亚洲莲全基因组SSR的基本特征与遗传变异

doi:10.3969/j.issn.1004-1524.20250455

浙江农业学报 ›› 2026, Vol. 38 ›› Issue (8): 1574-1588.DOI: 10.3969/j.issn.1004-1524.20250455

亚洲莲全基因组SSR的基本特征与遗传变异

黄国洪¹^,²(), 马艺妮², 何佳欣², 屠莉², 廖伟彪¹^,^*(), 刘凤栾²^,^*()

¹ 甘肃农业大学园艺学院, 甘肃兰州 730070
² 上海辰山植物园上海市资源植物功能基因组学重点实验室, 上海 201602

收稿日期:2025-06-21 出版日期:2026-08-25 发布日期:2026-09-14
作者简介:黄国洪,研究方向为观赏荷花遗传育种。E-mail:hgh19962024@163.com
通讯作者: *廖伟彪,E-mail:liaowb@gsau.edu.cn;刘凤栾,E-mail:19liu19@163.com
基金资助:
国家自然科学基金(32071821)

Basic characteristics and genetic variation of genome-wide simple sequence repeats in Asian lotus (Nelumbo nucifera)

HUANG Guohong¹^,²(), MA Yini², HE Jiaxin², TU Li², LIAO Weibiao¹^,^*(), LIU Fengluan²^,^*()

¹ College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China
² Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China

Received:2025-06-21 Published:2026-08-25 Online:2026-09-14

摘要/Abstract

摘要：

为深入了解亚洲莲(Nelumbo nucifera)全基因组范围内简单重复序列(simple sequence repeat, SSR)的遗传特征,以33份代表性亚洲莲为材料,采用全基因组重测序技术,分析其全基因组SSR位点及其基序特征,并探讨种质来源、花色、瓣型和生态型等表型性状与SSR遗传变异之间的关联性。结果表明:亚洲莲全基因组SSR位点数量平均为64 253.8个,范围为25 961~119 777个。在不完全型c^*、复合型c、单核苷酸重复p1至六核苷酸重复p6共8种SSR类型中,p1和p2类型SSR的数量最多,占比分别为55.38%和29.91%。野生型、现代品种和地方品种的SSR数量呈逐渐增加的趋势;重瓣类型荷花的SSR数量为83 298.6个,为单瓣类型(51 874.6个)的1.6倍;温带莲和热带莲之间的SSR数量没有显著差异。完全型p1~p6 SSR分别平均包含2.0、4.0、10.0、23.6、49.8和88.6种基序,数量占比最大的3种基序依次为A/T(52.173%)、AG/CT(16.971%)和AT/AT(11.358%)。本研究揭示了亚洲莲代表性个体之间的全基因组SSR数量和基序组成的差异,发现8种SSR类型的占比模式十分保守,认为杂交和人为选择促进了基因组SSR位点数量的增加,并丰富了其基序种类。

关键词: 莲属, 亚洲莲, 简单重复序列(SSR), 基序, 花色, 生态型

Abstract:

To gain deeper insights into the genetic characteristics of simple sequence repeat (SSR) across the whole genome of Asian lotus (Nelumbo nucifera), 33 representative accessions were used as materials. Whole-genome resequencing was used to analyze genome-wide SSR loci and their motif features, and to investigate the associations between SSR genetic variation and phenotypic traits including germplasm origin, flower color, petal type, and ecotype. The results showed that the average number of SSR loci in the Asian lotus genome was 64 253.8, with a range of 25 961 to 119 777. Among the eight SSR types, namely imperfect (c^*), compound (c), and mononucleotide (p1) to hexanucleotide (p6) repeats, p1 and p2 SSRs were the most abundant, accounting for 55.38% and 29.91% of the total, respectively. SSR counts exhibited a gradually increasing trend from wild types to modern cultivars and landraces; the number of SSR loci in double-petal lotus was 83 298.6, which was 1.6 times that of the single-petal type (51 874.6). No significant difference in SSR number was observed between temperate and tropical lotus. Perfect p1 to p6 SSRs contained an average of 2.0, 4.0, 10.0, 23.6, 49.8, and 88.6 motif types, respectively, with the three most abundant motifs being A/T (52.173%), AG/CT (16.971%), and AT/AT (11.358%) in descending order. This study delineated the detailed differences in genome-wide SSR counts and motif composition among representative Asian lotus individuals, revealed a highly conserved proportional pattern across the eight SSR types, and suggested that hybridization and artificial selection have promoted both an increase in the number of genomic SSR loci and an enrichment of their motif diversity.

Key words: Nelumbo, Asian lotus (Nelumbo nucifera), simple sequence repeat (SSR), motif, flower color, ecotype

中图分类号:

S682.32

黄国洪, 马艺妮, 何佳欣, 屠莉, 廖伟彪, 刘凤栾. 亚洲莲全基因组SSR的基本特征与遗传变异[J]. 浙江农业学报, 2026, 38(8): 1574-1588.

HUANG Guohong, MA Yini, HE Jiaxin, TU Li, LIAO Weibiao, LIU Fengluan. Basic characteristics and genetic variation of genome-wide simple sequence repeats in Asian lotus (Nelumbo nucifera)[J]. Acta Agriculturae Zhejiangensis, 2026, 38(8): 1574-1588.

图/表 8

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序号 No.	名称 Name	样本来源 Sample origin	花色 Flower color	瓣数 Petal number	适生区域 Habitat	分布地域/资源亲本 Distribution area/germplasm parent
01	同江野生莲 Tongjiang lotus	野生莲 Wild	粉红 Pink-red	单瓣 Single	温带莲 Temperate	中国黑龙江省同江市 Tongjiang, Heilongjiang, China
02	图们江莲 Tumenjiang lotus	野生莲 Wild	粉红 Pink-red	单瓣 Single	温带莲 Temperate	中国吉林省珲春市 Hunchun, Jilin, China
03	图们江莲 Tumenjiang lotus	野生莲 Wild	粉红 Pink-red	单瓣 Single	温带莲 Temperate	中国吉林省珲春市 Hunchun, Jilin, China
04	普兰店古莲 Pulandian antique lotus	古代莲 Antique	红 Red	单瓣 Single	温带莲 Temperate	中国辽宁省大连市 Dalian, Liaoning, China
05	白洋淀红莲 Baiyangdian red lotus	野生莲 Wild	红 Red	单瓣 Single	温带莲 Temperate	中国河北省保定市白洋淀 Baiyangdian, Baoding, Hebei, China
06	白洋淀红莲 Baiyangdian red lotus	野生莲-3株混池 Wild-bulk DNA of 3 seedlings	红 Red	单瓣 Single	温带莲 Temperate	中国河北省保定市白洋淀 Baiyangdian, Baoding, Hebei, China
07	微山湖红莲 Weishanhu red lotus	野生莲 Wild	红 Red	单瓣 Single	温带莲 Temperate	中国山东省济宁市微山湖 Weishan Lake, Jining, Shandong, China
08	微山湖红莲 Weishanhu red lotus	野生莲-3株混池 Wild-bulk DNA of 3 seedlings	红 Red	单瓣 Single	温带莲 Temperate	中国山东省济宁市微山湖 Weishan Lake, Jining, Shandong, China
09	梁山古莲 Liangshan antique lotus	古代莲-3株混池 Antique-bulk DNA of 3 seedlings	红 Red	单瓣 Single	温带莲 Temperate	中国山东省济宁市梁山县,同株自交后代 Selfed progeny from the same plant, Liang- shan, Jining, Shandong, China
10	梁山古莲 Liangshan antique lotus	古代莲-3株混池 Antique-bulk DNA of 3 seedlings	红 Red	单瓣 Single	温带莲 Temperate	中国山东省济宁市梁山县,同株自交后代 Selfed progeny from the same plant, Liang- shan, Jining, Shandong, China
11	开封古莲 Kaifeng antiquelotus	古代莲 Antique	粉红 Pink-red	单瓣 Single	温带莲 Temperate	中国河南省开封市 Kaifeng, Henan, China
12	洪湖红莲 Honghu red lotus	野生莲 Wild	粉红 Pink-red	单瓣 Single	温带莲 Temperate	中国湖北省洪湖市洪湖 Honghu Lake, Honghu, Hubei, China
13	中山红台 Zhongshan Hongtai	地方传统品种 Landrace	红 Red	重瓣 Double	温带莲 Temperate	中国南方地区 Southern China
14	宜良千瓣 Yiliang thousand-petal	地方传统品种 Landrace	红 Red	千瓣 Thousand-petal	温带莲 Temperate	中国云南省宜良县 Yiliang, Yunnan, China
15	东山千瓣 Dongshan thousand-petal	地方传统品种 Landrace	红 Red	千瓣 Thousand-petal	温带莲 Temperate	中国云南省建水县 Jianshui, Yunnan, China
16	重台莲 Chongtai lotus	地方传统品种 Landrace	粉红 Pink-red	重瓣 Double	温带莲 Temperate	中国 China
17	红台莲 Hongtai lotus	地方传统品种 Landrace	红 Red	重瓣 Double	温带莲 Temperate	中国 China
18	单洒锦 Dan Sajin	地方传统品种 Landrace	洒锦 Variegated	单瓣 Single	温带莲 Temperate	中国 China
19	大洒锦 Da Sajin	地方传统品种 Landrace	洒锦 Variegated	重瓣 Double	温带莲 Temperate	中国 China
20	小洒锦 Xiao Sajin	地方传统品种 Landrace	洒锦 Variegated	重瓣 Double	温带莲 Temperate	中国 China
21	建选17号 Jianxuan No. 17	现代品种 Modern cultivar	白色粉尖 White with pink tip	单瓣 Single	温带莲 Temperate	中国,福建子莲,人工杂交 Artificial hybrid, seed lotus, Fujian, China
22	鄂莲6号 E’lian No. 6	现代品种 Modern cultivar	白 White	单瓣 Single	温带莲 Temperate	中国,湖北藕莲,人工杂交 Artificial hybrid, Rhizome lotus, Hubei, China
23	辰山飞燕 Chenshan Feiyan	现代品种 Modern cultivar	红 Red	单瓣 Single	温带莲 Temperate		中国山东省济宁市微山湖,莲子辐射变异 Radiation-induced mutation in lotus seeds, Weishan Lake, Jining, Shandong, China
24	嫦娥奔月 Chang’e Benyue	现代品种 Modern cultivar	白 White	重瓣 Double	温带莲 Temperate		中国,人工杂交 Artificial hybrid, China
25	红楼梦 Hongloumeng	现代品种 Modern cultivar	红 Red	重瓣 Double	温带莲 Temperate		中国,人工杂交 Artificial hybrid, China
26	粉凌云 Fen Lingyun	现代品种 Modern cultivar	粉红 Pink-red	重瓣 Double	温带莲 Temperate		中国,人工杂交 Artificial hybrid, China
27	L137	野生莲 Wild	粉红 Pink-red	单瓣 Single	热带莲 Tropical		越南,Tien Lu, Hung Yen Tien Lu, Hung Yen, Vietnam
28	G188	地方传统品种 Landrace	粉红 Pink-red	单瓣 Single	热带莲 Tropical		越南,藕莲 Rhizome lotus, Vietnam
29	粉红凌霄 Sattabongkot	现代品种 Modern cultivar	红 Red	重瓣 Double	热带莲 Tropical		泰国,选育方式未知 Unknown, Thailand
30	至高无上 Supreme	现代品种 Modern cultivar	淡绿 Light-green	重瓣 Double	热带莲 Tropical		泰国,选育方式未知 Unknown, Thailand
31	L134	推定的杂交个体 Putative hybrid individual	红 Red	单瓣 Single	热带莲 Tropical		泰国,选育方式未知 Unknown, Thailand
32	印度之谜 Indian Mystery	现代品种 Modern cultivar	红 Red	单瓣 Single	热带莲 Tropical		印度,由自然个体直接筛选而来 Directly selected from natural individuals, India
33	印度之宝 Indian Treasure	现代品种 Modern cultivar	白 White	重瓣 Double	热带莲 Tropical		印度,由自然个体直接筛选而来 Directly selected from natural individuals, India

序号 No.	名称 Name	样本来源 Sample origin	花色 Flower color	瓣数 Petal number	适生区域 Habitat	分布地域/资源亲本 Distribution area/germplasm parent
01	同江野生莲 Tongjiang lotus	野生莲 Wild	粉红 Pink-red	单瓣 Single	温带莲 Temperate	中国黑龙江省同江市 Tongjiang, Heilongjiang, China
02	图们江莲 Tumenjiang lotus	野生莲 Wild	粉红 Pink-red	单瓣 Single	温带莲 Temperate	中国吉林省珲春市 Hunchun, Jilin, China
03	图们江莲 Tumenjiang lotus	野生莲 Wild	粉红 Pink-red	单瓣 Single	温带莲 Temperate	中国吉林省珲春市 Hunchun, Jilin, China
04	普兰店古莲 Pulandian antique lotus	古代莲 Antique	红 Red	单瓣 Single	温带莲 Temperate	中国辽宁省大连市 Dalian, Liaoning, China
05	白洋淀红莲 Baiyangdian red lotus	野生莲 Wild	红 Red	单瓣 Single	温带莲 Temperate	中国河北省保定市白洋淀 Baiyangdian, Baoding, Hebei, China
06	白洋淀红莲 Baiyangdian red lotus	野生莲-3株混池 Wild-bulk DNA of 3 seedlings	红 Red	单瓣 Single	温带莲 Temperate	中国河北省保定市白洋淀 Baiyangdian, Baoding, Hebei, China
07	微山湖红莲 Weishanhu red lotus	野生莲 Wild	红 Red	单瓣 Single	温带莲 Temperate	中国山东省济宁市微山湖 Weishan Lake, Jining, Shandong, China
08	微山湖红莲 Weishanhu red lotus	野生莲-3株混池 Wild-bulk DNA of 3 seedlings	红 Red	单瓣 Single	温带莲 Temperate	中国山东省济宁市微山湖 Weishan Lake, Jining, Shandong, China
09	梁山古莲 Liangshan antique lotus	古代莲-3株混池 Antique-bulk DNA of 3 seedlings	红 Red	单瓣 Single	温带莲 Temperate	中国山东省济宁市梁山县,同株自交后代 Selfed progeny from the same plant, Liang- shan, Jining, Shandong, China
10	梁山古莲 Liangshan antique lotus	古代莲-3株混池 Antique-bulk DNA of 3 seedlings	红 Red	单瓣 Single	温带莲 Temperate	中国山东省济宁市梁山县,同株自交后代 Selfed progeny from the same plant, Liang- shan, Jining, Shandong, China
11	开封古莲 Kaifeng antiquelotus	古代莲 Antique	粉红 Pink-red	单瓣 Single	温带莲 Temperate	中国河南省开封市 Kaifeng, Henan, China
12	洪湖红莲 Honghu red lotus	野生莲 Wild	粉红 Pink-red	单瓣 Single	温带莲 Temperate	中国湖北省洪湖市洪湖 Honghu Lake, Honghu, Hubei, China
13	中山红台 Zhongshan Hongtai	地方传统品种 Landrace	红 Red	重瓣 Double	温带莲 Temperate	中国南方地区 Southern China
14	宜良千瓣 Yiliang thousand-petal	地方传统品种 Landrace	红 Red	千瓣 Thousand-petal	温带莲 Temperate	中国云南省宜良县 Yiliang, Yunnan, China
15	东山千瓣 Dongshan thousand-petal	地方传统品种 Landrace	红 Red	千瓣 Thousand-petal	温带莲 Temperate	中国云南省建水县 Jianshui, Yunnan, China
16	重台莲 Chongtai lotus	地方传统品种 Landrace	粉红 Pink-red	重瓣 Double	温带莲 Temperate	中国 China
17	红台莲 Hongtai lotus	地方传统品种 Landrace	红 Red	重瓣 Double	温带莲 Temperate	中国 China
18	单洒锦 Dan Sajin	地方传统品种 Landrace	洒锦 Variegated	单瓣 Single	温带莲 Temperate	中国 China
19	大洒锦 Da Sajin	地方传统品种 Landrace	洒锦 Variegated	重瓣 Double	温带莲 Temperate	中国 China
20	小洒锦 Xiao Sajin	地方传统品种 Landrace	洒锦 Variegated	重瓣 Double	温带莲 Temperate	中国 China
21	建选17号 Jianxuan No. 17	现代品种 Modern cultivar	白色粉尖 White with pink tip	单瓣 Single	温带莲 Temperate	中国,福建子莲,人工杂交 Artificial hybrid, seed lotus, Fujian, China
22	鄂莲6号 E’lian No. 6	现代品种 Modern cultivar	白 White	单瓣 Single	温带莲 Temperate	中国,湖北藕莲,人工杂交 Artificial hybrid, Rhizome lotus, Hubei, China
23	辰山飞燕 Chenshan Feiyan	现代品种 Modern cultivar	红 Red	单瓣 Single	温带莲 Temperate		中国山东省济宁市微山湖,莲子辐射变异 Radiation-induced mutation in lotus seeds, Weishan Lake, Jining, Shandong, China
24	嫦娥奔月 Chang’e Benyue	现代品种 Modern cultivar	白 White	重瓣 Double	温带莲 Temperate		中国,人工杂交 Artificial hybrid, China
25	红楼梦 Hongloumeng	现代品种 Modern cultivar	红 Red	重瓣 Double	温带莲 Temperate		中国,人工杂交 Artificial hybrid, China
26	粉凌云 Fen Lingyun	现代品种 Modern cultivar	粉红 Pink-red	重瓣 Double	温带莲 Temperate		中国,人工杂交 Artificial hybrid, China
27	L137	野生莲 Wild	粉红 Pink-red	单瓣 Single	热带莲 Tropical		越南,Tien Lu, Hung Yen Tien Lu, Hung Yen, Vietnam
28	G188	地方传统品种 Landrace	粉红 Pink-red	单瓣 Single	热带莲 Tropical		越南,藕莲 Rhizome lotus, Vietnam
29	粉红凌霄 Sattabongkot	现代品种 Modern cultivar	红 Red	重瓣 Double	热带莲 Tropical		泰国,选育方式未知 Unknown, Thailand
30	至高无上 Supreme	现代品种 Modern cultivar	淡绿 Light-green	重瓣 Double	热带莲 Tropical		泰国,选育方式未知 Unknown, Thailand
31	L134	推定的杂交个体 Putative hybrid individual	红 Red	单瓣 Single	热带莲 Tropical		泰国,选育方式未知 Unknown, Thailand
32	印度之谜 Indian Mystery	现代品种 Modern cultivar	红 Red	单瓣 Single	热带莲 Tropical		印度,由自然个体直接筛选而来 Directly selected from natural individuals, India
33	印度之宝 Indian Treasure	现代品种 Modern cultivar	白 White	重瓣 Double	热带莲 Tropical		印度,由自然个体直接筛选而来 Directly selected from natural individuals, India

样本编号 Sample No.	数量Number								总数 Total number
样本编号 Sample No.	c^*	c	p1	p2	p3	p4	p5	p6	总数 Total number
23	43	1 336	15 115	7 375	1 683	224	96	90	25 962
03	42	1 350	16 160	6 558	1 533	249	81	101	26 074
02	39	1 509	16 855	7 174	1 599	285	92	101	27 654
07	56	1 747	17 554	8 878	2 044	303	117	107	30 806
10	56	2 151	20 430	9 824	2 265	355	132	116	35 329
01	40	1 940	21 376	9 669	2 195	368	136	117	35 841
09	51	2 334	20 939	10 473	2 400	373	131	117	36 818
05	50	2 084	21 625	10 211	2 373	375	134	128	36 980
08	52	2 063	20 597	11 260	2 693	405	155	123	37 348
06	64	2 716	23 861	12 543	2 799	433	149	132	42 697
28	52	2 034	24 711	12 111	3 085	479	166	121	42 759
11	71	3 184	26 931	15 380	3 875	592	183	142	50 358
31	56	2 436	30 410	13 861	3 478	574	235	170	51 220
32	49	2 513	30 481	14 153	3 518	554	201	165	51 634
22	57	2 645	29 448	15 422	3 984	613	215	141	52 525
24	54	2 566	30 078	15 612	4 169	689	208	147	53 523
33	61	2 978	29 914	16 923	3 808	582	223	167	54 656
04	68	2 945	29 744	17 247	3 970	621	185	155	54 935
30	55	3 120	36 762	18 883	4 795	792	288	194	64 889
13	61	2 781	35 028	21 629	6 352	991	333	198	67 373
25	61	3 383	39 613	22 427	6 243	969	326	186	73 208
27	64	3 426	43 700	26 630	7 643	1 265	424	212	83 364
16	65	3 679	45 373	26 337	7 350	1 178	402	222	84 606
29	85	4 359	46 771	25 967	6 591	1 023	363	230	85 389
26	73	3 831	45 908	27 130	7 528	1 166	386	218	86 240
14	70	3 822	44 344	29 761	8 696	1 337	438	249	88 717
15	75	4 037	45 789	30 465	8 820	1 364	440	249	91 239
12	76	4 197	49 451	30 662	8 708	1 358	433	252	95 137
17	75	4 278	51 639	31 608	8 877	1 398	466	246	98 587
21	73	4 050	54 256	31 236	8 561	1 397	463	239	100 275
20	82	4 966	69 244	31 972	8 752	1 412	436	246	117 110
19	77	4 900	69 171	32 197	8 885	1 414	454	247	117 345
18	75	4 993	71 086	32 529	8 956	1 433	448	257	119 777
均值Average	61.5	3 041.0	35 586.8	19 215.4	5 097.8	805.2	270.9	175.3	64 253.8
均值占比/% Proportion of average/%	0.10	4.73	55.38	29.91	7.93	1.25	0.42	0.27	100

样本编号 Sample No.	数量Number								总数 Total number
样本编号 Sample No.	c^*	c	p1	p2	p3	p4	p5	p6	总数 Total number
23	43	1 336	15 115	7 375	1 683	224	96	90	25 962
03	42	1 350	16 160	6 558	1 533	249	81	101	26 074
02	39	1 509	16 855	7 174	1 599	285	92	101	27 654
07	56	1 747	17 554	8 878	2 044	303	117	107	30 806
10	56	2 151	20 430	9 824	2 265	355	132	116	35 329
01	40	1 940	21 376	9 669	2 195	368	136	117	35 841
09	51	2 334	20 939	10 473	2 400	373	131	117	36 818
05	50	2 084	21 625	10 211	2 373	375	134	128	36 980
08	52	2 063	20 597	11 260	2 693	405	155	123	37 348
06	64	2 716	23 861	12 543	2 799	433	149	132	42 697
28	52	2 034	24 711	12 111	3 085	479	166	121	42 759
11	71	3 184	26 931	15 380	3 875	592	183	142	50 358
31	56	2 436	30 410	13 861	3 478	574	235	170	51 220
32	49	2 513	30 481	14 153	3 518	554	201	165	51 634
22	57	2 645	29 448	15 422	3 984	613	215	141	52 525
24	54	2 566	30 078	15 612	4 169	689	208	147	53 523
33	61	2 978	29 914	16 923	3 808	582	223	167	54 656
04	68	2 945	29 744	17 247	3 970	621	185	155	54 935
30	55	3 120	36 762	18 883	4 795	792	288	194	64 889
13	61	2 781	35 028	21 629	6 352	991	333	198	67 373
25	61	3 383	39 613	22 427	6 243	969	326	186	73 208
27	64	3 426	43 700	26 630	7 643	1 265	424	212	83 364
16	65	3 679	45 373	26 337	7 350	1 178	402	222	84 606
29	85	4 359	46 771	25 967	6 591	1 023	363	230	85 389
26	73	3 831	45 908	27 130	7 528	1 166	386	218	86 240
14	70	3 822	44 344	29 761	8 696	1 337	438	249	88 717
15	75	4 037	45 789	30 465	8 820	1 364	440	249	91 239
12	76	4 197	49 451	30 662	8 708	1 358	433	252	95 137
17	75	4 278	51 639	31 608	8 877	1 398	466	246	98 587
21	73	4 050	54 256	31 236	8 561	1 397	463	239	100 275
20	82	4 966	69 244	31 972	8 752	1 412	436	246	117 110
19	77	4 900	69 171	32 197	8 885	1 414	454	247	117 345
18	75	4 993	71 086	32 529	8 956	1 433	448	257	119 777
均值Average	61.5	3 041.0	35 586.8	19 215.4	5 097.8	805.2	270.9	175.3	64 253.8
均值占比/% Proportion of average/%	0.10	4.73	55.38	29.91	7.93	1.25	0.42	0.27	100

样本来源 Sample origin	样本数 Sample number		c^*			c			p1				p2			p3
样本来源 Sample origin	样本数 Sample number		数量 Number	占比/% Proportion /%		数量 Number		占比/% Proportion /%	数量 Number		占比/% Proportion /%		数量 Number		占比/% Proportion /%	数量 Number		占比/% Proportion /%
野生型-混池 Wild lotus-bulk	4		55.7± 5.9 b	0.14		2 316.0± 289.6 b		6.09	21 456.7± 1 616.8 b		56.39		11 025.0± 1 169.9 c		28.98	2 539.3± 248.8 c		6.67
野生型-单株 Wild lotus- individual	9		56.2± 14.2 b	0.11		2 486.9± 984.9 b		5.07	27 044.0± 12 044.9 b		55.17		14 712.1± 8 705.9 b		30.01	3 771.1± 2 659.0 bc		7.69
现代品种 Modern lotus	10		61.1± 12.6 ab	0.09		3 078.1± 885.7 ab		4.75	35 834.6± 11 267.0 b		55.27		19 512.8 ±7 154.7 b		30.10	5 087.9± 2 094.0 b		7.85
地方品种 Landrace	9		70.2± 9.3 a	0.08		3 943.3± 1 016.4 a		4.29	50 709.4± 16 261.4 a		55.15		27 623.2± 6 806.6 a		30.04	7 752.6± 1 966.4 a		8.43
样本来源 Sample origin		p4					p5					p6					总数 Total number
样本来源 Sample origin		数量 Number			占比/% Proportion/%		数量 Number			占比/% Proportion/%		数量 Number		占比/% Proportion/%			总数 Total number
野生型-混池 Wild lotus-bulk		391.5±34.5 c			1.03		141.8±12.1 c			0.37		122.0±7.3 c		0.32			38 048.0± 3 215.0 c
野生型-单株 Wild lotus-individual		601.8±423.1 bc			1.23		198.3±135.1 bc			0.40		146.1±52.9 bc		0.30			49 016.6± 24 941.1 bc
现代品种 Modern lotus		800.9±342.5 b			1.24		276.9±108.8 b			0.43		177.7±45.6 ab		0.27			64 830.0± 21 795.3 b
地方品种 Landrace		1 222.9±314.1 a			1.33		398.1±95.6 a			0.43		226.1±43.4 a		0.25			91 946.0± 25 458.3 a

亚洲莲全基因组SSR的基本特征与遗传变异

Basic characteristics and genetic variation of genome-wide simple sequence repeats in Asian lotus (Nelumbo nucifera)

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样本分类 Sample classification	样本数 Sample number		c^*			c			p1				p2			p3
样本分类 Sample classification	样本数 Sample number		数量 Number	占比/% Proportion/%		数量 Number		占比/% Proportion/%	数量 Number		占比/% Proportion/%		数量 Number	占比/% Proportion/%		数量 Number		占比/% Proportion /%
单瓣 Single flower	20		56.7± 11.7 b	0.11		2 582.7± 979.4 b		4.98	29 236.5± 14 607.2 b		56.36		15 159.8± 8 314.4 b	29.22		3 868.1± 2 486.7 b		7.46
重瓣 Double flower	13		68.8± 10.0 a	0.08		3 746.2± 764.8 a		4.50	45 356.5± 12 470.5 a		54.45		25 454.7± 5 844.9 a	30.56		6 989.7± 1 847.5 a		8.39
温带莲 Temperate lotus	26		61.8± 12.8 a	0.10		3 057.2± 1 137.5 a		4.71	35 831.3± 17 401.6 a		55.24		19 445.3± 9 687.8 a	29.98		5 204.2± 2 934.6 a		8.02
热带莲 Tropical lotus	7		60.3± 12.0 a	0.10		2 980.9± 767.0 a		4.81	34 678.4± 8 060.7 a		55.94		18 361.1± 5 853.6 a	29.62		4 702.6± 1 757.9 a		7.59
样本分类 Sample classification		p4					p5					p6					总数 Total number
样本分类 Sample classification		数量 Number			占比/% Proportion/%		数量 Number			占比/% Proportion/%		数量 Number			占比/% Proportion/%		总数 Total number
单瓣 Single flower		612.8±403.6 b			1.18		208.8±126.2 b			0.40		149.3±51.5 b			0.29		51 874.6± 26 709.5 b
重瓣 Double flower		1 101.2±287.0 a			1.32		366.4±86.2 a			0.44		215.3±34.2 a			0.26		83 298.6± 20 503.2 a
温带莲 Temperate lotus		819.3±465.8 a			1.26		270.8±146.4 a			0.42		174.1±60.3 a			0.27		64 864.0± 31 415.9 a
热带莲 Tropical lotus		752.7±292.3 a			1.21		271.4±92.8 a			0.44		179.9±35.8 a			0.29		61 987.3± 16 631.4 a

SSR类型 SSR type	基序的总量/均值/单样本变化范围 Total number/mean value/range per sample of SSR motif	基序类型 Motif type	SSR平均数量 Average SSR count	占8类SSR的比例/% Percentage in eight SSR types/%
p1	2/2.0/2	A/T	33 523.0±15 216.3 a	52.173
		C/G	2 063.9±729.7 b	3.212
p2	4/4.0/3~4	AC/GT	1 009.6±608.1 c	1.571
		AG/CT	10 904.8±6 093.0 a	16.971
		AT/AT	7 298.0±2 560.4 b	11.358
		CG/CG	3.0±2.2 d	0.005
p3	10/10.0/10	AAC/GTT	157.5±105.3 d	0.245
		AAG/CTT	2 263.5±1 141.1 a	3.523
		AAT/ATT	1 639.0±840.0 b	2.551
		ACC/GGT	112.3±68.8 d	0.175
		ACG/CGT	24.3±18.0 d	0.038
		ACT/AGT	125.8±76.9 d	0.196
		AGC/CTG	72.1±47.6 d	0.112
		AGG/CCT	185.7±114.4 d	0.289
		ATC/ATG	506.7±322.6 c	0.789
		CCG/CGG	11.2±6.9 d	0.017
p4	31/23.6/14~30	ACAT/ATGT	253.5±112.4 a	0.395
		AAAT/ATTT	215.4±139.6 a	0.335
		AAAG/CTTT	113.6±65.0 b	0.177
		AGAT/ATCT	110.3±48.7 b	0.172
		AATT/AATT	29.6±20.3 c	0.046
p5	71/49.8/31~65	AAGAG/CTCTT	65.5±36.8 a	0.102
		AAAAT/ATTTT	24.5±13.3 b	0.038
		AAAAG/CTTTT	23.8±15.9 bc	0.037
		AACCC/GGGTT	18.0±9.4 cd	0.028
		AATAT/ATATT	15.3±7.8 d	0.024
p6	134/88.6/60~116	AAAAAC/GTTTTT	8.4±2.9 a	0.013
		AATATT/AATATT	7.0±3.2 ab	0.011
		AAAAAG/CTTTTT	6.8±3.2 bc	0.011
		AAATAT/ATATTT	6.0±2.6 bc	0.009
		AACCAC/GGTTGT	5.8±1.1 c	0.009

SSR类型 SSR type	基序类型 Motif type		荷花样本的SSR数量SSR number of lotus sample
SSR类型 SSR type	基序类型 Motif type		01		02		03		04		05		06		07		08		09		10		11		12		13		14		15		16		17
p1	A/T		19 755		15 600		14 985		27 761		20 063		21 208		16 620		19 563		18 603		18 322		24 247		47 076		33 659		42 677		44 069		43 014		49 213
p1	C/G		1 621		1 255		1 175		1 983		1 562		2 653		934		1 034		2 336		2 108		2 684		2 375		1 369		1 667		1 720		2 359		2 426
p2	AC/GT		400		297		254		772		414		426		342		443		367		343		590		1 764		1 267		1 718		1 743		1 550		1 824
p2	AG/CT		4 902		3 765		3 561		8 448		5 121		5 309		4 186		5 165		4 696		4 553		6 976		18 115		12 569		17 205		17 468		16 041		18 883
p2	AT/AT		4 366		3 111		2 741		8 025		4 675		6 806		4 350		5 651		5 409		4 927		7 813		10 779		7 790		10 833		11 248		8 742		10 896
p2	CG/CG		1		1		2		2		1		2		0		1		1		1		1		4		3		5		6		4		5
p3	AAC/GTT		53		38		40		95		46		46		51		67		39		42		87		281		207		295		290		255		298
p3	AAG/CTT		1 116		822		815		1 741		1 150		1 197		983		1 183		1 086		1 045		1 614		3 650		2 702		3 596		3 650		3 277		3 786
p3	AAT/ATT		667		445		410		1 428		779		1 179		694		1 017		947		868		1 574		2 917		2 062		2 929		3 001		2 185		2 871
p3	ACC/GGT		40		41		37		83		46		41		35		50		48		37		66		200		137		195		209		173		212
p3	ACG/CGT		5		4		3		12		5		8		6		9		6		5		11		46		36		45		47		40		46
p3	ACT/AGT		43		34		36		90		49		53		40		60		43		46		82		236		156		221		227		191		231
p3	AGC/CTG		19		14		13		58		29		26		28		32		21		20		40		130		101		136		136		121		128
p3	AGG/CCT		61		58		48		124		73		74		63		81		52		46		110		324		249		336		321		284		341
p3	ATC/ATG		188		141		129		330		194		172		138		187		154		153		282		906		688		923		918		807		945
p3	CCG/CGG		3		2		2		9		2		3		6		7		4		3		9		18		14		20		21		17		19
p4	AAAC/GTTT		7		5		5		15		7		7		4		7		5		4		10		25		23		31		28		27		31
p4	AAAG/CTTT		49		37		35		84		48		47		40		48		44		41		70		186		145		192		196		178		206
p4	AAAT/ATTT		75		50		48		151		76		80		71		103		65		65		127		398		307		398		403		335		401
p4	AACC/GGTT		0		0		0		0		0		0		0		1		0		0		1		2		1		3		4		3		3
p4	AAGG/CCTT		6		3		2		1		5		3		3		3		4		4		5		4		5		3		3		3		4
p4	AATC/ATTG		2		0		0		8		4		3		2		2		0		0		1		9		9		8		11		8		11
p4	AATG/ATTC		3		4		1		4		2		1		0		1		2		2		4		14		9		13		11		11		12
p4	AATT/AATT		10		7		5		21		11		11		11		13		8		10		22		61		35		57		61		44		61
p4	ACAG/CTGT		1		3		3		7		4		2		2		4		2		3		5		16		14		16		15		15		16
p4	ACAT/ATGT		137		117		94		207		141		186		110		142		168		161		226		393		262		380		390		351		400
p4	ACCC/GGGT		2		1		3		3		1		3		0		2		2		2		3		6		4		5		3		4		8
p4	ACTC/AGTG		1		1		1		2		0		0		1		1		0		0		1		8		8		9		9		9		10
p4	ACTG/AGTC		0		0		0		0		0		0		0		0		0		0		0		2		3		3		3		2		3
p4	AGAT/ATCT		66		49		45		94		66		79		53		71		61		54		99		178		130		167		178		135		170
p4	AGCG/CGCT		1		1		1		1		1		2		1		1		1		1		2		5		1		3		3		2		4
p4	AGCT/AGCT		1		0		0		3		0		0		0		0		0		0		1		6		4		8		6		5		7
p4	AGGG/CCCT		2		3		2		5		4		3		1		2		4		3		8		23		10		13		12		22		24
p4	ATCC/ATGG		2		2		2		3		1		0		1		1		2		2		2		6		8		9		9		8		9
p4	ATGC/ATGC		0		0		0		3		0		0		0		0		0		0		0		3		3		4		4		4		4
p1~p4基序类型的总量 Total of p1- p4 motif types			144		130		125		172		144		155		133		144		136		132		158		217		196		218		221		208		218
SSR类型 SSR type		基序类型 Motif type		荷花样本的SSR数量SSR number of lotus sample
SSR类型 SSR type		基序类型 Motif type		18		19		20		21		22		23		24		25		26		27		28		29		30		31		32		33
p1		A/T		67 685		65 922		65 688		51 371		27 560		14 406		28 205		37 495		43 515		41 370		23 228		43 280		34 493		28 711		28 701		28 189
p1		C/G		3 401		3 249		3 556		2 885		1 888		709		1 873		2 118		2 393		2 330		1 483		3 491		2 269		1 699		1 780		1 725
p2		AC/GT		2 017		1 947		1 890		1 864		747		331		847		1 237		1 583		1 608		596		1 138		937		715		674		671
p2		AG/CT		21 718		21 502		21 090		19 169		8 233		3 612		8 893		13 021		16 140		16 240		7 081		12 810		10 436		7 767		7 625		7 557
p2		AT/AT		8 787		8 741		8 985		10 198		6 442		3 432		5 868		8 167		9 400		8 777		4 433		12 016		7 508		5 375		5 851		8 693
p2		CG/CG		7		7		7		5		0		0		4		2		7		5		1		3		2		4		3		2
p3		AAC/GTT		320		316		305		309		117		47		147		198		252		280		95		162		125		96		98		99
p3		AAG/CTT		4 055		4 035		3 963		3 792		1 803		792		1 978		2 723		3 287		3 317		1 444		2 750		2 243		1 713		1 647		1 740
p3		AAT/ATT		2 616		2 569		2 572		2 485		1 293		544		1 140		2 003		2 321		2 254		880		2 535		1 473		955		1 093		1 380
p3		ACC/GGT		203		198		200		219		77		37		104		152		183		201		69		118		101		77		60		57
p3		ACG/CGT		50		50		49		50		14		4		19		35		43		47		17		28		21		11		16		13
p3		ACT/AGT		244		237		231		223		100		28		99		146		191		216		79		146		114		66		101		90
p3		AGC/CTG		143		140		134		140		43		20		63		96		114		126		44		76		63		46		38		40
p3		AGG/CCT		348		348		337		345		131		63		168		241		305		313		107		217		188		134		123		114
p3		ATC/ATG		956		969		941		979		398		142		445		633		814		872		343		542		457		373		334		267
p3		CCG/CGG		21		23		20		19		8		5		6		16		18		17		7		17		10		7		8		8
p4		AAAC/GTTT		27		28		28		28		13		3		14		18		25		29		10		19		14		14		13		11
p4		AAAG/CTTT		207		209		205		204		76		34		108		135		171		185		72		124		122		87		90		74
p4		AAAT/ATTT		418		410		399		417		157		63		167		262		327		385		125		254		201		128		126		116
p4		AACC/GGTT		2		3		3		4		1		0		2		2		4		3		1		0		0		1		2		2
p4		AAGG/CCTT		4		3		4		4		3		5		3		3		4		6		5		3		4		4		5		3
p4		AATC/ATTG		11		13		13		11		6		1		6		7		10		11		4		6		4		2		3		2
p4		AATG/ATTC		14		13		12		16		8		0		7		9		12		16		5		9		5		9		7		7
p4		AATT/AATT		59		48		59		61		17		9		19		39		42		53		16		39		24		17		11		17
p4		ACAG/CTGT		17		17		16		16		6		4		4		12		14		14		7		13		12		6		3		3
p4		ACAT/ATGT		417		419		428		379		217		63		226		308		345		354		139		349		257		191		183		224
p4		ACCC/GGGT		5		4		5		7		5		0		3		2		2		4		3		3		2		3		3		4
p4		ACTC/AGTG		9		9		9		9		3		1		2		6		5		9		3		6		3		2		1		3
p4		ACTG/AGTC		3		2		2		3		1		0		0		0		0		1		2		1		0		0		0		0
p4		AGAT/ATCT		189		185		181		174		74		37		104		123		151		139		66		152		108		84		88		104
p4		AGCG/CGCT		4		4		5		4		2		0		1		2		4		3		1		2		2		3		3		3
p4		AGCT/AGCT		7		7		7		7		1		0		2		4		3		4		2		4		1		3		1		0
p4		AGGG/CCCT		16		14		11		28		11		1		10		19		22		25		8		20		15		8		7		3
p4		ATCC/ATGG		8		9		8		8		4		1		2		6		8		9		4		4		5		2		4		3
p4		ATGC/ATGC		4		4		4		4		0		0		0		2		4		2		0		4		2		3		0		0
p1~p4基序类型的总量 Total of p1- p4 motif types				224		222		221		221		168		122		172		184		215		209		155		205		187		181		170		172

样本分类 Sample classification		样本数 Sample number	基序种类的均值The average number of SSR motif type
样本分类 Sample classification		样本数 Sample number	p4	p5	p6
来源	野生型Wild lotus	13	20.0±4.6 c	41.4±9.3 c	76.3±15.9 b
Origin	现代品种Modern cultivar	10	23.9±4.9 b	51.8±9.2 b	89.7±15.7 b
	地方传统品种Landrace	9	28.3±1.9 a	59.8±6.7 a	105.1±13.8 a
花色	红色Red	16	22.4±5.5 a	47.4±10.8 b	84.8±17.9 b
Flower color	粉红色Pink-red	9	23.4±5.4 a	47.8±12.8 b	86.2±20.7 b
	白色White	4	24.3±4.1 a	53.8±8.1 ab	89.0±16.0 b
	洒锦Variegated	3	29.0±0.0 a	63.7±0.6 a	113.7±2.1 a
瓣数	单瓣Single flower	20	21.2±5.0 b	44.8±10.9 b	79.9±17.9 b
Petal number	重瓣Double flower	13	26.8±3.0 a	56.8±6.2 a	100.4±10.3 a
适生区域	温带莲Temperate lotus	26	23.4±5.6 a	49.5±12.4 a	87.9±20.3 a
Habitat	热带莲Tropical lotus	7	24.3±3.6 a	51.1±5.3 a	91.3±11.8 a

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