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Acta Agronomica Sinica ›› 2019, Vol. 45 ›› Issue (2): 214-224.doi: 10.3724/SP.J.1006.2019.83008


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

Yuan LU1,2,Wei-Da AI3,Qing HAN1,2,Yi-Fa WANG1,Hong-Yang LI4,Yu-Ji QU5,Biao SHI1,2,*(),Xue-Fang SHEN1,2,*()   

  1. 1 Crop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
    2 CIMMYT: China Specialty Maize Research Center, Shanghai 201403, China
    3 College of Agriculture, Anshun University, Anshun 561000, Guizhou, China
    4 Sanya Sci-Tech Academy of Hainan National Breeding and Multiplication, Sanya 572000, Hainan, China
    5 Agricultural Service Center of Qingpu Town in Zhujiajiao District of Shanghai, Shanghai 201713, China
  • Received:2018-01-15 Accepted:2018-10-08 Online:2019-02-12 Published:2018-11-03
  • Contact: Biao SHI,Xue-Fang SHEN E-mail:18918162109@163.com;shenxuefang68@163.com
  • Supported by:
    This study was supported by the Shanghai Agriculture Applied Technology Development Program, China(20160103);the Research Project of Shanghai Science and Technology Commission, China(153919N1300);the Research Project of Shanghai Science and Technology Commission, China(17391900100);the Research Project of Shanghai Science and Technology Commission, China(17391902702);and the Shanghai Academy of Agricultural Sciences Excellence Team Project, China(2017B-08);the Youth Talent Development Plan of Shanghai Municipal Agricultural System, China(20150104);the Youth Talent Development Plan of Shanghai Municipal Agricultural System, China(20180106);and the Youth Science and Technology Personnel of Shanghai Academy of Agricultural Sciences


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

Supplementary table 1

List of 91 waxy maize germplasm resources and their pedigrees"

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
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
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

Table 1

Polymorphism parameters of 29 SSR markers used in this study"

Bin 等位基因数
No. of alleles
Major allele frequency
Gene diversity
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

Fig. 1

Frequency distributions of GS between waxy maize inbred lines"

Fig. 2

Cluster analysis of 87 waxy maize inbred lines by SSR markers"

Supplementary fig. 1

The line chart of ln P(D) value changing with K-value"

Fig. 3

Population genetic analysis of 87 waxy maize inbred lines A: the line chart of ΔK changing with K-value; B: the population structure of 87 waxy maize inbred lines estimated by Structure (K = 4)."

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