Maize Genomics and Genetics 2025, Vol.16, No.2, 70-79 http://cropscipublisher.com/index.php/mgg 74 5 Comparison of Genetic Diversity Analysis Methods 5.1 Analyses based on phenotypic data When it comes to studying the diversity of corn varieties, the most direct way is to see what they look like. Researchers usually measure visible and tangible characteristics such as plant height, ear height, and grain yield. This method is particularly commonly used in corn germplasm research. Although it sounds simple, it works surprisingly well. For example, in Egypt, scientists have used this method to study commercial hybrids (Al-Naggar et al., 2020). They found that after the morphological data of these corns were processed using PCA and UPGMA cluster analysis, the differences in agronomic traits of different varieties were clear at a glance. Interestingly, the same method was also used in southern Africa (He et al., 2017), and it was found that there were quite large differences between different brands of hybrids. These findings are of great reference value for corn classification and breeding. Although the method is traditional, it does work. 5.2 Analyses using molecular markers When it comes to analyzing the genetic diversity of corn, the most commonly used molecular markers are SSR and SNP. These technologies are indeed much more accurate than traditional methods. For example, in Portugal, when researchers used SSR markers to detect local corn germplasm (Franco-Duran et al., 2019), they found that the differences between different inbred lines were quite obvious, and confirmed that Portuguese corn is actually "hybrid". But what's interesting is that SNP markers give richer information. When using it to analyze global corn germplasm, temperate and tropical varieties are naturally divided into different groups, and the genetic differences between different hybrid advantage groups are also clearly seen. Even more surprising is the performance of tropical corn-SNP and haplotype analysis shows (Liu, 2024) that tropical corn not only has higher genetic diversity, but also has a faster decay of linkage disequilibrium, which is good news for future breeding work. 5.3 High-throughput analyses based on whole-genome data The means of studying corn genes are becoming more and more advanced. Take the IRAP technology, for example. It can reveal the ecological adaptation characteristics of corn varieties through retrotransposons, which is quite interesting. But even more powerful is the whole genome SNP analysis (Figure 2) (Yang et al., 2022). This technology has recently discovered more than 1 100 selected genomic regions in temperate and tropical corn. Interestingly, many of these regions are regulatory genes, which seem to play an important role in the process of corn improvement. These new methods have indeed deepened our understanding of the genetic structure of corn. Although the technology is complex, the information obtained is indeed comprehensive. 5.4 Advantages and limitations of different analytical methods When studying the genetic diversity of maize, we have several methods to choose from, but each has its pros and cons. The most traditional one is phenotypic analysis, which is simple and cost-effective, and can be used in many breeding projects (Ghonaim et al., 2020). But the problem is that what maize looks like is greatly affected by the environment, and the results measured by different people may be different. In contrast, molecular markers such as SSR and SNP are much more accurate and less interfered by environmental factors, but laboratory operations are complicated and costly. The most comprehensive one is whole genome analysis, which can even show which specific gene regions have been selected (Mhoswa et al., 2016). But to be honest, this method is not only expensive, but also requires a professional bioinformatics team to process massive amounts of data. So you see, the method you choose depends on specific needs and conditions, and there is no perfect method. 6 Conservation and Utilization of Genetic Diversity in Sweet Corn Germplasm 6.1 Identification and evaluation of superior germplasm resources To protect and utilize the genetic resources of fresh corn, we must first find those truly high-quality varieties. Researchers usually use a variety of molecular markers to evaluate these germplasm resources. For example, a study used microsatellite marker analysis to find that there is significant polymorphism and heterozygosity between different fresh corn varieties (Jompuk et al., 2020). Interestingly, if field observations and molecular testing are combined, more surprises can often be found-some inbred lines not only have outstanding yields, but also have excellent sweetness performance. Although each detection method has its own characteristics, the
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