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Acta Agronomica Sinica ›› 2024, Vol. 50 ›› Issue (5): 1115-1123.doi: 10.3724/SP.J.1006.2024.33052

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

Development of an optimal core SNP loci set for maize variety genuineness identification

TIAN Hong-Li1**(), YANG Yang1**(), FAN Ya-Ming1**(), YI Hong-Mei1, WANG Rui1, JIN Shi-Qiao2, JIN Fang2, ZHANG Yun-Long1, LIU Ya-Wei1, WANG Feng-Ge1,*(), ZHAO Jiu-Ran1,*()   

  1. 1Maize Research Institute, Beijing Academy of Agriculture and Forestry Sciences / Key Laboratory of Crop DNA Fingerprinting Innovation and Utilization of the Ministry of Agriculture and Rural Affairs (Co-construction by Ministry and Province) / Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing 100097, China
    2National Agricultural Technology Extension and Service Center, Beijing 100026, China
  • Received:2023-10-25 Accepted:2024-01-12 Online:2024-05-12 Published:2024-02-08
  • Contact: E-mail: maizezhao@126.com, Tel: 86-10-51503936; E-mail: gege0106@163.com, Tel: 86-10-51503558 E-mail:tianhongli9963@163.com;caurwx@163.com;13718078547@163.com;gege0106@163.com;maizezhao@126.com
  • About author:First author contact:

    **Contributed equally to this work

  • Supported by:
    National Scientific and Technological Innovation-Major Projects(2022ZD04019);Financial Project of Beijing Academy of Agriculture and Forestry Sciences(KJCX20230301);Financial Project of Beijing Academy of Agriculture and Forestry Sciences(CZZJ202206)

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Abstract:

Variety genuineness is an important indicator for seed quality monitoring. In order to establish accurate, reliable, fast, simple, high-throughput, and low-cost maize variety genuineness identification technology, we evaluated and determined a set of high discriminative power core SNP loci set including 96 SNPs based on SNP fingerprint data of 5816 maize hybrids and 3274 inbred lines using the genetic algorithm and variety recognition rate. All 96 SNPs were located in the intra-gene region, generally distributed evenly on 10 pairs of chromosomes. The evaluation results using the above hybrid and inbred line data showed that 96 SNPs set had high polymorphism and variety discrimination power. The average values of PIC, MAF, and DP were 0.36, 0.40, 0.60, and 0.36, 0.39, 0.48 for hybrids and inbred lines, respectively. The variety discrimination power for hybrids and inbred lines reached 99.14% and 99.24%, respectively. Pairwise comparison between varieties showed that 99.99% of the comparisons had at least three differential loci. About 96.74% of hybrids and 95.67% of inbred lines mostly had the 30-65 and 30-60 differential loci between varieties, respectively. Compared with the 40 SSRs genotype dataset using 221 hybrids, the 96-SNPs set had high consistency in the identification results of the two marker sets. In summary, the optimal core SNPs set reported in this study had the advantage of the minimum number of loci, the highest discrimination power, the strongest differentiation platforms, and the automatic genotyping. It is expected that the extensive application of this core SNP loci set will be widely used in maize variety genuineness monitor and seed quality control for maintaining seed market order, so as to defend the breeders’ rights and protecting interests of farmers.

Key words: maize variety, genuineness identification, SNP loci set, high discrimination power

Fig. 1

Variety discrimination power curve based on the optimal loci set The abscissa is the number of loci included in the loci combination, and the ordinate is the rate of variety discrimination power."

Fig. 2

Distribution of 96 core SNP loci on maize nuclear genome"

Fig. 3

Distribution of PIC, MAF, DP, and heterozygous genotype values (AB rate) of 96 SNPs evaluated by 5816 hybrids and 3274 inbred lines The abscissa is the SNP loci sorted by PIC value in descending order, the ordinate is the values of each evaluation parameter. PIC: polymorphism information content; MAF: minor allele frequency; DP: discrimination power; AB rate: AB heterozygous genotype rate."

Fig. 4

Distribution of the number of different SNPs obtained by pairwise analysis of maize hybrids and inbred lines"

Fig. 5

Correlation analysis of 96 SNPs and 40 SSRs data based on pairwise Nei 1973 genetic distances (GD) of 221 hybrids"

Fig. 6

Overall display of SNP-DNA fingerprints of 96 loci in 20 sets triad (F1 hybrid and its parents) samples Each row represents one variety, each three rows represent one set of triplet samples, N01-N20 are the numbers of the triplet samples; each column represents one SNP locus sorted by physical location on genome; DNA fingerprints are displayed in different colors."

[1] 赵久然, 王凤格, 郭景伦, 吕波, 胡长远, 堵苑苑. 玉米品种鉴定DNA指纹方法. 中华人民共和国农业行业标准, NY/T1432- 2007, 2007.
Zhao J R, Wang F G, Guo J L, Lyu B, Hu C Y, Du Y Y. Maize Variety Identification Molecular Techniques. Agricultural Industry Standards of the People’s Republic of China, NY/T 1432- 2007, 2007 (in Chinese).
[2] 王凤格, 易红梅, 赵久然, 刘平, 张新明, 田红丽, 堵苑苑. 玉米品种鉴定技术规程 SSR标记法. 中华人民共和国农业行业标准, NY/T1432- 2014, 2014.
Wang F G, Yi H M, Zhao J R, Liu P, Zhang X M, Tian H L, Du Y Y. Protocol for the Identification of Maize Varieties-SSR Marker Method. Agricultural Industry Standards of the People’s Republic of China, NY/T 1432- 2014, 2014 (in Chinese).
[3] 王凤格, 支巨振, 易红梅, 赵建宗, 张力科, 田红丽, 律宝春. 主要农作物品种真实性和纯度SSR分子标记检测玉米. 中华人民共和国国家标准, GB/T39914- 2021, 2021.
Wang F G, Zhi J Z, Yi H M, Zhao J Z, Zhang L K, Tian H L, Lyu B C. Variety Genuineness and Purity Testing of Main Crops with SSR Markers-Maize. National Standards of the People’s Republic of China, GB/T 39914- 2021, 2021 (in Chinese).
[4] 王凤格, 杨扬, 易红梅, 赵久然, 任洁, 王璐, 葛建镕, 江彬, 张宪晨, 田红丽, 侯振华. 中国玉米审定品种标准SSR指纹库的构建. 中国农业科学, 2017, 50: 1-14.
Wang F G, Yang Y, Yi H M, Zhao J R, Ren J, Wang L, Ge J R, Jiang B, Zhang X C, Tian H L, Hou Z H. Construction of an SSR-based standard fingerprint database for corn variety authorized in China. Sci Agric Sin, 2017, 50: 1-14 (in Chinese).
[5] 王凤格, 赵久然, 杨扬. 国家审定玉米品种SSR指纹图谱. 北京: 中国农业科学技术出版社, 2015.
Wang F G, Zhao J R, Yang Y. SSR Fingerprinting Data of National Approval of Maize Cultivars. Beijing: China Agricultural Science and Technology Press, 2015 (in Chinese).
[6] Lai J S, Li R Q, Xu X, Jin W W, Xu M L, Zhao H N, Xiang X K, Song W B, Ying K, Zhang M, Jiao Y P, Ni P X, Zhang J G, Li D, Guo X S, Ye K X, Jian M, Wang B, Zheng H S, Liang H Q, Zhang X Q, Wang S C, Chen S J, Li J S, Fu Y, Springer N M, Yang H M, Wang J, Dai J R, Schnable P S, Wang J. Genome-wide patterns of genetic variation among elite maize inbred lines. Nat Genet, 2010, 42:1027-1030.
[7] Jiao Y P, Zhao H N, Ren L H, Song W B, Zeng B, Guo J J, Wang B B, Liu Z P, Chen J, Li W, Zhang M, Xie S J, Lai J S. Genome-wide genetic changes during modern breeding of maize. Nat Genet, 2012, 44:812-817.
doi: 10.1038/ng.2312 pmid: 22660547
[8] Chia J M, Song C, Bradbury P J, Costich D, Leon N D, Doebley J, Elshire R J, Gaut B, Geller L, Glaubitz J C, Gore M, Guill K E, Holland J, Hufford M B, Lai J S, Li M, Liu X, Lu Y L, McCombie R, Nelson R, Poland J, Prasanna B M, Pyhäjärvi T, Rong T Z, Sekhon R S, Sun Q, Tenaillon M I, Tian F, Wang J, Xu X, Zhang Z U, Kaeppler S M, Ross-Ibarra J, McMullen M D, Buckler E S, Zhang G Y, Xu Y B, Ware D. Maize HapMap2 identifies extant variation from a genome in flux. Nat Genet, 2012, 44: 803-809.
doi: 10.1038/ng.2313
[9] Jiao Y P, Peluso P, Shi J H, Liang T, Stitzer M C, Wang B, Campbell M S, Stein J C, Wei X H, Chin C S, Guill K, Regulski M, Kumari S, Olson A, Gent J, Schneider K L, Wolfgruber T K, May M R, Springer N M, Antoniou E, McCombie W R, Presting G G, McMullen M, Ross-Ibarra J, Dawe R K, Hastie A, Rank D R, Ware D. Improved maize reference genome with single-molecular technologies. Nature, 2017, 546: 524-527.
[10] Bukowski R, Guo X, Lu Y L, Zou C, He B, Rong Z Q, Wang B, Xu D W, Yang B C, Xie C X, Fan L J, Gao S B, Xu X, Zhang G Y, Li Y R, Jiao Y P, Doebley J F, Ross-Ibarra J, Lorant A, Buffalo V, Romay M C, Buckler E S, Ware D, Lai J S, Sun Q, Xu Y B. Construction of the third-generation Zea mays haplotype map. GigaScience, 2018, 7: 1-12.
doi: 10.1093/gigascience/gix134 pmid: 29300887
[11] Semagn K, Babu R, Hearne S, Olsen M. Single nucleotide polymorphism genotyping using Kompetitive Allele Specific PCR (KASP): overview of the technology and its application in crop improvement. Mol Breed, 2014, 33, 1-14.
doi: 10.1007/s11032-013-9917-x
[12] Tian H L, Wang F G, Zhao J R, Yi H M, Wang L, Wang R, Yang Y, Song W. Development of maizeSNP3072, a high-throughput compatible SNP array, for DNA fingerprinting identification of Chinese maize varieties. Mol Breed, 2015, 35: 136.
doi: 10.1007/s11032-015-0335-0
[13] 田红丽, 杨扬, 王璐, 王蕊, 易红梅, 许理文, 张云龙, 葛建镕, 王凤格, 赵久然. 兼容型maizeSNP384标记筛选与玉米杂交种DNA指纹图谱构建. 作物学报, 2020, 46: 1006-1015.
doi: 10.3724/SP.J.1006.2020.93048
Tian H L, Yang Y, Wang L, Wang R, Yi H M, Xu L W, Zhang Y L, Ge J R, Wang F G, Zhao J R. Screening of compatible maizeSNP384 markers and the construction of DNA fingerprints of maize varieties. Acta Agron Sin, 2020, 46: 1006-1015 (in Chinese with English abstract).
doi: 10.3724/SP.J.1006.2020.93048
[14] Tian H L, Yang Y, Yi H M, Xu L W, He H, Fan Y M, Wang L, Ge J R, Liu Y W, Wang F G, Zhao J R. New resources for genetic studies in maize (Zea mays L.): a genome-wide maize 6H-60K single nucleotide polymorphism array and its application. Plant J, 2021, 105: 1113-1122.
doi: 10.1111/tpj.v105.4
[15] Tian H L, Yang Y, Wang R, Fan Y M, Yi H M, Jiang B, Wang L, Ren J, Xu L W, Zhang Y L, Ge J R, Liu Y W, Wang F G, Zhao J R. Screening of 200 core SNPs and the construction of a systematic SNP-DNA standard fingerprint database with more than 20,000 maize varieties. Agriculture, 2021, 11: 597.
[16] 王凤格, 晋芳, 田红丽, 易红梅, 赵久然, 金石桥, 杨扬, 王蕊, 葛建镕, 支巨振, 赵建宗. 玉米品种真实性鉴定 SNP标记法. 中华人民共和国农业行业标准, NY/T4022- 2021, 2021.
Wang F G, Jin F, Tian H L, Yi H M, Zhao J R, Jin S Q, Yang Y, Wang R, Ge J R, Zhi J Z, Zhao J Z. Maize (Zea mays L.) Variety Genuineness Identification: SNP Based Method. Agricultural Industry Standards of the People’s Republic of China, NY/T 4022- 2021, 2021 (in Chinese).
[17] 魏兴华, 刘丰泽, 韩斌, 徐群, 冯旗, 赵妍, 支巨振, 周泽宇, 杨窑龙, 冯跃, 任雪贞, 王珊, 章孟臣. 水稻品种真实性鉴定 SNP标记法. 中华人民共和国农业行业标准, NY/T2745- 2021, 2021.
Wei X H, Liu F Z, Han B, Xu Q, Feng Q, Zhao Y, Zhi J Z, Zhou Z Y, Yang Y L, Feng Y, Ren X Z, Wang S, Zhang M C. Rice (Oryza sativa L.) Variety Genuineness Identification: SNP Based Method. Agricultural Industry Standards of the People’s Republic of China, NY/T 2745- 2021, 2021 (in Chinese).
[18] 庞斌双, 任雪贞, 刘丽华, 赵昌平, 张明明, 金石桥, 李宏博, 刘阳娜, 周泽宇, 张风廷, 张立平, 张胜全, 马锦绣, 权威, 王穆穆, 张旭, 侯建, 关海涛, 傅友兰, 王卫红. 小麦品种真实性鉴定 SNP标记法. 中华人民共和国农业行业标准, NY/T4021- 2021, 2021.
Pang B S, Ren X Z, Liu L H, Zhao C P, Zhang M M, Jin S Q, Li H B, Liu Y N, Zhou Z Y, Zhang F T, Zhang L P, Zhang S Q, Ma J X, Quan W, Wang M M, Zhang X, Hou J, Guan H T, Fu Y L, Wang W H. Wheat (Triticum aestivum L.) Variety Genuineness Identification: SNP Based Method. Agricultural Industry Standards of the People’s Republic of China, NY/T 4021- 2021, 2021 (in Chinese).
[19] 李志远, 于海龙, 方智远, 杨丽梅, 刘玉梅, 庄木, 吕红豪, 张扬勇. 甘蓝SNP标记开发及主要品种的DNA指纹图谱构建. 中国农业科学, 2018, 51: 2771-2787.
doi: 10.3864/j.issn.0578-1752.2018.14.014
Li Z Y, Yu H L, Fang Z Y, Yang L M, Liu Y M, Zhuang M, Lyu H H, Zhang Y Y. Development of SNP markers in cabbage and construction of DNA fingerprinting of main varieties. Sci Agric Sin, 2018, 51: 2771-2787 (in Chinese with English abstract).
[20] 颜廷进, 蒲艳艳, 张文兰, 田茜, 王栋, 李群, 戴双, 丁汉凤. 基于SNP标记的菜豆品种真实性和纯度鉴定技术. 山东农业科学, 2019, 51(12): 111-119.
Yan T J, Pu Y Y, Zhang W L, Tian Q, Wang D, Li Q, Dai S, Ding H F. Identification technology of genuineness and purity for common bean varieties based on SNP markers. Shandong Agric Sci, 2019, 51(12): 111-119 (in Chinese with English abstract).
[21] 任海龙, 许东林, 张晶, 邹集文, 李光光, 周贤玉, 肖婉钰, 孙艺嘉. 菜薹KASP-SNP指纹图谱构建及品种鉴定. 园艺学报, 2023, 50: 307-318.
doi: 10.16420/j.issn.0513-353x.2021-1046
Ren H L, Xu D L, Zhang J, Zou J W, Li G G, Zhou X Y, Xiao W Y, Sun Y J. Establishment of SNP fingerprinting and identification of Chinese flowering cabbage varieties based on KASP genotyping. Acta Hortic Sin, 2023, 50: 307-318.
doi: 10.16420/j.issn.0513-353x.2021-1046
[22] 王凤格, 赵久然, 杨扬. 基于遗传算法的植物品种真实性鉴定位点筛选方法. 中国发明专利, 2013, ZL201310629676.2.
Wang F G, Zhao J R, Yang Y. The Method of Locus Selecting for Plant Variety Authenticity Identification Based on Genetic Algorithm. Chinese Invention Patent, 2013, ZL201310629676.2 (in Chinese).
[23] Yang Y, Tian H L, Wang R, Wang L, Yi H M, Liu Y W, Xu L W, Fan Y M, Zhao J R, Wang F G. Variety Discrimination Power: an appraisal index for loci combination screening applied to plant variety discrimination. Front Plant Sci, 12: 566796.
doi: 10.3389/fpls.2021.566796
[24] 赵久然, 王凤格, 田红丽, 易红梅, 王蕊, 葛建镕. 适于农作物品种分子身份鉴别和确权鉴定的检测方法. 中国发明专利, 2017, ZL 201710527354.5.
Zhao J R, Wang F G, Tian H L, Yi H M, Wang R, Ge J R. Detection Methods for Identity Distinguish and Intellectual Property Confirmation of Crop Varieties Using Molecular Markers. Chinese Invention Patent, 2017, ZL 201710527354.5 (in Chinese).
[25] 王凤格, 田红丽, 易红梅, 赵涵, 霍永学, 匡猛, 张力科, 吕远大, 丁曼卿, 赵久然. 植物品种DNA指纹鉴定原理及其鉴定方案. 分子植物育种, 2018, 16: 4756-4766.
Wang F G, Tian H L, Yi H M, Zhao H, Huo Y X, Kuang M, Zhang L K, Lyu Y D, Ding M Q, Zhao J R. Principle and strategy of DNA fingerprint identification of plant variety. Mol Plant Breed, 2018, 16: 4756-4766 (in Chinese with English abstract).
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