Triticeae Genomics and Genetics 2024, Vol.15 http://cropscipublisher.com/index.php/tgg © 2024 CropSci Publisher, registered at the publishing platform that is operated by Sophia Publishing Group, founded in British Columbia of Canada. All Rights Reserved. -
Triticeae Genomics and Genetics 2024, Vol.15 http://cropscipublisher.com/index.php/tgg © 2024 CropSci Publisher, registered at the publishing platform that is operated by Sophia Publishing Group, founded in British Columbia of Canada. All Rights Reserved. CropSci Publisher is an international Open Access publishing specializing in maize genome, trait-controlling, maize gene expression and regulation at the publishing platform that is operated by Sophia Publishing Group (SPG), founded in British Columbia of Canada Publisher CropSci Publisher Edited by Editorial Team of Triticeae Genomics and Genetics Email: edit@tgg.cropscipublisher.com Website: http://cropscipublisher.com/index.php/tgg Address: 11388 Stevenston Hwy, PO Box 96016, Richmond, V7A 5J5, British Columbia Canada Triticeae Genomics and Genetics (ISSN 1925-203X) is an open access, peer reviewed journal published online by CropSci Publisher. The journal publishes original papers involving in all aspects of Triticeae sciences. Subject areas covered comprise classical genetics analysis, structural and functional analysis of Triticeae genome, gene expression and regulation, efficient breeding of improved varieties, as well as transgenic varieties. It is positioned to meet the needs of breeders, geneticists, molecular biologists, and anyone, worldwide, engaged in the field of Triticeae research. All the articles published in Triticeae Genomics and Genetics are Open Access, and are distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. CropSci Publisher uses CrossCheck service to identify academic plagiarism through the world’s leading plagiarism prevention tool, iParadigms, and to protect the original authors’ copyrights.
Triticeae Genomics and Genetics (online), 2024, Vol. 15, No.3 ISSN 1925-203X http://cropscipublisher.com/index.php/tgg © 2024 CropSci Publisher, registered at the publishing platform that is operated by Sophia Publishing Group, founded in British Columbia of Canada. All Rights Reserved. Latest Content Discovering Genes that Enhance Yield in Drought Conditions within Turkish Winter Wheat JianLi Zhong Triticeae Genomics and Genetics, 2024, Vol. 15, No. 3, 121-124 Taxonomy and Genetic Resources of Triticeae: Exploring Wild and Cultivated Species Zhengqi Ma, Zhongying Liu, Wei Wang Triticeae Genomics and Genetics, 2024, Vol. 15, No. 3, 125-136 High-Density Genetic Mapping in Wheat: Methodologies and Achievements Xian Zhang, Xuemei Liu Triticeae Genomics and Genetics, 2024, Vol. 15, No. 3, 137-151 Harnessing Genetic Diversity for Wheat Improvement Using Exotic Germplasm ShaoMin Yang Triticeae Genomics and Genetics, 2024, Vol. 15, No. 3, 152-161 The Impact of Hexaploid Genetics on Wheat Breeding Strategies Xingzhu Feng Triticeae Genomics and Genetics, 2024, Vol. 15, No. 3, 162-171
Triticeae Genomics and Genetics, 2024, Vol.15, No.3, 121-124 http://cropscipublisher.com/index.php/tgg 121 Scientific Review Open Access Discovering Genes that Enhance Yield in Drought Conditions within Turkish Winter Wheat JianLi Zhong Hainan Institute of Tropical Agricultural Resources, Sanya, 572024, China Corresponding email: zhongjianli8888@gmail.com Triticeae Genomics and Genetics, 2024, Vol.15, No.3 doi: 10.5376/tgg.2024.15.0012 Received: 11 Apr., 2024 Accepted: 14 May., 2024 Published: 26 May., 2024 Copyright © 2024 Zhong, This is an open access article published under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Preferred citation for this article: Zhong J.L., 2024, Discovering genes that enhance yield in drought conditions within turkish winter wheat, Triticeae Genomics and Genetics, 15(3): 121-124 (doi: 10.5376/tgg.2024.15.0012) On April 10, 2024, a collaborative research result by the International Maize and Wheat Improvement Center in Mexico, Syngenta's Jealott's Hill International Research Center, and Kazakhstan's Scientific Production Grain Center was published in the journal Scientific Reports. The paper, authored by D. Sehgal as the first author and A. Morgounov as the corresponding author, is titled "Genomic wide association study and selective sweep analysis identify genes associated with improved yield under drought in Turkish winter wheat germplasm." This research was jointly funded by the FAO's International Treaty on Plant Genetic Resources for Food and Agriculture (W2B-PR-41-TURKEY) and the BMGF/FCDO project on Accelerating Genetic Gains in Maize and Wheat for Improved Livelihoods (AGG) (INV-003439). The study employed genome-wide association studies (GWAS) and selective sweep analysis to explore genes and genomic regions related to drought resistance and increased yield within Turkish winter wheat germplasm. The research involved genotyping 84 local Turkish winter wheat varieties and 73 modern varieties using a 25K wheat SNP array and phenotyped agronomic traits in 2018 and 2019. The year 2018 was considered a drought environment due to extremely low rainfall, while 2019 was deemed a favorable environment. The results indicated several genomic regions associated with yield and yield-related traits. 1 Experimental Data Analysis The GWAS results identified 18 genomic regions associated with grain yield (GY) and related traits, such as TaERF3-3A and TaERF3-3B. Selective sweep analysis revealed 39 selection signals, 15 of which were close to genes known to control flowering, yield, and yield components. The study also found that specific haplotype blocks exhibited a significant increase in yield (over 700 kg/ha) during the drought season. Figure 1 clearly reflects the comparison between the wheat yield and related traits during the drought season of 2018 and the favorable season of 2019. In the drought season of 2018, the average wheat yield (shown in Figure a) significantly decreased, and its distribution showed a wide range, indicating considerable variability in performance under drought conditions among different local or modern varieties. At the same time, related yield parameters such as the number of spikelets per spike (Figure b) and thousand-grain weight (Figure c) also showed significant declines under drought conditions, suggesting that drought not only affects the overall wheat yield but also its constituent elements. Changes in spike length (Figure d) and the number of spikes (Figure e) also displayed significant differences between the two seasons, indicating that wheat growth and development were restricted under drought conditions, potentially affecting overall yield. However, these traits recovered under favorable conditions in 2019, indicating some adaptability of wheat varieties to environmental conditions. Additionally, the harvest index (Figure f), which is the ratio of the harvestable part weight to the total plant weight, also showed a downward trend in the drought year, reflecting a decrease in crop conversion efficiency under drought conditions. Although the response to these traits varied significantly among different varieties, the overall trend is consistent: drought conditions significantly affect wheat growth and yield.
Triticeae Genomics and Genetics, 2024, Vol.15, No.3, 121-124 http://cropscipublisher.com/index.php/tgg 122 Figure 1 Wheat yield and yield-related traits in drought season of 2018 vs favorable season of 2019 The results of the statistical significance tests (p-values) further validated the credibility of these observations. For example, the significance level for the decrease in grain weight was less than 0.01, and the reduction in the number of spikelets was less than 0.001. Decreases in thousand-grain weight, spike length, and the number of spikes also showed varying degrees of statistical significance, indicating that drought has a statistically significant impact on wheat yield parameters. Therefore, these data reveal the extensive negative impact of drought on wheat production traits, particularly yield-related traits. This finding is crucial for guiding future wheat breeding work for drought resistance because it provides direct evidence of wheat growth traits under drought conditions and emphasizes the importance of considering drought resistance and yield improvement in wheat breeding. The relationship between the genetic diversity and geographic distribution of wheat varieties is depicted through a three-dimensional principal component analysis (PCA) plot (Figure 2). In Figure 2a, two broad groups are identified: local varieties (LR) and modern varieties (MV). The data points for the LR group are more dispersed within the PCA space, indicating greater genetic variability among these varieties; conversely, the MV group is relatively concentrated, suggesting higher genetic similarity among modern varieties. Figure 2b further subdivides the LR group into three subgroups based on geographical origin, consisting of local varieties from Afghanistan, Iran, and Turkey, while the MV group is shown as a separate cluster. It is observable that LR groups from different geographic origins are distinctly separated in the PCA plot, demonstrating genetic differences based on geographic distribution. Although the MV group is separated from the LR groups in the PCA plot, it also shows a tendency to be close to the Turkish LR group in Figure 2b, which may reflect that modern varieties have potentially retained or borrowed genetic traits from local varieties during the breeding process. Additionally, the lines between points in Figure 2b represent the fixation index (Fst) between groups, with Fst values providing a quantitative measure of genetic differentiation between populations. Higher Fst values indicate greater genetic differentiation. The Fst values in the figure indicate some level of genetic differentiation between different LR groups, and the Fst values between the MV group and each LR group further confirm the genetic distinction between modern and local varieties. Therefore, the significant genetic diversity of local varieties reflects the genetic variations accumulated by wheat in different regions adapting to local environmental conditions. Although modern varieties exhibit lower genetic diversity, they may possess genetic connections across geographical boundaries, which is a valuable resource for future wheat breeding because these relationships can be utilized to introduce new, beneficial genetic traits.
Triticeae Genomics and Genetics, 2024, Vol.15, No.3, 121-124 http://cropscipublisher.com/index.php/tgg 123 Moreover, the integration of this genetic information helps us better understand and utilize wheat's genetic resources, especially in the face of climate change and environmental pressures. Protecting and exploiting this diversity is crucial for ensuring food security. Figure 2 Three-dimensional PCA plot of LR subgroups and MV group Figure 3 originates from the EigenGWAS analysis of Turkish local and modern wheat varieties, highlighting SNPs that exhibit selection signals. The x-axis represents chromosome numbers, while the y-axis represents the adjusted P-values, also known as PGC values. The Manhattan plot is a commonly used chart in genetics to visually display the results of genome-wide association studies (GWAS). Each point on the plot represents the statistical significance of an association between a specific SNP and a trait. In this plot, different colors of the points represent different chromosomes, and the vertical position of a point indicates its -log10 P-value; the higher the position, the greater the statistical significance of the association with the trait. A blue horizontal line across the chart represents the significance threshold, with SNPs above this threshold considered to exhibit selection signals. It is evident that points on certain chromosomes, particularly on chromosomes like 3B, 5A, and 5B, are notably high, suggesting that SNPs in these regions might have undergone strong selection during the evolution of wheat varieties, related to important agronomic traits. Thus, this provides direct evidence of genetic selection within Turkish wheat varieties, revealing key genetic regions that affect important wheat traits. This information is crucial for guiding the genetic improvement and enhancement of crop performance in wheat. Figure 3 Manhattan plot from EigenGWAS showing distribution of SNPs with selection signals in turkish landraces and modern varieties
Triticeae Genomics and Genetics, 2024, Vol.15, No.3, 121-124 http://cropscipublisher.com/index.php/tgg 124 2 Research Results Analysis This study effectively identified genes and genomic regions associated with drought resistance and yield improvement in wheat by combining GWAS and selective sweep analysis. It also highlighted the potential value of utilizing the genetic diversity in local varieties for modern breeding practices. 3 Research Evaluation The study leveraged the genetic resources of Turkish winter wheat, utilizing advanced molecular marker technologies and statistical methods to effectively identify genes and genomic regions that contribute to drought resistance and yield enhancement. These findings provide valuable genetic resources for drought-resistant breeding in wheat. 4 Conclusion The GWAS and selective sweep analysis of Turkish winter wheat germplasm successfully identified several key genes and genomic regions associated with improved drought resistance and yield, providing important molecular markers for future wheat breeding against adverse conditions. 5 Access the Full Text Sehgal, D., Rathan, N.D., Özdemir, F. et al. Genomic wide association study and selective sweep analysis identify genes associated with improved yield under drought in Turkish winter wheat germplasm. Sci Rep 14, 8431 (2024). https://doi.org/10.1038/s41598-024-57469-1. Acknowledgements I am deeply grateful to Scientific Reports for its service of providing open access to articles,, especially for the groundbreaking study published by Sehgal et al. in 2024, titled“Identifying genes that enhance yield in drought conditions in Turkish winter wheat.”This service allows me to deeply understand the latest research developments in this field and share them with peers, thereby contributing to the continuous development of the scientific community.
Triticeae Genomics and Genetics, 2024, Vol.15, No.3, 125-136 http://cropscipublisher.com/index.php/tgg 125 Review Article Open Access Taxonomy and Genetic Resources of Triticeae: Exploring Wild and Cultivated Species Zhengqi Ma, Zhongying Liu, Wei Wang Institute of Life Science, Jiyang College of Zhejiang A&F University, Zhuji, 311800, Zhejiang, China Corresponding author: 2741098603@qq.com Triticeae Genomics and Genetics, 2024, Vol.15, No.3 doi: 10.5376/tgg.2024.15.0013 Received: 15 Apr., 2024 Accepted: 18 May., 2024 Published: 30 May., 2024 Copyright © 2024 Ma et al., This is an open access article published under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Preferred citation for this article: Ma Z.Q., Liu Z.Y., and Wang W., 2024, Taxonomy and genetic resources of Triticeae: exploring wild and cultivated species, Triticeae Genomics and Genetics, 15(3): 125-136 (doi: 10.5376/tgg.2024.15.0013) Abstract As an important component of global agricultural production, the Triticeae family holds significant meanings for crop improvement and food security in terms of its classification and genetic resources research. This study discusses the taxonomic progress of Triticeae, the genetic diversity of wild and cultivated species, the protection strategies of genetic resources, and the methods of genetic improvement. By reviewing historical classification systems, analyzing the ecological roles and evolutionary significance of key species, and exploring the domestication history and agronomic traits of major cultivated species, the study aims to reveal the richness and complexity of Triticeae genetic resources. Meanwhile, facing challenges such as genetic complexity and resistance to abiotic/biotic stresses, this study emphasizes the importance of genetic resource protection and proposes directions and priorities for future research, including strengthening genetic improvement through emerging technologies and international cooperation, and providing theoretical support and resource foundation for future genetic improvement and crop breeding, thereby ensuring the sustainable utilization of Triticeae genetic resources. Keywords Triticeae; Taxonomy; Genetic resources; Genetic improvement; Protection strategy 1 Introducion The Triticeae tribe, a taxon within the Poaceae family, encompasses several of the world's most vital cereal crops, including wheat, barley, and rye, as well as numerous forage grasses (Yen and Yang, 2009). These species have been fundamental to human agriculture since the dawn of civilization, particularly in temperate regions where they serve as primary food sources (Mascher et al., 2017),. The tribe consists of approximately 325 species, with around 250 being perennials that are crucial for forage. The cultivated members of Triticeae, such as wheat and barley, are globally significant, while rye holds regional importance (Merker, 2008). The genetic diversity within this tribe is immense, providing a vast reservoir of traits that can be harnessed for crop improvement, particularly in response to environmental and biotic stresses (Feuillet et al., 2008). Understanding the taxonomy and genetic resources of the Triticeae tribe is essential for several reasons. Firstly, taxonomic classification provides a framework for identifying and categorizing species, which is crucial for the effective utilization of germplasm in breeding programs (Yen and Yang, 2009). Traditional taxonomic methods based on morphology have limitations, often leading to misclassification due to environmental influences on phenotypic traits. Modern approaches incorporating cytogenetic and molecular genomic analyses offer more accurate classifications, reflecting true phylogenetic relationships (Yen and Yang, 2009). Secondly, the genetic resources within Triticeae, including wild and weedy taxa, represent a gigantic gene pool that is invaluable for crop improvement (Bothmer et al., 2008). These resources are particularly important for enhancing traits such as drought and salt tolerance, which are critical for adapting to climate change and ensuring food security (Nevo and Chen, 2010). The integration of genetic information through databases and advanced breeding techniques further accelerates the discovery and utilization of key loci involved in plant productivity (Mochida et al., 2008). This study aims to comprehensively explore the taxonomy and genetic resources of the Triticeae family, particularly focusing on in-depth analysis of wild and cultivated species. By collecting, organizing, and analyzing a vast amount of Triticeae species information, the study intends to reveal the diversity, distribution patterns,
Triticeae Genomics and Genetics, 2024, Vol.15, No.3, 125-136 http://cropscipublisher.com/index.php/tgg 126 evolutionary history, and the current status of distribution and utilization of genetic resources within the Triticeae family. Additionally, the study will explore protection strategies and utilization approaches for Triticeae genetic resources, providing scientific evidence and references for breeding improvement, genetic resource conservation, and sustainable agricultural production of Triticeae crops. This is not only significant for the research and application of Triticeae crops, but also plays an active role in promoting the progress and development of global agricultural production. 2 Taxonomy of Triticeae 2.1 Historical background and classification systems The tribe Triticeae, a significant group within the Poaceae family, has been the subject of extensive taxonomic studies due to its inclusion of major cereal crops such as wheat, barley, and rye, as well as numerous forage grasses. Historically, taxonomic treatments of Triticeae were primarily based on comparative morphology and geography. Morphological characters, which are phenotypic expressions resulting from the interaction of dominant genes and environmental factors, were the main criteria for classification. However, this approach often led to misclassifications due to morphological convergence in distantly related taxa and divergence in closely related taxa under different environmental conditions (Yen and Yang, 2009). With the emergence of cytogenetics and molecular genomic analysis, traditional classification systems have been developed, providing more accurate insights into the phylogenetic relationships within the wheat family. For example, Hyun et al. (2020) obtained single nucleotide polymorphism (SNP) markers covering all seven chromosomes from 283 wheat related genotypes using GBS technology. These SNP markers provide rich genetic information for the phylogenetic relationships between different species within the wheat genus. Based on these SNP data, researchers successfully constructed the first high-resolution phylogenetic tree of the wheat genus, providing new insights into the species classification and evolutionary relationships of the wheat genus (Figure 1). Hyun et al. (2020) demonstrated the genetic relationships of 114 Triticum species and subspecies through a Bayesian phylogenetic tree. The color-coded and labeled branches help to understand the genetic grouping and chromosomal composition among different accessions. Additionally, the Bayesian posterior probabilities provide confidence information on these genetic relationships and offer valuable insights into the genetic relationships among Triticum species and subspecies, aiding in the further understanding of their evolutionary history and genetic diversity. 2.2 Current taxonomic classification and key species The current taxonomic classification of Triticeae integrates both morphological and genomic data to provide a more comprehensive understanding of the tribe's diversity. Recent genomic investigations have recognized approximately 30 genera within the Triticeae, reflecting a more refined and accurate classification system (Yen and Yang, 2009). Key species within this tribe include the major cereal crops wheat (Triticum spp.), barley (Hordeum spp.), and rye (Secale spp.), as well as important forage grasses such as elymus and agropyron (Bothmer et al., 2008; Knüpffer, 2009). Chen et al. (2020) investigated the genetic relationships among different species and genomes in the Triticae family (Figure 2). They subdivided the Triticae family into wild-type, cultivated type, and hybrid type genomes based on the discovery that they originated from a common ancestor, and explained the genome naming method, emphasizing the differences between different genera, species, and strains within the same family, revealing the diversity of the wheat genome and its close relationship with species classification. The genomic resources available for Triticeae have significantly advanced our understanding of these species. For example, the whole genomes of barley, wheat, Tausch’s goatgrass (Aegilops tauschii), and wild einkorn wheat (Triticum urartu) have been sequenced, providing valuable data for comparative genomics and crop improvement (Mochida and Shinozaki, 2013). These genomic tools are crucial for identifying new genes and understanding the evolutionary relationships within the tribe.
Triticeae Genomics and Genetics, 2024, Vol.15, No.3, 125-136 http://cropscipublisher.com/index.php/tgg 127 Figure 1 Genetic relationships between genotypes (access lines) of 114 Triticumspecies and subspecies (Adapted from Hyun et al., 2020) Image caption: The genotype was obtained through genotype sequencing (GBS) and analyzed using 14188 single nucleotide polymorphisms (SNPs) data (with a deletion level of 80%) (Adapted from Hyun et al., 2020)
Triticeae Genomics and Genetics, 2024, Vol.15, No.3, 125-136 http://cropscipublisher.com/index.php/tgg 128 Figure 2 Genomic diversity and taxonomic tree of Triticae species (Adapted from Chen et al., 2020) Image caption: The A-tree structure indicates the common ancestor of all Triticae species, from which different species and genomes gradually differentiate, forming the diversity of modern Triticae species; B further refined this classification, displaying different types of genomes such as wild-type, cultivated type, and hybrid type (Adapted from Chen et al., 2020) 2.3 Challenges and controversies inTriticeae taxonomy Despite advances in wheat taxonomy, there are still some challenges and controversies. A major issue is that the descriptions of genera and species are incomplete and sometimes inconsistent. For example, evaluations of some genome classification systems have shown that many operational taxonomic units (OTUs) cannot be resolved due to the presence of homoplasticity and parallel homology, indicating the need for a more comprehensive approach to treat all attributes equally (Rodriguez-R et al., 2018) Another challenge is the morphological identification of genomic genera, particularly in perennial species with solitary spikelets. While it is possible to distinguish these groups based on morphology, it requires the examination of characters that have not been traditionally emphasized, such as the length of middle inflorescence internodes and the morphology of glumes (Barkworth et al., 2009). This highlights the ongoing need for detailed morphological studies to complement genomic data. Moreover, the integration of wild and weedy taxa into the taxonomic framework poses additional difficulties. These taxa are often underrepresented in genetic studies, and there is limited knowledge about their seed physiology, genetic diversity, and seed handling techniques (Bothmer et al., 2008). Addressing these gaps is essential for a more comprehensive understanding of Triticeae taxonomy and for the effective utilization of these genetic resources in crop improvement. In conclusion, the taxonomy of Triticeae is a complex and evolving field that requires the integration of morphological, cytogenetic, and genomic data. While significant progress has been made, ongoing research and refinement of classification systems are necessary to address the remaining challenges and controversies. 3 Wild Species of Triticeae 3.1 Overview of wildTriticeae species The tribe Triticeae encompasses approximately 350 wild taxa, which form a significant gene pool for temperate cereals such as wheat, barley, and Rye, as well as several important forage grasses(Bothmer et al., 2008). Despite the vast number of species, the primary focus has traditionally been on the primary gene pools of cultivated species, with wild and weedy taxa receiving less attention until recent years(Bothmer et al., 2008). The wild species, which include around 250 perennial species, are crucial for their genetic diversity and potential to improve cultivated varieties.
Triticeae Genomics and Genetics, 2024, Vol.15, No.3, 125-136 http://cropscipublisher.com/index.php/tgg 129 3.2 Ecological roles and natural habitats Wild Triticeae species occupy diverse ecological niches and play significant roles in their natural habitats. These species are found across various regions, often thriving in environments where cultivated species may not survive. For instance, many wild species are adapted to extreme conditions, contributing to the ecological stability and resilience of their habitats (Bothmer et al., 2008). The perennial species, which make up a substantial portion of the Triticeae tribe, are particularly important as forage grasses, supporting both natural ecosystems and agricultural systems. 3.3 Genetic diversity and evolutionary significance The genetic diversity within wild Triticeae species is immense and holds considerable evolutionary significance. This diversity is not only crucial for the adaptation and survival of these species in their natural habitats but also provides a valuable genetic reservoir for breeding programs aimed at improving cultivated cereals(Bothmer et al., 2008; Uauy, 2011). The structural polymorphisms observed in the chromosomes of wild species, such as those in the St, P, and Y genomes, highlight the evolutionary processes and genetic variability within the tribe (Wang et al., 2010). Understanding and utilizing this genetic diversity is essential for advancing our knowledge of Triticeae evolution and for the sustainable improvement of cereal crops (Uauy, 2011; Mochida and Shinozaki, 2013). 4 Cultivated Species of Triticeae 4.1 Major cultivated species The Triticeae tribe includes several major cultivated species that are of significant agricultural importance globally. The primary cultivated species are wheat (Triticum spp.), barley (Hordeum vulgare), and rye (Secale cereale) (Bothmer et al., 2008; Merker, 2008). Wheat is one of the most widely grown crops worldwide, providing a staple food source for a large portion of the global population. Barley is primarily used for animal feed, brewing, and as a food grain, while rye is cultivated mainly in cooler climates and is used for bread, beer, and animal fodder (Merker, 2008). 4.2 Domestication history and agronomic traits The domestication of these major Triticeae species has a rich history that dates back thousands of years. Wheat, for instance, was domesticated from wild emmer (Triticum dicoccoides) and other wild relatives in the Fertile Crescent around 10,000 years ago (Xie and Nevo, 2008). Barley was also domesticated in the same region and time period, while rye's domestication occurred later, primarily in Europe (Merker, 2008). Agronomic traits of these species have been extensively studied and improved through breeding programs. Key traits include disease resistance, drought tolerance, and grain quality. For example, wild emmer harbors genes for abiotic stress tolerances (e.g., salt, drought, and heat) and biotic stress tolerances (e.g., powdery mildew, rusts) that have been transferred to cultivated wheat to enhance its resilience and productivity (Xie and Nevo, 2008). Similarly, the genetic diversity within Triticum urartu has been explored to identify alleles that can improve wheat agronomy and quality (Talini et al., 2019). 4.3 Genetic diversity within cultivated species Genetic diversity within cultivated Triticeae species is crucial for their continued improvement and adaptation to changing environmental conditions. Wheat, barley, and rye have benefited from the genetic resources of their wild relatives, which provide a vast reservoir of alleles for various agronomic traits (Bothmer et al., 2008; Merker, 2008). For instance, the North American Triticale Genetic Resources Collection (NATGRC) has been established to conserve and evaluate the genetic diversity of triticale, a hybrid of wheat and rye, highlighting the importance of preserving unique gene combinations for future breeding efforts. The genetic diversity within these species is also evident in the various genotypic and phenotypic traits observed in different accessions. For example, a study on Triticum urartu reported significant variation in phenology, plant architecture, and seed features(Figure 3), demonstrating the potential of this wild wheat relative to contribute valuable alleles for wheat improvement (Talini et al., 2019). Similarly, the diversity indices and principal
Triticeae Genomics and Genetics, 2024, Vol.15, No.3, 125-136 http://cropscipublisher.com/index.php/tgg 130 component analyses of triticale accessions from different regions have shown considerable genetic variation, which is essential for breeding programs aimed at enhancing crop performance. Figure 3 Diversity analysis of the Triticum uratuset (Adapted from Talini et al., 2019) Image caption: (a) It is a principal component analysis (PCA) based on phenotypic diversity, where the first two principal components (PCs) are displayed, different points represent different varieties, colors are classified based on their geographical origins, and vectors represent the load of original traits on derived principal components; (b) The PCA is based on single nucleotide polymorphism (SNP) diversity, and the point representation is the same as in Figure (a) (Adapted from Talini et al., 2019) Talini et al. (2019) were able to reveal genetic and phenotypic differences among different varieties through PCA analysis, and further investigate how these differences are influenced by environmental factors such as geography and climate (Figure 3). These differences reflect genetic diversity, where different strains have undergone long-term adaptation and evolution in different geographical environments, forming their own unique genotype and phenotype characteristics. Through PCA analysis, it is clear that this diversity is reflected at the genetic and phenotypic levels, providing important data support for the study of genetic diversity, crop breeding, and ecological adaptation. 5 Genetic Resources and Conservation 5.1 Importance of conserving triticeae genetic resources The conservation of Triticeae genetic resources is crucial for several reasons. Firstly, Triticeae, which includes economically significant crops such as wheat, barley, and rye, forms a vital part of global food security. The genetic diversity within this tribe provides a reservoir of traits that can be harnessed for crop improvement, including resistance to diseases, tolerance to abiotic stresses, and enhanced nutritional qualities (Bothmer et al., 2008; Lu and Ellstrand, 2014). The loss of genetic diversity in these crops could severely impact agricultural productivity and sustainability, making conservation efforts essential (Uauy, 2011; Guzzon and Ardenghi, 2018). 5.2 Ex situ and in situ conservation strategies Conservation strategies for Triticeae genetic resources can be broadly categorized into ex situ and in situ methods. Ex situ conservation involves the preservation of genetic material outside its natural habitat, typically in gene banks. This method allows for the long-term storage and easy accessibility of genetic resources for research and breeding purposes (Uauy, 2011). However, it is not without challenges, such as the need for accurate taxonomic identification to ensure the usability of the conserved material (Guzzon and Ardenghi, 2018).
Triticeae Genomics and Genetics, 2024, Vol.15, No.3, 125-136 http://cropscipublisher.com/index.php/tgg 131 In situ conservation, on the other hand, involves the protection of species within their natural habitats. This method helps maintain the evolutionary processes and ecological interactions that contribute to genetic diversity. Both strategies are complementary; while ex situ conservation provides a backup for genetic material that might be lost in nature, in situ conservation ensures the ongoing adaptation and evolution of species in their natural environments (Greene et al., 2014). 5.3 Role of gene banks and international collaborations Gene banks play a pivotal role in the conservation of Triticeae genetic resources. They serve as repositories for a vast array of genetic material, ensuring its availability for future research and breeding programs. The effectiveness of gene banks depends on accurate documentation and regular updates to maintain the integrity of the conserved material. International collaborations are also crucial in this context. They facilitate the sharing of resources, knowledge, and technologies, thereby enhancing the global capacity for genetic conservation (Khoury et al., 2019). Collaborative efforts, such as those under the Convention on Biological Diversity and the International Treaty on Plant Genetic Resources for Food and Agriculture, aim to create comprehensive conservation strategies and set ambitious targets for safeguarding genetic diversity (Khoury et al., 2019). These collaborations help address the gaps in current conservation efforts and promote the development of effective conservation indicators and methodologies (Khoury et al., 2019). 6 Genetic Improvement and Breeding 6.1 Traditional breeding methods inTriticeae Traditional breeding methods in Triticeae have long relied on the utilization of both cultivated and wild relatives to enhance desirable traits in crops such as wheat, barley, and rye. These methods primarily involve the selection and cross-breeding of plants to combine favorable traits from different varieties. For instance, wheat breeders have successfully incorporated disease resistance traits from wild relatives into cultivated wheat varieties through traditional cross-breeding techniques (Merker, 2008). The primary gene pools, which include the most closely related species, have been the main focus of these efforts due to their higher compatibility and ease of gene transfer (Bothmer et al., 2008). However, the wild and weedy taxa have also gained attention for their potential to introduce novel traits into cultivated species, despite the challenges posed by their genetic diversity and the need for specialized seed handling techniques (Bothmer et al., 2008). 6.2 Modern genetic tools and biotechnological approaches The advent of modern genetic tools and biotechnological approaches has revolutionized the breeding of Triticeae species. Techniques such as genome-wide association studies (GWAS), molecular markers, and next-generation sequencing have enabled more precise and efficient identification and incorporation of beneficial traits. For example, a genome-wide association study on Triticum urartu identified significant quantitative trait nucleotides (QTNs) for various agronomic and quality traits, highlighting the potential of this wild wheat relative as a valuable genetic resource for wheat improvement (Talini et al., 2019). Additionally, the sequencing of whole genomes of key Triticeae species, including wheat and barley, has provided comprehensive genomic resources that facilitate the discovery of new genes and the functional analysis of existing ones (Mochida and Shinozaki, 2013). These advancements have also enabled the integration of genomic data from model organisms like Brachypodium distachyon, further enhancing the understanding and manipulation of Triticeae genomes(Mochida and Shinozaki, 2013). 6.3 Case studies of successful genetic improvement Several case studies illustrate the successful application of both traditional and modern breeding methods in the genetic improvement of Triticeae species. One notable example is the North American Triticale Genetic Resources Collection, which assembled over 3 000 accessions of triticale from various breeding programs. This collection has been extensively characterized and evaluated, revealing significant genetic diversity and providing a valuable resource for future breeding efforts. Another example is the use of wild relatives in wheat breeding,
Triticeae Genomics and Genetics, 2024, Vol.15, No.3, 125-136 http://cropscipublisher.com/index.php/tgg 132 where traits such as disease resistance have been successfully transferred from wild species to cultivated wheat, demonstrating the practical benefits of utilizing the genetic diversity within the Triticeae tribe (Merker, 2008). Furthermore, the development of genomic tools and resources, such as those provided by the transplant project, has facilitated the integration and analysis of complex genomic data, thereby accelerating the breeding and improvement of Triticeae crops (Spannagl et al., 2016). 7 Challenges inTriticeae Genetic Research 7.1 Genetic complexity and genome organization The genetic complexity and genome organization of Triticeae species present significant challenges in genetic research. The tribe includes both diploid and polyploid species, with polyploids arising from hybridization events and genome duplications, leading to intricate genome structures (Maestra and Naranjo, 2000). The large and complex genomes of Triticeae species, such as wheat, barley, and rye, complicate genetic mapping and the identification of specific genes responsible for desirable traits (Uauy, 2011). Additionally, the presence of repetitive DNA sequences and transposable elements further complicates genome assembly and annotation (Uauy, 2011). Despite these challenges, advances in molecular markers, chromosome genomics, and comparative genomics have facilitated the study of these complex genomes (Uauy, 2011). 7.2 Abiotic and biotic stress resistance Abiotic and biotic stress resistance is a critical area of research in Triticeae genetics due to the significant impact of environmental stresses on crop yield and quality. Wild relatives of Triticeae species, such as Triticum dicoccoides and Hordeum spontaneum, possess valuable genetic resources for drought and salt tolerance, which have been identified and transferred to cultivated wheat and barley (Nevo and Chen, 2010). Similarly, genes conferring resistance to diseases like powdery mildew and leaf rust have been tracked in wild relatives such as Triticum boeoticumand T. urartu, providing valuable resources for breeding programs (Hovhannisyan et al., 2018). However, the introgression of these resistance genes into cultivated varieties remains challenging due to the genetic complexity and potential linkage drag associated with wild germplasm (Merker, 2008). 7.3 Socio-economic and policy-related challenges Socio-economic and policy-related challenges also play a significant role in Triticeae genetic research. The conservation and utilization of genetic resources from wild and weedy taxa are often hindered by limited knowledge of seed physiology, seed handling techniques, and genetic diversity. Additionally, the collection and evaluation of these resources are constrained by socio-political factors, such as access to germplasm and international regulations on genetic resource exchange (Bothmer et al., 2008). Furthermore, the integration of advanced genetic research into practical breeding programs requires substantial investment and collaboration between public and private sectors, which can be challenging to achieve. Addressing these socio-economic and policy-related challenges is crucial for the effective utilization of Triticeae genetic resources in crop improvement and ensuring global food security (Lu and Ellstrand, 2014). In summary, the genetic complexity and genome organization of Triticeae species, the need for abiotic and biotic stress resistance, and socio-economic and policy-related challenges are significant hurdles in Triticeae genetic research. Overcoming these challenges requires a multidisciplinary approach, combining advances in genomics, breeding techniques, and international collaboration to harness the full potential of Triticeae genetic resources for crop improvement. 8 Future Directions and Research Priorities 8.1. Emerging trends and technologies inTriticeae research Recent advancements in Triticeae research have been significantly influenced by the integration of genomic technologies and bioinformatics tools. The development of high-throughput genotyping platforms, such as SNP-based marker systems, has facilitated the screening of genetic diversity and the introgression of desirable traits from wild relatives into cultivated species (Przewieslik-Allen et al., 2019). Additionally, the creation of
Triticeae Genomics and Genetics, 2024, Vol.15, No.3, 125-136 http://cropscipublisher.com/index.php/tgg 133 extensive EST libraries and SSR markers for perennial Triticeae species has expanded the genomic resources available for genetic mapping and diversity studies (Bushman et al., 2008). These technologies are crucial for advancing our understanding of the genetic basis of important traits and for improving breeding programs. Moreover, the Triticeae Toolbox (T3) database has emerged as a pivotal resource, enabling researchers to combine, visualize, and analyze phenotype and genotype data. This tool supports various applications, including genome-wide association studies and genomic prediction, which are essential for modern plant breeding (Blake et al., 2016). The integration of these technologies is expected to accelerate the development of improved Triticeae cultivars with enhanced traits such as stress tolerance, disease resistance, and yield. 8.2 Integration of genomic and phenotypic data The integration of genomic and phenotypic data is a critical area of focus in Triticeae research. The comprehensive characterization of genetic resources, including both cultivated and wild taxa, provides a vast gene pool for crop improvement (Bothmer et al., 2008; Lu and Ellstrand, 2014). The use of genomic tools to analyze these resources has revealed significant insights into the evolutionary relationships and genetic diversity within the tribe (Yen and Yang, 2009; Kawahara, 2009). For instance, the Triticeae Toolbox (T3) facilitates the integration of phenotype and genotype data, allowing researchers to define specific datasets for various analyses (Blake et al., 2016). This integration is essential for identifying genetic markers associated with desirable traits and for understanding the genetic architecture of complex traits. Additionally, the development of genomic resources for perennial Triticeae species has enabled comparative mapping and the identification of syntenous regions across different species, further enhancing our understanding of their genetic relationships (Bushman et al., 2008). 8.3 Collaborative efforts and funding opportunities Collaborative efforts and funding opportunities are vital for advancing Triticeae research. The establishment of large-scale genetic resource collections, such as the North American Triticale Genetic Resources Collection (NATGRC), highlights the importance of international collaboration in conserving and utilizing genetic diversity. These collections provide valuable resources for researchers worldwide and facilitate the exchange of germplasm and knowledge. Funding opportunities from governmental and non-governmental organizations are essential for supporting research initiatives and fostering collaboration. Programs like the Triticeae Coordinated Agricultural Project (TCAP) have played a significant role in advancing Triticeae research by providing financial support and promoting collaborative efforts among researchers (Blake et al., 2016). Continued investment in such programs is crucial for addressing the challenges of food security and sustainable agriculture. In conclusion, the future of Triticeae research lies in the continued development and integration of advanced genomic technologies, the comprehensive characterization of genetic resources, and the promotion of collaborative efforts and funding opportunities. These strategies will enable researchers to harness the full potential of Triticeae species for crop improvement and contribute to global food security. 9 Concluding Remarks Through the aforementioned research, it is evident that the Triticeae family exhibits remarkable species diversity and genetic resource abundance, which are indispensable for agricultural production and crop improvement. Wild and cultivated species differ significantly in genetic traits and adaptability, providing a valuable gene pool for crop breeding. Furthermore, in-depth studies in Triticeae taxonomy not only aid in understanding the genetic relationships and evolutionary history among species, but also provide crucial references for the protection and rational utilization of genetic resources. For researchers, a comprehensive understanding of Triticeae taxonomy and genetic resources will facilitate breakthroughs in crop breeding, genetic improvement, and biotechnology research. For farmers, utilizing these genetic resources can significantly enhance crop yield, quality, and stress resistance, thereby strengthening the
Triticeae Genomics and Genetics, 2024, Vol.15, No.3, 125-136 http://cropscipublisher.com/index.php/tgg 134 stability and sustainability of agricultural production. For policymakers, emphasizing the importance of genetic resource protection and adopting appropriate strategies for their conservation and management is crucial to ensure their sustainable utilization. Despite significant progress in Triticeae taxonomy and genetic resource research, further exploration is still needed. Therefore, future researchers can continue to delve into the genetic characteristics and evolutionary mechanisms of Triticeae, discovering more valuable genetic resources. At the same time, governments and various sectors of society should also strengthen the protection and management of genetic resources to ensure their sustainable utilization. Through global cooperation and joint efforts, it is expected to make greater contributions to the development of global agricultural production and the maintenance of food security. Acknowledgments Heartfelt thanks to the peer reviewers for their invaluable feedback on the initial draft of this manuscript. Conflict of Interest Disclosure The authors affirm that this research was conducted without any commercial or financial relationships that could be construed as a potential conflict of interest. References Barkworth M., Cutler D., Rollo J., Jacobs S., and Rashid A., 2009, Morphological identification of genomic genera in the Triticeae, Breeding Science, 59: 561-570. https://doi.org/10.1270/jsbbs.59.561 Blake V., Birkett C., Matthews D., Hane D., Bradbury P., and Jannink J., 2016, The Triticeae toolbox: combining phenotype and genotype data to advance small‐grains breeding, The Plant Genome, 9(2): 0099. https://doi.org/10.3835/plantgenome2014.12.0099 PMid:27898834 Bushman B., Larson S., Mott I., Cliften P., Wang R., Chatterton N., Hernandez A., Ali S., Kim R., Thimmapuram J., Gong G., Liu L., and Mikel M., 2008, Development and annotation of perennial Triticeae ESTs and SSR markers, Genome, 51(10): 779-788. https://doi.org/10.1139/G08-062 PMid:18923529 Bothmer R., Seberg O., and Jacobsen N., 2008, Genetic resources in the Triticeae, Hereditas, 116: 141-150. https://doi.org/10.1111/j.1601-5223.1992.tb00814.x Chen Y., Song W., Xie X., Wang Z., Guan P., Peng H., Jiao Y., Ni Z., Sun Q., and Guo W., 2020, A Collinearity-incorporating homology inference strategy for connecting emerging assemblies in Triticeae tribe as a pilot practice in the plant pangenomic era, Molecular plant, 13(12): 1694-1708. https://doi.org/10.1016/j.molp.2020.09.019 PMid:32979565 Feuillet C., Langridge P., and Waugh R., 2008, Cereal breeding takes a walk on the wild side, Trends in genetics: TIG, 24(1): 24-32. https://doi.org/10.1016/j.tig.2007.11.001 PMid:18054117 Guzzon F., and Ardenghi N., 2018, Could taxonomic misnaming threaten the ex situ conservation and the usage of plant genetic resources? Biodiversity and Conservation, 27: 1157-1172. https://doi.org/10.1007/s10531-017-1485-7 Greene S., Kisha T., Yu L., and Parra‐Quijano M., 2014, Conserving Plants in Gene Banks and Nature: Investigating Complementarity with Trifolium thompsonii Morton, PLoS ONE, 9(8): e105145. https://doi.org/10.1371/journal.pone.0105145 PMid:25121602 PMCid:PMC4133347 Hovhannisyan N., Dulloo M., Yesayan A., Knüpffer H., and Amri A., 2018, Tracking of powdery mildew and leaf rust resistance genes in Triticum boeoticum and T. urartu, wild relatives of common wheat, Czech Journal of Genetics and Plant Breeding, 47: 45-57. https://doi.org/10.17221/127/2010-CJGPB Hyun D., Sebastin R., Lee K., Lee G., Shin M., Kim S., Lee J., and Cho G., 2020, Genotyping-by-sequencing derived single nucleotide polymorphisms provide the first well-resolved phylogeny for the genus Triticum(Poaceae), Frontiers in Plant Science, 11: 688. https://doi.org/10.3389/fpls.2020.00688 PMid:32625218 PMCid:PMC7311657 Kawahara T., 2009, Molecular phylogeny among Triticum-Aegilops species and of the tribe Triticeae, Breeding Science, 59: 499-504. https://doi.org/10.1270/jsbbs.59.499
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