Screening of 200 Core SNPs and the Construction of a Systematic SNP-DNA Standard Fingerprint Database with More Than 20,000 Maize Varieties

Hongli Tian, Yang Yang, Rui Wang, Yaming Fan, Hongmei Yi, Bin Jiang, Lu Wang, Jie Ren, Liwen Xu, Yunlong Zhang, Jianrong Ge, Yawei Liu, Fengge Wang and Jiuran Zhao
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Hongli Tian: Maize Research Center, Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
Yang Yang: Maize Research Center, Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
Rui Wang: Maize Research Center, Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
Yaming Fan: Maize Research Center, Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
Hongmei Yi: Maize Research Center, Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
Bin Jiang: Maize Research Center, Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
Lu Wang: Maize Research Center, Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
Jie Ren: Maize Research Center, Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
Liwen Xu: Maize Research Center, Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
Yunlong Zhang: Maize Research Center, Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
Jianrong Ge: Maize Research Center, Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
Yawei Liu: Maize Research Center, Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
Fengge Wang: Maize Research Center, Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
Jiuran Zhao: Maize Research Center, Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China

Agriculture, 2021, vol. 11, issue 7, 1-14

Abstract: To strengthen the management of maize varieties and the protection of intellectual property rights to new varieties, we constructed a comprehensive single nucleotide polymorphism (SNP)-DNA standard fingerprint database of 20,075 materials covering nationally and provincially approved maize hybrid lines, hybridized combinations, and inbred lines. The database was based on 200 core SNPs selected from 60 K SNPs distributed in intragenic regions, including 106 (53.0%) located in exons. Average minor allele frequencies (MAF) of the 200 SNPs in 6755 maize hybrids, 7837 hybridized combinations, and 3478 inbred lines were 0.385, 0.350, and 0.378, respectively, with corresponding average polymorphism information content (PIC) values of 0.354, 0.335, and 0.351. Heterozygous genotype frequencies of maize hybrids, hybridized combinations, and inbred lines averaged 0.48, 0.47, and 0.012, respectively. The number of different loci in the three different maize groups ranged from one up to 164, 160, and 140, respectively. The percentage of different SNPs within 5% (the number of difference SNPs is less than 10) accounted for 0.013%, 0.011%, and 0.030% among pairwise comparisons of samples within hybrid lines, hybridized combinations and inbred lines, respectively. Genetic distances between varieties based on the 200 core SNPs were highly correlated with those obtained using 60 K SNPs, with a correlation coefficient of 0.82 and 0.87 in in inbred and hybrid lines, respectively. The maize SNP-DNA fingerprint database established in this study can play an important role in variety authentication, purity determination and the protection of variety rights, thereby providing reliable, comprehensive data support for use in the seed industry.

Keywords: Maize ( Zea mays L.); 200 core SNPs; fingerprint database; variety identification; protection of variety rights (search for similar items in EconPapers)
JEL-codes: Q1 Q10 Q11 Q12 Q13 Q14 Q15 Q16 Q17 Q18 (search for similar items in EconPapers)
Date: 2021
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