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Shows crop domestication and plant breeding timeline reformations, for example, artificial selection breeding, hybrid breeding, molecular breeding, and precise breeding for crop improvement in traditional and modern agriculture.
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Climate change biotic and abiotic stressors lead to unpredictable crop yield losses, threatening global food and nutritional security. In the past, traditional breeding has been instrumental in fulfilling food demand; however, owing to its low efficiency, dependence on environmental conditions, labor intensity, and time consumption, it fails to mai...
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... Oil palm compactness is a quantitative trait likely influenced by multiple genes, environmental factors and their interactions (Yaakub et al. 2020). To accelerate the introduction of compactness-associated alleles into high-yielding varieties, molecular breeding techniques such as marker-assisted selection (MAS) and genomic selection (GS) are viable molecular tools to enhance breeders' selection decisions and overall breeding efficiency (Kumar et al. 2024;Tyagi et al. 2024). Molecular strategies have been widely adopted in crop breeding for its ability to improve selection accuracy, including in rice and wheat (Das et al. 2017;Song et al. 2023). ...
Breeding for oil palm with a compact architecture is beneficial, as it facilitates harvesting and enhances yield in commercial plantations through high-density planting. In this study, we conducted a genome-wide association study to identify markers associated with nine compactness traits across a total of 475 Tenera palms from eight biparental families, each containing 42–78 offsprings. These families were derived from the Deli, Nigeria, and Yangambi genetic backgrounds. A Q-matrix of K = 6 was used as a fixed effect to account for population structure. As a result, a total of 27 single nucleotide polymorphism (SNP) markers linked to seven of the nine traits examined, including rachis length, petiole width, petiole depth, and petiole cross-section were successfully identified. Given the complex nature of the traits, SNP markers with small genetic effects were generally identified, and these have the potential to accelerate the introgression of desirable alleles into commercial lines. Among these, seven SNPs co-localised to similar regions with markers identified in previous studies, whereas the remaining markers are novel and can offer important insights into the development of compact palms. Additionally, our findings provide a foundation for further research to uncover the genes responsible for the compactness traits in oil palm.
... This information can be used to develop climate-smart crops that maintain yield stability despite environmental challenges. Understanding the molecular mechanisms underlying stress tolerance enables targeted biotechnological interventions, such as genetic engineering or CRISPR-based modifications aimed at enhancing specific traits related to abiotic or biotic resistance [6,7]. By developing crops that can withstand adverse conditions such as drought or salinity, integrated omics approaches contribute to sustainable agricultural practices that ensure food security in a changing climate [8,9]. ...
... Recent advancements in technology and data analysis further enhance this integration, paving the way for innovative solutions that improve crop performance under challenging environmental conditions. As these approaches continue to evolve, they promise to develop resilient crops capable of thriving in an increasingly unpredictable climate [3,7]. ...
Plants face an array of environmental stresses, including both abiotic and biotic stresses. These stresses significantly impact plant lifespan and reduce agricultural crop productivity. Abiotic stresses, such as ultraviolet (UV) radiation, high and low temperatures, salinity, drought, floods, heavy metal toxicity, etc., contribute to widespread crop losses globally. On the other hand, biotic stresses, such as those caused by insects, fungi, and weeds, further exacerbate these challenges. These stressors can hinder plant systems at various levels, including molecular, cellular, and development processes. To overcome these challenges, multi-omics computational approaches offer a significant tool for characterizing the plant’s biomolecular pool, which is crucial for maintaining homeostasis and signaling response to environmental changes. Integrating multiple layers of omics data, such as proteomics, metabolomics, ionomics, interactomics, and phenomics, simplifies the study of plant resistance mechanisms. This comprehensive approach enables the development of regulatory networks and pathway maps, identifying potential targets for improving resistance through genetic engineering or breeding strategies. This review highlights the valuable insights from integrating multi-omics approaches to unravel plant stress responses to both biotic and abiotic factors. By decoding gene regulation and transcriptional networks, these techniques reveal critical mechanisms underlying stress tolerance. Furthermore, the role of secondary metabolites in bio-based products in enhancing plant stress mitigation is discussed. Genome editing tools offer promising strategies for improving plant resilience, as evidenced by successful case studies combating various stressors. On the whole, this review extensively discusses an advanced multi-omics approach that aids in understanding the molecular basis of resistance and developing novel strategies to improve crops’ or organisms’ resilience to abiotic and biotic stresses.
... Additionally, traditional breeding often fails to address biotic and abiotic stressors, with climate change's new abiotic pressures like heat and drought potentially exacerbating biotic stresses and causing severe crop losses (Wijerathna-Yapa and Hiti-Bandaralage, 2023). Consequently, the incapacity of traditional breeding to concurrently address these interrelated pressures may result in a failure to generate crops that are strong enough to endure the diverse difficulties provided by a changing environment (Tyagi et al., 2024). In this situation, CRISPR-Casmediated genome editing may develop desirable features, boost quality and production, and improve agricultural plants in less time compared to traditional breeding . ...
Plant development is mainly impacted by biotic stresses, including disease and pests, reducing agricultural production. Genome editing methods have high efficiency, controlled, and directional editing qualities, so their use in agriculture has increased significantly in recent years. Breeding-resistant variants might greatly benefit from the deployment of genome editing methods. These strategies have produced amazing results when it comes to the resistant breeding of significant agricultural crops. One of the most effective, practical, and quick methods for successfully manipulating the target gene is the clustered regularly interspaced short palindromic repeats (CRISPR)-Cas (CRISPR-associated) system. The Cas9 protein, an RNA-guided DNA endonuclease, causes a site-specific double-strand break that starts a DNA repair process and modifies the genome. Despite possessing two layers of defensive mechanisms: Effectors-triggered immunity (ETI) and PAMP-triggered immunity (PTI) responses, plants are susceptible to phytopathogens (bacteria, fungi, viruses). The genome has been edited using CRISPR-Cas technology to strengthen plant immunity and provide long-term resistance to pathogens and insects. To improve plant life and resistance, this review explains the functions of CRISPR-Cas-mediated genome editing in plants against various biotic stresses. This review also points out the limitations of CRISPR-Cas systems, which will be the subject of future research.
... For example, in soybean, researchers developed highdensity SNP arrays, such as Soy50K and SoySNP arrays, to facilitate the identification of key traits such as seed composition, flooding tolerance, and disease resistance. Advancements in soybean genomics accelerated breeding for improved yield and stress resilience [60,61]. Similarly, in cotton, genomic resources were employed to improve fiber quality [62]. ...
Genomic selection (GS) is an effective approach to address the growing need for increasing and improving food production and quality, respectively, under challenging environmental conditions. In Korea, GS significantly advanced major crops such as rice and wheat by improving critical agronomic traits. However, minor crops such as mung bean and sesame still require development because of limited resources and breeding infrastructure. These crops, though less prioritized, are vital for their nutritional and functional properties and contribute significantly to agricultural diversity and rural livelihoods. Addressing the research gap in minor crops is essential to prevent the loss of genetic diversity and to enhance their resilience to environmental changes. Unlike traditional selection methods, GS enhances the accuracy of complex trait selection, accelerates breeding cycles, and boosts genetic gain. It leverages genome-wide markers to predict genomic estimated breeding values (GEBVs) with high precision, enabling faster and more effective breeding strategies, especially for traits controlled by multiple genes. Genotyping techniques, such as Genotyping by Sequencing and Whole Genome Resequencing, are integral to GS, each offering specific benefits and limitations. Multispecies single nucleotide polymorphism arrays present a cost-effective solution for improving GS in minor crops by capturing the genetic diversity across species and enabling cross-species data integration. Expanding the GS in minor crops is essential for preserving genetic diversity, improving adaptability, and supporting sustainable agriculture and food security in South Korea. By addressing these challenges, GS can transform breeding programs, ensuring a sustainable and resilient agricultural system for the future.
... Also, this finding can be applied to breeding programs to develop superior Gladiolus genotypes with desirable traits. For instance, marker-assisted selection (MAS) programs can be employed to accelerate the breeding process by selecting plants that carry favorable alleles for these traits (Tyagi et al., 2024). However, it is worth mentioning that the direct application of the results of association analyses requires validation in larger populations with a greater number of molecular markers and confirmation of the results. ...
Gladiolus is considered one of the most significant globally ornamental crops, extensively utilized as a cut flower and for outdoor landscaping. However, the local destruction of Iranian Gladiolus as a weed threatens the biodiversity of this species. This research aimed to compare Iranian Gladiolus populations. A total of 76 Iranian Gladiolus accessions were collected. These accessions exhibited significant phenotypic variability across all the studied traits. Geographical factors were found to significantly contribute to this diversity. Additionally, to explore the association between genetic markers and phenotypic traits, both ISSR and IRAP markers were employed. Significant correlations were identified between stem length and latitude (r = 0.746, p < 0.01). Moreover, floret number showed a strong correlation with spike length and longitude (r = 0.777, p < 0.01 and r = 0.658, p < 0.05, respectively). The Hmdn8 population from Hamedan province exhibited superior values across all phenotypic traits. Furthermore, the Krdstn4 population from Kurdistan province, known for its superior inflorescence traits, was identified as suitable for specific breeding purposes. The climatic conditions of Kurdistan, characterized by a cold semi-humid climate and high annual rainfall, indicate that higher latitudes and colder periods are favorable for Gladiolus growth and flowering. A total of 146 polymorphic bands were produced from two types of markers, ISSR and IRAP. The association analysis revealed that the ISSR4-3, ISSR2-20 and ISSR5-24 markers showed significant correlations with stem length and floret number. Additionally, informative markers were identified for other traits, demonstrating significant associations with multiple traits in Gladiolus. These findings are crucial for identifying crucial genomic regions for Gladiolus breeding programs.
... Metabolic engineering can enhance the synthesis and recycling of antioxidants like ascorbate and glutathione, improving redox homeostasis and ROS scavenging capacity. Marker-assisted selection and genomic prediction further accelerate the breeding of cultivars with superior antioxidant profiles (Gantait et al., 2019;Rana et al., 2019;Tyagi et al., 2024;Wani et al., 2018). Integrative approaches that combine gene editing, omics-based discovery, and precision phenotyping enable researchers to translate fundamental insights into breeding pipelines (Kumar et al., 2021;Roychowdhury et al., 2023). ...
... In addition, HBB can utilize historical recombination events, offering insights into the evolutionary and domestication history and functional significance of specific haplotypes, which can be leveraged to predict and select advantageous genetic combinations more effectively. Integrating HBB with SB amplifies these benefits by dramatically reducing the breeding cycle duration, allowing for multiple generations to be grown and evaluated annually (Tyagi et al., 2024). SB uses controlled environments with extended photoperiods and optimized growth conditions to accelerate plant development and flowering times. ...
Wheat (Triticum spp.) is a primary dietary staple food for humanity. Many wheat genetic resources with variable genomes have a record of domestication history and are widespread throughout the world. To develop elite wheat varieties, agronomical and stress-responsive trait characterization is foremost for evaluating existing germ-plasm to promote breeding. However, genomic complexity is one of the primary impediments to trait mining and characterization. Multiple reference genomes and cutting-edge technologies like haplotype mapping, genomic selection, precise gene editing tools, high-throughput phenotyping platforms, high-efficiency genetic transformation systems, and speed-breeding facilities are transforming wheat functional genomics research to understand the genomic diversity of polyploidy. This review focuses on the research achievements in wheat genomics, the available omics approaches, and bioinformatic resources developed in the past decades. Advances in genomics and system biology approaches are highlighted to circumvent bottlenecks in genomic and phenotypic selection, as well as gene transfer. In addition, we propose conducting precise functional genomic studies and developing sustainable breeding strategies for wheat. These developments in understanding wheat traits have speed up the creation of high-yielding, stress-resistant, and nutritionally enhanced wheat varieties, which will help in addressing global food security and agricultural sustainability in the era of climate change.
The application of genomic approaches in improving abiotic stress tolerance has revolutionized plant breeding, providing precise, efficient, and accelerated methods for developing climate-resilient crops. The integration of genomic selection (GS), transcriptomics, proteomics, and metabolomics has enabled breeders to identify key stress-responsive genes, ensuring the rapid selection of drought-, heat-, salinity-, and cold-tolerant varieties. The advancement of CRISPR-Cas gene editing has further enhanced breeding efficiency by enabling targeted modifications of stress-related pathways, reducing dependency on traditional breeding cycles. High-throughput phenomics and remote sensing technologies have improved the accuracy of stress trait evaluation, allowing for real-time monitoring of plant responses under dynamic environmental conditions. Multi-omics integration, combined with artificial intelligence (AI) and machine learning, has enabled predictive modeling for stress adaptation, optimizing selection strategies for multi-trait improvement. Marker-assisted backcrossing (MABC) and genomic estimated breeding values (GEBVs) have accelerated the introgression of stress-tolerance alleles into elite cultivars, ensuring the development of high-yielding stress-adapted hybrids. Speed breeding, combined with GS, has shortened breeding cycles for major crops such as wheat, rice, and maize, enhancing productivity under adverse environmental conditions. The successful application of these genomic tools has led to the development of climate-smart agriculture, ensuring stable food production in an era of rising global temperatures and erratic rainfall patterns. Future research in synthetic biology and systems biology will refine stress adaptation mechanisms by engineering novel gene networks, optimizing metabolic pathways, and enhancing transgenerational stress memory.
In the realm of crop enhancement, plant molecular breeding has revolutionized the ability to manipulate traits with precision and efficiency. This chapter delves into the integration of conventional and molecular breeding approaches, starting with an explanation of the significance of genetic markers and the biotechnological tools driving molecular breeding advancements. Breeders can now precisely improve both qualitative and quantitative traits using techniques like marker-assisted selection, gene pyramiding, backcrossing, and recurrent selection. Genomic selection expands breeding horizons by enabling accurate prediction of individual plant performance through vast genomic datasets. Despite challenges like complex trait inheritance and marker-trait associations, the emergence of CRISPR-Cas9 gene editing holds promise for precision breeding. Looking ahead, the field is on the brink of a transformative era, where technology, data, and innovation converge to shape a sustainable agricultural future. As the need for sustainable agriculture grows amidst climate change and global food security challenges, plant molecular breeding emerges as a pivotal tool for developing climate-resilient crops and increasing agricultural productivity. This chapter provides a comprehensive guide to the dynamic and ever-evolving landscape of plant molecular breeding, offering valuable insights and reflections for researchers, breeders, and students navigating the complexities of plant genetics.
