Maize Genomics and Genetics 2024, Vol.15, No.4, 204-217 http://cropscipublisher.com/index.php/mgg 207 3.2 Development and application of molecular markers Molecular markers are essential tools in modern plant breeding, providing a means to track genetic variations associated with desirable traits. The development of various types of molecular markers, such as single nucleotide polymorphisms (SNPs), has revolutionized the field. These markers are used in MAS to assist phenotypic selections, thereby improving the accuracy and efficiency of breeding programs (Eathington et al., 2007; He et al., 2014; Hasan et al., 2021). The advent of next-generation sequencing (NGS) technologies has further expanded the utility of molecular markers. Techniques like genotyping-by-sequencing (GBS) have enabled the simultaneous discovery and genotyping of SNPs in large crop genomes, such as maize. GBS involves the digestion of genomic DNA with restriction enzymes, followed by the ligation of barcode adapters, PCR amplification, and sequencing. This high-throughput approach has been successfully used in genome-wide association studies (GWAS), genetic diversity studies, and genomic selection, making it a cost-effective and powerful tool for large-scale plant breeding programs (He et al., 2014). In addition to SNPs, other molecular markers such as quantitative trait loci (QTL) have been extensively mapped for various plant species. These markers have been used in MAS to improve traits like drought tolerance, disease resistance, and yield. The integration of molecular markers into breeding programs has significantly shortened the time required to develop new crop varieties, thereby enhancing the overall productivity and sustainability of agricultural systems (Varshney et al., 2013; Hasan et al., 2021). 3.3 Integration of genomic selection in breeding programs The integration of GS into breeding programs requires a strategic approach to optimize its benefits. Traditional breeding programs need to be restructured to incorporate GS effectively. This involves reorganizing field designs, training populations, and increasing the number of lines evaluated. Leveraging large amounts of genomic and phenotypic data collected across different growing seasons and environments is crucial to increase heritability estimates, selection intensity, and selection accuracy (Merrick et al., 2022). One of the key advantages of GS is its ability to improve selection accuracy while minimizing the need for extensive phenotyping. This is particularly beneficial for traits that are difficult or expensive to measure. By using GEBVs, breeders can select the best candidates for the next breeding cycle more efficiently, thereby reducing the overall time and cost associated with developing new varieties (Jannink et al., 2010; Budhlakoti et al., 2022). GS has been successfully integrated into maize breeding programs, where it has been used to enhance traits such as yield, stress tolerance, and disease resistance. The use of advanced statistical models and high-throughput phenotyping techniques has further improved the accuracy of GS predictions. For instance, hyperspectral imaging technology can be combined with GS to provide detailed phenotypic data, which can be used to refine prediction models and enhance breeding outcomes (Crossa et al., 2017; Budhlakoti et al., 2022). In conclusion, the integration of GS and molecular markers into maize breeding programs represents a significant advancement in crop improvement. By leveraging genome-wide marker data and advanced statistical models, breeders can achieve faster genetic gains and develop superior crop varieties with enhanced traits. The continued refinement and application of these genomic tools will play a crucial role in meeting the growing demands for food security and sustainable agriculture. 4 CRISPR and Genome Editing Techniques in Maize 4.1 Overview of CRISPR technology The CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) technology, coupled with CRISPR-associated proteins (Cas), has revolutionized the field of genome editing. Initially discovered as a bacterial immune mechanism, CRISPR/Cas systems have been adapted for precise genome editing in various organisms, including plants and animals. The CRISPR/Cas9 system, in particular, has gained widespread use due to its simplicity, efficiency, and versatility (Figure 2) (Manghwar et al., 2019; Li et al., 2021; Wang and Doudna, 2023).
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