Maize Genomics and Genetics 2024, Vol.15, No.5, 247-256 http://cropscipublisher.com/index.php/mgg 251 4 Role of High-Throughput Sequencing in Maize Genetic Diversity Studies 4.1 Assessment of genetic diversity High-throughput sequencing (HTS) technologies, such as genotyping-by-sequencing (GBS), have revolutionized the evaluation of genetic diversity in maize germplasm. For instance, the comprehensive genotyping of the USA national maize inbred seed bank utilized GBS to genotype 2 815 maize inbred accessions, resulting in the identification of 681 257 single-nucleotide polymorphism (SNP) markers across the genome. This extensive genotypic data revealed significant population stratification and moderate differentiation among major maize subpopulations, highlighting the utility of HTS in capturing the genetic diversity present in maize germplasm collections (Romay et al., 2013). Additionally, the use of inter-retrotransposon-amplified polymorphisms (IRAPs) has been effective in assessing genetic diversity, with studies showing high polymorphism rates and the ability to identify genetic similarities among maize lines (Ghonaim et al., 2020). HTS data supports the conservation and utilization of maize germplasm by providing detailed genetic information that can guide breeding programs. For example, the development of high-resolution multiple-SNP arrays through genotyping by target sequencing (GBTS) has enabled the creation of marker panels that are powerful for genetic diversity detection and linkage disequilibrium decay analysis. These tools facilitate genome-wide association studies and the efficient management of genetic resources, ensuring that diverse germplasm is conserved and utilized effectively in breeding programs (Guo et al., 2019; Guo et al., 2021). 4.2 Population structure analysis and genetic linkage mapping HTS data is instrumental in conducting population structure analysis in maize. The genotyping of diverse maize inbred lines using RNA-sequencing (RNA-seq) identified over 351 710 polymorphic loci, which were used to reveal tight clustering of distinct heterotic groups and exotic lines. This clustering provides insights into the genetic structure of maize populations, which is crucial for understanding the genetic basis of important traits and for designing effective breeding strategies (Hansey et al., 2012). Similarly, the phased genotyping-by-sequencing approach has enhanced the analysis of genetic diversity and revealed divergent copy number variants, further contributing to the understanding of population structure (Manching et al., 2017). HTS technologies have enabled the construction of high-density genetic linkage maps, which are essential for quantitative trait loci (QTL) mapping of complex traits in maize. For instance, the GBS approach has been used to map roughly 200 000 sequence tags in maize recombinant inbred populations, providing a dense genetic map that supports the identification of QTLs associated with important agronomic traits (Elshire et al., 2011). These high-density maps are invaluable for dissecting the genetic architecture of complex traits and for facilitating marker-assisted selection in breeding programs. 4.3 Natural populations and domestication history studies HTS has provided new insights into the domestication history and evolutionary processes of maize. By analyzing genetic diversity and population structure, researchers can trace the origins and spread of domesticated maize. For example, the comprehensive genotyping of maize germplasm has revealed patterns of genetic variation that reflect the domestication and subsequent breeding of maize, shedding light on the evolutionary processes that have shaped its current genetic makeup (Romay et al., 2013; Ghonaim et al., 2020). HTS data has also been used to study gene flow between wild maize and domesticated varieties. The detailed genetic information obtained from HTS allows researchers to detect introgression events and to understand the impact of gene flow on the genetic diversity of domesticated maize. This information is crucial for maintaining genetic diversity and for the continued improvement of maize through breeding programs (Hansey et al., 2012; Romay et al., 2013). 5 Applications of High-Throughput Sequencing in Resistance Breeding 5.1 Identification of disease resistance genes High-throughput sequencing (HTS) has significantly advanced the identification of disease resistance genes in maize. By enabling the comprehensive analysis of genetic variations, HTS facilitates the discovery of quantitative
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