基于简化基因组测序高粱育种材料亲缘关系的分析

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

摘要/Abstract

摘要：

探明高粱育种材料的遗传结构和亲缘关系,为今后高粱杂交育种、种质创新及杂种优势群构建提供理论依据。采用简化基因组测序技术（Specific-locus amplified fragment sequencing,SLAF-seq）对37份高粱材料进行测序,以高粱（Sorghum bicolor_v3.1）基因组为参考基因组进行酶切预测,以水稻品种日本晴为对照进行比对分析,开发单核苷酸多态性（Single nucleotide polymorphism,SNP）标记并将其应用于育种材料的遗传结构和亲缘关系分析。结果表明,从37份高粱材料中共获得106.19 Mb的读长数据,不同材料的读长个数在1 461 206-4 628 462;对照数据的双端比对效率为92.15%,酶切效率为89.69%,SLAF建库正常。测序质量值Q30平均为89.60%,所有样品GC含量均值为45.71%,共开发了226 724个SLAF标签,其中多态性SLAF标签有105 053个,通过序列分析共获得185 451个有效标记。群体遗传结构分析和主成分分析都将37份高粱育种材料划分为2个类群,保持系和国外材料聚为一类,恢复系和中国材料聚为一类,分群结果与实际系谱基本相符。根据SNP标记估算材料间的遗传距离,距离值范围为0.0098-0.8841,L2R与L17R遗传距离最小,3765白B与L17R遗传距离最大。本研究明确了部分外引材料的血缘关系,并发现都拉类型、卡佛尔/顶尖类型的不育系与倾中国高粱的恢复系亲缘关系最远,在高粱杂交育种选配亲本上应加以重视。

关键词: 高粱, SLAF-seq, 育种材料, 遗传结构, 亲缘关系

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

张一中, 范昕琦, 杨慧勇, 张晓娟, 邵强, 梁笃, 郭琦, 柳青山, 杜维俊. 基于简化基因组测序高粱育种材料亲缘关系的分析[J]. 生物技术通报, 2020, 36(12): 21-33.

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.

图/表 14

参考文献 36

[1]	Huang RD. Research progress on plant tolerance to soil salinity and alkalinity in sorghum[J]. Journal of Integrative Agriculture, 2018,17(4):739-746.
[2]	Fujimoto R, Uezono K, Ishikura S, et al. Recent research on the mechanism of heterosis is important for crop and vegetable breeding systems[J]. Breeding Science, 2018,68(2):145-158. URL pmid: 29875598
[3]	Rakshit S, Hariprasanna K, Gomashe S, et al. Changes in area, yield gains, and yield stability of sorghum in major sorghum-producing countries, 1970 to 2009[J]. Crop Science, 2014,54:1571-1584.
[4]	王瑞, 王金胜, 张福耀, 等. 1970s—2000s中国高粱杂交种亲本遗传距离演变的SSR分析[J]. 中国农业科学, 2015,48(3):415-425.
	Wang R, Wang JS, Zhang FY, et al. Evolution of genetic distance between parental lines of Chinese sorghum hybrids from1970s-2000s based on SSR analysis[J]. Scientia Agricultura Sinica, 2015,48(3):415-425.
[5]	侯荷亭, 杜志宏, 赵根弟. 高粱亲本遗传距离与杂种优势和特殊配合力的关系[J]. 遗传, 1995,17(1):30-33.
	Hou HT, Du ZH, Zhao GD. Studies on the relationships of genetic distance of sorghum parental lines with heterosis and specific combining ability[J]. Hereditas(Beijing), 1995,17(1):30-33.
[6]	Wang LM, Jiao SJ, Jiang YX, et al. Genetic diversity in parent lines of sweet sorghum based on agronomical traits and SSR markers[J]. Field Crops Research, 2013,149:11-19.
[7]	Basahi MA. ISSR-based analysis of genetic diversity among sorghum landraces growing in some parts of Saudi Arabia and Yemen[J]. Comptes Rendus Biologies, 2015,338(11):723-727. URL pmid: 26496867
[8]	高旭, 周棱波, 张国兵, 等. 基于SSR标记的粒用高粱资源遗传多样性及群体结构[J]. 贵州农业科学, 2016,44(9):13-19.
	Gao X, Zhou LB, Zhang GB, et al. Genetic diversity and population structure of grain sorghum germplasm resources based on SSR marker[J]. Guizhou Agricultural Sciences, 2016,44(9):13-19.
[9]	李萌, 秦慧彬, 王宇楠, 等. 基于SSR标记的山西高粱地方品种遗传多样性和遗传结构分析[J]. 分子植物育种, 2020-06-01, http://kns.cnki.net/kcms/detail/46.1068.S.20191011.0902.002.html. URL pmid: 31598026
	Li M, Qin HB, Wang YN, et al. Genetic diversity and structure of sorghum landrace germplasm in Shanxi based on SSR markers[J]. Molecular Plant Breeding, 2020-06-01, http://kns.cnki.net/kcms/detail/46.1068.S.20191011.0902.002.html. URL pmid: 31598026
[10]	石璇, 王茹媛, 唐君, 等. 利用简化基因组技术分析甘薯种间单核苷酸多态性[J]. 作物学报, 2016,42(5):641-647.
	Shi X, Wang RY, Tang J, et al. Analysis of interspecific SNPs in sweet potato using a reduced-representation genotyping technology[J]. Acta Agronomica Sinica, 2016,42(5):641-647.
[11]	Sun XW, Liu DY, Zhang XF, et al. SLAF-seq:an efficient method of large-scale de novo SNP discovery and genotyping using high-throughput sequencing[J]. PLoS One, 2013,8(3):e58700. URL pmid: 23527008
[12]	杨光, 孙兰英, 段亚东, 等. 基于简化基因组测序的树莓(Rubus corchorifolius)遗传分析[J]. 分子植物育种, 2019,17(22):7338-7343.
	Yang G, Sun LY, Duan YD, et al. Genetic analysis of Rubus corchorifolius based on simplified genome sequencing[J]. Molecular Plant Breeding, 2019,17(22):7338-7343.
[13]	Shen C, Jin X, Zhu D, et al. Uncovering SNP and indel variations of tetraploid cottons by SLAF-seq[J]. BMC Genomics, 2017,18:247.
[14]	Su WJ, Wang LJ, Lei J, et al. Genome-wide assessment of population structure and genetic diversity and development of a core germplasm set for sweet potato based on specific length amplified fragment(SLAF)sequencing[J]. PLoS One, 2017,12(2):e0172066.
[15]	籍贵苏, 吕芃, 杜瑞恒, 等. 高粱单核苷酸多态性(SNP)标记开发研究初报[J]. 华北农学报, 2018,33(2):119-125.
	Ji GS, Lv P, Du RH, et al. A primary study on developing SNP markers in sorghum[J]. Acta Agriculturae Boreali-Sinica, 2018,33(2):119-125.
[16]	Ji GS, Zhang QS, Du RH, et al. Construction of a high-density genetic map using specific-locus amplified fragments in sorghum[J]. BMC Genomics, 2017,18(1):51. URL pmid: 28061813
[17]	Han YC, Lv P, Hou SL, et al. Combining next generation sequencing with bulked segregant analysis to fine map a stem moisture locus in Sorghum(Sorghum bicolor L. Moench)[J]. PLoS One, 2015,10(5):e0127065. URL pmid: 25984727
[18]	王瑞, 凌亮, 詹鹏杰, 等. 控制高粱分蘖与主茎株高一致性的基因定位[J]. 作物学报, 2019,45(6):829-838.
	Wang R, Ling L, Zhan PJ, et al. Mapping of genes confessing same height of tiller and main stem in sorghum[J]. Acta Agronomica Sinica, 2019,45(6):829-838.
[19]	张一中. 高粱育种材料主要性状综合评价及骨干亲本亲缘关系鉴定[D]. 太谷:山西农业大学, 2017.
	Zhang YZ. Comprehensive evaluation of main characters of sorghum breeding materials and identification of genetic relationships among the backone parents[D]. Taigu: Shanxi Agricultural University, 2017.
[20]	Kozich JJ, Westcott SL, Baxter NT, et al. Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the Miseq Illumina sequencing platform[J]. Applied and Environmental Microbiology, 2013,79(17):5112-5120. doi: 10.1128/AEM.01043-13 URL pmid: 23793624
[21]	俞奔驰, 韦丽君, 雷开文, 等. 基于SLAF-seq技术的木薯SNP标记开发[J]. 植物生理学报, 2018,54(6):1029-1037.
	Yu BC, Wei LJ, Lei KW, et al. Development of SNP markers in cas-sava(Manihot esculenta Crantz)based on SLAF-seq technology[J]. Plant Physiology Journal, 2018,54(6):1029-1037.
[22]	Li H, Handsaker B, Wysoker A, et al. The sequence alignment/map format and samtools[J]. Bioinformatics, 2009,25(16):2078-2079. URL pmid: 19505943
[23]	Mckenna A, Hanna M, Banks E, et al. The Genome Analysis Toolkit:A MapReduce framework for analyzing next-generation DNA sequencing data[J]. Genome Research, 2010,20(9):1297-1303. doi: 10.1101/gr.107524.110 URL pmid: 20644199
[24]	Alexander DH, Novembre J, Lange K. Fast model-based estimation of ancestry in unrelated individuals[J]. Genome Research, 2009,19(9):1655-1664. URL pmid: 19648217
[25]	Tamura K, Peterson D, Peterson N, et al. MEGA5:Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods[J]. Molecular Biology & Evolution, 2011,28(10):2731-2739. URL pmid: 21546353
[26]	Price AL, Patterson NJ, Plenge RM, et al. Principal components analysis corrects for stratification in genome-wide association studies[J]. Nature Genetics, 2006,38(8):904-909.
[27]	Li RQ, Yu C, Li YR, et al. SOAP2:an improved ultrafast tool for short read alignment[J]. Bioinformatics, 2009,25(15):1966-1967.
[28]	赵秀华, 刘家裕, 柏德华, 等. 高粱恢复系“4003”及其衍生系的选育与利用研究[J]. 辽宁农业科学, 1995(1):37-41.
	Zhao XH, Liu JY, Bai DH, et al. Breeding and utilization of sorghum restorer line ‘4003' and its derivative lines[J]. Liaoning Agricultural Sciences, 1995(1):37-41.
[29]	王瑞, 张福耀, 王花云, 等. 高粱抗旱种质筛选及遗传多样性的SSR分析[J]. 植物遗传资源学报, 2014,15(4):871-876.
	Wang R, Zhang FY, Wang HY, et al. Drought resistance screening and genetic diversity by SSR markers in sorghum[J]. Journal of Plant Genetic Resources, 2014,15(1):871-876.
[30]	倪先林, 赵甘霖, 刘天朋, 等. SSR分子标记在糯高粱种质资源遗传多样性分析中的应用[J]. 江苏农业学报, 2015,31(1):16-22.
	Ni XL, Zhao GL, Liu TP, et al. Genetic diversity analysis of glutinous sorghum germplasm by simple sequence repeat[J]. Jiangsu Journal of Agricultural Sciences, 2015,31(1):16-22.
[31]	Adugna A. Analysis of in situ diversity and population structure in ethiopian cultivated Sorghum bicolor(L.)landraces using phenotypic traits and SSR markers[J]. Springer Plus, 2014,3:212. URL pmid: 24877027
[32]	Wang YH, Upadhyaya HD, Burrell AM, et al. Genetic structure and linkage disequilibrium in a diverse, representative collection of the C4 model plant, Sorghum bicolor[J]. Genes Genomes Genetics, 2013,3:783-793. doi: 10.1534/g3.112.004861 URL pmid: 23704283
[33]	屈洋, 周瑜, 王钊, 等. 苦荞产区种质资源遗传多样性和遗传结构分析[J]. 中国农业科学, 2016,49(11):2049-2062.
	Qu Y, Zhou Y, Wang Z, et al. Analysis of genetic diversity and structure of tartary buckwheat resources from production regions[J]. Scientia Agricultura Sinica, 2016,49(11):2049-2062.
[34]	蒙祖庆, 宋丰萍, 刘婷. 西藏玉米地方品种与国内骨干自交系间的遗传关系分析[J]. 核农学报, 2018,32(7):1298-1308.
	Meng ZQ, Song FP, Liu T. Analysis of genetic relationship between the Tibetan maize landraces and the key inbred lines[J]. Journal of Nuclear Agricultural Sciences, 2018,32(7):1298-1308.
[35]	Xu Q, Yuan XP, Wang S, et al. The genetic diversity and structure of indica rice in China as detected by single nucleotide polymorphism analysis[J]. BMC Genetics, 2016,17(1):53.
[36]	高士杰, 刘晓辉, 郭中校, 等. 中国杂交高粱的种质基础及优势利用模式研究[J]. 中国农学通报, 2005,21(10):106-108.
	Gao SJ, Liu XH, Guo ZX, et al. Chinese hybrid sorghum idioplasm foundation and superiority use pattern[J]. Chinses Agricultural Science Bulletin, 2005,21(10):106-108.

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