1 Introduction

Teosinte (Zea mays ssp. parviglumis) is the wild ancestor of modern maize (Zea mays ssp. mays). The transformation of teosinte into maize is a prime example of domestication that has significantly impacted agricultural practices. Teosinte and maize differ drastically in their morphological traits, such as the structure of their inflorescences and kernels, yet they share a common genetic foundation. The morphological differences are primarily controlled by a few key genetic loci, such as teosinte branched1 (tb1), which influences plant architecture and inflorescence development (Doebley et al., 1995).

Comparative genomics, the study of similarities and differences in the genetic material of different organisms, plays a crucial role in understanding the evolutionary processes and genetic modifications underlying domestication. By comparing the genomes of teosinte and maize, researchers can identify genetic variations that have been selected during domestication, such as copy number variations (CNVs) and presence-absence variations (PAVs) (Swanson-Wagner et al., 2010). These insights are vital for improving modern maize varieties through the introduction of beneficial alleles from teosinte, enhancing genetic diversity, and increasing resilience to environmental stresses (Liu et al., 2016).

This study aims to synthesize current research on the comparative genomics of teosinte and maize and its agricultural implications. It seeks to elucidate the genetic differences and similarities between teosinte and maize by examining key genetic loci and their roles in plant morphology and domestication traits (Doebley and Stec, 1991). Additionally, the study highlights the advances in genomic technologies, such as next-generation sequencing, that facilitate the study of these genetic relationships (Hufford et al., 2012). Understanding these genetic underpinnings is vital for improving modern maize varieties through the introduction of beneficial alleles from teosinte, enhancing genetic diversity, and increasing resilience to environmental stresses (Liu et al., 2016). By leveraging the genetic resources of teosinte, researchers aim to develop maize varieties that are more robust, high-yielding, and capable of thriving in diverse environments Oaxaca, indicates that agricultural selection of domesticated teosinte was underway by around 4 200 B.C. (Benz, 2001). The transition from foraging to farming marked a pivotal change in human societies, allowing for settled communities and the development of complex civilizations.

Maize (Zea mays ssp. mays) and its closest wild relatives, the teosintes (Zea mays ssp. parviglumis and Zea mays ssp. mexicana), exhibit stark differences in morphology despite their genetic similarities. This domestication process involved significant modifications to teosinte's physical characteristics, making it more suitable for human consumption and cultivation (Panda et al., 2020).

2 Origin and Domestication

2.1 Historical context of teosinte and maize domestication

The domestication of maize from its wild ancestor, teosinte, represents one of the most significant agricultural transformations in human history. This process began approximately 9 000 years ago in the Balsas River Valley of southern Mexico. Archaeological evidence from Guilá Naquitz, Oaxaca, indicates that agricultural selection of domesticated teosinte was underway by around 4 200 B.C. (Benz, 2001). The transition from foraging to farming marked a pivotal change in human societies, allowing for settled communities and the development of complex civilizations.

Maize (Zea mays ssp. mays) and its closest wild relatives, the teosintes (Zea mays ssp. parviglumis and Zea mays ssp. mexicana), exhibit stark differences in morphology despite their genetic similarities. This domestication process involved significant modifications to teosinte's physical characteristics, making it more suitable for human consumption and cultivation (Panda et al., 2020).

2.2 Genetic evidence for domestication events

Genetic studies have played a crucial role in unraveling the complex history of maize domestication. Phylogenetic analyses based on multilocus microsatellite genotyping indicate that all modern maize varieties descended from a single domestication event in southern Mexico about 9,000 years ago (Matsuoka et al., 2002). This finding challenges earlier hypotheses that proposed multiple independent domestication events.

The genetic diversity observed in maize today can be attributed to gene flow from various teosinte taxa into the maize gene pool, both during and after domestication. Gene flow from teosinte has contributed to the genetic variability seen in maize, allowing for adaptation to diverse environments and resilience to biotic and abiotic stresses (Warburton et al., 2011).

Comparative genomics studies have identified significant genetic variations, such as copy number variations (CNVs) and presence-absence variations (PAVs), between maize and teosinte. These genetic differences have been crucial in understanding the domestication process and identifying genes under strong selection during this period (Swanson-Wagner et al., 2010).

2.3 Morphological changes during domestication

The domestication of maize involved dramatic morphological changes from its wild ancestor, teosinte. These changes were primarily driven by human selection for traits that enhanced the utility and productivity of the plant. One of the most significant morphological changes was the modification of the ear structure. In teosinte, the ear is composed of a few small, hard kernels enclosed in a hard casing, making it difficult for human consumption. In contrast, domesticated maize has large, exposed kernels that are easily accessible (Wang et al., 2005).

The teosinte branched1 (tb1) gene played a critical role in this transformation. The tb1 gene controls the plant's branching architecture, with the domesticated version of tb1 leading to fewer branches and a single, large central stalk, which supports a larger ear (Doebley et al., 1995). This change made maize more suitable for cultivation and harvesting.

Another significant gene, teosinte glume architecture1 (tga1), influenced the development of the maize kernel's protective casing. The domesticated allele of tga1 led to the reduction of the hard glumes that enclose the kernels in teosinte, resulting in the "naked" kernels of maize that are easily accessible (Wang et al., 2005).

In addition to these genetic changes, the domestication process also involved alterations in the plant's reproductive structures. The transformation of the inflorescence from a teosinte-like structure to the modern maize ear involved changes in the expression and regulation of multiple genes, leading to the development of female ears on the central stalk and male tassels at the top (Doebley et al., 1990).

The domestication of maize also involved metabolic changes. Comparative metabolomics studies have shown that domesticated maize and teosinte have distinct metabolic profiles, with maize having adapted to different environmental conditions through changes in metabolic pathways. These adaptations include the evolution of specific metabolites that enhance the plant's growth and resistance to pests and diseases (Xu et al., 2019). The domestication of maize from teosinte involved significant genetic and morphological changes driven by human selection. These changes enhanced the plant's suitability for cultivation, consumption, and adaptation to diverse environments, transforming it into one of the world's most important staple crops.

3 Genomic Comparisons

3.1 Genome structure and organization

The genome structure and organization of maize and teosinte exhibit both similarities and significant differences, reflecting the evolutionary changes brought about by domestication. Teosinte (Zea mays ssp. parviglumis) and maize (Zea mays ssp. mays) share the same basic chromosome number (2n=20) and largely similar chromosomal structures, which allows for interbreeding and the production of fertile hybrids (Doebley and Stec, 1991). However, structural variations such as copy number variations (CNVs) and presence-absence variations (PAVs) are prominent in their genomes, contributing to their phenotypic diversity (Swanson-Wagner et al., 2010).

Genomic analyses have identified significant gene content variation among different maize inbreds and teosinte genotypes. For instance, teosinte possesses a higher number of genes with copy number variations compared to maize. These CNVs and PAVs are often found in multiple genotypes, indicating that they predate domestication and have been maintained despite selection pressures (Li et al., 2021).

3.2 Key genetic differences between teosinte and maize

The key genetic differences between teosinte and maize are primarily associated with loci that control traits relevant to domestication and agriculture. One of the most notable genetic loci is teosinte branched1 (tb1), which plays a critical role in the plant's architecture. In teosinte, the tb1 gene promotes the development of long lateral branches, while in maize, a mutation in tb1 results in reduced branching and a more compact plant structure suitable for cultivation (Doebley et al., 1995).

Another significant locus is teosinte glume architecture1 (tga1), which affects the hardness and coverage of the kernels. In teosinte, the kernels are encased in a hard fruitcase, whereas in maize, a mutation in tga1 disrupts this structure, exposing the kernels and making them accessible for consumption (Dorweiler and Doebley, 1997).

There are genes associated with metabolic processes that differ significantly between maize and teosinte. For example, genes involved in the synthesis of secondary metabolites such as alkaloids, terpenoids, and benzoxazinoids exhibit divergence between these two subspecies. This metabolic divergence reflects the adaptation of maize to different environmental conditions and human agricultural practices (Xu et al., 2019).

3.3 Genomic regions associated with domestication traits

Genomic regions associated with domestication traits in maize have been identified through quantitative trait loci (QTL) mapping and other genetic analyses. These regions typically contain genes that have undergone strong selection during the domestication process. One such region is the locus on chromosome 1 that includes tb1, which significantly affects plant architecture and branching patterns (Doebley et al., 1995).

Another critical region is the one containing the tga1 gene on chromosome 4, which controls the hardness and protection of the kernels. The domestication of maize involved selecting for mutations in this region that led to the development of softer, exposed kernels, which are easier to harvest and consume (Dorweiler and Doebley, 1997).

Recent studies have also highlighted the role of other genomic regions and genes in the domestication and improvement of maize. For instance, the presence-absence variations (PAVs) and CNVs in certain genes contribute to phenotypic diversity and adaptation to different environments. These structural variations are often found in genes involved in stress responses, growth regulation, and metabolic processes (Li et al., 2021).

Moreover, comparative transcriptomic studies have revealed that around 75% of genes are highly conserved between maize and teosinte, while the remaining genes exhibit divergence due to selection pressures during domestication. This includes genes with strong selection signals that contribute to important agronomic traits such as yield, stress tolerance, and nutrient use efficiency (Huang et al., 2016).

The genomic comparisons between teosinte and maize have provided valuable insights into the genetic changes associated with domestication. Key genetic loci such as tb1 and tga1 play crucial roles in defining the morphological and physiological traits that distinguish maize from its wild ancestor. Understanding these genetic differences and the associated genomic regions can aid in the development of improved maize varieties through the incorporation of beneficial alleles from teosinte.

4 Functional Genomics and Gene Expression

4.1 Identification of functional genes in teosinte and maize

The identification of functional genes in teosinte and maize has provided crucial insights into the genetic basis of domestication and the adaptation of maize to diverse environments. Comparative genomic studies have revealed that approximately 75% of the genes are highly conserved between maize and teosinte. These genes are involved in essential biological processes and metabolic pathways, underscoring their fundamental roles in both species (Huang et al., 2016).

The transcriptome analysis of teosinte has identified specific genes that show adaptive sequence divergence. For instance, around 1516 unigenes are uniquely expressed in teosinte, indicating their potential role in environmental adaptation and stress responses. Additionally, 99 unigenes with strong selection signals and 57 unigenes with high Ka/Ks ratios suggest that these genes have been under strong selection during maize domestication and improvement (Huang et al., 2016).

4.2 Gene expression patterns and their agricultural relevance

Gene expression patterns play a crucial role in determining the phenotypic traits of maize and teosinte. The regulation of gene expression is influenced by both genetic and environmental factors, which together shape the plant's ability to adapt to different conditions. For example, the gene expression analysis of the maize-teosinte population has identified 25, 60 expression quantitative trait loci (eQTL) for 17 311 genes, revealing a significant range of expression variation (Wang et al., 2017) (Figure 1).

Figure 1 Characterization of eQTL and eQTL-regulated genes (Adopted from Wang et al., 2017) Image caption: (A) Number of eQTL mapped for each gene; The x axis and y axis represent the number of eQTL mapped for each gene and the number of genes in each group, respectively; (B) The expression variation explained by local and distant eQTL. Local eQTL explains more expression variation than distant eQTL; (C) The distribution of genes regulated by local and/or distant eQTL; (D) Functional enrichment analysis for local eQTL-regulated genes; Each bubble stands for one functional class and the size of bubble indicates the number of enriched genes in each class; The y axis shows the P value of hypergeometric test with Benjamini and Hochberg multiple test correction (Adopted from Wang et al., 2017)

4.3 Regulatory networks and pathways

The regulatory networks and pathways governing gene expression in maize and teosinte are complex and involve numerous genes and regulatory elements. One of the key regulatory genes is teosinte branched1 (tb1), which controls plant architecture by suppressing the growth of axillary branches. The expression patterns of tb1 in maize and teosinte are highly correlated with the plant's growth suppression, highlighting its role in the domestication process (Hubbard et al., 2002).

Another significant regulatory pathway involves the teosinte glume architecture1 (tga1) gene, which influences kernel casing and exposure. The tga1 gene has been crucial in the transition from encased kernels in teosinte to exposed kernels in maize, facilitating easier harvest and consumption (Dorweiler et al., 1993).

Furthermore, recent studies have uncovered the role of long non-coding RNAs (lncRNAs) in regulating gene expression. In maize, around 18 165 high-confidence lncRNAs have been identified, with 6 873 conserved between maize and teosinte. These lncRNAs exhibit distinct genomic characteristics and play a role in gene regulation, indicating their potential impact on the plant's phenotype and adaptation (Han et al., 2018).

The regulatory networks and pathways in maize and teosinte are further influenced by transposable elements, which contribute to genomic and transcriptomic variation. Transposable elements can affect gene expression by altering the chromatin structure and creating new regulatory elements, thereby impacting the plant's adaptability and evolution (Li et al., 2021).

The functional genomics and gene expression studies of teosinte and maize have provided valuable insights into the genetic and regulatory mechanisms underlying their domestication and adaptation. Identifying functional genes, understanding gene expression patterns, and elucidating regulatory networks are essential for improving maize breeding and developing varieties with enhanced agronomic traits.

One notable finding is the presence of co-regulated gene clusters in both maize and teosinte. These clusters often consist of genes with related functions and shared chromatin modifications, indicating a coordinated regulation of gene expression. For instance, genes involved in flavonoid biosynthesis and glycolysis are regulated by specific transcription factors such as the bHLH transcription factor R1 and hexokinase HEX9, respectively. These regulatory networks are crucial for the plant's metabolic processes and stress responses (Wang et al., 2017).

Domestication and subsequent breeding have significantly impacted the gene expression patterns in maize. Many genes targeted by selection during domestication exhibit coordinated cis-regulatory divergence. For example, the Bx genes involved in benzoxazinoid biosynthesis have undergone significant cis-regulatory changes, which are associated with maize's adaptation to temperate environments and its distinct herbivore community (Wang et al., 2017).

5 Agricultural Impact

5.1 Yield and productivity improvements

The domestication and subsequent breeding of maize from its wild ancestor teosinte have resulted in significant yield and productivity improvements. Modern maize exhibits a compact plant structure with a single dominant stalk and large, easily accessible ears, traits that have been heavily selected to maximize yield. One of the key loci involved in these changes is the teosinte branched1 (tb1) gene, which controls plant architecture by suppressing the growth of axillary branches, thus allowing the plant to focus resources on the main stalk and ear development (Doebley et al., 1995).

The introgression of favorable alleles from teosinte into modern maize has also been instrumental in improving yield. Studies have shown that teosinte harbors alleles that can enhance kernel composition traits, such as protein, oil, and starch content. For instance, genetic analysis of teosinte near-isogenic lines (NILs) has identified alleles that significantly increase kernel oil content, which is crucial for both nutritional value and industrial uses (Karn et al., 2017).

5.2 Stress tolerance and disease resistance

One of the major challenges in agriculture is the ability to develop crops that can withstand various environmental stresses and resist diseases. Teosinte, being a wild relative, has adapted to a range of environmental conditions and exhibits a broader genetic diversity compared to cultivated maize. This diversity includes alleles that confer resistance to biotic and abiotic stresses.

For example, the genetic diversity found in teosinte has been shown to include alleles for enhanced drought tolerance. The introgression of these alleles into maize has led to the development of drought-resistant maize varieties that can maintain yield under water-limited conditions. Similarly, alleles from teosinte have been used to improve maize's resistance to pests and diseases. The maize-teosinte introgression populations have shown increased resistance to common pests like the corn borer and diseases such as northern corn leaf blight (Hufford et al., 2012).

Teosinte also exhibits a rich metabolic profile, including higher concentrations of secondary metabolites like phenolic compounds, which play a crucial role in plant defense mechanisms. Screening teosinte populations for phenolic content has identified specific compounds that contribute to enhanced antioxidant activity, which can be leveraged to improve the health benefits and stress tolerance of maize (Zavala-López et al., 2018).

5.3 Nutritional enhancements

The nutritional quality of maize is a critical aspect of its value as a staple food crop. Teosinte, despite its smaller kernel size, contains higher protein content compared to modern maize. Studies on the genetic basis of kernel composition have shown that teosinte alleles can enhance the protein content of maize kernels, making them more nutritious. For instance, teosinte has been found to have a higher average alpha zein content, a type of storage protein, which is essential for the nutritional quality of the grain (Flint-Garcia et al., 2009).

Moreover, the genetic introgression from teosinte has also been utilized to improve the oil content in maize kernels. Higher oil content not only increases the caloric value of maize but also provides essential fatty acids that are beneficial for human health. The identification of QTLs associated with high oil content in teosinte has enabled breeders to enhance this trait in maize through selective breeding programs (Karn et al., 2017) (Figure 2).

Figure 2 Distribution of kernel starch, protein, and oil content in the teosinte NILs, The least squares mean (LSMean) for B73 is indicated by a black arrow (Adapted from Karn et al., 2017) Image caption: The figure presents histograms depicting the distribution of three key compositional traits in maize: starch content, protein content, and oil content; Each histogram shows the frequency of maize samples with specific percentages of these traits; Top Histogram: The distribution of starch content (%) in maize samples, with the LSMean (Least Squares Mean) for the B73 variety indicated at 71.53%. The distribution is approximately normal, centered around this mean value. Middle Histogram: The distribution of protein content (%) in maize samples, with the LSMean for the B73 variety indicated at 10.51%; This distribution is also approximately normal, centered around the mean value; Bottom Histogram: The distribution of oil content (%) in maize samples, with the LSMean for the B73 variety indicated at 3.85%. This distribution shows a slightly skewed normal distribution centered around the mean value. Overall, the histograms illustrate the natural variability in these traits within the maize population, with B73 values marked to highlight its position within these distributions; The LSMean values for B73 indicate that it falls near the average for starch and protein content, and slightly above the average for oil content, within this sample population (Adapted from Karn et al., 2017).

In addition to protein and oil content, the genetic diversity of teosinte has been explored to enhance other nutritional aspects of maize. For example, teosinte has been found to possess unique metabolites with potential health benefits. The diversity in phenolic compounds and their antioxidant properties in teosinte can be utilized to develop maize varieties with improved nutritional and health-promoting properties (Zavala-López et al., 2018).

The comparative genomics of teosinte and maize has significantly impacted agricultural practices by enhancing yield and productivity, improving stress tolerance and disease resistance, and enhancing the nutritional quality of maize. The continued exploration and utilization of teosinte genetic resources hold promise for the future improvement of maize, ensuring its resilience and nutritional value in the face of changing environmental conditions and growing global food demand.

6 Biotechnological Applications

6.1 Genetic engineering and CRISPR technologies

The application of genetic engineering and CRISPR technologies in maize has revolutionized the ability to manipulate its genome with precision. One of the most significant advancements has been the use of CRISPR/Cas9 to target specific genes associated with desirable traits. CRISPR technology allows for precise editing of the maize genome, enabling the introduction of beneficial traits from teosinte or the correction of deleterious mutations. For example, the teosinte branched1 (tb1) gene, which plays a critical role in the plant's architecture, can be modified to enhance maize's yield and adaptability (Doebley et al., 1995).

CRISPR has also been used to enhance maize's resistance to pests and diseases. By targeting genes associated with susceptibility, such as those involved in the plant's immune response, researchers can create maize varieties that are more resilient. For instance, the Bx genes involved in benzoxazinoid biosynthesis, which contribute to pest resistance, have been targeted for modification to improve maize's defense mechanisms (Wang et al., 2017).

6.2 Breeding programs and hybrid development

Breeding programs have significantly benefited from the genetic diversity found in teosinte. Traditional breeding methods, combined with modern genomic tools, have facilitated the introgression of beneficial alleles from teosinte into maize. This has resulted in the development of hybrids with enhanced traits such as higher yield, improved stress tolerance, and better nutritional quality.

Teosinte has been used to introduce traits such as drought tolerance and disease resistance into maize. For example, breeding programs have utilized teosinte-derived alleles to develop maize varieties that can thrive under water-limited conditions, thereby ensuring food security in arid regions (Hufford et al., 2012). Furthermore, the introgression of teosinte alleles has enhanced maize's resistance to pests and diseases, reducing the need for chemical pesticides and promoting sustainable agriculture.

Hybrid development has also been enhanced through the use of molecular markers and genomic selection. Microsatellites and single nucleotide polymorphism (SNP) markers have been used to identify and select for desirable traits in breeding populations. This approach has accelerated the development of high-yielding and resilient maize hybrids (Tang et al., 2005).

6.3 Future prospects in crop improvement

The future prospects for crop improvement using teosinte and maize genomics are promising. As genomic technologies continue to advance, the ability to explore and utilize the genetic diversity of teosinte will be further enhanced. The use of high-throughput sequencing, transcriptomics, and metabolomics will provide deeper insights into the genetic and molecular mechanisms underlying important agronomic traits.

One of the key areas of future research is the exploration of epigenetic modifications and their role in trait development. Epigenetic changes, such as DNA methylation and histone modifications, can influence gene expression and phenotypic traits without altering the DNA sequence. Understanding these modifications in teosinte and maize can lead to the development of crops with improved traits through epigenetic engineering (Huang et al., 2016).

Another promising area is the integration of artificial intelligence (AI) and machine learning in crop breeding. AI can analyze large datasets generated from genomic, phenotypic, and environmental data to predict and select for optimal breeding strategies. This approach can significantly accelerate the breeding process and enhance the efficiency of developing new maize varieties (Li et al., 2021).

The development of synthetic biology tools also holds great potential for crop improvement. Synthetic biology involves designing and constructing new biological parts, devices, and systems for desired functions. In maize, synthetic biology can be used to engineer metabolic pathways for enhanced nutrient content, biofuel production, and stress resilience. For instance, metabolic engineering of the flavonoid biosynthesis pathway can enhance the nutritional value and health benefits of maize (Wang et al., 2017).

The integration of genetic engineering, advanced breeding programs, and emerging biotechnological tools will continue to drive the improvement of maize. The genetic resources of teosinte offer a rich reservoir of traits that can be harnessed to develop maize varieties that meet the challenges of modern agriculture, including climate change, food security, and sustainable farming practices.

7 Conservation and Biodiversity

7.1 Preservation of teosinte genetic resources

Teosinte, the wild ancestor of maize, is a critical genetic reservoir for the future improvement of maize. However, teosinte populations are under significant threat due to habitat loss, agricultural expansion, and climate change. For instance, the Balsas teosinte population in Mexico, once covering vast areas, has drastically declined due to changing land use and agricultural policies influenced by international trade agreements (Wilkes, 2007). The preservation of teosinte genetic resources requires urgent in situ and ex situ conservation strategies. In situ conservation involves protecting teosinte in its natural habitat, which can be facilitated by establishing protected areas and engaging local communities in conservation efforts. Ex situ conservation, on the other hand, includes the collection and storage of teosinte seeds in gene banks, such as those maintained by the International Maize and Wheat Improvement Center (CIMMYT) and other global repositories.

7.2 Role of teosinte in maize genetic diversity

Teosinte plays a pivotal role in maintaining and enhancing the genetic diversity of maize. Genetic diversity is essential for the adaptability and resilience of crops to environmental changes and biotic stresses. Studies have shown that teosinte harbors higher levels of genetic diversity compared to domesticated maize, making it a valuable resource for breeding programs (Warburton et al., 2011). Gene flow from teosinte to maize has historically contributed to the genetic makeup of modern maize varieties, introducing alleles that confer beneficial traits such as drought tolerance, disease resistance, and nutritional improvements (Flint-Garcia et al., 2009).

Teosinte populations exhibit significant genetic variability, which can be tapped into through hybridization and backcrossing techniques to enhance maize germplasm. The genetic diversity within teosinte populations, such as those found in Nicaraguan teosinte (Zea nicaraguensis), provides a rich source of alleles that can be used to improve maize's adaptability to various environmental conditions (Loáisiga et al., 2011).

7.3 Strategies for sustainable utilization

Sustainable utilization of teosinte genetic resources involves a multifaceted approach that integrates conservation, research, and breeding programs. Key strategies include:

In Situ Conservation: Establishing protected areas in regions where teosinte naturally occurs is vital. These areas should be managed in collaboration with local communities to ensure sustainable land use practices that support both agriculture and biodiversity. For example, conservation efforts in southern Brazil, where teosinte coexists with local maize landraces, highlight the importance of protecting these genetic reservoirs (Silva et al., 2015).

Ex Situ Conservation: Maintaining and expanding seed banks with diverse teosinte accessions ensures the availability of genetic resources for future breeding programs. The genetic analysis and characterization of teosinte populations, as done by various researchers, provide valuable data for selecting and preserving high-diversity lines (Fukunaga et al., 2005).

Genetic Research and Breeding: Advances in genomic technologies facilitate the identification of beneficial alleles in teosinte that can be introgressed into maize. Techniques such as CRISPR/Cas9 and marker-assisted selection can accelerate the development of maize varieties with improved traits. For example, research on the genetic diversity and structure of teosinte populations has identified key alleles associated with stress tolerance and nutrient use efficiency (Gasca-Pineda et al., 2019).

Policy and Education: Effective conservation and sustainable utilization require supportive policies and public awareness. Governments and international organizations should implement policies that promote the conservation of wild relatives of crops and support research initiatives. Educational programs can engage local communities and stakeholders in conservation efforts, emphasizing the ecological and agricultural importance of teosinte.

In conclusion, the conservation and sustainable utilization of teosinte genetic resources are crucial for maintaining maize's genetic diversity and enhancing its resilience to future challenges. By integrating conservation strategies, advancing genetic research, and promoting sustainable breeding practices, we can ensure the long-term availability of these valuable genetic resources for the improvement of maize and global food security.

8 Challenges and Future Directions

8.1 Current gaps in knowledge

Despite significant progress in the study of teosinte and maize genomics, several gaps in knowledge remain. One primary area of concern is the incomplete understanding of the genetic and molecular basis of key domestication traits. While numerous quantitative trait loci (QTLs) associated with domestication have been identified, the exact genes and mechanisms involved in these traits are not fully understood. For example, many of the genes controlling morphological differences between maize and teosinte, such as inflorescence architecture, are yet to be fully characterized (Doebley and Stec, 1993).

Another significant gap is the limited availability of comprehensive transcriptomic and genomic data for various teosinte accessions. Although some progress has been made in sequencing and annotating the teosinte transcriptome (Huang et al., 2016), there is still a lack of detailed functional genomics studies that can elucidate the roles of specific genes in teosinte's adaptation and domestication.

Additionally, the environmental and ecological contexts of teosinte's genetic diversity are not fully understood. Understanding how environmental factors and ecological interactions influence genetic diversity and adaptation in teosinte can provide insights into how these factors might be leveraged for maize improvement (Hufford et al., 2012).

8.2 Technological and methodological advances

Recent technological and methodological advances offer promising avenues to address these knowledge gaps. Next-generation sequencing (NGS) technologies have revolutionized the ability to generate comprehensive genomic and transcriptomic data. Techniques such as whole-genome sequencing (WGS), RNA sequencing (RNA-seq), and single-cell RNA-seq can provide high-resolution insights into the genetic and functional diversity of teosinte and maize (Swanson-Wagner et al., 2010).

CRISPR/Cas9 and other gene-editing technologies have also opened new possibilities for functional genomics. These tools allow for precise manipulation of the maize and teosinte genomes, enabling the identification and validation of genes associated with key traits. By creating knockouts or introducing specific mutations, researchers can study the phenotypic effects of individual genes and their interactions with other genetic elements (Doebley et al., 1995).

Advances in bioinformatics and computational biology are also critical for analyzing and integrating large datasets generated from genomic and transcriptomic studies. Machine learning algorithms and artificial intelligence (AI) techniques can help identify patterns and predict gene functions, facilitating the discovery of novel genetic variants and their potential applications in breeding programs (Kumar et al., 2022).

8.3 Potential research areas

Several promising research areas can be explored to further enhance our understanding and utilization of teosinte and maize genomics:

Functional Characterization of Domestication Genes: Detailed studies on the function and regulation of genes associated with domestication traits, such as tb1 and tga1, can provide deeper insights into the molecular mechanisms underlying these traits. Functional genomics approaches, including gene editing and transcriptomic analyses, can be employed to dissect the roles of these genes (Doebley and Stec, 1991).

Exploration of Epigenetic Modifications: Epigenetic changes, such as DNA methylation and histone modifications, play a crucial role in gene regulation and trait expression. Studying the epigenetic landscape of teosinte and maize can reveal how these modifications influence domestication and adaptation processes (Huang et al., 2016).

Climate Resilience and Adaptation: Investigating the genetic basis of stress tolerance in teosinte can lead to the development of maize varieties that are more resilient to climate change. Identifying and introgressing alleles associated with drought, heat, and disease resistance can enhance maize's adaptability to changing environmental conditions (Hufford et al., 2012).

Integration of Omics Data: Integrating genomics, transcriptomics, proteomics, and metabolomics data can provide a holistic understanding of the biological processes in teosinte and maize. Multi-omics approaches can uncover complex interactions between genes, proteins, and metabolites, leading to more comprehensive breeding strategies (Swanson-Wagner et al., 2010).

Conservation Genomics: Applying genomic tools to conservation efforts can help preserve the genetic diversity of teosinte. Understanding the population structure, genetic diversity, and adaptive potential of teosinte populations can inform conservation strategies and ensure the availability of these genetic resources for future breeding programs (Warburton et al., 2011).

In conclusion, addressing the current gaps in knowledge and leveraging technological and methodological advances can significantly enhance our understanding of teosinte and maize genomics. Future research in these areas holds the potential to develop maize varieties that are more productive, resilient, and sustainable, ensuring food security in the face of global challenges.

9 Concluding Remarks

The comparative genomics of teosinte and maize has elucidated several critical insights into the domestication and evolution of maize. Firstly, significant genetic diversity exists between teosinte and maize, with teosinte harboring a broader range of genetic variations that can be leveraged for maize improvement. Key genes such as teosinte branched1 (tb1) and teosinte glume architecture1 (tga1) have been identified as central to the morphological differences between the two species, highlighting the impact of human selection during domestication.

Functional genomics has revealed that many genes associated with stress tolerance and nutritional content in teosinte can be introgressed into maize, enhancing its resilience and nutritional value. Moreover, the advent of CRISPR and other genomic tools has enabled precise modifications in the maize genome, further accelerating the improvement of desirable traits.

The findings from comparative genomics studies between teosinte and maize have profound implications for agriculture and biotechnology. The genetic diversity present in teosinte provides a valuable resource for breeding programs aimed at improving maize. This diversity can be harnessed to develop maize varieties with enhanced stress tolerance, disease resistance, and improved nutritional profiles. For instance, introgressing alleles associated with drought tolerance from teosinte into maize can help develop varieties that are more resilient to climate change.

The application of biotechnological tools such as CRISPR/Cas9 allows for the targeted editing of maize genes to enhance specific traits. This technology can accelerate the development of high-yielding and resilient maize varieties by enabling precise modifications at the genomic level. Additionally, advances in transcriptomics and metabolomics provide deeper insights into the gene regulatory networks and metabolic pathways that underlie key agronomic traits.

The integration of teosinte genetic resources into maize breeding programs holds great promise for the future of agriculture. However, several challenges and future directions need to be addressed to fully realize this potential. Firstly, comprehensive genomic and transcriptomic data for various teosinte accessions need to be generated and made accessible. This will facilitate the identification and utilization of beneficial alleles in breeding programs. In situ and ex situ conservation efforts for teosinte populations must be strengthened to preserve their genetic diversity. Protected areas and gene banks play crucial roles in ensuring the availability of teosinte genetic resources for future research and breeding efforts.

Moreover, there is a need for interdisciplinary research that integrates genomics, phenomics, and environmental data to develop a holistic understanding of the genetic and ecological factors influencing teosinte and maize. This integrative approach can inform breeding strategies that not only enhance yield and resilience but also promote sustainable agricultural practices. Policy frameworks should support the conservation and sustainable utilization of teosinte genetic resources. Governments and international organizations must implement policies that encourage the preservation of wild relatives of crops and support research initiatives aimed at improving crop resilience and productivity.

Acknowledgments

I would like to express my gratitude to the two anonymous peer reviewers for their critical assessment and constructive suggestions on our manuscript.

Conflict of Interest Disclosure

The author affirms that this research was conducted without any commercial or financial relationships that could be construed as a potential conflict of interest.

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