糯玉米自交系SSR标记遗传多样性及群体遗传结构分析

doi:10.3724/SP.J.1006.2019.83008

Abstract

Abstract:

To understand the genetic basis of waxy maize (Zea mays L. var. ceratina Kulesh), 87 waxy maize inbred lines were screened by 29 pairs of SSR markers for genetic diversity analysis. Totally, 180 alleles were detected in this population, with an average of 6 alleles per locus. Polymorphic information content (PIC) ranged from 0.308 to 0.915, with an average of 0.572. The genetic similarity between materials ranged from 0.49 to 0.93 with an average of 0.66. Based on the UPGMA (unweighted pair-group method with arithmetic means) cluster analysis, divided 87 waxy maize inbred lines into four groups with genetic similarity of 0.64, including 9, 66, 10, and 2 materials. In addition, 87 waxy maize inbred lines were also divided into four genetic subpopulations, including 24, 25, 19, and 19 materials, by the population genetic structure analysis. Further study showed that genetic variation among most of waxy maize inbred lines in this population was relatively simple. This study provides a germplasm base and theoretical basis for new variety breeding and evolutionary genetics analysis of waxy maize.

Key words: waxy maize, genetic diversity, population structure

Yuan LU,Wei-Da AI,Qing HAN,Yi-Fa WANG,Hong-Yang LI,Yu-Ji QU,Biao SHI,Xue-Fang SHEN. Genetic diversity and population structure analysis by SSR markers in waxy maize[J].Acta Agronomica Sinica, 2019, 45(2): 214-224.

Figures/Tables 6

Supplementary table 1

List of 91 waxy maize germplasm resources and their pedigrees"

编号 No.	名称 Name	系谱 Pedigree		来源 Origin
N1	16SW-122	W97/玉美头601♀ W97/Yumeitou 601♀		上海 Shanghai
N2	W97	不详 Unknown		上海 Shanghai
N3	W148	不详 Unknown		上海Shanghai
N4	16SW-292	W75/W95		上海Shanghai
N5	16SW-296	(江南花糯二环系/白478)/W22 (Second cycle lines from Jiangnanhuanuo/Bai 478) /W22		江苏 Jiangsu
N6	通系5 Tongxi 5	不详 Unknown		江苏 Jiangsu
N7	16SW-311	申W22/H54 Shen W22/H54		上海 Shanghai
N8	16SW-312	京W♂/W100 JingW♂/W100		北京 Beijing
N9	16SW-320	W82/(W88/紫黑W1号) W82/(W88/Zihei W1)		上海 Shanghai
N10	16SW-321	申W22/(南汇黑/申W13) Shen W22/(Nanhuihei/Shen W13)		上海 Shanghai
N11	16SW-322	W96/张红 W96 / Zhanghong		甘肃 Gansu
N12	16SW-324	W75/[江南花糯二环系/(祝西/5003)] W75/[Second cycle lines from Jiangnanhuanuo/(Zhuxi/5003)]		江苏 Jiangsu
N13	16SW-327	W75/玉美头601♀ W75/Yumeitou 601♀		广西 Guangxi
N14	京W♂ Jing W♂	不详 Unknown		北京 Beijing
N15	16SW-333	申W48/张红 Shen W48/Zhanghong		甘肃 Gansu
N16	W153	不详 Unknown		上海 Shanghai
N17	W152	不详 Unknown		上海 Shanghai
N18	W158	不详 Unknown		上海 Shanghai
N19	16SW-347	W93/京W♂ W93/Jing W♂		北京 Beijing
N20	16SW-349	申W22/H88 Shen W22/H88		上海 Shanghai
N21	16SW-350	京W♂/H54 JingW♂/H54		北京 Beijing
N22	16SW-363	(江南花糯二环系/衡白522)/(江南花糯二环系/G478) (Second cycle lines from Jiangnanhuanuo/Hengbai 522)/(Second cycle lines from Jiangnanhuanuo/G478)		江苏 Jiangsu
N23	16SW-365	美玉8号二环系 Second cycle lines from Meiyu8		广西 Guangxi
N24	16SW-367	(通系5/昌7-2)/W88 (Tongxi 5/Chang 7-2)/W88		不详 Unknown
N25	16SW-369	[江南花糯二环系/(祝西/5003)]/(江南花糯二环系/衡白522) [Second cycle lines from Jiangnanhuanuo/(Zhuxi/5003)]/(Second cycle lines from Jiangnanhuanuo/Hengbai 522)		江苏 Jiangsu
N26	16SW-373	07东N-1/玉美头601♀ 07DongN-1/Yumeitou 601♀		广西 Guangxi
N27	16SW-374	W95/玉美头601♀ W95/Yumeitou 601♀		广西 Guangxi
N28	16SW-424	W93/西星黑糯1号二环系 W93/Second cycle lines from Xixingheinuo 1		山东 Shandong
N29	W116	不详 Unknown		上海 Shanghai
N30	16SW-426	W88/申W22 W88/Shen W22		上海 Shanghai
N31	16SW-427	W75/[(W01/申W48)/W01] W75/[(W01/Shen W48)/W01]		上海 Shanghai
N32	16SW-429	W01/中糯1号OP W01/Zhongnuo 1 OP		北京 Beijing
N33	16SW-437	苏玉糯1号二环系 Second cycle lines from Suyunuo1		江苏 Jiangsu
N34	16SW-438	[通系5/(515/小黄糯)]/江南花糯二环系 [Tongxi 5/(515/Xiaohuangnuo)]/ Second cycle lines from Jiangnanhuanuo		云南 Yunnan
N35	16SW-439	[通系5/(515/小黄糯)]/(申W13/通系5) [Tongxi 5/(515/ Xiaohuangnuo)]/(Shen W13/Tongxi 5)		云南 Yunnan
编号 No.	名称 Name	系谱 Pedigree		来源 Origin
N36	16SW-441	申W22/小黄糯 Shen W22/ Xiaohuangnuo		云南 Yunnan
N37	16SW-442	D049/杂1-4 D049/Za1-4		上海 Shanghai
N38	16SW-444	[通系5/(515/小黄糯)]/通系5 [Tongxi 5/(515/Xiaohuangnuo)]/Tongxi 5		云南 Yunnan
N39	16SW-447	申W13/W27 Shen W13/W27		上海 Shanghai
N40	16SW-449	(W01/申W13)/申W22 (W01/Shen W13)/Shen W22		上海 Shanghai
N41	16SW-450	(申W48/紫黑1号)/[(申W48/W01)/申W48] (Shen W48/Zihei 1)/[(Shen W48/W01)/Shen W48]		上海 Shanghai
N42	16SW-451	文山红糯/申W22 Wenshanhongnuo/Shen W22		云南 Yunnan
N43	16SW-452	{[通系5/(515/小黄糯)]/通系5}/江南花糯二环系 {[Tongxi 5/(515/Xiaohuangnuo)]/Tongxi 5}/Second cycle lines from Jiangnanhuanuo		云南 Yunnan
N44	16SW-455	(W01/申W48)/W01 (W01/Shen W48)/W01		上海 Shanghai
N45	16SW-456	(申W13/通系5)/{[通系5/(通系5/515)]/通系5} (Shen W13/Tongxi 5)/{[Tongxi 5/(Tongxi 5/515)]/Tongxi 5}		上海 Shanghai
N46	16SW-457	(W01/申W13)/W01 (W01/Shen W13)/W01		上海 Shanghai
N47	16SW-458	田白糯1号二环系 Second cycle lines from Tianbainuo1		广东 Guangdong
N48	16SW-459	(江南花糯二环系/白478)/申W48 (Second cycle lines from Jiangnanhuanuo /Bai 478)/Shen W48		江苏 Jiangsu
N49	16SW-460	申W48/郑白糯6号二环系 Shen W48/Second cycle lines from Zhengbainuo6		河南 Henan
N50	16SW-465	[(七宝紫/申W22)/江南花糯二环系]/[江南花糯二环系/(祝西/5003)] [(Qibaozi/Shen W22)/Second cycle lines from Jiangnanhuanuo]/[Second cycle lines from Jiangnanhuanuo/(Zhuxi/5003)]		上海 Shanghai
N51	16SW-466	{[通系5/(515/小黄糯)]/通系5}/[江南花糯二环系/(祝西/5003))] {[Tongxi 5/(515/Xiaohuangnuo)]/Tongxi 5}/[Second cycle lines from Jiangnanhuanuo/(Zhuxi/5003)]		江苏 Jiangsu
N52	16SW-468	{{[通5/(515/小黄糯)]/通系5}/江南花糯二环系}/[江南花糯二环系/(祝西/5003)] {{[Tongxi 5/(515/Xiaohuangnuo)]/Tongxi5}/Second cycle lines from Jiangnanhuanuo}/[Second cycle lines from Jiangnanhuanuo/(Zhuxi/5003)]		江苏 Jiangsu
N53	16SW-470	W88/W96		上海 Shanghai
N54	16SW-471	W88/[江南花糯二环系/(祝西/5003)] W88/[Second cycle lines from Jiangnanhuanuo/(Zhuxi/5003)]		江苏 Jiangsu
N55	16SW-475	[W97/(七宝紫/申W22)]/{[通系5/(515/小黄糯)]/通系5} [W97/(Qibaozi/Shen W22)]/{[Tongxi 5/(515/Xiaohuangnuo)]/Tongxi 5}		上海 Shanghai
N56	16SW-476	[(七宝紫/申W22)/江南花糯二环系]/{[通系5/(515/小黄糯)]/通系5} [(Qibaozi/Shen W22)/Second cycle lines from Jiangnanhuanuo]/{[Tongxi 5/(515/ Xiaohuangnuo)]/Tongxi 5}		上海 Shanghai
N57	16SW-478	W01/京W♂ W01/JingW♂		北京 Beijing
N58	16SW-480	[通系5(488/5003)]/W88 [Tongxi 5(488/5003)]/W88		上海 Shanghai
N59	16SW-481	[(申W13/通系5)/昌7-2]/W88 [(Shen W13/Tongxi 5)/Chang 7-2]/W88		江苏 Jiangsu
N60	16SW-484	(文山红糯/申W22)/申W22 (Wenshanhongnuo/Shen W22)/Shen W22		云南 Yunnan
N61	16SW-485	W75/白478 W75/Bai 478		山东 Shandong
N62	16SW-487	申W13/(江南花糯二环系/白478) Shen W13/(Second cycle lines from Jiangnanhuanuo/Bai 478)		江苏 Jiangsu
N63	W108	不详 Unknown		上海 Shanghai
N64	W107	不详 Unknown		上海 Shanghai
N65	W01	不详 Unknown		上海 Shanghai
N66	W75	不详 Unknown		上海 Shanghai
编号 No.	名称 Name		系谱 Pedigree	来源 Origin
N67	W151		不详 Unknown	上海 Shanghai
N68	W114		不详 Unknown	上海 Shanghai
N69	张改♀ Zhanggai ♀		不详 Unknown	上海 Shanghai
N70	wh-2		不详 Unknown	上海 Shanghai
N71	16HW-31		(江南花糯二环系/白478)/W95 (Second cycle lines from Jiangnanhuanuo/Bai 478)/W95	山东 Shandong
N72	16HW-46		(W96/张红)/申W22 (W96/Zhanghong)/Shen W22	甘肃 Gansu
N73	16AW-1001		引种大/W95 Yinzhongda/W95	上海 Shanghai
N74	16AW-1003		申W48/[(申W48/紫黑1号)/申W48] Shen W48/[(Shen W48/Zihei 1)/Shen W48]	上海 Shanghai
N75	16AW-1004		[(申W48/W01)/申W48]/[(申W48/紫黑1号)/申W48] [(Shen W48/W01)/Shen W48]/[(Shen W48/Zihei 1)/Shen W48]	上海 Shanghai
N76	16AW-1005		[(江南花糯二环系/白478)/郑白糯6号二环系]/京W♂ [(Second cycle lines from Jiangnanhuanuo/Bai 478)/Second cycle lines from Zhengbainuo6]/Jing W♂	河南 Henan
N77	16AW-1006		[(W48/5003)/W48]/中糯2号二环系 [(W48/5003)/W48]/Second cycle lines from Zhongnuo 2	北京 Beijing
N78	查12at-1385 Cha 12at-1385		不详 Unknown	上海 Shanghai
N79	16AW-1008		张红/[江南花糯二环系/(祝西/5003)] Zhanghong/[Second cycle lines from Jiangnanhuanuo/(Zhuxi/5003)]	江苏 Jiangsu
N80	09N-5M		不详 Unknown	上海 Shanghai
N81	09N-6M		不详 Unknown	上海 Shanghai
N82	09N-S150P		不详 Unknown	上海 Shanghai
N83	16AW-1015		[(申W48/紫黑1号)/(申W48/W01)]/申W22 [(Shen W48/Zihei 1)/(Shen W48/W01)]/Shen W22	上海 Shanghai
N84	16AW-1019		申W48/郑白糯6号二环系 Shen W48/Second cycle lines from Zhengbainuo 6	河南 Henan
N85	W-109		不详 Unknown	上海 Shanghai
N86	申W93 Shen W93		荆黑糯2号二环系 Second cycle lines from Jingheinuo 2	上海 Shanghai
N87	黄W-♀ Huang W- ♀		不详 Unknown	上海 Shanghai
N88	16HW-LY5		16HW-31/申W48 16HW-31/Shen W48	上海 Shanghai
N89	16HW-LY8		16HW-4/16HW-46	上海 Shanghai
N90	沪紫黑糯2号 Huziheinuo 2		申W74/申W93 Shen W74/Shen W93	上海 Shanghai
N91	五彩甜糯2号 Wucaitiannuo 2		申W93/wh-2 Shen W93/wh-2	上海 Shanghai

Supplementary table 1

Table 1

Fig. 1

Fig. 2

Supplementary fig. 1

Fig. 3

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编号 No.	标记位点 Locus	Bin	等位基因数 No. of alleles	主等位基因频率 Major allele frequency	基因多样性 Gene diversity	多态性信息含量 Polymorphic information content
1	umc1147y4	1.07	4	0.54	0.575	0.496
2	bnlg1671y17	1.10	4	0.60	0.579	0.531
3	phi96100y1	2.00	4	0.67	0.504	0.458
4	umc1823	2.02	4	0.45	0.640	0.571
5	b1	2.03	6	0.39	0.743	0.705
6	zpu1	2.05	4	0.40	0.663	0.599
7	pbf1	2.05	4	0.80	0.333	0.308
8	umc2253	2.05	4	0.59	0.554	0.483
9	umc1875	2.06	4	0.53	0.570	0.484
10	umc1536k9	2.07	4	0.78	0.358	0.320
11	bnlg1520K1	2.09	7	0.39	0.722	0.675
12	umc2105k3	3.00	4	0.75	0.412	0.379
13	umc1746	3.00	4	0.76	0.402	0.375
14	umc2257	3.01	4	0.53	0.590	0.515
15	umc1495	3.04	13	0.26	0.843	0.826
16	umc2264	3.04	7	0.34	0.769	0.734
17	phi053k2	3.05	8	0.43	0.734	0.699
18	phys2	3.05	20	0.13	0.921	0.915
19	umc1027	3.06	5	0.82	0.323	0.308
20	umc1489y3	3.07	7	0.46	0.668	0.611
21	mtl1	4.01	4	0.45	0.650	0.580
22	bnlg490y4	4.04	4	0.57	0.591	0.536
23	umc1705w1	5.03	4	0.52	0.620	0.553
24	bnlg2305k4	5.07	5	0.51	0.631	0.569
25	bnlg161k8	6.00	8	0.34	0.786	0.758
26	bnlg1702k1	6.05	8	0.55	0.629	0.588
27	phi065k9	9.03	5	0.48	0.599	0.519
28	umc1492y13	9.04	6	0.53	0.647	0.602
29	umc1432y6	10.02	15	0.20	0.889	0.879
	平均值 Mean		6	0.51	0.619	0.572

Genetic diversity and population structure analysis by SSR markers in waxy maize

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