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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."

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