Genetic Relationship Analysis of Sorghum Breeding Materials Based on Simplified Genome Sequencing

doi:10.13560/j.cnki.biotech.bull.1985.2020-0344

Abstract

Abstract:

The objective of this study is to explore the genetic structure and relationship of sorghum breeding materials,and to provide theoretical basis for crossbreeding,germplasm innovation and heterosis group construction in the future. Specific-locus amplified fragment sequencing（SLAF-seq）was used to sequence 37 sorghum materials. The sorghum genome（Sorghum_bicolor_v3.1）was used as the reference genome for enzyme digestion prediction and the Nipponbare rice were as the control,and single nucleotide polymorphism（SNP）markers were developed and applied to genetic structure and genetic relationship analysis of breeding materials. Results showed that 106.19 Mb reads length data were obtained by sequencing from the 37 sorghum materials. The reads of the samples varied from 1 461 206 to 4 628 462. The paired-end mapped reads efficiency of the control data was 92.15%,the enzyme digestion efficiency was 89.69%,which indicated that SLAF database was normal. The average quality of sequencing Q30 was 89.60%,and the average GC content of all samples was 45.71%. A total of 226 724 SLAF tags were developed,of which 105 053 were polymorphic SLAF tags. A total 185 451 effective single nucleotide polymorphisms（SNPs）were obtained by sequence analysis. Based on these SNPs,37 sorghum breeding materials were divided into two groups by genetic structure analysis and principal component analysis. The maintenance lines and foreign materials were grouped into one,the restoration lines and Chinese materials were grouped into another one,and the grouping result was basically consistent with the actual genealogy. The genetic distance between materials was estimated based on SNP markers and the distance ranged from 0.0098 to 0.8841. The genetic distance between L2R and L17R was the smallest,and the genetic distance between 3765 white B and L17R was the largest. In this study,the blood relationship of some foreign materials was clarified. It was further found that the sterility lines of Durra and Kafir-caudatum were most distantly related to trend Kaoliang restoration lines,and more attentions should be paid to it in selecting parents for sorghum cross breeding.

Key words: sorghum, specific-locus amplified fragment sequencing, breeding materials, genetic structure, genetic relationship

ZHANG Yi-zhong, FAN Xin-qi, YANG Hui-yong, ZHANG Xiao-juan, SHAO Qiang, LIANG Du, GUO Qi, LIU Qing-shan, DU Wei-jun. Genetic Relationship Analysis of Sorghum Breeding Materials Based on Simplified Genome Sequencing[J]. Biotechnology Bulletin, 2020, 36(12): 21-33.

Figures/Tables 14

References 36

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编号	材料名称	类型	来源	编号	材料名称	类型	来源
1	L2R	恢复系	中国四川	20	10480B	保持系	中国山西
2	L17R	恢复系	中国山西	21	1383-2	恢复系	中国山西
3	忻粱7号	恢复系	中国山西	22	5-26	恢复系	中国辽宁
4	LNR-4	恢复系	中国辽宁	23	LgB/R5M874B-I	保持系	中国山西
5	3560R	恢复系	中国四川	24	LgB/R5M874B-III	保持系	中国山西
6	R111	恢复系	中国山西	25	11494B	保持系	中国山西
7	锦Y15	恢复系	中国辽宁	26	7B大粒/TB	保持系	中国山西
8	LR233	恢复系	中国山西	27	5-27	恢复系	中国辽宁
9	铁10612	保持系	中国辽宁	28	0-30	恢复系	中国辽宁
10	L早615	恢复系	中国山西	29	非洲高粱	地方品种	马达加斯加
11	吉12	恢复系	中国吉林	30	吉2055B	保持系	中国吉林
12	H02079	恢复系	中国黑龙江	31	L407B	保持系	中国辽宁
13	072198	恢复系	中国黑龙江	32	AGR-1B	保持系	中国四川
14	晋粱5号	恢复系	中国山西	33	棒洛三	地方品种	中国山西
15	V4B	保持系	印度	34	三尺三	地方品种	中国山西
16	8808B	保持系	中国四川	35	吉R105	恢复系	中国吉林
17	45B	保持系	中国四川	36	Tx3197B	保持系	美国
18	3765红B	保持系	中国山西	37	Tx623B	保持系	美国
19	3765白B	保持系	中国山西

编号	材料名称	类型	来源	编号	材料名称	类型	来源
1	L2R	恢复系	中国四川	20	10480B	保持系	中国山西
2	L17R	恢复系	中国山西	21	1383-2	恢复系	中国山西
3	忻粱7号	恢复系	中国山西	22	5-26	恢复系	中国辽宁
4	LNR-4	恢复系	中国辽宁	23	LgB/R5M874B-I	保持系	中国山西
5	3560R	恢复系	中国四川	24	LgB/R5M874B-III	保持系	中国山西
6	R111	恢复系	中国山西	25	11494B	保持系	中国山西
7	锦Y15	恢复系	中国辽宁	26	7B大粒/TB	保持系	中国山西
8	LR233	恢复系	中国山西	27	5-27	恢复系	中国辽宁
9	铁10612	保持系	中国辽宁	28	0-30	恢复系	中国辽宁
10	L早615	恢复系	中国山西	29	非洲高粱	地方品种	马达加斯加
11	吉12	恢复系	中国吉林	30	吉2055B	保持系	中国吉林
12	H02079	恢复系	中国黑龙江	31	L407B	保持系	中国辽宁
13	072198	恢复系	中国黑龙江	32	AGR-1B	保持系	中国四川
14	晋粱5号	恢复系	中国山西	33	棒洛三	地方品种	中国山西
15	V4B	保持系	印度	34	三尺三	地方品种	中国山西
16	8808B	保持系	中国四川	35	吉R105	恢复系	中国吉林
17	45B	保持系	中国四川	36	Tx3197B	保持系	美国
18	3765红B	保持系	中国山西	37	Tx623B	保持系	美国
19	3765白B	保持系	中国山西

编号	测序片段数/个	GC含量/%	Q30值/%	编号	测序片段数/个	GC含量/%	Q30值/%
1	3 567 939	46.21	89.83	20	1 946 504	45.94	89.49
2	4 628 462	45.53	89.73	21	2 460 604	45.70	90.16
3	3 166 760	46.23	89.80	22	2 646 261	45.80	89.97
4	3 885 523	45.36	90.09	23	2 440 775	45.58	89.38
5	3 933 701	46.01	90.26	24	2 601 176	45.37	90.05
6	3 024 122	46.41	89.90	25	2 282 802	45.97	89.35
7	3 579 391	45.64	90.00	26	2 952 467	45.34	89.93
8	3 532 436	45.20	90.12	27	2 353 719	45.80	89.67
9	2 734 469	45.80	89.70	28	3 851 721	45.29	89.22
10	1 497 466	46.53	90.16	29	3 927 558	44.51	90.26
11	2 022 644	46.15	89.63	30	3 133 975	45.48	89.27
12	1 461 206	46.28	90.91	31	2 745 391	45.41	89.09
13	1 633 119	46.08	89.54	32	3 952 510	45.16	88.96
14	2 323 181	46.77	89.30	33	3 014 449	45.64	89.42
15	1 919 156	46.26	90.03	34	2 963 041	45.71	89.35
16	2 224 406	46.14	90.15	35	3 311 922	45.26	88.00
17	2 375 725	45.73	89.44	36	3 862 422	44.58	88.47
18	2 275 153	46.14	88.83	37	3 680 028	44.73	88.38
19	2 285 308	45.66	89.31	对照	484 025	43.18	88.87

编号	测序片段数/个	GC含量/%	Q30值/%	编号	测序片段数/个	GC含量/%	Q30值/%
1	3 567 939	46.21	89.83	20	1 946 504	45.94	89.49
2	4 628 462	45.53	89.73	21	2 460 604	45.70	90.16
3	3 166 760	46.23	89.80	22	2 646 261	45.80	89.97
4	3 885 523	45.36	90.09	23	2 440 775	45.58	89.38
5	3 933 701	46.01	90.26	24	2 601 176	45.37	90.05
6	3 024 122	46.41	89.90	25	2 282 802	45.97	89.35
7	3 579 391	45.64	90.00	26	2 952 467	45.34	89.93
8	3 532 436	45.20	90.12	27	2 353 719	45.80	89.67
9	2 734 469	45.80	89.70	28	3 851 721	45.29	89.22
10	1 497 466	46.53	90.16	29	3 927 558	44.51	90.26
11	2 022 644	46.15	89.63	30	3 133 975	45.48	89.27
12	1 461 206	46.28	90.91	31	2 745 391	45.41	89.09
13	1 633 119	46.08	89.54	32	3 952 510	45.16	88.96
14	2 323 181	46.77	89.30	33	3 014 449	45.64	89.42
15	1 919 156	46.26	90.03	34	2 963 041	45.71	89.35
16	2 224 406	46.14	90.15	35	3 311 922	45.26	88.00
17	2 375 725	45.73	89.44	36	3 862 422	44.58	88.47
18	2 275 153	46.14	88.83	37	3 680 028	44.73	88.38
19	2 285 308	45.66	89.31	对照	484 025	43.18	88.87

编号	SLAF标签数/个	平均测序深度/×	SNP个数/个	SNP完整度/%	SNP杂合率/%
1	183 156	15.90	333 872	47.26	5.11
2	185 016	21.61	311 459	44.09	4.79
3	180 402	14.77	297 415	42.10	4.50
4	190 803	17.56	302 139	42.77	12.81
5	187 939	17.25	342 316	48.46	5.48
6	183 062	13.51	321 331	45.49	7.91
7	182 682	16.60	308 210	43.63	4.88
8	184 786	15.90	316 840	44.85	4.41
9	181 967	12.61	293 483	41.54	3.13
10	155 692	7.15	263 779	37.34	4.91
11	165 815	9.55	272 674	38.60	4.95
12	154 623	7.05	256 240	36.27	4.27
13	160 222	8.28	239 963	33.97	5.14
14	167 159	11.39	264 921	37.50	4.49
15	166 553	8.99	276 512	39.14	3.75
16	176 033	9.81	304 536	43.11	3.31
17	175 330	11.26	273 048	38.65	2.49
18	175 129	10.63	275 800	39.04	2.58
19	172 299	11.05	263 219	37.26	2.73
20	169 084	9.35	261 891	37.07	3.57
21	171 602	11.85	272 682	38.60	4.29
22	177 676	12.00	298 725	42.29	3.80
23	175 244	11.61	269 964	38.21	5.11
24	175 560	12.20	283 319	40.10	3.71
25	177 840	10.40	284 973	40.34	3.22
26	181 621	13.63	290 251	41.09	2.95
27	172 939	10.99	283 654	40.15	3.88
28	183 861	17.91	291 301	41.23	4.59
29	184 381	18.14	300 566	42.55	3.76
30	184 919	14.17	309 217	43.77	3.42
31	181 436	12.87	273 308	38.69	3.42
32	190 434	17.71	315 042	44.60	2.70
33	181 663	13.58	310 318	43.93	4.44
34	191 999	12.83	308 762	43.71	13.32
35	182 399	15.28	296 553	41.98	4.73
36	185 333	18.20	278 585	39.43	3.30
37	191 557	16.65	294 393	41.67	1.79