1 Introduction

Genetic diversity is a cornerstone of crop improvement, providing the raw material for breeding programs to develop new varieties with enhanced traits. The erosion of genetic diversity in cultivated crops due to the widespread adoption of high-yielding varieties has led to increased vulnerability to pests, diseases, and environmental stresses. Therefore, harnessing genetic diversity is critical to ensure food security, resilience, and sustainability in agriculture. Wild relatives of crops, such as wild rice, are invaluable reservoirs of genetic diversity. They possess unique alleles that can introduce beneficial traits such as disease resistance, stress tolerance, and improved nutritional quality into cultivated varieties (Swain et al., 2017).

Wild rice species, particularly Oryza rufipogon, have evolved over millennia to adapt to diverse and challenging environments, resulting in a rich genetic pool. These species harbor alleles that have been lost during the domestication of cultivated rice (Oryza sativa). These alleles include those conferring resistance to biotic and abiotic stresses, which are crucial for the development of resilient rice varieties. Recent advancements in genomic technologies have facilitated the identification and utilization of these alleles in breeding programs. Studies have shown that wild rice can significantly enhance traits such as salt tolerance, drought resistance, and yield stability in cultivated rice (Stein et al., 2018; Zhang et al., 2020).

This study aims to consolidate current knowledge on the genetic diversity of wild rice and its potential impact on cultivated rice varieties. Highlight the importance of genetic diversity in crop improvement. Provide an overview of the beneficial alleles found in wild rice species. Discuss the methodologies used to introgress these alleles into cultivated rice. Evaluate the impact of wild rice alleles on the agronomic traits of cultivated varieties. Identify future research directions and potential challenges in harnessing wild rice for crop improvement.

2 Genetic Diversity in Wild Rice

2.1 Taxonomy and distribution of wild rice species

Wild rice species, belonging to the genus Oryza, are distributed across various regions globally, with significant diversity observed in Asia and Africa. The genus Oryza includes two cultivated species, Oryza sativa and Oryza glaberrima, and 22 wild species that represent 10 distinct genome types (Ammiraju et al., 2010). Oryza rufipogon, the progenitor of Asian cultivated rice, is widely distributed in Asia, particularly in China, India, and Southeast Asia (Sun et al., 2001; Liu et al., 2015). In Africa, Oryza longistaminata and Oryza barthii are notable wild species, with O. longistaminata found at the edge of its distribution in Ethiopia (Lakew et al., 2021). These wild species are crucial for understanding the evolutionary history and genetic diversity of rice.

2.2 Genetic variability in wild rice

Wild rice species exhibit remarkable genetic variability, which is essential for rice breeding and improvement. Studies have shown that Oryza rufipogon possesses higher genetic diversity compared to cultivated rice, with significant polymorphism observed in various populations (Sun et al., 2001). For instance, the genetic diversity of O. rufipogon in China is notably high, with a mean polymorphism information content (PIC) of 0.64, indicating a high level of genetic variation (Liu et al., 2015). Similarly, African wild rice, O. longistaminata, exhibits unique genetic variations at the edge of its distribution, which are valuable for future rice breeding (Lakew et al., 2021). The genetic diversity in wild rice is also reflected in the presence of numerous single nucleotide polymorphisms (SNPs) and structural variations, contributing to the overall genetic variability (Zhang et al., 2020).

2.3 Conservation of wild rice germplasm

The conservation of wild rice germplasm is critical for maintaining genetic diversity and ensuring the availability of valuable genetic resources for rice improvement. Efforts have been made to develop core collections of wild rice accessions for ex situ conservation. For example, a core collection of 130 accessions of Oryza rufipogon was developed in China, retaining over 90% of the alleles at 36 marker loci (Liu et al., 2015). Additionally, the Oryza Map Alignment Project (OMAP) aims to leverage the novel genetic diversity from wild relatives for rice improvement by providing comprehensive genus-wide BAC resources (Ammiraju et al., 2010). These conservation efforts are essential for preserving the genetic diversity of wild rice and utilizing it for the development of improved rice varieties with enhanced agronomic traits.

The genetic diversity in wild rice species, their taxonomy and distribution, and the conservation of their germplasm are crucial for harnessing natural genetic diversity to improve cultivated rice varieties. The rich genetic variability in wild rice provides a valuable reservoir of alleles that can be utilized for rice breeding and the development of resilient and high-yielding rice varieties.

3 Molecular Basis of Wild Rice Alleles

3.1 Identification and characterization of wild rice alleles

The identification and characterization of wild rice alleles have been pivotal in understanding the genetic diversity and potential of wild rice species. Studies have shown that wild rice species, such as Oryza rufipogon and Oryza nivara, harbor a wealth of genetic diversity that has been largely untapped in cultivated varieties. For instance, the resequencing of 50 accessions of both cultivated and wild rice has revealed thousands of genes with significantly lower diversity in cultivated rice, indicating regions selected during domestication that may contain important agronomic traits (Xu et al., 2011). Additionally, the use of molecular markers, such as microsatellites, has been effective in evaluating genetic diversity within rice subspecies, providing a reliable tool for germplasm conservation and cultivar identification (Ni et al., 2002).

3.2 Genomic tools for analyzing wild rice

Advancements in genomic tools have significantly enhanced the analysis of wild rice. The development of high-density single-nucleotide polymorphism (SNP) arrays and other genomic resources has facilitated the identification of valuable alleles from wild rice species. Chromosome segment substitution lines (CSSLs) and backcross inbred lines (BILs) are particularly powerful tools for introgressing favorable genes from wild species into cultivated rice. These tools allow for the dissection of quantitative traits and the evaluation of gene action as single factors, thereby uncovering new alleles from unadapted wild rice accessions (Ali et al., 2020). Furthermore, the availability of genome-wide information on wild rice species through specialized databases has provided a valuable resource for identifying novel genes and alleles, designing molecular markers, and conducting comparative analyses (Figure 1) (Kamboj et al., 2020).

Figure 1 Schematic diagram shows the denovo domestication of Australian wild rice through genome editing (Adopted from Kamboj et al., 2020) Image caption: Comprehensive workflow for developing improved rice varieties using CRISPR-Cas9, genome sequencing and gene mining to identify target genes, followed by precise gene editing and plant transformation, edited plants are screened, regenerated, genotyped and phenotyped, followed by field trials, the end result is a transgene-free genome-edited rice variety with improved traits for agricultural deployment (Adopted from Kamboj et al., 2020)

3.3 Functional genomics of wild rice traits

Functional genomics has played a crucial role in elucidating the traits of wild rice that can be beneficial for cultivated varieties. Introgression lines (ILs) developed through backcross strategies combined with marker-assisted selection (MAS) have been instrumental in broadening the genetic base of existing cultivars. These ILs have high power for mapping quantitative trait loci (QTLs) and are used for evaluating the genetic effects of QTLs and detecting gene-by-gene or gene-by-environment interactions (Chen et al., 2019). Additionally, genome-wide association studies (GWAS) have identified numerous loci associated with important traits such as flowering time and grain yield, further enhancing our understanding of the genetic basis of these traits in rice (Huang et al., 2011). The integration of genomic approaches has also revealed the genomic architecture of rice heterosis, providing insights into the genetic diversity and domestication of Oryza species (Chen et al., 2019). The molecular basis of wild rice alleles encompasses the identification and characterization of genetic diversity, the utilization of advanced genomic tools, and the application of functional genomics to uncover valuable traits. These efforts collectively contribute to the enhancement of cultivated rice varieties by harnessing the natural genetic diversity present in wild rice species.

4 Introgression of Wild Rice Alleles into Cultivated Varieties

4.1 Introgression techniques and strategies

Traditional breeding approaches for introgressing wild rice alleles into cultivated varieties primarily involve backcrossing. This method entails crossing a cultivated variety with a wild relative and then repeatedly backcrossing the progeny with the cultivated parent. This process aims to incorporate desirable traits from the wild species while retaining the agronomic characteristics of the cultivated variety. For instance, introgression lines (ILs) developed through backcrossing have been instrumental in broadening the genetic base of rice cultivars, allowing for the mapping of quantitative trait loci (QTLs) and the identification of elite alleles (Huang et al., 2011). These ILs serve as valuable resources for functional genomics research and breeding, enabling the genetic improvement of various traits such as drought resistance and grain quality (Figure 2) (Zhang et al., 2022).

Figure 2 Construction of rice ILs and their application in functional genomics research and breeding (Adopted from Zhang et al., 2022) Image caption: The figure outlines an integrated breeding strategy that combines genetic diversity from various hybrid types (interspecific, intersubspecific, and intrasubspecific) with advanced technologies such as MAS and QTL aggregation. This approach aims to improve rice yield, quality, and stress resistance, ultimately creating superior rice varieties (Adopted from Zhang et al., 2022)

Marker-assisted selection (MAS) enhances the efficiency of traditional breeding by using molecular markers to track the presence of specific alleles associated with desirable traits. This technique allows for the precise selection of progeny carrying the target alleles, thereby accelerating the breeding process. In rice, MAS has been successfully employed to develop ILs with improved agronomic traits by utilizing markers distributed across the genome (Zhang et al., 2022). The integration of genotyping-by-sequencing (GBS) and single-nucleotide polymorphism (SNP) typing further refines this process, enabling the identification of novel SNPs and the assessment of donor introgression patterns in early-backcross populations (Ali et al., 2018). These advancements facilitate the development of markers that support genomic applications in molecular breeding programs.

4.2 Challenges in introgression breeding

One of the primary challenges in introgression breeding is linkage drag, which occurs when undesirable traits from the wild donor are co-inherited with the target alleles. This phenomenon can hinder the performance of the cultivated variety and complicate the breeding process. For example, while introgressing beneficial alleles for traits such as drought resistance or disease resistance, breeders may inadvertently introduce alleles that negatively affect yield or other agronomic traits (Zhang et al., 2022). Strategies to mitigate linkage drag include fine mapping of QTLs and the use of advanced backcrossing techniques to break undesirable linkages.

Reproductive barriers between wild and cultivated rice species pose another significant challenge in introgression breeding. These barriers can manifest as pre-zygotic or post-zygotic incompatibilities, leading to reduced fertility or hybrid sterility. Overcoming these barriers requires careful selection of compatible parental lines and the use of techniques such as embryo rescue or bridge crossing. Additionally, the genetic structure of wild populations can be altered by gene introgression from cultivated rice, which may impact the conservation of wild relatives (Jin et al., 2017). Therefore, effective in situ conservation measures are necessary to maintain the genetic integrity of wild rice populations while harnessing their genetic diversity for crop improvement.

The introgression of wild rice alleles into cultivated varieties involves a combination of traditional breeding approaches and modern molecular techniques. While challenges such as linkage drag and reproductive barriers exist, ongoing advancements in genomics and breeding strategies continue to enhance the efficiency and effectiveness of introgression breeding in rice.

5 Impact on Agronomic Traits

5.1 Yield enhancement

The integration of wild rice alleles into cultivated varieties has shown significant potential in enhancing yield. Wild relatives of rice, such as Oryza rufipogon and Oryza nivara, possess genetic diversity that has been largely lost in domesticated rice due to selective breeding practices. By resequencing the genomes of these wild progenitors, researchers have identified numerous single nucleotide polymorphisms (SNPs) that are associated with yield-related traits. These SNPs can be used as molecular markers to guide breeding programs aimed at increasing yield in cultivated rice varieties (Xu et al., 2011). Additionally, the development of introgression libraries, which involve crossing wild rice species with elite cultivars, has led to the identification of novel allelic variations that significantly impact grain size and weight, further contributing to yield enhancement (Zhang et al., 2022).

5.2 Stress tolerance

Wild rice species are known for their resilience to various biotic and abiotic stresses, which are critical for maintaining crop productivity in the face of climate change and evolving pathogens. The genetic diversity found in wild rice has been harnessed to improve stress tolerance in cultivated varieties. For instance, wild relatives of rice have been shown to possess alleles that confer resistance to drought, aerobic conditions, and blast disease. These traits have been successfully introgressed into cultivated rice, enhancing their ability to withstand adverse environmental conditions (Zhang et al., 2022). Moreover, the use of modern genomic technologies has accelerated the identification and transfer of stress-tolerance genes from wild rice to cultivated varieties, making it possible to develop rice strains that are more resilient to environmental stresses (Xie and Liu, 2021).

5.3 Nutritional quality and grain characteristics

The nutritional quality and grain characteristics of rice are also significantly influenced by the alleles derived from wild rice species. Wild rice relatives contain a wealth of genetic diversity that can be tapped to improve the nutritional profile of cultivated rice. For example, the introgression of alleles from wild rice has led to the development of rice varieties with enhanced grain size, pericarp color, and kernel color, which are important for both consumer preference and nutritional value (Zhang et al., 2022). Additionally, the pan-genome analysis of wild soybean, a close relative of rice, has revealed genes associated with seed composition and organ size, suggesting that similar approaches could be applied to rice to enhance its nutritional quality (Li et al., 2014). The identification of these beneficial alleles and their incorporation into breeding programs hold great promise for improving the overall quality of rice grains (Kamboj et al., 2020).

The utilization of wild rice alleles has a profound impact on the agronomic traits of cultivated rice, including yield enhancement, stress tolerance, and nutritional quality. The integration of these alleles through advanced genomic and breeding techniques offers a sustainable approach to meeting the growing global food demand and ensuring food security in the face of environmental challenges.

6 Case Studies of Successful Utilization

6.1 Examples of wild alleles in cultivated rice

The utilization of wild rice alleles has significantly contributed to enhancing disease resistance in cultivated rice varieties. For instance, Indian rice landraces have been found to harbor a diverse array of blast resistance genes. A study identified twenty-four significant blast resistance gene loci in landraces from various rice ecologies in India, with some landraces containing up to nineteen resistance genes. These genes have been crucial in developing rice varieties with enhanced resistance to blast disease, a major threat to rice production. Additionally, the genetic diversity within these landraces provides a valuable resource for future genomic studies and rice improvement strategies aimed at disease resistance (Yadav et al., 2019).

Wild rice alleles have also been instrumental in improving abiotic stress tolerance in cultivated rice. For example, the introgression of salt-tolerant genes from wild rice into cultivated varieties has shown promising results. A study on the salt-tolerant line DJ15, derived from a cross between Dongxiang wild rice and the cultivated variety Ningjing16, identified several quantitative trait loci (QTL) associated with salt tolerance. These QTLs, particularly qST1.2 and qST6, have been shown to significantly enhance salt tolerance in rice, demonstrating the potential of wild rice genes in improving abiotic stress tolerance (Quan et al., 2018). Moreover, the genetic diversity analysis of stress-tolerant rice genotypes has revealed the presence of alleles that contribute to tolerance against various abiotic stresses, such as drought and submergence, further highlighting the importance of wild rice alleles in breeding programs (Islam et al., 2012).

6.2 Comparative analysis of cultivars with wild alleles

Comparative studies of rice cultivars with and without wild alleles have provided insights into the benefits of utilizing wild genetic resources. For instance, the salt-tolerant line DJ15, which contains wild rice alleles, exhibited superior performance under salt-stress conditions compared to its cultivated parent, Ningjing16. This demonstrates the effectiveness of wild alleles in enhancing stress tolerance (Quan et al., 2018). Similarly, the genetic diversity analysis of aromatic and quality rice landraces from North-Eastern India has shown that these landraces possess unique alleles that contribute to their adaptation to local environmental conditions. These alleles can be harnessed to improve the stress tolerance and quality traits of modern rice cultivars (Roy et al., 2015).

6.3 Lessons learned from past successes

The successful utilization of wild rice alleles in cultivated varieties has provided several key lessons for future breeding programs. Firstly, the genetic diversity present in wild rice and landraces is a valuable resource that can be leveraged to address various biotic and abiotic stresses. Studies have shown that landraces and wild relatives harbor unique alleles that are not present in modern cultivars, making them essential for broadening the genetic base of cultivated rice (Mammadov et al., 2018). The integration of modern molecular and genomic technologies has accelerated the identification and transfer of beneficial alleles from wild rice to cultivated varieties. Techniques such as QTL mapping and genomic resequencing have been instrumental in pinpointing specific genes associated with desirable traits, facilitating their incorporation into breeding programs (Quan et al., 2018). The importance of maintaining and utilizing genetic diversity cannot be overstated. The narrow genetic base of modern cultivars poses a significant challenge to crop improvement efforts, and the use of wild rice alleles offers a promising solution to enhance the resilience and productivity of cultivated rice (Mammadov et al., 2018). By learning from these past successes, future breeding programs can more effectively harness the natural genetic diversity present in wild rice to develop improved rice varieties that meet the growing demands for food security and environmental sustainability.

7 Future Prospects and Challenges

7.1 Advances in genomic technologies

The rapid advancements in genomic technologies have significantly enhanced our ability to harness the genetic diversity present in wild rice species. Techniques such as CRISPR/Cas genome editing and high-throughput sequencing have revolutionized the identification and utilization of beneficial alleles from wild rice relatives. For instance, the CRISPR/Cas system has been effectively used to modify genes in Australian wild rice, enabling the introduction of traits such as stress resistance and disease tolerance into cultivated varieties (Abdullah et al., 2022). Additionally, the de novo domestication of wild allotetraploid rice using advanced tissue culture and genome editing systems has shown promising results in improving agronomically important traits (Yu et al., 2021). These technological advancements not only accelerate the pace of trait discovery but also facilitate the efficient transfer of these traits into cultivated rice, thereby enhancing crop resilience and productivity (Mammadov et al., 2018).

7.2 Sustainable use of genetic resources

The sustainable use of genetic resources from wild rice is crucial for long-term agricultural sustainability. Wild rice species, such as Oryza rufipogon and Oryza nivara, possess a wealth of genetic diversity that can be tapped into for improving cultivated rice varieties. The development of core collections of wild rice populations, as demonstrated in China, ensures the conservation of genetic diversity and provides a valuable resource for future breeding programs (Liu et al., 2015). Moreover, the integration of molecular markers and next-generation sequencing technologies has facilitated the identification of quantitative trait loci (QTL) alleles that can enhance traits such as yield, disease resistance, and stress tolerance in cultivated rice (Xu et al., 2011). However, the challenge lies in balancing the exploitation of these genetic resources with their conservation to prevent the erosion of genetic diversity.

7.3 Policy and regulatory frameworks

The successful integration of wild rice alleles into cultivated varieties also depends on supportive policy and regulatory frameworks. Policies that promote the conservation of wild rice habitats and the sustainable use of genetic resources are essential. Additionally, regulatory frameworks that facilitate the use of advanced genomic technologies in breeding programs are crucial. For example, the establishment of databases harboring genome-wide information on wild rice species has been instrumental in rice breeding programs (Kamboj et al., 2020). However, there is a need for international collaboration and harmonization of regulations to ensure the safe and effective use of these technologies. Addressing intellectual property rights and benefit-sharing mechanisms is also important to ensure that the benefits derived from the use of wild rice genetic resources are equitably distributed (Nevo, 2006).

The future prospects of harnessing natural genetic diversity from wild rice are promising, thanks to advances in genomic technologies, sustainable use practices, and supportive policy frameworks. However, challenges remain in ensuring the conservation of genetic resources and the equitable distribution of benefits. Continued research and international collaboration will be key to overcoming these challenges and realizing the full potential of wild rice alleles in improving cultivated varieties.

8 Concluding Remarks

The exploration of natural genetic diversity in wild rice has revealed significant insights into the genetic basis of important agronomic traits in cultivated rice. Key findings include the identification of the GSE5 gene, which controls grain size through variations in its promoter region, contributing to grain size diversity in rice. The development of an introgression library from various AA genome Oryza species has provided a valuable resource for rice improvement, identifying novel allelic variations associated with traits such as grain length and width. Resequencing efforts have highlighted the genetic markers and candidate regions selected during rice domestication, which are crucial for breeding programs. Additionally, the de novo domestication of wild allotetraploid rice has demonstrated the potential to develop new staple cereals with enhanced traits. The genetic diversity in wild rice populations has been systematically evaluated, leading to the creation of a core collection for conservation and future breeding efforts.

The findings underscore the importance of harnessing natural genetic diversity from wild rice to enhance cultivated varieties. Future research should focus on further characterizing the genetic basis of agronomically important traits and exploring the potential of wild rice alleles in breeding programs. The introgression of beneficial alleles from wild species into elite cultivars can broaden the genetic base and improve traits such as yield, stress resistance, and grain quality. Advanced genomic tools and genome editing technologies offer promising avenues for accelerating the domestication process and developing new crop varieties with desirable traits. Additionally, the conservation of genetic diversity through core collections and ex situ conservation efforts is crucial for maintaining a reservoir of genetic resources for future breeding initiatives.

The integration of wild rice alleles into cultivated varieties holds great promise for addressing the challenges of food security and climate change. By leveraging the genetic diversity present in wild rice, breeders can develop more resilient and high-yielding rice varieties. Continued research and collaboration among geneticists, breeders, and agronomists will be essential to fully realize the potential of natural genetic diversity in rice improvement. The advancements in genomic technologies and the establishment of comprehensive genetic resources will play a pivotal role in shaping the future of rice breeding and ensuring sustainable agricultural practices.

Acknowledgments

The author extends sincere thanks to two anonymous peer reviewers for their invaluable feedback on the 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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