Genetic Structure Analysis of Picea crassifolia Based on Genome-wide SNP Molecular Markers

doi:10.7525/j.issn.1673-5102.2022.03.007

Abstract

Abstract:

A total of 106 clones of Picea crassifolia in Longqu P. crassifolia Clone Seed Orchard in Zhangye were used as materials， and the genomic DNA of P. crassifolia was extracted by improved CTAB method， the SLAF library was constructed and sequenced with high flux， and then the SLAF sequencing data were analyzed and SNP sites were screened， and the clustering of samples was obtained based on adjacency analysis respectively. The results showed that the efficiency of two terminal alignment was 95.33%， indicated that the SLAF database was successfully established. The Q30 of the sequence measured and the sequencing quality was high， but the error rate of base sequencing was low. A total of 4 058 883 SLAF tags were developed， and the average sequencing depth of the tags was 21.21×. A total of 12 275 765 P. crassifolia SNP markers were developed， and the number of SNPs in each P. crassifolia sample ranged from 1 890 934-4 487 841. Using the developed high quality SNP markers of P. crassifolia， 106 phylogenetic trees of P. crassifolia were constructed. It was found that P. crassifolia from different provenances were evenly distributed in each group， and P. crassifolia from different provenances mostly were clustered into one class. By SNP markers and principal component analysis， these clones were more likely to be derived from the same ancestor， indicated that the genetic relationship between clones was similar. It provids basic data for the analysis of genetic diversity and the construction of genetic map in the future， and also provids a basis for the elite seeds selection in P. crassifolia primary seed orchard， and lays a foundation for the construction of high generation seed orchard.

Key words: Picea crassifolia, DNA extraction, SLAF label, genetic structure analysis

CLC Number:

S722.5

Hongbin ZHANG, Dong LÜ, Ming ZHAO, Hu ZHAO, Xingpeng ZHAO, Wei LI. Genetic Structure Analysis of Picea crassifolia Based on Genome-wide SNP Molecular Markers[J]. Bulletin of Botanical Research, 2022, 42(3): 373-382.

Figures/Tables 6

Table 1

Table 2

Sequencing result of P. crassifolia

样品 Sample	Reads数量 Reads number	GC碱基比例 GC percentage /%	Q30 /%	样品 Sample	Reads数量 Reads number	GC碱基比例 GC Percentage /%	Q30 /%
2	12 146 243	39.66	97.34	75	27 070 087	40.57	94.28
3	24 241 911	40.45	92.31	76	13 240 839	40.53	93.85
4	8 152 218	41.63	93.37	77	7 634 863	40.79	94.37
5	16 862 228	40.43	94.15	79	10 089 736	40.30	94.13
6	14 751 714	40.16	93.61	80	8 736 905	40.67	93.46
7	30 427 534	40.59	94.21	82	14 917 563	39.95	97.10
9	10 048 409	40.65	94.02	83	15 371 612	39.73	97.82
10	11 555 933	39.78	97.68	85	14 684 553	39.68	97.30
11	19 330 765	39.94	93.09	87	20 033 110	39.34	97.57
12	8 841 081	40.21	94.52	88	28 707 808	39.65	97.71
14	8 576 004	40.60	93.99	89	9 351 352	40.30	93.38
15	17 319 977	41.00	93.19	90	8 111 089	40.14	93.35
17	8 990 525	39.73	97.52	91	14 487 381	40.19	93.43
18	18 189 255	40.65	93.17	92	14 917 678	39.53	97.63
19	14 768 755	40.08	93.98	93	13 759 732	39.90	97.61
20	5 030 643	40.45	94.28	94	10 413 249	39.48	97.57
21	9 138 350	40.64	93.87	95	11 396 311	39.62	97.74
22	13 998 204	41.42	94.11	96	8 028 318	39.67	97.54
23	10 909 007	40.73	92.91	97	22 758 710	39.97	92.50
25	12 353 762	41.39	93.38	98	15 850 692	39.19	97.67
26	4 800 937	40.30	94.25	101	18 092 780	40.20	93.55
27	15 072 877	40.81	93.43	103	9 349 642	41.09	93.82
28	12 689 902	40.38	93.76	105	9 812 558	40.02	94.24
30	5 167 434	42.14	94.46	106	4 556 284	40.13	94.55
31	10 644 008	39.75	97.67	107	7 358 455	40.11	94.43
32	12 885 735	43.62	92.31	108	13 981 084	40.04	97.81
33	6 805 875	40.10	94.39	109	12 592 356	41.23	97.58
34	21 616 266	40.13	97.79	111	8 842 740	40.45	93.98
35	11 611 262	40.77	93.93	116	8 385 599	41.02	94.01
36	4 411 192	40.76	93.78	118	15 464 622	39.86	97.77
39	12 226 428	39.98	97.70	123	8 839 070	39.19	97.62
42	9 675 424	41.50	94.28	124	8 077 398	40.49	93.26
45	9 145 446	40.71	93.51	125	19 127 204	41.42	93.77
48	10 170 557	39.52	97.40	128	24 215 373	39.61	94.39
49	12 403 724	39.82	97.63	130	5 449 712	41.56	94.05
51	10 368 220	39.57	97.43	132	17 452 700	40.03	97.41
52	19 183 107	39.58	97.51	133	14 656 193	39.81	97.70
54	11 692 092	39.59	97.71	135	14 908 559	40.97	94.36
55	7 235 883	39.88	97.48	138	14 464 740	40.72	94.16
56	14 602 000	39.71	97.54	140	8 795 260	39.42	97.66
57	21 325 095	40.15	97.41	142	10 900 920	40.73	93.51
60	9 268 409	39.98	97.64	145	13 401 810	39.79	97.75
61	11 063 287	39.65	97.78	146	11 524 254	39.64	97.51
62	11 532 628	39.77	97.78	148	11 297 193	40.15	97.44
64	13 724 591	40.12	97.33	150	15 421 893	39.73	97.45
66	8 816 718	39.73	97.73	152	9 091 753	40.62	94.40
67	7 304 810	40.90	94.39	153	21 765 056	40.38	97.64
68	13 542 675	40.85	92.67	154	13 367 005	40.33	97.55
69	8 165 970	40.08	97.20	155	10 172 094	40.41	97.63
70	22 365 733	40.65	92.75	156	13 494 970	39.21	97.79
71	21 941 923	40.17	90.97	158	16 212 064	39.49	97.74
72	7 773 989	41.66	94.24	161	19 033 231	39.74	97.68
73	7 717 213	40.03	93.11	164	13 327 258	39.19	97.82

Table 2

Table 3

SLAF tag statistics of P. crassifolia

样品 Sample	SLAF标签数 SLAF number	测序总深度 Total depth	平均测序深度 Average sequencing depth /×	样品 Sample	SLAF标签数 SLAF number	测序总深度 Total depth	平均测序深度 Average sequencing depth /×
2	283 717	7 873 658	27.75	75	634 128	17 396 837	27.43
3	659 680	15 347 986	23.27	76	403 787	8 450 911	20.93
4	344 102	5 229 683	15.20	77	325 372	4 842 419	14.88
5	482 133	10 804 488	22.41	79	350 373	6 373 063	18.19
6	495 908	9 454 803	19.07	80	336 768	5 611 089	16.66
7	708 255	19 752 908	27.89	82	330 756	9 563 151	28.91
9	371 375	6 449 443	17.37	83	356 480	9 985 631	28.01
10	331 478	7 421 661	22.39	85	322 277	9 426 340	29.25
11	494 355	12 659 785	25.61	87	566 876	12 911 648	22.78
12	376 358	5 800 464	15.41	88	607 100	18 258 838	30.08
14	441 006	5 429 629	12.31	89	349 540	5 936 414	16.98
15	491 444	10 983 018	22.35	90	325 755	5 236 638	16.08
17	325 156	5 812 190	17.88	91	403 779	9 277 664	22.98
18	505 319	11 543 410	22.84	92	329 819	9 579 711	29.05
19	430 073	9 550 710	22.21	93	342 438	8 918 869	26.05
20	305 926	3 281 598	10.73	94	644 360	6 612 971	10.26
21	364 661	5 836 862	16.01	95	312 698	7 402 699	23.67
22	439 626	8 824 107	20.07	96	309 093	5 190 628	16.79
23	415 196	6 900 230	16.62	97	544 451	14 562 977	26.75
25	473 236	7 799 968	16.48	98	429 471	10 039 734	23.38
26	316 568	3 134 561	9.90	101	464 833	11 586 985	24.93
27	437 772	9 622 570	21.98	103	383 368	5 938 816	15.49
28	428 672	8 121 110	18.94	105	330 137	6 307 582	19.11
30	300 021	3 266 162	10.89	106	282 123	2 996 839	10.62
31	310 233	6 894 152	22.22	107	336 957	4 845 120	14.38
32	450 419	7 617 695	16.91	108	333 343	9 067 734	27.20
33	318 282	4 496 327	14.13	109	363 929	8 027 585	22.06
34	423 593	13 973 551	32.99	111	363 390	5 668 890	15.60
35	424 551	7 498 549	17.66	116	374 221	5 291 881	14.14
36	270 596	2 815 411	10.40	118	356 171	10 005 848	28.09
39	336 312	7 935 385	23.60	123	369 445	5 619 881	15.21
42	395 383	6 185 133	15.64	124	314 201	5 204 019	16.56
45	319 732	5 801 761	18.15	125	436 450	12 148 040	27.83
48	302 612	6 537 445	21.60	128	519 047	15 632 012	30.12
49	297 968	7 990 841	26.82	130	319 221	3 423 360	10.72
51	270 600	6 709 651	24.80	132	305 735	11 260 150	36.83
52	699 363	12 170 897	17.40	133	353 696	9 479 624	26.80
54	610 820	7 354 427	12.04	135	423 032	9 580 803	22.65
55	316 164	4 628 653	14.64	138	366 512	9 298 310	25.37
56	398 646	9 299 796	23.33	140	296 040	5 719 814	19.32
57	367 385	13 590 078	36.99	142	349 964	6 995 137	19.99
60	334 384	5 958 739	17.82	145	345 367	8 712 936	25.23
61	308 031	7 192 502	23.35	146	284 569	7 445 141	26.16
62	338 272	7 458 343	22.05	148	347 636	7 280 860	20.94
64	424 361	8 729 259	20.57	150	305 218	9 867 284	32.33
66	310 171	5 713 877	18.42	152	319 674	5 823 188	18.22
67	345 644	4 710 390	13.63	153	475 857	14 030 436	29.48
68	422 843	8 621 261	20.39	154	356 950	8 542 542	23.93
69	328 370	5 232 840	15.94	155	325 592	6 509 041	19.99
70	563 993	14 204 545	25.19	156	426 427	8 758 461	20.54
71	439 168	14 049 337	31.99	158	308 212	10 467 617	33.96
72	368 468	4 907 444	13.32	161	320 028	12 378 938	38.68
73	327 831	4 977 618	15.18	164	353 721	8 651 293	24.46

Table 3

Table 4

SNP information statistics of P. crassifolia

样品 Sample	SNP数量 SNP number	完整度 Integrity ratio /%	杂合率 Heter ratio /%	样品 Sample	SNP数量 SNP number	完整度 Integrity ratio /%	杂合率 Heter ratio /%
2	1 971 193	16.06	7.69	75	4 136 952	33.70	9.80
3	4 136 822	33.70	9.52	76	2 717 377	22.14	5.76
4	2 396 731	19.52	8.27	77	2 217 145	18.06	7.03
5	3 108 723	25.32	7.76	79	2 366 746	19.28	7.24
6	3 178 543	25.89	7.92	80	2 282 147	18.59	6.86
7	4 487 841	36.56	10.99	82	2 286 061	18.62	8.11
9	2 533 393	20.64	7.59	83	2 430 707	19.80	9.06
10	2 251 295	18.34	8.95	85	2 242 174	18.27	8.32
11	3 241 100	26.40	9.10	87	3 338 208	27.19	7.88
12	2 522 359	20.55	7.28	88	3 531 028	28.76	8.70
14	2 950 389	24.03	8.62	89	2 389 125	19.46	7.24
15	3 267 024	26.61	9.08	90	2 193 067	17.87	6.88
17	2 201 266	17.93	9.06	91	2 656 046	21.64	7.34
18	3 377 556	27.51	8.86	92	2 267 242	18.47	9.15
19	2 828 634	23.04	7.60	93	2 348 631	19.13	9.14
20	2 090 116	17.03	6.36	94	3 606 123	29.38	8.47
21	2 475 276	20.16	7.20	95	2 139 811	17.43	8.81
22	3 052 930	24.87	9.11	96	2 120 259	17.27	9.08
23	2 898 300	23.61	8.49	97	3 541 604	28.85	9.12
25	3 261 249	26.57	9.47	98	2 564 309	20.89	6.67
26	2 145 298	17.48	6.49	101	3 007 490	24.50	8.63
27	3 058 956	24.92	8.93	103	2 710 974	22.08	9.07
28	2 956 993	24.09	8.62	105	2 222 120	18.10	6.81
30	2 099 746	17.10	6.67	106	1 939 562	15.80	6.45
31	2 128 003	17.33	8.80	107	2 352 208	19.16	7.60
32	3 058 296	24.91	8.95	108	2 301 940	18.75	8.35
33	2 144 399	17.47	6.63	109	2 525 069	20.57	9.42
34	2 858 436	23.29	9.14	111	2 431 938	19.81	7.25
35	2 906 011	23.67	8.17	116	2 573 445	20.96	7.21
36	1 915 028	15.60	6.53	118	2 429 920	19.79	9.23
39	2 316 925	18.87	8.84	123	2 303 375	18.76	6.68
42	2 761 907	22.50	8.36	124	2 159 104	17.59	6.92
45	2 185 404	17.80	6.15	125	3 014 132	24.55	8.47
48	2 090 766	17.03	9.28	128	3 279 851	26.72	7.99
49	2 074 937	16.90	8.40	130	2 262 880	18.43	7.88
51	1 890 934	15.40	8.42	132	2 132 709	17.37	5.41
52	4 049 531	32.99	8.99	133	2 433 809	19.83	9.36
54	3 291 325	26.81	7.87	135	2 927 258	23.85	8.41
55	2 156 368	17.57	8.88	138	2 546 908	20.75	7.98
56	2 587 466	21.08	7.95	140	2 032 448	16.56	8.58
57	2 558 408	20.84	9.02	142	2 439 976	19.88	7.85
60	2 272 844	18.51	9.29	145	2 363 702	19.26	9.27
61	2 102 345	17.13	8.59	146	1 971 986	16.06	8.18
62	2 332 513	19.00	9.23	148	2 378 440	19.38	9.11
64	2 844 988	23.18	9.43	150	2 123 625	17.30	8.35
66	2 134 550	17.39	8.99	152	2 152 132	17.53	6.54
67	2 397 443	19.53	7.18	153	3 065 469	24.97	8.70
68	2 925 591	23.83	9.08	154	2 466 491	20.09	9.72
69	2 252 820	18.35	8.94	155	2 218 384	18.07	8.88
70	3 739 016	30.46	9.51	156	2 737 463	22.30	8.11
71	3 043 281	24.79	8.62	158	2 117 277	17.25	7.96
72	2 476 112	20.17	6.96	161	2 208 835	17.99	8.50
73	2 248 977	18.32	7.24	164	2 321 578	18.91	7.34

Table 4

Fig.1

Fig.2

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材料来源 Material sources	北纬度 Latitude（N）	东经度 Longitude（E）	海拔 Elevation /m
西水林区（XS）	38°23′~38°48′	100°3′~100°23′	2 400~4 000
连城林区（LC）	36°33′~36°48′	102°26′~102°55′	1 870~3 616
大黄山林区（DHS）	38°20′~38°30′	101°~101°30′	2 400~3 977
哈溪林区（HX）	37°16′~37°45′	102°1′~102°51′	2 500~4 500
东大山林区（DDS）	39°~39°4′	100°45′~100°51′	2 500~3 600
隆畅河林区（LCH）	38°39′~38°56′	99°32′~100°1′	2 000~3 900
古城林区（GC）	36°45′~37°7′	102°26′~102°51′	2 050~3 500
大河口林区（DHK）	37°54′~38°31′	100°31′~100°56′	2 400~4 000
祁连林区（QL）	37°31′~37°51′	102°6′~102°25′	2 300~4 500
西营河林区（XYH）	37°34′~38°5′	101°26′~102°23′	2 400~4 800
寺大隆林区（SDL）	38°13′~38°42′	99°30′~100°15′	2 800~4 800

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