Maize Genomics and Genetics 2024, Vol.15, No.4, 204-217 http://cropscipublisher.com/index.php/mgg 205 2 Development of Maize Genomic Resources 2.1 Sequencing of the maize genome: milestones and progress The sequencing of the maize genome has undergone significant advancements over the past decade, driven by the development of new sequencing technologies and methodologies. One of the most notable milestones was the assembly and annotation of the maize genome using Single Molecule Real-Time (SMRT) sequencing and high-resolution optical mapping. This approach resulted in a 52-fold increase in contig length compared to previous reference genomes, with substantial improvements in the assembly of intergenic spaces and centromeres. The characterization of the repetitive portion of the genome revealed over 130 000 intact transposable elements, providing insights into transposable element lineage expansions unique to maize. Additionally, gene annotations were updated using 111 000 full-length transcripts obtained by SMRT sequencing (Jiao et al., 2017). Another significant contribution to maize genomics was the draft genome sequence of the elite maize line HuangZaoSi (HZS). This genome sequence provided insights into genomic variation and the improvement history of maize. The study revealed that more than 60% of identified selective sweeps were clustered in identity-by-descent conserved regions, and yield-related genes/QTLs were enriched in HZS characteristic selected regions. This research expanded our understanding of the breadth of genomic variation and the historical improvement of maize (Li et al., 2019). 2.2 Public databases and genomic repositories Public databases and genomic repositories play a crucial role in the dissemination and utilization of maize genomic resources. The USA National Plant Germplasm System, for instance, has utilized genotyping-by-sequencing (GBS) to genotype 2 815 maize inbred accessions. This effort produced 681 257 single-nucleotide polymorphism (SNP) markers distributed across the entire genome, enabling the detection of rare alleles with high confidence. The genotypic information from this publicly available panel allows researchers to explore genetic diversity and perform genome-wide association studies, thereby addressing challenges in sustainable agriculture (Romay et al., 2013). Genotyping-by-sequencing (GBS) has emerged as a powerful tool for marker-assisted selection (MAS) in plant breeding. GBS combines molecular marker discovery and genotyping, making it a cost-effective technique for large-scale plant breeding programs. It has been successfully used in genome-wide association studies (GWAS), genomic diversity studies, genetic linkage analysis, and molecular marker discovery, significantly accelerating the breeding process (Bevan et al., 2017). 2.3 Comparative genomics and evolutionary insights Comparative genomics has provided valuable evolutionary insights into maize and its relatives. The detailed characterization of plant genomes and genetic diversity has been instrumental in identifying a wide spectrum of genetic variation and associating it with diverse agronomic phenotypes. Advances in genome sequencing and assembly have enabled researchers to access the large and complex genomes of crops and their wild relatives, facilitating the identification of genetic diversity and its association with agronomic traits (Figure 1) (Andorf et al., 2019). The comparative analysis of maize genomes has also revealed the prevalence of deletions in regions of low gene density and maize lineage-specific genes. This information is crucial for understanding the evolutionary history of maize and its adaptation to different environments (Jiao et al., 2017). Furthermore, the proteome clustering of six completed maize genomes identified 638 proteins falling into 264 HZS-specific gene families, with the majority of contributions from tandem duplication events. This study provided novel insights into the genomic variation and improvement history of maize, highlighting the importance of comparative genomics in crop improvement (Li et al., 2019). In summary, the development of maize genomic resources has been marked by significant milestones in genome sequencing, the establishment of public databases and genomic repositories, and the application of comparative genomics. These advancements have provided a solid foundation for enhanced crop breeding, enabling
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