SNP Markers Development and Genetic Relationship Analysis of Dendrobium Germplasms Using SLAF-seq Technology

doi:10.13560/j.cnki.biotech.bull.1985.2022-1386

Abstract

Abstract:

The genetic relationship of the collected Dendrobium germplasm resources was analyzed by SNP marker technology to provide theoretical basis for the selection of new varieties breeding parents. Total 60 Dendrobium germplasm resources were used for SNP marker development and genetic relationship analysis using specific-locus amplified fragment sequencing technology（SLAF-seq）. The sequencing data of each sample were statistically analyzed, and 157.34 Mb Clean Reads data were obtained. The Reads data of each sample ranged from 576 195 to 5 359 710. The average sequencing quality value（Q30）and GC content of samples was 93.85% and 40.16%. Through sequencing data analysis, a total of 1 337 217 SLAF tags and 1 049 638 polymorphic SLAF tags were obtained. The average sequencing depth of the tags was 9.63×. A total of 11 248 186 population SNP markers were developed. The number of SNP markers in each sample ranged from 694 015 to 6 367 379. The integrity ratio was 2.71% to 24.89%, and the hetloci ratio was 1.13% to 5.74%. The population SNPs were filtered, and a total of 31 499 highly consistent and effective SNP markers were obtained. The phylogenetic tree was constructed by using the SNP markers obtained. The 60 Dendrobium germplasm resources were divided into 3 subgroups. These three subgroups contained germplasm resources: Q1（3）, Q2（21）, and Q3（36）. The results of germplasm clustering were basically consistent with the morphological classification. Using SLAF-seq technology can efficiently and accurately develop SNP markers suitable for the genetic analysis of Dendrobium. The SNP markers developed may provide molecular basis for Dendrobium breeding, genetic map construction, variety identification and association analysis of agronomic traits.

Key words: Dendrobium, SLAF-seq, SLAF tags, SNP marker, population structure, phylogenetic tree, genetic relationship

CUI Xue-qiang, HUANG Chang-yan, DENG Jie-ling, LI Xian-min, LI Xiu-ling, ZHANG Zi-bin. SNP Markers Development and Genetic Relationship Analysis of Dendrobium Germplasms Using SLAF-seq Technology[J]. Biotechnology Bulletin, 2023, 39(6): 141-148.

Figures/Tables 5

References 25

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种质编号 Germplasm No.	总读数 Total reads	GC含量 GC content/%	Q30含量 Q30 content/%	种质编号 Germplasm No.	总读数 Total reads	GC含量 GC content/%	Q30含量 Q30 content/%
1	2 206 424	40.80	94.43	32	5 359 710	39.13	92.60
2	3 392 758	39.52	94.06	33	1 927 034	39.04	91.41
3	1 685 725	40.68	94.30	34	1 001 860	40.88	89.71
4	2 397 802	41.36	93.61	35	1 738 186	38.96	91.29
5	2 407 877	40.88	94.25	36	1 570 013	38.62	90.59
6	3 816 221	37.99	93.65	37	2 817 541	42.10	94.61
7	1 236 847	45.65	92.95	38	2 262 024	41.10	94.49
8	2 603 097	40.01	94.46	39	1 506 192	40.21	94.35
9	2 266 706	40.64	94.09	40	1 658 896	39.49	94.57
10	2 741 663	39.42	93.77	41	2 398 814	41.12	94.63
11	2 888 849	39.57	94.72	42	2 010 374	39.09	94.46
12	5 033 204	39.52	94.34	43	2 253 253	38.95	94.61
13	1 177 834	39.60	93.56	44	2 443 737	39.60	94.03
14	1 558 521	39.04	93.06	45	3 295 369	39.07	94.86
15	3 350 246	42.91	94.67	46	1 067 643	38.75	94.67
16	2 508 628	39.29	93.40	47	2 170 007	39.61	94.40
17	3 008 190	39.45	93.23	48	1 954 914	39.23	94.37
18	2 892 775	42.48	94.54	49	2 394 534	39.06	94.48
19	3 799 474	41.30	94.54	50	2 899 967	39.27	94.52
20	3 265 332	41.98	94.56	51	2 199 124	46.38	94.72
21	2 223 263	38.82	93.44	52	3 270 085	40.08	94.66
22	2 536 748	40.32	94.25	53	1 303 118	39.41	94.51
23	3 663 842	40.96	94.71	54	3 465 111	38.97	94.13
24	576 195	42.98	93.34	55	2 955 467	39.29	94.76
25	5 218 665	39.01	93.00	56	4 757 901	39.73	94.79
26	2 318 866	39.08	93.03	57	4 802 384	40.06	94.62
27	2 752 538	41.06	94.50	58	2 339 558	40.16	94.63
28	1 709 658	38.85	90.70	59	2 787 875	38.80	94.67
29	3 965 547	38.44	94.48	60	1 857 241	42.29	93.80
30	1 831 691	38.73	91.14	SD	7 293 431	42.86	94.33
31	3 836 959	40.67	94.49

种质编号 Germplasm No.	总读数 Total reads	GC含量 GC content/%	Q30含量 Q30 content/%	种质编号 Germplasm No.	总读数 Total reads	GC含量 GC content/%	Q30含量 Q30 content/%
1	2 206 424	40.80	94.43	32	5 359 710	39.13	92.60
2	3 392 758	39.52	94.06	33	1 927 034	39.04	91.41
3	1 685 725	40.68	94.30	34	1 001 860	40.88	89.71
4	2 397 802	41.36	93.61	35	1 738 186	38.96	91.29
5	2 407 877	40.88	94.25	36	1 570 013	38.62	90.59
6	3 816 221	37.99	93.65	37	2 817 541	42.10	94.61
7	1 236 847	45.65	92.95	38	2 262 024	41.10	94.49
8	2 603 097	40.01	94.46	39	1 506 192	40.21	94.35
9	2 266 706	40.64	94.09	40	1 658 896	39.49	94.57
10	2 741 663	39.42	93.77	41	2 398 814	41.12	94.63
11	2 888 849	39.57	94.72	42	2 010 374	39.09	94.46
12	5 033 204	39.52	94.34	43	2 253 253	38.95	94.61
13	1 177 834	39.60	93.56	44	2 443 737	39.60	94.03
14	1 558 521	39.04	93.06	45	3 295 369	39.07	94.86
15	3 350 246	42.91	94.67	46	1 067 643	38.75	94.67
16	2 508 628	39.29	93.40	47	2 170 007	39.61	94.40
17	3 008 190	39.45	93.23	48	1 954 914	39.23	94.37
18	2 892 775	42.48	94.54	49	2 394 534	39.06	94.48
19	3 799 474	41.30	94.54	50	2 899 967	39.27	94.52
20	3 265 332	41.98	94.56	51	2 199 124	46.38	94.72
21	2 223 263	38.82	93.44	52	3 270 085	40.08	94.66
22	2 536 748	40.32	94.25	53	1 303 118	39.41	94.51
23	3 663 842	40.96	94.71	54	3 465 111	38.97	94.13
24	576 195	42.98	93.34	55	2 955 467	39.29	94.76
25	5 218 665	39.01	93.00	56	4 757 901	39.73	94.79
26	2 318 866	39.08	93.03	57	4 802 384	40.06	94.62
27	2 752 538	41.06	94.50	58	2 339 558	40.16	94.63
28	1 709 658	38.85	90.70	59	2 787 875	38.80	94.67
29	3 965 547	38.44	94.48	60	1 857 241	42.29	93.80
30	1 831 691	38.73	91.14	SD	7 293 431	42.86	94.33
31	3 836 959	40.67	94.49