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Acta Agronomica Sinica ›› 2020, Vol. 46 ›› Issue (7): 1006-1015.doi: 10.3724/SP.J.1006.2020.93048

• CROP GENETICS & BREEDING·GERMPLASM RESOURCES·MOLECULAR GENETICS • Previous Articles     Next Articles

Screening of compatible maizeSNP384 markers and the construction of DNA fingerprints of maize varieties

TIAN Hong-Li**,YANG Yang**,WANG Lu,WANG Rui,YI Hong-Mei,XU Li-Wen,ZHANG Yun-Long,GE Jian-Rong,WANG Feng-Ge(),ZHAO Jiu-Ran()   

  1. Maize Research Center, Beijing Academy of Agriculture and Forestry Sciences / Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing 100097, China
  • Received:2019-08-30 Accepted:2020-03-24 Online:2020-07-12 Published:2020-04-17
  • Contact: Feng-Ge WANG,Jiu-Ran ZHAO E-mail:gege0106@163.com;maizezhao@126.com
  • About author:** Contributed equally to this work
  • Supported by:
    13th Five-Year National Key Research and Development Program of China(2017YFD0102001-003);Beijing Scholars Program(BSP041)

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Abstract:

In order to improve the management of maize varieties and the protection of intellectual property rights, a compatible multiple platform loci combination maizeSNP384 was developed as a means of identifying varieties of maize. SNP-DNA fingerprints of 335 maize hybrids were constructed. All the 384 SNPs were located in the intra-genic region, showing good polymorphism. The average MAF, PIC, and DP of 384 loci were 0.39, 0.36, and 0.60, respectively. MAF in 88% of the 384 loci was most than 0.30, PIC in 98% was most than 0.30, and DP in 98% was most than 0.50. Pairwise comparative analysis of 335 maize hybrids using genetic similarity showed that the range of variation of GD (1-Nei genetic distance) was 0.60-0.99, and the ratios of GD value greater than or equal to 0.98, 0.95, and 0.90 were 0.10%, 0.38%, and 1.40%, respectively. The range of variation of GS (same allele ratio) was 0.50-0.99, and the ratios of GS value greater than or equal to 0.98, 0.95, and 0.90 were 0.03%, 0.11%, and 0.35%, respectively. The optimal locus combination was extracted from 384 SNPs, with the variety discrimination power of 0.99 when 12 SNPs were extracted; the combination of 20 SNPs was able to identify all 335 varieties. In summary, 384 core SNPs reported in this study are compatible with multiple platforms, highly stable, highly repeatable and having high variety discrimination power. SNP-DNA fingerprints of 335 maize hybrids were constructed based on these core SNPs, which provides key data support for molecular identification, fingerprint data construction, and molecular breeding of maize.

Key words: maize, SNP, loci combination, variety molecular identification, DNA fingerprint, chip

Table 1

Sample information of 30 sets hybrids and their parents for SNPs evaluation"

编号
No.		 品种
Variety		 母本
Female parent		 父本
Male parent
T01 SC704 B73 Mo17
T02 丹玉39 Danyu 39 C8605-2 丹598 Dan 598
T03 登海11 Denghai 11 DH65232 DH40
T04 登海9号 Denghai 9 DH65232 8723
T05 东单60 Dongdan 60 A801 丹598 Dan 598
T06 会单4号 Huidan 4 SW1611 掖107 Ye 107
T07 吉单180 Jidan 180 吉853 Ji 853 Mo17
T08 吉单209 Jidan 209 8902 吉853 Ji 853
T09 京科968 Jingke 968 京724 Jing 724 京92 Jing 92
T10 京科糯2000 Jingkenuo 2000 京糯6 Jingnuo 6 白糯6 Bainuo 6
T11 浚单20 Xundan 20 浚9058 Xun 9058 浚92-8 Xun 92-8
T12 蠡玉6号 Liyu 6 543 连87 Lian 87
T13 龙单13 Longdan 13 K10 龙抗11 Longkang 11
T14 鲁单981 Ludan 981 齐319 Qi 319 Lx 9801
T15 农大108 Nongda 108 X178 黄C Huang C
T16 农大3138 Nongda 3138 综31 Zong 31 P138
T17 农华101 Nonghua 101 NH60 S121
T18 沈单10 Shendan 10 沈137 Shen 137 Q1261
T19 沈单16 Shendan 16 K12 沈137 Shen 137
T20 四单19 Sidan 19 444 Mo17
T21 苏玉糯1号 Suyunuo 1 通系5号 Tongxi 5 衡白522 Hengbai 522
T22 苏玉糯5号 Suyunuo 5 通系5号 Tongxi 5 通366 Tong 366
T23 先玉335 Xianyu 335 PH6WC PH4CV
T24 掖单13 Yedan 13 掖478 Ye 478 丹340 Dan 340
T25 渝单8号 Yudan 8 掖478 Ye 478 渝561 Yu 561
T26 渝糯7号 Yunuo 7 S147 S181
T27 豫玉22 Yuyu 22 综3 Zong 3 豫自87-1 Yuzi 87-1
T28 正大619 Zhengda 619 F06 F19
T29 郑单958 Zhengdan 958 郑58 Zheng 58 昌7-2 Chang 7-2
T30 中单2号 Zhongdan 2 Mo17 自330 Zi 330

Fig. 1

Genotyping patterns of MG004 SNP locus on three different chip platforms A: illumine GGGT platform; B: illumina infinium platform; C: affymetrix-axiom platform. Each point is an actual genotype call, the data points of the same genotype gather together; the red and blue data points on both sides are homozygous genotypes, the data point on the middle group are heterozygous genotypes."

Table S1

Detailed information of the 384 SNPs for maize molecular identification, the physical location is based on B73 (AGP-V3) reference sequence"

位点
Locus		 染色体
Chr.		 物理位置
Physical location		 等位基因A Allele A 等位基因B Allele B MAF DP PIC AB Rate
MG001 1 2304391 A G 0.49 0.62 0.38 0.51
MG002 1 8974336 A G 0.50 0.62 0.38 0.51
MG003 1 11486897 A G 0.43 0.63 0.37 0.47
MG004 1 17738926 G A 0.41 0.60 0.37 0.53
MG005 1 21466180 C T 0.33 0.60 0.35 0.42
MG006 1 24584752 T G 0.43 0.61 0.37 0.51
MG007 1 27804659 C T 0.39 0.61 0.36 0.47
MG008 1 32232188 G A 0.33 0.60 0.35 0.43
MG009 1 35047741 A G 0.43 0.64 0.37 0.44
MG010 1 39118219 A G 0.32 0.59 0.34 0.42
MG011 1 42927856 T C 0.25 0.54 0.31 0.37
MG012 1 44545185 C A 0.36 0.56 0.36 0.55
MG013 1 51014726 G A 0.47 0.57 0.37 0.58
MG014 1 56566037 C A 0.30 0.58 0.33 0.42
MG015 1 61632511 T C 0.45 0.60 0.37 0.54
MG016 1 67735307 C T 0.50 0.57 0.38 0.59
MG017 1 77806149 C T 0.25 0.54 0.31 0.38
MG018 1 79425465 C T 0.46 0.64 0.37 0.47
MG019 1 92354027 G A 0.35 0.58 0.35 0.49
MG020 1 97688251 C A 0.42 0.62 0.37 0.49
MG021 1 111288396 G A 0.42 0.63 0.37 0.47
MG022 1 121979974 T G 0.38 0.60 0.36 0.49
MG023 1 155443646 G A 0.33 0.58 0.35 0.47
MG024 1 156554418 G T 0.38 0.60 0.36 0.49
MG025 1 161723857 C T 0.32 0.58 0.34 0.47
MG026 1 162755217 A G 0.35 0.59 0.35 0.48
MG027 1 164572994 T C 0.18 0.45 0.25 0.26
MG028 1 171553774 C T 0.34 0.57 0.35 0.51
MG029 1 180966708 T G 0.32 0.57 0.34 0.47
MG030 1 198287528 A G 0.46 0.65 0.37 0.44
MG031 1 200899746 T C 0.45 0.62 0.37 0.51
MG032 1 209627876 G A 0.32 0.59 0.34 0.43
MG033 1 220359715 C T 0.33 0.60 0.34 0.43
MG034 1 243187260 G C 0.30 0.58 0.33 0.43
MG035 1 245753063 A G 0.48 0.59 0.37 0.56
MG036 1 248798195 T C 0.25 0.54 0.31 0.36
MG037 1 253565722 C T 0.30 0.58 0.33 0.43
MG038 1 263219431 G A 0.35 0.60 0.35 0.44
MG039 1 265515707 A C 0.42 0.63 0.37 0.45
MG040 1 269419877 T G 0.26 0.55 0.32 0.41
MG041 1 272938380 A G 0.31 0.56 0.34 0.49
MG042 1 276881002 C T 0.36 0.60 0.35 0.46
MG043 1 277668429 G A 0.41 0.61 0.37 0.49
MG044 1 279336197 T C 0.41 0.62 0.37 0.48
MG045 1 281272643 G A 0.41 0.60 0.37 0.51
MG046 1 282748902 T C 0.45 0.58 0.37 0.56
MG047 1 285846709 C T 0.35 0.61 0.35 0.43
MG048 1 287789543 T C 0.36 0.61 0.35 0.42
MG049 1 289408285 T C 0.46 0.58 0.37 0.57
MG050 1 290379030 T C 0.49 0.64 0.38 0.48
MG051 1 292481023 T C 0.46 0.64 0.37 0.47
MG052 1 296850785 C T 0.33 0.59 0.35 0.46
MG053 1 298863606 C T 0.49 0.62 0.38 0.51
MG054 2 2500805 C T 0.33 0.58 0.35 0.48
MG055 2 3743906 A G 0.49 0.60 0.40 0.55
MG056 2 4697714 C A 0.31 0.56 0.34 0.49
MG057 2 6915357 A G 0.36 0.56 0.36 0.54
MG058 2 8914166 T C 0.46 0.61 0.37 0.53
MG059 2 22258930 G A 0.36 0.57 0.36 0.53
MG060 2 34162472 G A 0.36 0.58 0.35 0.51
MG061 2 47154261 A G 0.40 0.61 0.37 0.50
MG062 2 47789173 T C 0.35 0.60 0.35 0.47
MG063 2 57693847 G A 0.28 0.55 0.32 0.46
MG064 2 109563976 G T 0.34 0.54 0.35 0.56
MG065 2 111835040 C A 0.45 0.65 0.37 0.43
MG066 2 113226924 A C 0.45 0.55 0.37 0.61
MG067 2 145265362 T C 0.47 0.57 0.37 0.59
MG068 2 152240139 G T 0.27 0.56 0.32 0.35
MG069 2 156515220 A C 0.45 0.55 0.37 0.60
MG070 2 160621095 C T 0.47 0.56 0.37 0.60
MG071 2 182623845 G A 0.49 0.57 0.38 0.59
MG072 2 186339948 T G 0.47 0.60 0.37 0.54
MG073 2 191081573 C T 0.48 0.57 0.38 0.59
MG074 2 195937060 C A 0.45 0.62 0.37 0.50
MG075 2 196568843 T G 0.34 0.59 0.35 0.45
MG076 2 199837334 C T 0.27 0.56 0.32 0.40
MG077 2 201108308 C A 0.42 0.61 0.37 0.50
MG078 2 204601534 C T 0.37 0.60 0.36 0.49
MG079 2 207814715 A G 0.37 0.63 0.36 0.37
MG080 2 213018299 G A 0.39 0.61 0.36 0.48
MG081 2 216183437 T C 0.25 0.53 0.30 0.41
MG082 2 219129445 T C 0.27 0.54 0.32 0.44
MG083 2 221291383 C A 0.31 0.59 0.34 0.39
MG084 2 223977328 T G 0.42 0.62 0.37 0.48
MG085 2 225264554 T G 0.25 0.54 0.30 0.38
MG086 2 226199968 A G 0.40 0.61 0.37 0.49
MG087 2 235077065 C T 0.45 0.59 0.37 0.55
MG088 3 8979286 C T 0.37 0.58 0.36 0.51
MG089 3 15222625 G T 0.37 0.62 0.36 0.41
MG090 3 24225424 A G 0.34 0.57 0.35 0.50
MG091 3 25866687 G A 0.30 0.58 0.33 0.39
MG092 3 27775731 T C 0.47 0.54 0.37 0.63
MG093 3 29213820 T G 0.46 0.62 0.37 0.51
MG094 3 54969279 G T 0.49 0.59 0.38 0.56
MG095 3 57091132 C A 0.31 0.58 0.34 0.44
MG096 3 58082419 A G 0.30 0.56 0.33 0.47
MG097 3 67702516 G A 0.43 0.63 0.37 0.47
MG098 3 92555979 T C 0.36 0.59 0.35 0.50
MG099 3 88400489 C T 0.46 0.63 0.37 0.48
MG100 3 117106253 C A 0.37 0.61 0.36 0.46
MG101 3 118083714 C A 0.49 0.51 0.38 0.66
MG102 3 122901197 C T 0.49 0.61 0.38 0.52
MG103 3 126128781 C T 0.44 0.57 0.37 0.57
MG104 3 132489439 C T 0.46 0.62 0.37 0.51
MG105 3 134796979 A C 0.45 0.60 0.37 0.54
MG106 3 141646415 C T 0.50 0.63 0.38 0.50
MG107 3 142724956 T C 0.30 0.55 0.33 0.48
MG108 3 151086172 T C 0.40 0.61 0.36 0.50
MG109 3 152533264 A G 0.36 0.59 0.35 0.48
MG110 3 155358367 G A 0.34 0.61 0.35 0.42
MG111 3 156325759 A G 0.41 0.59 0.37 0.53
MG112 3 161301281 A G 0.48 0.63 0.38 0.49
MG113 3 162340416 G A 0.39 0.62 0.36 0.46
MG114 3 169261670 A G 0.48 0.65 0.38 0.45
MG115 3 173048348 T C 0.40 0.63 0.37 0.45
MG116 3 174581037 T C 0.33 0.58 0.35 0.48
MG117 3 179842209 A G 0.49 0.61 0.38 0.53
MG118 3 181032542 T C 0.34 0.60 0.35 0.43
MG119 3 184176645 T G 0.36 0.59 0.36 0.50
MG120 3 196000794 C T 0.44 0.62 0.37 0.49
MG121 3 200262266 T C 0.38 0.62 0.36 0.45
MG122 3 201757644 G A 0.49 0.60 0.38 0.54
MG123 3 203824251 A C 0.42 0.61 0.37 0.51
MG124 3 206611097 G A 0.30 0.58 0.33 0.37
MG125 3 208142658 T C 0.35 0.61 0.35 0.41
MG126 3 209109183 T G 0.30 0.59 0.33 0.38
MG127 3 212050055 A C 0.46 0.57 0.37 0.58
MG128 3 218112568 T C 0.44 0.62 0.37 0.50
MG129 3 221653490 A C 0.26 0.55 0.31 0.34
MG130 3 226343075 A G 0.46 0.62 0.37 0.50
MG131 3 229397149 T G 0.38 0.63 0.36 0.41
MG132 4 1487851 G A 0.26 0.55 0.31 0.37
MG133 4 14131426 A G 0.42 0.58 0.37 0.56
MG134 4 18832691 A C 0.41 0.60 0.37 0.51
MG135 4 20077010 G T 0.39 0.59 0.36 0.51
MG136 4 20761638 A C 0.21 0.49 0.27 0.31
MG137 4 22576276 T C 0.28 0.56 0.32 0.41
MG138 4 31743151 T G 0.30 0.58 0.33 0.40
MG139 4 33150343 T C 0.45 0.65 0.37 0.40
MG140 4 37381509 A T 0.33 0.61 0.34 0.37
MG141 4 39828005 T C 0.39 0.62 0.36 0.46
MG142 4 45151079 C T 0.47 0.60 0.37 0.55
MG143 4 50184084 T G 0.35 0.57 0.35 0.52
MG144 4 53473032 A G 0.41 0.60 0.37 0.51
MG145 4 55889650 C T 0.49 0.64 0.38 0.47
MG146 4 67519590 T C 0.48 0.63 0.37 0.49
MG147 4 77234543 A G 0.49 0.62 0.38 0.52
MG148 4 128874466 G T 0.33 0.58 0.35 0.47
MG149 4 145650338 A G 0.35 0.58 0.35 0.51
MG150 4 149311096 G A 0.39 0.64 0.36 0.35
MG151 4 151253200 A G 0.37 0.62 0.36 0.44
MG152 4 153661937 G A 0.44 0.64 0.37 0.45
MG153 4 154880065 C T 0.41 0.61 0.37 0.51
MG154 4 164294138 C T 0.30 0.56 0.33 0.47
MG155 4 169994302 G A 0.49 0.63 0.38 0.49
MG156 4 173238441 A G 0.31 0.59 0.34 0.39
MG157 4 177180130 A G 0.46 0.58 0.37 0.57
MG158 4 179824742 C T 0.48 0.61 0.38 0.53
MG159 4 184328972 G A 0.26 0.55 0.31 0.38
MG160 4 193937034 T C 0.39 0.59 0.36 0.52
MG161 4 201638107 A G 0.41 0.62 0.37 0.47
MG162 4 208661194 T C 0.32 0.58 0.34 0.46
MG163 4 215441456 A G 0.32 0.58 0.34 0.45
MG164 4 221839256 G T 0.34 0.61 0.35 0.40
MG165 4 223648151 G A 0.45 0.61 0.37 0.51
MG166 4 230935341 T G 0.40 0.58 0.37 0.55
MG167 4 232019010 A C 0.40 0.59 0.36 0.52
MG168 4 234081042 G T 0.31 0.56 0.34 0.50
MG169 4 236715495 C T 0.42 0.62 0.37 0.49
MG170 4 238918388 G A 0.35 0.61 0.35 0.43
MG171 4 240891845 T G 0.39 0.58 0.36 0.53
MG172 5 6881507 A G 0.40 0.63 0.37 0.45
MG173 5 8507286 C T 0.33 0.60 0.34 0.40
MG174 5 11356449 T C 0.32 0.56 0.34 0.51
MG175 5 13402375 T C 0.45 0.60 0.37 0.54
MG176 5 15452020 C T 0.27 0.55 0.32 0.43
MG177 5 17881372 G A 0.49 0.64 0.38 0.47
MG178 5 21008784 T C 0.39 0.61 0.36 0.47
MG179 5 29937148 C T 0.42 0.63 0.37 0.44
MG180 5 31668063 C T 0.48 0.65 0.37 0.44
MG181 5 33072014 G A 0.43 0.58 0.37 0.56
MG182 5 35669253 G A 0.29 0.57 0.33 0.40
MG183 5 38831562 T C 0.17 0.44 0.25 0.24
MG184 5 48413218 G T 0.47 0.63 0.37 0.50
MG185 5 59068812 T C 0.48 0.63 0.38 0.48
MG186 5 60955626 C T 0.37 0.59 0.36 0.51
MG187 5 62137456 A G 0.26 0.54 0.31 0.40
MG188 5 64134193 G A 0.33 0.57 0.34 0.49
MG189 5 72721863 C T 0.31 0.58 0.33 0.41
MG190 5 74941891 A G 0.27 0.56 0.32 0.39
MG191 5 80839340 G A 0.45 0.60 0.37 0.54
MG192 5 86070543 C T 0.33 0.57 0.34 0.49
MG193 5 88226330 G A 0.40 0.61 0.37 0.48
MG194 5 93618116 A G 0.30 0.57 0.33 0.43
MG195 5 130860915 T C 0.48 0.62 0.37 0.51
MG196 5 141206885 C T 0.44 0.65 0.37 0.42
MG197 5 161040798 G T 0.30 0.58 0.33 0.39
MG198 5 163451299 C T 0.37 0.63 0.36 0.38
MG199 5 166437548 T C 0.38 0.63 0.36 0.40
MG200 5 173209693 G A 0.38 0.62 0.36 0.44
MG201 5 174352063 A G 0.46 0.63 0.37 0.49
MG202 5 176085344 G A 0.43 0.59 0.37 0.55
MG203 5 178878084 T C 0.42 0.64 0.37 0.42
MG204 5 181267545 A G 0.36 0.60 0.36 0.48
MG205 5 190533458 G A 0.48 0.64 0.38 0.47
MG206 5 199812574 T C 0.49 0.61 0.38 0.53
MG207 5 204879476 G A 0.39 0.58 0.36 0.54
MG208 5 215521126 T C 0.35 0.62 0.35 0.39
MG209 5 217664096 C T 0.49 0.62 0.38 0.51
MG210 6 3592433 A G 0.45 0.61 0.37 0.52
MG211 6 4843861 T C 0.40 0.63 0.37 0.43
MG212 6 6530602 G A 0.38 0.61 0.36 0.47
MG213 6 8111698 A C 0.35 0.59 0.35 0.49
MG214 6 33247659 G A 0.48 0.64 0.37 0.48
MG215 6 39822979 C T 0.50 0.55 0.38 0.62
MG216 6 42757005 T G 0.48 0.60 0.38 0.54
MG217 6 45872006 G T 0.37 0.60 0.36 0.49
MG218 6 53883513 T G 0.27 0.56 0.32 0.36
MG219 6 56274915 G A 0.25 0.53 0.30 0.42
MG220 6 56968490 C G 0.36 0.60 0.36 0.47
MG221 6 61133030 G T 0.49 0.62 0.40 0.53
MG222 6 80804393 C T 0.37 0.58 0.36 0.52
MG223 6 83130638 G A 0.50 0.64 0.38 0.47
MG224 6 86421059 T A 0.32 0.57 0.34 0.49
MG225 6 93160349 A G 0.40 0.59 0.37 0.53
MG226 6 110465918 C T 0.50 0.66 0.38 0.41
MG227 6 111230603 C T 0.40 0.61 0.37 0.49
MG228 6 108233804 A T 0.37 0.62 0.36 0.43
MG229 6 110053930 G A 0.49 0.63 0.38 0.49
MG230 6 114361855 C T 0.47 0.59 0.37 0.55
MG231 6 118325927 C A 0.44 0.61 0.37 0.51
MG232 6 120823677 A G 0.33 0.60 0.34 0.39
MG233 6 123789176 C T 0.36 0.59 0.35 0.48
MG234 6 125370735 G A 0.42 0.58 0.37 0.56
MG235 6 132222944 T C 0.31 0.57 0.34 0.45
MG236 6 133537579 C T 0.48 0.62 0.37 0.51
MG237 6 134282494 C T 0.38 0.61 0.36 0.48
MG238 6 136548390 T C 0.34 0.59 0.35 0.45
MG239 6 139059651 T C 0.21 0.50 0.28 0.38
MG240 6 141476300 T G 0.43 0.61 0.37 0.52
MG241 6 144146341 G A 0.34 0.59 0.35 0.46
MG242 6 151680442 T C 0.37 0.61 0.36 0.45
MG243 6 153168568 C T 0.30 0.56 0.33 0.48
MG244 6 154359722 A G 0.37 0.62 0.36 0.44
MG245 6 158855833 A G 0.47 0.62 0.37 0.50
MG246 6 161650242 G A 0.49 0.62 0.38 0.51
MG247 6 164878483 T C 0.35 0.62 0.35 0.40
MG248 7 1196275 T C 0.33 0.58 0.35 0.49
MG249 7 5558292 T C 0.49 0.63 0.38 0.49
MG250 7 8069959 G A 0.41 0.64 0.37 0.42
MG251 7 9336550 A G 0.35 0.61 0.35 0.42
MG252 7 13214476 C A 0.34 0.59 0.35 0.47
MG253 7 20905062 C T 0.47 0.61 0.37 0.53
MG254 7 40598911 T C 0.25 0.54 0.30 0.36
MG255 7 44152949 A G 0.43 0.63 0.37 0.46
MG256 7 50103439 T C 0.46 0.62 0.37 0.51
MG257 7 54347237 G A 0.36 0.60 0.35 0.47
MG258 7 82347040 G A 0.30 0.57 0.33 0.43
MG259 7 86087257 A G 0.34 0.59 0.35 0.48
MG260 7 88150664 T G 0.36 0.62 0.36 0.40
MG261 7 94053087 T C 0.30 0.57 0.33 0.43
MG262 7 66727257 C A 0.32 0.58 0.34 0.47
MG263 7 98592776 G A 0.43 0.56 0.37 0.58
MG264 7 101605140 A C 0.35 0.60 0.35 0.46
MG265 7 106782474 C T 0.45 0.62 0.37 0.49
MG266 7 109082463 T G 0.45 0.64 0.37 0.46
MG267 7 117397385 T G 0.37 0.59 0.36 0.51
MG268 7 120009353 G A 0.35 0.58 0.35 0.49
MG269 7 123883434 G A 0.46 0.64 0.37 0.45
MG270 7 126677146 C A 0.33 0.58 0.34 0.47
MG271 7 132197633 A G 0.36 0.57 0.35 0.52
MG272 7 133597448 C T 0.36 0.59 0.36 0.49
MG273 7 136307948 T C 0.38 0.62 0.36 0.44
MG274 7 137524243 G A 0.32 0.59 0.34 0.40
MG275 7 143446474 G A 0.39 0.62 0.36 0.45
MG276 7 144541791 G A 0.29 0.57 0.33 0.41
MG277 7 148219064 A G 0.38 0.63 0.36 0.43
MG278 7 153138112 A G 0.43 0.62 0.37 0.50
MG279 7 155821714 A G 0.42 0.61 0.37 0.50
MG280 7 157609773 A C 0.35 0.62 0.35 0.34
MG281 7 158991658 C T 0.45 0.65 0.37 0.42
MG282 7 162196275 A G 0.37 0.57 0.36 0.54
MG283 7 163637365 C T 0.47 0.63 0.37 0.48
MG284 7 169245453 C T 0.48 0.64 0.37 0.47
MG285 7 172200651 T C 0.36 0.57 0.36 0.53
MG286 7 175252105 G A 0.43 0.65 0.37 0.38
MG287 8 2761824 G A 0.43 0.62 0.37 0.48
MG288 8 4177172 G T 0.48 0.59 0.38 0.56
MG289 8 7624059 T G 0.28 0.56 0.32 0.43
MG290 8 10124026 T C 0.48 0.63 0.38 0.49
MG291 8 14102678 C T 0.39 0.62 0.36 0.44
MG292 8 15996125 G A 0.39 0.60 0.36 0.50
MG293 8 20978845 T G 0.45 0.61 0.37 0.52
MG294 8 26588701 G A 0.34 0.58 0.35 0.48
MG295 8 40391144 A G 0.39 0.63 0.36 0.44
MG296 8 59490912 G A 0.37 0.63 0.36 0.39
MG297 8 65658110 A C 0.29 0.55 0.33 0.47
MG298 8 67244579 G A 0.49 0.60 0.38 0.55
MG299 8 70314230 G A 0.31 0.57 0.34 0.45
MG300 8 73372505 C A 0.32 0.60 0.34 0.40
MG301 8 77266692 C T 0.37 0.62 0.36 0.42
MG302 8 78372314 A G 0.45 0.58 0.37 0.57
MG303 8 84128111 T C 0.31 0.57 0.34 0.45
MG304 8 85385460 T C 0.44 0.60 0.37 0.54
MG305 8 97932001 G A 0.34 0.59 0.35 0.46
MG306 8 100450253 A G 0.23 0.52 0.29 0.35
MG307 8 109898576 C G 0.20 0.48 0.27 0.31
MG308 8 111252477 A G 0.30 0.58 0.33 0.43
MG309 8 113184750 T C 0.42 0.65 0.37 0.41
MG310 8 117143671 A G 0.40 0.62 0.36 0.47
MG311 8 118299376 C T 0.36 0.54 0.35 0.57
MG312 8 124844061 A G 0.42 0.62 0.37 0.49
MG313 8 126875542 T C 0.31 0.58 0.34 0.43
MG314 8 137758805 G A 0.33 0.59 0.34 0.45
MG315 8 139128429 C T 0.35 0.59 0.35 0.48
MG316 8 144758077 T C 0.35 0.59 0.35 0.49
MG317 8 146150639 G T 0.24 0.52 0.30 0.42
MG318 8 147803381 T C 0.43 0.65 0.39 0.44
MG319 8 152624007 G A 0.37 0.58 0.36 0.51
MG320 8 153398996 C T 0.30 0.56 0.33 0.47
MG321 8 158931728 T C 0.31 0.58 0.34 0.43
MG322 8 161316216 C A 0.30 0.58 0.33 0.42
MG323 8 164483853 A G 0.39 0.62 0.36 0.46
MG324 8 165927214 G T 0.48 0.64 0.38 0.46
MG325 8 170942747 A G 0.41 0.62 0.37 0.48
MG326 8 172618390 T C 0.48 0.65 0.37 0.45
MG327 8 174329510 G A 0.32 0.59 0.34 0.42
MG328 9 1025355 G A 0.44 0.57 0.37 0.59
MG329 9 3857368 T C 0.44 0.59 0.37 0.54
MG330 9 7191207 A G 0.38 0.59 0.36 0.51
MG331 9 11505100 C T 0.47 0.61 0.37 0.53
MG332 9 12582466 G A 0.34 0.59 0.35 0.46
MG333 9 15999332 A C 0.30 0.57 0.33 0.44
MG334 9 17446904 G T 0.41 0.62 0.37 0.47
MG335 9 24162919 T A 0.33 0.56 0.34 0.52
MG336 9 27238881 A G 0.33 0.57 0.35 0.49
MG337 6 117204743 A G 0.47 0.64 0.37 0.45
MG338 9 48613774 T C 0.39 0.64 0.36 0.37
MG339 9 56522105 C T 0.36 0.56 0.35 0.54
MG340 9 61772043 C T 0.37 0.63 0.36 0.32
MG341 9 65041502 A G 0.43 0.61 0.37 0.52
MG342 9 68085408 T G 0.32 0.60 0.34 0.37
MG343 9 89991829 G A 0.39 0.63 0.36 0.44
MG344 9 96747891 T C 0.50 0.63 0.38 0.48
MG345 9 98400029 G T 0.46 0.63 0.37 0.48
MG346 9 102277066 T C 0.46 0.61 0.37 0.53
MG347 9 104695670 A G 0.42 0.55 0.37 0.60
MG348 9 124089293 G A 0.33 0.60 0.34 0.43
MG349 9 127197714 A G 0.50 0.55 0.38 0.62
MG350 9 143433554 C T 0.46 0.62 0.37 0.51
MG351 9 148627045 C T 0.49 0.56 0.38 0.60
MG352 9 149308774 A C 0.49 0.65 0.38 0.42
MG353 9 150911119 G A 0.45 0.58 0.37 0.56
MG354 9 151542506 A G 0.49 0.61 0.38 0.53
MG355 9 155054804 G A 0.32 0.57 0.34 0.48
MG356 10 2802838 T G 0.43 0.62 0.37 0.48
MG357 10 10674490 C T 0.21 0.49 0.27 0.35
MG358 10 22133988 C T 0.30 0.57 0.33 0.43
MG359 10 32194186 T C 0.30 0.56 0.33 0.47
MG360 10 58207909 T C 0.45 0.64 0.37 0.45
MG361 10 39960289 C T 0.48 0.59 0.40 0.57
MG362 10 61011906 G A 0.49 0.65 0.38 0.45
MG363 10 76655433 T G 0.50 0.66 0.38 0.40
MG364 10 82039366 G A 0.48 0.61 0.38 0.53
MG365 10 84110544 T G 0.33 0.59 0.35 0.44
MG366 10 89433313 G A 0.36 0.60 0.36 0.46
MG367 10 95929973 A G 0.46 0.59 0.37 0.55
MG368 10 103380111 A G 0.47 0.62 0.37 0.50
MG369 10 109396730 G A 0.49 0.61 0.38 0.53
MG370 10 114217715 G A 0.49 0.64 0.38 0.46
MG371 10 117773469 T G 0.38 0.60 0.36 0.50
MG372 10 121559630 G A 0.50 0.63 0.38 0.50
MG373 10 129486606 A G 0.30 0.58 0.33 0.39
MG374 10 130399835 A G 0.32 0.58 0.34 0.45
MG375 10 131065538 T C 0.43 0.65 0.37 0.42
MG376 10 131912401 T C 0.49 0.65 0.38 0.44
MG377 10 132535283 G A 0.28 0.55 0.32 0.45
MG378 10 133905339 G A 0.28 0.57 0.32 0.36
MG379 10 135351702 C T 0.35 0.61 0.35 0.41
MG380 10 135937058 T C 0.32 0.59 0.34 0.41
MG381 10 137192651 A C 0.42 0.62 0.37 0.48
MG382 10 139565935 A G 0.41 0.59 0.37 0.54
MG383 10 144384643 A C 0.49 0.64 0.38 0.47
MG384 10 147014927 G A 0.29 0.57 0.33 0.41

Fig. 2

Distribution of maizeSNP384 combinations A: the distribution of 384 SNPs on maize 10 chromosomes; B: the distribution of SNPs in different gene regions."

Fig. 3

Distribution of MAF and PIC values of 384 SNP loci The abscissa is the interval value of MAF and PIC, and the ordinate is the number of SNP loci."

Fig. 4

The overall display of SNP-DNA fingerprints of 335 maize hybrids Each row represents one variety sorted by national approval number; each column represents one SNP locus, sorted by physical location in genome; DNA fingerprints are displayed in different colors."

Fig. 5

Analysis of heterozygous genotype rate and genetic difference of 335 maize hybrid lines A: the heterozygous genotype rate of the 335 maize hybrid lines (number of loci for heterozygous genotypes/384). B: distribution of different locus number obtained by pairwise comparative analysis of 335 maize hybrid lines, the abscissa is the number of differential loci, and the ordinate is the number of paired comparisons. C: distribution of genetic similarity coefficient obtained by pairwise comparative analysis of 335 maize hybrid lines, the abscissa is percentage of genetic similarity coefficient, and the ordinate is the number of paired comparisons."

Fig. 6

Variety identity probability curve based on the optimal loci combination"

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