTTGATGGATT	（ATT）n	VIII	51.7
16	S170	CGCAAATCTTCATCCGATTC	TCCGGCGGATAATACTTGTT	（GAC）n	VIII	53.0
17	C54	TGGCTGCAGAAATCAAGATG	TGAAACCACTGGGAGGACTT	（AT）n	VI	51.4
18	STM0019a	AATAGGTGTACTGACTCTCAATG	TTGAAGTAAAAGTCCTAGTATGTG	（AT）n（GT）n（AT）n（GT）n（GC）n（GT）n	VI	53.0
19	STL003	ACCATCCACCATGTCAATGC	CTCATGGATGGTGTCATTGG	（CAG）n	VIII	54.1
20	S7	GACTGGCTGACCCTGAACTC	GACAAAATTACAGGAACTGCAAA	（CGA）n（GAA）n（TCT）n	II	55.6
21	STM1014	AGAAACTGAGTTGTGTGTTGGGA	TCAACAGTCTCAGAAACCCTCT	（TCT）n	III	54.6
22	C58	GCTGCTAAACACTCAAGCAGAA	CAACTACAAGATTCCATCCACAG	（TCA）n	VI	55.1
23	S184	TCATCACAACGTGACCCCA	GGGCTTGAATGATGTGAAGCTC	（TG）n（AT）n	II	53.3
24	S192	ACTTCTGCATCTGGTGAAGC	GGTCTGGATTCCCAGGTTG	（ATA）n	III	54.9
25	SSR59	TTCGTTGAAGAAGATGATGGTC	CAAAGAGGGCAAGCATCCAAGA	（AAG）n（ATA）n（TCT）n	VIII	54.7
26	STM3023	AAGCTGTTACTTGATTGCTGCA	GTTCTGGCATTTCCATCTAGAGA	（GA）9 （GA）8 （GA）4	IV	52.5
27	C3	CCGGGAGAATTAGACGATGA	TTTATGGGGAGCAGTTGAGG	（GAT）n	XI	55.5
28	STM1104	TGATTCTCTTGCCTACTGTAATCG	GAAAGTGGTGTGAAGCTGTGA	（TCT）n	VIII	54.8
29	STI049	TCATCACAACGTGACCCC	CGGGCTTGAATGATGTGAAGCT	（TG）n（AT）n	II	54.8
30	SSR0707	AGAAATTGGCAGAGCATTTAGCTG	GGATTAGACAAACCTTCTTTTCCACA	（TA）n（AC）n	III	56.6
31	S180	ACTGCTGTGGTTGGCGTC	ACGGCATAGATTTGGAAGCATC	（TAA）n	VIII	55.5
32	PM0936	AGTTGTGTCTCAATCCTTTCACGA	TGCTTAAAAATCTGACTTTGGTGTTC	（GA）n	XII	56.4
33	SSR0675	GCTGTGTTTTCAATTTCTTCAGCA	GTCTCGTTGTTCATCAAA	（AC）n	VI	50.6
34	STM0037	AATTTAACTTAGAAGATTAGTCTC	ATTTGGTTGGGTATGATA	（TC）n（AC）nAA（AC）n（AT）n	VI	44.6
35	STI0012	GAAGCGACTTCCAAAATCAGA	AAAGGGAGGATTAGAAACCAAAA	（ATT）n	IV	52.4
36	STM1106	TCCAGCTGATTGGTTAGGTTG	ATGCGAATCTACTCGTCATGG	（ATT）n	X	53.9
37	STG0016	AGCTGCTCAGCATCAAGAGA	ACCACCTCAGGCACTTCATC	（AGA）n	I	55.0

性状 Trait	最大值 Max	最小值 Min	极差 Range	平均值 Mean	标准差 SD	变异系数 CV （%）	Simpson指数 Simpson index
主茎数 Number of main stems	11.00	1.00	10.00	3.56	1.60	45.03	0.992 6
分支数 Number of branches	14.00	0.00	14.00	4.07	2.60	63.90	0.990 7
株高 Plant height （cm）	130.0	22.00	108.00	60.45	16.08	26.60	0.991 6
茎粗 Stem diameter （mm）	20.61	4.45	16.16	12.08	2.34	19.40	0.992 4
单株产量 Yield per plant （kg）	2.64	0.06	2.58	0.99	0.36	36.60	0.999 1
单株结薯数 Number of potatoes per plant	47.00	1.00	46.00	8.38	3.69	44.03	0.991 4
大中薯 Number of large and medium potatoes	11.00	0.00	11.00	4.50	1.92	42.70	0.992 3
大中薯重 Weight of large and medium potato （kg）	2.38	0.00	2.38	0.79	0.34	42.34	1.001 0