Yang Yang

Maize(Zea mays. L) is a globally important crop, and understanding its genetic diversity is crucial for plant breeding phylogenetic analyses and comparative genetics. While nuclear markers have been extensively used for mapping agriculturally important genes, they are limited in recognizing characteristics, such as cytoplasmic male sterility and reciprocal cross hybrids. In this study, we performed next-generation sequencing of 176samples, and the maize cultivars represented five distinct groups. A total of 89 single nucleotide polymorphisms (SNPs) and 11 insertion/deletion polymorphisms (InDels) were identified. To enable high-throughput detection, we successfully amplified and confirmed 49 SNP and InDel markers, which were defined as a Varietal Chloroplast Panel (VCP) using the Kompetitive Allele Specific PCR (KASP). The specific markers provided a valuable tool for identifying chloroplast groups. The verification experiment, focusing on the identification of reciprocal cross hybrids and cytoplasmic male sterility hybrids, demonstrated the significant advantages of VCP markers in maternal inheritance characterization. Furthermore, only a small subset of these markers is needed to provide useful information, showcasing the effectiveness of these markers in elucidating the artificial selection process of elite maize lines.

The standard fingerprint construction and genetic diversity analysis of maize varieties approved in Jilin province can provide data support for variety approval, protection, and market monitoring. It is also of great significance for variety breeding and germplasm innovation. In this study, 40 pairs of SSR markers were used to construct the standard SSR-DNA fingerprints of 290 maize varieties approved in Jilin province from 2010 to 2017, and the genetic diversity was analyzed. The results showed that the average number of alleles detected by 40 SSRs was 11.85 and the average PIC was 0.64. The average frequency of heterozygous genotypes of varieties was 0.66. The different loci number among varieties was ≥ 2. The genetic diversity analysis of six maturity groups revealed that there were more varieties with middle and late maturity, accounting for 71.72%, and fewer varieties with extremely early maturity, early maturity, and late maturity. The early maturity group had the highest gene diversity parameter of 0.69, and the mid-late maturity group with the largest number of varieties had a relatively low gene diversity value. Clustering results indicated that the varieties approved and popularized in Jilin province were divided into three categories: sweet waxy and popcorn, extremely early and early middle, medium or late maturity. The middle or late maturing varieties had two major trends, representing the differences in the selection of heterozygous groups, the different breeding units, the differences in variety types and so on. This study provides an important theoretical and data basis for maize variety management, variety breeding, and germplasm innovation in Jilin province.

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.

Silage corn is a high-quality feed crop, which is of great significance to the vigorous development of animal husbandry. In order to explore the current status of genetic diversity of silage corn varieties, 141 silage corn varieties approved by national or provincial (municipal) were used as materials. From the perspective of ecological regions, the genetic diversity of the test varieties was analyzed by agronomic and quality traits and SSR markers. The results showed that the coefficient of variation of the 13 agronomic and quality traits ranged from 10.30% to 30.31%, with an average of 16.01%; the diversity index ranged from 0.50 to 0.71, with an average of 0.60. According to the cluster analysis of tested varieties based on agronomic and quality traits, all the varieties were divided into five groups, and most of them from the same ecological region were classified into the same group. A total of 482 allelic variants were detected for 40 SSR markers, with an average of 12.05 per locus, and the polymorphic information content (PIC) ranged from 0.27 to 0.89, with an average of 0.68. The genetic distances between South varieties and Northeast, Huang-Huai-Hai, or Northwest varieties are relatively far with a value of 0.054, 0.047, and 0.046, respectively, and most of South varieties are clustered in the same group. The analysis results of the two methods show both commonalities and differences. South varieties show specificity in both agronomic and quality traits and SSR markers, while Northwest and Huang-Huai-Hai varieties show specificity only in agronomic and quality traits. Combination of the two methods can thus help us understand the genetic background of silage corn varieties more comprehensively and accurately, and provide basis and reference for the selection and promotion of new varieties in different ecological regions.

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.