Scientia Agricultura Sinica ›› 2024, Vol. 57 ›› Issue (2): 236-249.doi: 10.3864/j.issn.0578-1752.2024.02.002


The Construction and Application of SSR and SNP Molecular ID for Maize Germplasm Resources of Jilin Province

ZHANG MingQi1,3(), WANG Rui1(), ZHANG ChunXiao2, SUN Bo1,3, REN Jie1, LI ShuFang4, WANG Lu1, ZHU ShaoXi1, ZHANG JiangBin1, SHI XinChen1, WANG HaiJie1, ZHANG YunLong1, TIAN HongLi1, ZHAO YiKun1, KUANG Meng3, WANG YuanDong1, YI HongMei1, LI XiaoHui2(), WANG FengGe1()   

  1. 1 Maize Research Institute, Beijing Academy of Agricultural and Forestry Sciences/Key Laboratory of Crop DNA Fingerprinting Innovation and Utilization (Co-construction by Ministry and Province)/Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing 100097
    2 Maize Research Institute, Jilin Academy of Agricultural Sciences, Gongzhuling 136100, Jilin
    3 Institute of Cotton Research of Chunese Academy of Agricultural Sciences/State Key Laboratory of Cotton Biology, Anyang 455000, Henan
    4 Crop Germplasm Resources Institute, Jilin Academy of Agricultural Sciences, Gongzhuling 136100, Jilin
  • Received:2023-06-05 Accepted:2023-08-01 Online:2024-01-16 Published:2024-01-19


【Objective】 Crop germplasm resources hold a crucial strategic position. The Maize Germplasm Resources Bank in Jilin Province safeguards a collection of germplasm resources distinctively representative of the Northern Spring Maize Region. Traditional germplasm resource management faces challenges in ascertaining accurate identity information. To address this issue, molecular marker technology has been employed to establish a process for the construction and classification of molecular IDs for germplasm resources, thereby enabling precise identification and bolstering categorical management. Thorough exploration of the exceptional resources within Jilin Province's Maize Germplasm Resources Bank is intended to advance the shared utilization of these valuable germplasm resources. 【Method】 A total of 2 918 maize germplasm resources were utilized from the Jilin Provincial Maize Germplasm Resources Bank as subjects of the study, the molecular IDs were constructed by using 40 pairs of SSR markers and 61 214 SNP markers recommended in maize variety identification standards. Based on the molecular ID information, the germplasm resources were categorized into core, closely related, heterogeneous, and population groups for management purposes. Furthermore, the core germplasms were analyzed on genetic diversity. 【Result】 In this investigation, the SSR molecular IDs were constructed for 2 918 maize germplasm resources, while the SNP molecular IDs were constructed for 2 502 maize germplasm resources, excluding heterogeneous germplasm. The standards for the construction of SSR and SNP molecular IDs were established for maize germplasm resources. The SSR molecular ID is composed of a combination of three-digit numbers and one-letter code converted from 40 SSR loci fingerprints, stored in the form of a QR code. The SNP molecular ID converts the fingerprints of 61 214 SNP loci into visual barcodes. Based on the features of sample homozygosity and fingerprint specificity, the samples were categorized into 1 561 cores, 705 closely related, 416 heterogeneous, and 236 population types of germplasm resources. Genetic diversity analysis indicates that domestic germplasm resources, represented by Lüdahonggu and Huanggai groups, constituting the main germplasm resources in the Jilin Provincial Maize Germplasm Resources Bank, accounting for 64.38% of all core germplasm resources. 【Conclusion】 This research outlines a methodology for constructing molecular IDs for maize germplasm resources. The SSR molecular IDs were constructed for 2 918 accessions stored in the Jilin Provincial Maize Germplasm Resources Bank and the SNP molecular IDs were constructed for 2 502 among them. The germplasm resources were categorized into core, closely related, heterogeneous, and population types to achieve the classification management.

Key words: maize, germplasm resource, Jilin, SSR, SNP, molecular ID

Fig. 1

Schematic diagram of the process for constructing molecular IDs of germplasm resources"

Fig. 2

Comparison of the DNA fingerprinting profile between the core germplasm resource Ji754 and the landrace Zhengbai1 by the top ten SSR loci"

Fig. 3

A distribution chart of the proportion of homozygosity of maize germplasm resources of Jilin Province"

Table 1

Molecular IDs table of SSR markers of representative germplasm"

Sample name
1 2 3 4 5 6 7 8 9 10
Ⅰ组 Group Ⅰ 325Y 238Y 246Y 354Y 291Y 362Y 433Y 380Y 273Y 248Y
Ⅱ组 Group Ⅱ 183Y 267Y 202Y 169Y 221Y 212Y 393Y 278Y 229Y 178Y
Ⅲ组 Group Ⅲ 167Y 186Y 253Y 232Y 173Y 233Y 271Y 197Y 284Y 126Y
Ⅳ组 Group Ⅳ 280Y 234Y 215Y 172Y 183Y 204Y 183Y 261Y 312Y 310Y
Ⅰ组 Group Ⅰ 320N 252Y 248Y 359N 314N 343N 421Y 364N 275N 260Y
Ⅱ组 Group Ⅱ 183Y 267N 202N 154Y 221N 212N 413N 284Y 222Y 185N
Ⅲ组 Group Ⅲ 154Y 184N 253N 232N 175Y 233N 297N 197N 284N 134N
Ⅳ组 Group Ⅳ 263N 000N 207Y 170Y 180N 215N 185N 261Y 304N 299Y

Fig. 4

Molecular IDs of SSR markers of representative germplasm resources"

Table 2

Maize germplasm resources classification management information table (sample table)"

Sample barcode number
Sample name
ID of SSR markers
ID of SNP markers
Homozygosity (%)
Proportion of identical loci (%)
Phenotypic data
The first propagation number
重量Storage weight
1 NZ00556 大红袍137
有Yes 有Yes 核心Core 95.00 无No 有Yes 02725Y14G0195 12W1429 58
2 NZ01291 遗501 Yi501 有Yes 有Yes 核心Core 95.00 无No 有Yes 03458Y14G0928 13J1166 113
3 NZ01447 郑58(山东)
有Yes 有Yes 核心Core 97.50 无No 有Yes 03621Y14G1091 13J1333 178
4 NZ00693 系14 Xi14 有Yes 有Yes 核心Core 90.00 无No 有Yes 02859Y14G0329 12W1568 30
5 NZ02361 43朝系43Chaoxi 有Yes 有Yes 核心Core 95.00 无No 有Yes 04550Y14G2020 13J1827 118
6 NZ02364 大器Daqi 有Yes 有Yes 核心Core 90.00 无No 有Yes 04555Y14G2025 100168 14
7 NZ02400 inbyed45 有Yes 有Yes 核心Core 90.00 无No 有Yes 04595Y14G2065 100217 144
8 NZ02519 大白棒Dabaibang 有Yes 有Yes 核心Core 92.50 无No 有Yes 04719Y14G2189 100370 55
9 NZ02526 秧Yang 有Yes 有Yes 核心Core 95.00 无No 有Yes 04727Y14G2197 100378 30
10 NZ00132 Mo17 有Yes 有Yes 核心Core 92.50 无No 有Yes WG208NZ00132 18G3830 201
11 NZ01465 郑58(河南)
有Yes 有Yes 其它Others 100.00 无No 无No 03639Y14G1109 13J1351 106
12 NZ01555 K4H6003 有Yes 有Yes 群体Population 90.00 92.34 无No 03726Y14G1196 13W1201 101
13 NZ01556 K4H6004 有Yes 有Yes 群体Population 92.50 96.15 无No 03727Y14G1197 13W1202 197
14 NZ01557 K4H6005 有Yes 有Yes 群体Population 92.50 94.92 无No 03728Y14G1198 13W1203 179
15 NZ01559 K4H6002 有Yes 有Yes 群体Population 92.50 94.92 无No 03730Y14G1200 13W1205 139
16 NZ00942 MO17“c"cms 有Yes 有Yes 同近源
Closely related
92.50 98.90 有Yes 03107Y14G0577 13W0960 205
17 NZ00960 FRMO17 O2 有Yes 有Yes 同近源
Closely related
92.50 98.90 有Yes 03126Y14G0596 13W0980 102
18 NZ01377 系14 Xi14 有Yes 有Yes 同近源
Closely related
90.00 93.67 有Yes 03549Y14G1019 13J1260 130
19 NZ02308 FRM017Rfc 有Yes 有Yes 同近源
Closely related
90.00 98.70 有Yes 04496Y14G1966 13W1534 108
20 NZ02309 FRM017rhm 有Yes 有Yes 同近源
Closely related
92.50 98.50 有Yes 04497Y14G1967 13W1535 124
21 NZ02809 75-217 有Yes 有Yes 同近源
Closely related
90.00 99.98 有Yes 05027Y14G2497-2粉轴
05027Y14G2497-2 Pink cob
13J2310 78
22 NZ02810 75-217 有Yes 有Yes 同近源
Closely related
90.00 99.98 有Yes 05027Y14G2497-3圆粒
05027Y14G2497-3 Round grains
13J2310 100
23 NZ01899 K4H6001 有Yes 无No 异质性Heterogeneous 87.50 无No 无No 04055Y14G1525 13W1533 144
24 NZ00544 自16 Zi16 有Yes 无No 异质性Heterogeneous 85.00 无No 无No 02712Y14G0182 12W1416 99
25 NZ00570 大黄46
有Yes 无No 异质性Heterogeneous 52.50 无No 无No 02740Y14G0210 12W1447 13
26 NZ00822 郑白1
有Yes 无No 异质性Heterogeneous 40.00 无No 无No 02985Y14G0455 12W0838 370
27 NZ01240 系14
有Yes 无No 异质性Heterogeneous 77.50 无No 无No 03407Y14G0877 13J1114 71
28 NZ02719 MO17 有Yes 无No 异质性Heterogeneous 82.50 无No 无No 04930Y14G2400 13J2212 62
29 NZ02808 75-217 有Yes 无No 异质性Heterogeneous 55.00 无No 无No 05027Y14G2497-1红轴
05027Y14G2497-1 Red cob
13J2310 333

Fig. 5

Molecular IDs of representative germplasm resources based on SNP markers Black is AA genotype, white is BB genotype, dark gray is AB genotype, light gray means missing loci. Ten color bands correspond to ten chromosomes of maize"

Fig. 6

The graph of the pairwise comparison of Jilin core and homologous-resources using SSR and SNP markers"

Fig. 7

Genetic diversity analysis of germplasm resources based on SNP markers"

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