Plant Gene and Trait 2024, Vol.15 http://genbreedpublisher.com/index.php/pgt © 2024 GenBreed Publisher, registered at the publishing platform that is operated by Sophia Publishing Group, founded in British Columbia of Canada. All Rights Reserved.
Plant Gene and Trait 2024, Vol.15 http://genbreedpublisher.com/index.php/pgt © 2024 GenBreed Publisher, registered at the publishing platform that is operated by Sophia Publishing Group, founded in British Columbia of Canada. All Rights Reserved. GenBreed Publisher is an international Open Access publisher specializing in plant protection, plant breeding, molecular genetics, proteomics and genetic diversity registered at the publishing platform that is operated by Sophia Publishing Group (SPG), founded in British Columbia of Canada. Publisher GenBreed Publisher Editedby Editorial Team of Plant Gene and Trait Email: edit@pgt.genbreedpublisher.com Website: http://genbreedpublisher.com/index.php/pgt Address: 11388 Stevenston Hwy, PO Box 96016, Richmond, V7A 5J5, British Columbia Canada Plant Gene and Trait (ISSN 1925-2013) is an open access, peer reviewed journal published online by GenBreed Publisher. The journal publishes articles that address the fundamental nature of genes and genomes at any level, either experimental or computational approaches, in plants as well as algae, including applications of novel techniques to plant biology and plant trait improvement. All papers chosen for publishing should be innovative research work in fields of plant genes or traits, plant protection, plant breeding, particular in the areas of functional genomics, genomic tools, genome technologies, transgene, genome sequencing analysis, molecular genetics, proteomics, genetic diversity, heterosis, genetic characteristics, genetic modification, genotype-phenotype relationships, stress resistance characteristics, QTL analysis, biochemistry, physiology and morphology. All the articles published in Plant Gene and Trait 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. GenBreed Publisher uses CrossCheck service to identify academic plagiarism through the world’s leading plagiarism prevention tool, iParadigms, and to protect the original authors’ copyrights.
Plant Gene and Trait (online), 2024, Vol. 15 ISSN 1925-2013 http://genbreedpublisher.com/index.php/pgt © 2024 GenBreed Publisher, an online publishing platform of Sophia Publishing Group. All Rights Reserved. Sophia Publishing Group (SPG), founded in British Columbia of Canada, is a multilingual publisher Latest Content Genetic Diversity in Sweet Potato: A Review of Global Germplasm Hongyun Zhang, Lin Zhao Plant Gene and Trait, 2024, Vol. 15, No. 6, 275-284 Identification of Sex-Specific Markers in Eucommia ulmoides Xi Chen, Yue Yang, Degang Zhao Plant Gene and Trait, 2024, Vol. 15, No. 6, 285-294 Current Status of Collection, Evaluation, and Utilization of Sorghum Germplasm Resources Chunxin Cao, Nuan Wang, Yubing Liu, Hongming Huang, Meijuan Wu, Xinhua Liu Plant Gene and Trait, 2024, Vol. 15, No. 6, 295-304 Case Study of Sweet Potato Breeding for Enhanced Agronomic Traits Xiangqun Yu, Ning Shen, Jiang Shi, Lin Zhao, Yueqing Zhu Plant Gene and Trait, 2024, Vol. 15, No. 6, 305-313 A Systematic Review of the Molecular Mechanisms of Cysteine Synthase Gene GRA78 in Regulating Rice Leaf Color Jianquan Li Plant Gene and Trait, 2024, Vol. 15, No. 6, 314-322
Plant Gene and Trait 2024, Vol.15, No.6, 275-284 http://genbreedpublisher.com/index.php/pgt 275 Review Article Open Access Genetic Diversity in Sweet Potato: A Review of Global Germplasm Hongyun Zhang1, LinZhao2 1 Zhejiang Wuwangnong Seeds shareholding Co., Ltd., Hangzhou, 310000, Zhejiang, China 2 Hangzhou Academy of Agricultural Sciences, Institute of Crop (Ecology) Research, Hangzhou, 310024, Zhejiang, China Corresponding email: zhaolin0227@163.com Plant Gene and Trait, 2024, Vol.15, No.6 doi: 10.5376/pgt.2024.15.0027 Received: 11 Oct., 2024 Accepted: 13 Nov., 2024 Published: 21 Nov., 2024 Copyright © 2024 Zhang and Zhao, 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: Zhang H.Y., and Zhao L., 2024, Genetic diversity in sweet potato: a review of global germplasm, Plant Gene and Trait, 15(6): 275-284 (doi: 10.5376/pgt.2024.15.0027) Abstract Sweet potato (Ipomoea batatas L. Lam) is a globally significant food crop with extensive genetic diversity. This study synthesizes findings from various studies on the genetic diversity of sweet potato germplasm collected worldwide. Chloroplast SSR markers have revealed low genetic diversity among female parents in the National Agrobiodiversity Center’s collection, indicating a need for broader germplasm collection. Retrotransposon-based insertion polymorphism (RBIP) markers have demonstrated significant intergroup genetic variation, suggesting limited evolutionary diversification despite geographic speciation. Genome-wide assessments using SNPs have identified three major genetic groups, with a core germplasm set developed for future breeding. Morphological, biochemical, and molecular markers have been used to characterize genetic diversity, highlighting promising genotypes for yield and antioxidant content. AFLP analysis has shown low genetic diversity among Tanzanian accessions, with significant within-region variation. These findings underscore the importance of comprehensive germplasm characterization and conservation to support sweet potato breeding programs. Keywords Sweet potato; Genetic diversity; Germplasm; Chloroplast SSR markers; Retrotransposon-based insertion polymorphism (RBIP) 1 Introduction Sweet potato (Ipomoea batatas L. Lam) is a vital food crop with significant agricultural and economic contributions worldwide. It ranks as the sixth most important food crop globally, with China leading its production in a market valued at USD 45 trillion (Escobar-Puentes et al., 2022). Sweet potato is not only a staple food in many developing countries but also a crucial source of income and nutrition for poor farming communities (Lamaro et al., 2022). Its rich nutritional profile, including sugars, slow digestible/resistant starch, vitamins, minerals, and bioactive compounds, makes it a valuable crop for both food security and health benefits (Mohanraj and Sivasankar, 2014). Additionally, sweet potato's versatility extends to its use in agroindustry and medicinal applications, further enhancing its economic importance. The study of genetic diversity and germplasm conservation in sweet potato is essential for several reasons. Firstly, understanding the genetic diversity within sweet potato cultivars can help in the development of improved varieties with higher yields, disease resistance, and better adaptability to different environmental conditions (Lamaro et al., 2022). For instance, genetic diversity studies using various markers such as SSR, AFLP, and RBIP have revealed significant variability among sweet potato accessions, which is crucial for breeding programs (ELameen et al., 2008; Meng et al., 2021). Secondly, conserving sweet potato germplasm ensures the preservation of unique genetic traits that may be lost due to environmental changes or agricultural practices (Roullier et al., 2013; Winnicki et al., 2021). This is particularly important in regions like New Guinea, where traditional landraces have accumulated impressive genetic diversity due to farmers' management practices (Roullier et al., 2016). Lastly, germplasm conservation supports the reinvigoration of cultural heritage and local markets, as seen with the traditional Hawaiian sweet potato varieties (Winnicki et al., 2021). This study reviews the current status of genetic diversity in global sweet potato germplasm resources, discusses the importance of their conservation, and provides an overview of commonly used diversity assessment markers and methods (such as SSR, AFLP, and RBIP). It analyzes the role of regional germplasm banks (such as the
Plant Gene and Trait 2024, Vol.15, No.6, 275-284 http://genbreedpublisher.com/index.php/pgt 276 National Agricultural Biodiversity Center, as well as those in Tanzania and Burkina Faso) in preserving genetic diversity, and proposes measures like on-farm conservation programs and core sample distribution to enhance local adaptability and resilience. Using examples from Hawaii and New Guinea, it explores the economic and cultural impacts of sweet potato genetic diversity, aiming to provide a theoretical basis and practical guidance for the effective conservation and sustainable utilization of global sweet potato germplasm resources. 2 Historical Overview of Sweet Potato Domestication 2.1 The origin and domestication process of sweet potato The domestication of sweet potato (Ipomoea batatas) is a complex process that has intrigued researchers for decades. The origins of this hexaploid species have been debated, with hypotheses suggesting either an autopolyploid origin from the diploid I. trifida or an allopolyploid origin involving genomes of I. trifida and I. triloba. Recent molecular genetic data, however, support an autopolyploid origin of sweet potato from an ancestor shared with I. trifida, which might be similar to currently observed tetraploid wild Ipomoea accessions. This suggests that cultivated I. batatas evolved from at least two distinct autopolyploidization events in polymorphic wild populations of a single progenitor species (Roullier et al., 2013). Additionally, cytogenetic studies have reinforced the close relationship between I. trifida and I. batatas, indicating that I. trifida might be the progenitor of I. batatas (Srisuwan et al., 2006). 2.2 Global distribution of sweet potato germplasm resources Sweet potato is now cultivated globally, with significant genetic diversity observed across different regions. The germplasm resources of sweet potato are distributed widely, with notable centers of diversity in Central and South America, where the crop is believed to have originated. Molecular marker analysis has revealed high genetic diversity in sweet potato germplasms from these regions, particularly in Central America, which is considered a primary center of origin (Murthy et al., 2021). New Guinea is recognized as a secondary center of diversity, where the introduction of sweet potato from the Northern neotropical genepool and subsequent recombination with local genotypes have led to significant genetic variation (Roullier et al., 2013). Furthermore, studies using chloroplast SSR markers have shown that sweet potato accessions from Korea, Japan, Taiwan, and the USA form distinct clusters, indicating regional differentiation in germplasm resources (Lee et al., 2019). 2.3 Historical development and evolution of sweet potato varieties in different regions The historical development and evolution of sweet potato varieties have been shaped by both natural and human-mediated processes. In New Guinea, the diversification of sweet potato is primarily attributed to the active management of the crop's reproductive biology by local farmers, who frequently incorporate plants from true seeds, leading to a high number of variants (Roullier et al., 2013). In Polynesia, archaeological evidence suggests that sweet potato was introduced pre-Columbian times, with cultivation practices adapting to local climatic conditions. For instance, in New Zealand, the discovery of ancient storage pits for sweet potato (kūmara) in the cooler southern regions indicates that early Polynesian settlers developed strategies to grow and store the crop despite challenging environmental conditions. This historical adaptation highlights the resilience and versatility of sweet potato as it spread across different regions and climates. 3 Current Status of Sweet Potato Germplasm Collection 3.1 Current state of the collection and preservation of sweet potato germplasm worldwide The global collection and preservation of sweet potato germplasm have seen significant advancements, with numerous accessions being conserved in various germplasm banks. For instance, the National Agrobiodiversity Center (NAC) has a collection of 558 sweet potato accessions, which have been analyzed for genetic diversity using chloroplast simple sequence repeat (cpSSR) markers. This analysis revealed a relatively low genetic diversity among the female parents of these accessions, indicating a need for further collection efforts to enhance the genetic base (Lee et al., 2019). Similarly, the International Potato Center (CIP) houses one of the largest collections, with nearly 6,000 accessions of cultivated sweet potato and over 1,000 accessions of crop wild relatives. This extensive collection has been genotyped to assess genetic identity, diversity, and population structure, uncovering high levels of redundancy and some genetic identity errors (Anglin et al., 2021).
Plant Gene and Trait 2024, Vol.15, No.6, 275-284 http://genbreedpublisher.com/index.php/pgt 277 3.2 The role of major germplasm banks and research institutions Major germplasm banks and research institutions play a crucial role in the collection, preservation, and characterization of sweet potato germplasm. The CIP, for example, not only maintains a vast collection but also conducts genotyping and phenotyping to ensure the accuracy and utility of the germplasm. Their efforts have identified significant genetic diversity and population structure within their collection, which is essential for breeding and conservation programs (Anglin et al., 2021). The NAC in South Korea also contributes significantly by maintaining a diverse collection and conducting genetic diversity assessments to inform future preservation and breeding strategies (Lee et al., 2019). These institutions provide valuable resources and data that support global sweet potato improvement efforts. 3.3 Advances in germplasm preservation technologies Recent advances in germplasm preservation technologies have greatly enhanced the ability to maintain and utilize sweet potato genetic resources. Techniques such as retrotransposon-based insertion polymorphism (RBIP) markers have been developed to study genetic diversity and population structure in sweet potato. These markers have proven effective in revealing high levels of polymorphism and genetic variation among sweet potato accessions, which is crucial for identifying and preserving diverse genetic traits (Meng et al., 2021). Additionally, genome-wide assessments using specific length amplified fragment (SLAF) sequencing have provided detailed insights into the genetic relationships and population structure of sweet potato accessions, facilitating the development of core germplasm sets for targeted breeding programs (Su et al., 2017). These technological advancements are instrumental in ensuring the long-term conservation and effective utilization of sweet potato germplasm. 4 Genetic Diversity in Sweet Potato 4.1 Progress in studying sweet potato genetic diversity using molecular markers The use of molecular markers, particularly simple sequence repeats (SSRs), has significantly advanced the study of genetic diversity in sweet potato. SSR markers are highly polymorphic and reproducible, making them ideal for genetic studies. For instance, a high-density SSR genetic linkage map was developed for sweet potato, which included 5 057 SSR markers covering 13 299.9 cM with a marker density of 2.6 cM in one parent map and 3 009 SSR markers covering 1 122.9 cM with a marker density of 3.7 cM in another parent map. This map is consistent with the autohexaploid nature of sweet potato and provides a robust foundation for quantitative trait locus (QTL) mapping and marker-assisted breeding (Meng et al., 2021). Additionally, SSR markers have been used to assess the genetic diversity of sweet potato germplasms collected worldwide, revealing significant polymorphisms and genetic variability among accessions (Lee et al., 2019). 4.2 Application of genomic analysis in revealing genetic structure and diversity Genomic analysis using SSR markers has been instrumental in uncovering the genetic structure and diversity of sweet potato. For example, a study using nine chloroplast SSR markers on 558 sweet potato accessions from the National Agrobiodiversity Center (NAC) identified 33 chlorotypes and divided the accessions into four clusters based on their genetic relationships. This analysis highlighted the low genetic diversity of female parents in the NAC collection, suggesting the need for more diverse germplasm collection (Lee et al., 2019). Another study on Brazilian sweet potato landraces using SSR markers found high genetic and intravarietal diversity, with most variability distributed within households rather than between communities. This indicates the influence of outcrossing and anthropic factors such as selection and maintenance of different varieties within small plots and home gardens (Veasey et al., 2008). 4.3 Research on genetic differences and phylogenetic relationships among sweet potato germplasm Research on genetic differences and phylogenetic relationships among sweet potato germplasm has provided insights into the evolutionary history and breeding potential of this crop. The development of SSR linkage maps has facilitated the identification of homologous groups and the understanding of the genetic architecture of sweet potato (Meng et al., 2021). Furthermore, studies using SSR markers have revealed significant genetic diversity among sweet potato accessions from different geographical regions. For instance, the genetic diversity assessment
Plant Gene and Trait 2024, Vol.15, No.6, 275-284 http://genbreedpublisher.com/index.php/pgt 278 of sweet potato accessions from Brazil showed a high level of genetic variability, which is crucial for breeding programs aiming to improve sweet potato traits (Ghebreslassie et al., 2016). These findings underscore the importance of molecular approaches in enhancing our understanding of sweet potato genetic diversity and guiding conservation and breeding efforts. 5 Genetic Diversity in Sweet Potato Germplasm from Asia 5.1 Genetic diversity analysis of sweet potato germplasm in Asia The genetic diversity of sweet potato germplasm in Asia has been extensively studied using various molecular markers. For instance, a genome-wide assessment of 197 sweet potato accessions, primarily from China, utilized 62 363 SNPs to evaluate genetic diversity and population structure. This study identified three distinct genetic groups and highlighted significant genetic variation within the accessions, with a mean genetic distance ranging from 0.290 to 0.311 (Figure 1) (Su et al., 2017). Another study employed retrotransposon-based insertion polymorphism (RBIP) markers to analyze 105 sweet potato germplasm resources from China, Japan, and America. This analysis revealed high polymorphism (91.07%) and significant genetic variation among the accessions, which were divided into three groups (Meng et al., 2021). Figure 1 Location of the sweet potato accessions from around the world, highlighting China (Adopted from Su et al., 2017) 5.2 Research background and data sources The research on sweet potato genetic diversity in Asia has been driven by the need to enhance breeding programs and conserve genetic resources. The studies have utilized germplasm collections from various national and international gene banks. For example, the National Agrobiodiversity Center (NAC) in South Korea has been a significant source of germplasm for genetic diversity studies. One study analyzed 558 sweet potato accessions from the NAC using chloroplast SSR markers, revealing low genetic diversity among the female parents and the need for more diverse collections (Lee et al., 2019). Additionally, the International Potato Center (CIP) has contributed to the understanding of genetic diversity by maintaining a vast collection of sweet potato accessions from around the world, including Asia (Zhang et al., 2000). 5.3 Key findings and their significance for global sweet potato diversity conservation The key findings from these studies underscore the rich genetic diversity present in Asian sweet potato germplasm. The identification of distinct genetic groups and high levels of polymorphism suggests that Asian germplasm can significantly contribute to global sweet potato breeding programs. The low genetic diversity observed in some collections, such as those from the NAC, highlights the importance of expanding germplasm collections to include more diverse accessions (Figure 2) (Lee et al., 2019; Luo et al., 2023). The development of core germplasm sets, as seen in the study using SNP markers, provides valuable resources for future breeding efforts. Furthermore, the use of advanced molecular markers like RBIP and SSRs has proven effective in characterizing genetic diversity and can be applied to other regions to enhance global conservation strategies (Monteros-Altamirano et al., 2020). These findings are crucial for the conservation of sweet potato genetic resources, as they provide insights into the genetic structure and diversity of germplasm collections. By identifying areas with low genetic diversity, researchers can prioritize these regions for new germplasm collection efforts. Additionally, the development of core germplasm sets ensures that the most genetically diverse and representative accessions are preserved and utilized in breeding programs, ultimately contributing to the sustainability and improvement of sweet potato crops worldwide.
Plant Gene and Trait 2024, Vol.15, No.6, 275-284 http://genbreedpublisher.com/index.php/pgt 279 Figure 2 Phenotypic codes and pictures for sweet potato germplasm (Adopted from Luo et al., 2023) 6 Environmental and Agronomic Factors Influencing Genetic Diversity 6.1 Effects of different environmental conditions on sweet potato genetic diversity Environmental conditions such as climate and soil significantly influence the genetic diversity of sweet potato. For instance, sweet potato genotypes exhibit varying degrees of adaptation to different environmental conditions, which is crucial for breeding programs aimed at improving crop resilience. Studies have shown that sweet potato genotypes can be selected based on their performance across multiple environments, incorporating traits such as yield, quality, and plant architecture (Rosero et al., 2023; Liu and Chen, 2024). Additionally, the genetic diversity of sweet potato is influenced by the specific environmental conditions of the regions where they are cultivated. For example, sweet potato accessions from Korea, Japan, Taiwan, and the USA showed distinct genetic clusters, indicating that regional environmental conditions play a role in shaping genetic diversity (Lee et al., 2019). 6.2 Impact of agronomic management and cultivation practices Agronomic management and cultivation practices also have a profound impact on the genetic diversity and performance of sweet potato. Practices such as fertilization, crop protection, and rotational designs can influence crop yield and nutritional quality. For example, organic fertilization has been shown to result in higher concentrations of phenolics and other nutritionally desirable phytochemicals in crops, while also reducing the concentrations of toxic metals like cadmium and nickel (Rempelos et al., 2023). Moreover, the selection of sweet potato genotypes based on multi-trait indices and stability analysis helps in identifying superior varieties that perform well under different agronomic conditions (Rosero et al., 2023). This approach ensures that the selected genotypes are not only high-yielding but also stable across various environmental conditions, thereby maintaining genetic diversity.
Plant Gene and Trait 2024, Vol.15, No.6, 275-284 http://genbreedpublisher.com/index.php/pgt 280 6.3 Challenges posed by global warming to sweet potato germplasm resources and diversity Global warming poses significant challenges to the genetic diversity and germplasm resources of sweet potato. Increasing temperatures and extreme weather events can negatively impact the productivity and resilience of sweet potato genotypes. For instance, heat stress is a major concern, and studies have identified specific sweet potato cultivars that exhibit heat tolerance, which is crucial for maintaining crop resilience in the face of climate change (Heider et al., 2020). Additionally, drought stress is another critical factor that affects sweet potato cultivation. Breeding programs are focusing on developing drought-tolerant varieties by studying the physiological and biochemical features of different genotypes (Monteros-Altamirano et al., 2023). These efforts are essential to ensure that sweet potato remains a viable crop under changing climatic conditions, thereby preserving its genetic diversity. 7 Utilization of Sweet Potato Germplasm for Breeding and Improvement 7.1 Breeding strategies to enhance yield, disease resistance, and nutritional value using genetic diversity Breeding strategies for sweet potato have increasingly focused on leveraging the extensive genetic diversity present within global germplasm collections. The use of morphological, biochemical, and molecular markers has been pivotal in identifying and selecting genotypes with desirable traits. For instance, the study by Paliwal et al. (2020) demonstrated the use of RAPD markers to assess genetic diversity among 21 sweet potato genotypes, identifying promising candidates for yield improvement and disease resistance. Similarly, the analysis of chloroplast SSR markers in 558 sweet potato accessions highlighted the need for broader genetic diversity in breeding programs to enhance traits such as yield and disease resistance (Lee et al., 2019). Moreover, the integration of advanced genomic tools has revolutionized breeding strategies. Techniques such as marker-assisted selection (MAS) and genomic selection (GS) enable breeders to track and manipulate specific DNA sequences associated with desirable traits, thereby increasing the efficiency of breeding programs (Bethke et al., 2019; Tiwari et al., 2020). These strategies are complemented by traditional breeding methods, which continue to play a significant role in the development of new cultivars with improved nutritional value, such as higher carotene and antioxidant content (Solankey et al., 2015). 7.2 Analysis of successful breeding cases and insights for future breeding Several successful breeding cases underscore the potential of utilizing genetic diversity for sweet potato improvement. For example, the study by (Vargas et al., 2018) highlighted the significant genetic variability among sweet potato accessions collected from traditional communities, which can be harnessed for breeding programs aimed at enhancing yield and disease resistance. The identification of genotypes with high phenolic and antioxidant content, as reported by (Paliwal et al., 2020), provides a foundation for developing nutritionally superior sweet potato varieties. Future breeding efforts can benefit from the insights gained through these studies. The use of high-throughput marker systems, such as retrotransposon-based insertion polymorphism (RBIP) markers, has proven effective in assessing genetic diversity and identifying unique genetic resources for breeding (Meng et al., 2021). Additionally, the application of genomic tools, including genome editing and multi-omics platforms, offers new avenues for the precise manipulation of genetic traits, thereby accelerating the development of improved sweet potato cultivars (Tiwari et al., 2022). 7.3 Challenges faced in breeding processes and potential solutions Despite the advancements in breeding strategies, several challenges persist in the breeding of sweet potato. One major challenge is the limited genetic diversity within certain germplasm collections, which can hinder the development of new varieties with enhanced traits (Lee et al., 2019). To address this, it is crucial to expand germplasm collections by incorporating accessions from diverse geographical regions and traditional farming communities (Vargas et al., 2018). Another challenge is the complexity of sweet potato genetics, which can complicate the identification and manipulation of desirable traits. The use of advanced genomic tools and high-throughput marker systems can
Plant Gene and Trait 2024, Vol.15, No.6, 275-284 http://genbreedpublisher.com/index.php/pgt 281 mitigate this issue by providing more precise and efficient methods for trait selection and breeding (Bethke et al., 2019; Meng et al., 2021). Additionally, the integration of phenotypic and genotypic data through association mapping can enhance the understanding of trait inheritance and facilitate the development of superior sweet potato varieties (Gebhardt et al., 2004). 8 Conservation Strategies for Sweet Potato Genetic Resources 8.1 Strategies for maintaining and managing sweet potato genetic diversity Maintaining and managing the genetic diversity of sweet potato is crucial for ensuring the crop's resilience and adaptability to changing environmental conditions. One effective strategy is the collection and characterization of diverse sweet potato accessions from various geographical regions. For instance, the National Agrobiodiversity Center (NAC) has utilized chloroplast simple sequence repeat (cpSSR) markers to analyze the genetic diversity of 558 sweet potato accessions, revealing the need for more diverse collections to enhance genetic variability (Lee et al., 2019). Similarly, in Puerto Rico, genetic diversity assessments using SSR markers have shown high levels of heterozygosity and genetic diversity among local landraces, underscoring the importance of preserving these genetic resources (Rodríguez-Bonilla et al., 2014). 8.2 Comprehensive applications of in vitro conservation, field gene banks, and community-based germplasm conservation In vitro conservation, field gene banks, and community-based germplasm conservation are complementary approaches to preserving sweet potato genetic resources. In vitro conservation techniques, such as cryopreservation and tissue culture, allow for the long-term storage of genetic material under controlled conditions, minimizing the risk of genetic erosion (Salgotra and Chauhan, 2023). Field gene banks, on the other hand, maintain living collections of sweet potato accessions, providing a dynamic resource for breeding and research. For example, the Texas A&M University Potato Breeding Program has maintained a collection of advanced clones in vitro over a 40-year period, facilitating the conservation and utilization of genetic diversity (Pandey et al., 2021). Community-based germplasm conservation involves local farmers and communities in the preservation of sweet potato varieties. This approach not only helps maintain genetic diversity but also ensures the continued use and adaptation of traditional varieties to local conditions. In Ethiopia, local collections of sweet potato have shown significant genetic diversity and better performance compared to improved varieties, highlighting the value of community-based conservation efforts (Mohammed et al., 2015). 8.3 Importance of international cooperation and policy support for the conservation of sweet potato genetic resources International cooperation and policy support are essential for the effective conservation of sweet potato genetic resources. Collaborative efforts between countries and institutions can facilitate the exchange of germplasm, knowledge, and technologies, enhancing global conservation strategies. For instance, the identification of heat-tolerant sweet potato cultivars through international field experiments underscores the importance of shared research initiatives in addressing climate change challenges (Heider et al., 2020). Policy support at national and international levels is also critical for the sustainable conservation of genetic resources. Policies that promote the establishment of gene banks, support community-based conservation programs, and facilitate the exchange of genetic material can significantly enhance conservation efforts. The integration of biotechnological tools, such as next-generation sequencing and molecular markers, into conservation policies can further improve the characterization and preservation of sweet potato genetic diversity (Salgotra and Chauhan, 2023). 9 Conclusion The current status of sweet potato genetic diversity conservation and utilization reveals a complex yet promising landscape. Studies have shown that sweet potato germplasm collections exhibit significant genetic diversity, although there are areas that require further attention. For instance, the genetic diversity of sweet potato
Plant Gene and Trait 2024, Vol.15, No.6, 275-284 http://genbreedpublisher.com/index.php/pgt 282 accessions conserved at the National Agrobiodiversity Center (NAC) is relatively low, indicating a need for more extensive collection efforts to enhance the genetic base. Retrotransposon-based insertion polymorphism (RBIP) markers have been effectively used to assess genetic diversity, revealing substantial polymorphism and genetic variation among sweet potato germplasms. Additionally, genome-wide assessments using specific length amplified fragment (SLAF) sequencing have provided detailed insights into the population structure and genetic relationships among sweet potato accessions, further highlighting the genetic richness within the species. Despite these advancements, the genetic diversity within sweet potato germplasms is not uniformly distributed, with some studies indicating limited evolutionary diversification and geographic speciation. Overall, while significant progress has been made in understanding and conserving sweet potato genetic diversity, there remains a need for continued efforts to expand and utilize these genetic resources effectively. Looking forward, several key areas of research and germplasm resource management need to be prioritized to ensure the sustainable conservation and utilization of sweet potato genetic diversity. First, expanding the collection of sweet potato germplasms, particularly from underrepresented regions, is crucial to enhance the genetic base and ensure the availability of diverse genetic material for breeding programs. Advanced molecular techniques, such as RBIP markers and SLAF sequencing, should continue to be employed to provide comprehensive assessments of genetic diversity and population structure, facilitating the identification of core germplasm sets for targeted breeding efforts. Additionally, integrating ex situ and in situ conservation strategies will be essential to safeguard the genetic diversity of sweet potato and its wild relatives, as demonstrated by successful conservation efforts in Brazil. Collaborative international initiatives, such as those supported by the Global Crop Diversity Trust, can play a pivotal role in coordinating these efforts and ensuring the global exchange of germplasm resources. Furthermore, leveraging the economic benefits of conserved germplasm, as evidenced by the significant contributions of the International Potato Center (CIP) genebank to crop improvement, can provide a strong incentive for continued investment in germplasm conservation and utilization. By addressing these future prospects, researchers and policymakers can ensure the sustainable management of sweet potato genetic resources, ultimately contributing to global food security and agricultural resilience. Acknowledgments We would like to thank Prof. Guan for his meticulous reading of the manuscript, providing comprehensive academic suggestions and for editing this article. We’re also grateful to the two anonymous peer reviewers for their academic revisions. 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 Anglin N., Robles R., Rossel G., Alagon R., Panta A., Jarret R., Manrique N., and Ellis D., 2021, Genetic identity, diversity, and population structure of CIP’s sweetpotato’s (I. batatas) germplasm collection, Frontiers in Plant Science, 12: 660012. https://doi.org/10.3389/fpls.2021.660012 PMid:34777403 PMCid:PMC8589021 Bethke P., Halterman D., and Jansky S., 2019, Potato germplasm enhancement enters the genomics era, Agronomy, 9(10): 575. https://doi.org/10.3390/agronomy9100575 ELameen A., Fjellheim S., Larsen A., Rognli O., Sundheim L., Msolla S., Masumba E., Mtunda K., and Klemsdal S., 2008, Analysis of genetic diversity in a sweet potato (Ipomoea batatas L.) germplasm collection from Tanzania as revealed by AFLP, Genetic Resources and Crop Evolution, 55: 397-408. https://doi.org/10.1007/s10722-007-9247-0 Escobar-Puentes A., Palomo I., Rodríguez L., Fuentes E., Villegas-Ochoa M., González-Aguilar G., Olivas-Aguirre F., and Wall-Medrano A., 2022, Sweet potato (Ipomoea batatas L.) phenotypes: from agroindustry to health effects, Foods, 11(7): 1058. https://doi.org/10.3390/foods11071058 PMid:35407143 PMCid:PMC8997864
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Plant Gene and Trait 2024, Vol.15, No.6, 285-294 http://genbreedpublisher.com/index.php/pgt 285 Research Insight Open Access Identification of Sex-Specific Markers inEucommia ulmoides Xi Chen1, YueYang2, Degang Zhao1,2 1 Plant Conservation & Breeding Technology Center, Guizhou Key Laboratory of Agricultural Biotechnology / Guizhou Institute of Prataculture, Guizhou Academy of Agricultural Sciences, Guiyang, 550006, China 2 National-local Joint Engineering Research Center of Karst Region Plant Resources Utilization & Breeding (Guizhou), College of Life Sciences/Institute of Agro- Bioengineering, Guizhou University, Guiyang, 550025, China Corresponding email: dgzhao@gzu.edu.cn Plant Gene and Trait, 2024, Vol.15, No.6 doi: 10.5376/pgt.2024.15.0028 Received: 23 Oct., 2024 Accepted: 25 Nov., 2024 Published: 03 Dec., 2024 Copyright © 2024 Chen 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: Chen X., Yang Y., and Zhao D.G., 2024, Identification of sex-specific markers in Eucommia ulmoides, Plant Gene and Trait, 15(6): 285-294 (doi: 10.5376/pgt.2024.15.0028) Abstract Eucommia ulmoides is a dioecious plant with significant ecological and economic value, but its sex is difficult to identify at the juvenile stage using traditional morphological methods, resulting in low breeding efficiency and affecting commercial cultivation. To address this challenge, this study provides an in-depth analysis of the application of several sex-specific molecular markers in sex identification of E. ulmoides, with a focus on the male-specific markers that have been identified, such as the MSL4 locus and the 247 bp SCAR marker. These molecular markers can accurately distinguish male and female individuals at an early developmental stage, demonstrating high reliability and stability. They offer significant advantages in improving breeding efficiency, accelerating seedling selection, and optimizing resource allocation. Furthermore, these markers play a crucial role in promoting the commercial cultivation and resource management of E. ulmoides, providing technical support for industry development. Future research will focus on optimizing the application of these molecular markers and exploring their potential in other dioecious plants. This study provides a strong theoretical basis and technical guidance for sex identification and molecular breeding in related species. Keywords Eucommia ulmoides; Sex-specific markers; Dioecious plants; Molecular breeding; Marker-assisted selection 1 Introduction Eucommia ulmoides, commonly known as the hardy rubber tree, is a dioecious species native to China, meaning it has distinct male and female individuals. This species is highly valued for its medicinal properties and its ability to produce rubber, making it economically significant (Du et al., 2023; You et al., 2023). However, one of the major challenges in cultivating E. ulmoides is the inability to determine the sex of the plants at the juvenile stage, which can last for several years. This limitation hinders efficient breeding and commercial production, as the pistillate (female) plants are generally more economically valuable than the staminate (male) plants. Recent advancements in molecular biology have provided new methods for early sex identification in E. ulmoides. Techniques such as Amplified Fragment Length Polymorphism (AFLP), Random Amplified Polymorphic DNA (RAPD), and double-digest restriction site-associated DNA sequencing (ddRAD-seq) have been employed to develop sex-specific markers. These markers allow for the identification of male and female plants at an early developmental stage, thus facilitating more efficient breeding programs and resource allocation (Xu et al., 2004; Wang et al., 2011; Wang et al., 2020). The ability to determine the sex of individuals in dioecious plants like Eucommia ulmoides at an early developmental stage is crucial for several reasons. On one hand, it facilitates selective breeding programs aimed at improving desirable traits such as increased rubber yield and the production of medicinal compounds (Montgomery et al., 2019; Fu et al., 2020). Secondly, early sex identification can significantly improve the efficiency of commercial cropping by ensuring the optimal ratio of male to female plants, which is essential for maximizing yield and resource allocation. Traditional morphological methods for sex determination are often unreliable and time-consuming, necessitating the development of molecular markers for accurate and rapid sex identification (Wang et al., 2020; Du et al., 2023; Zhang et al., 2023).
Plant Gene and Trait 2024, Vol.15, No.6, 285-294 http://genbreedpublisher.com/index.php/pgt 286 This study delves into the application potential of sex-specific molecular markers in E. ulmoides by analyzing existing genomic and transcriptomic data. The research summarizes several sex-related molecular markers and evaluates their reliability and stability in early sex identification. It focuses on reviewing current marker technologies and analyzing their application in the breeding of E. ulmoides, providing a theoretical foundation for future sex identification and efficient breeding strategies. By conducting an in-depth analysis of existing techniques, this study aims to offer valuable insights for optimizing breeding processes and resource allocation in E. ulmoides, while also exploring new directions for research and applications in other dioecious plants. 2 Biological Characteristics and Reproductive Biology of Eucommia ulmoides 2.1 Biological traits of Eucommia ulmoides Eucommia ulmoides, commonly known as the hardy rubber tree, is a dioecious perennial tree native to China. It is the sole species of the family Eucommiaceae and is highly valued for its medicinal and industrial applications, particularly for its rubber-producing capabilities (Wang et al., 2018; Wang et al., 2020). The species is characterized by its unisexual flowers, which are borne on separate male and female individuals from the earliest stages of stamen/pistil primordium formation (Zhang et al., 2023). The tree has a long juvenile phase during which it is difficult to distinguish between male and female plants based on morphological traits alone (Wang et al., 2011). 2.2 Reproductive biology of dioecious plants Dioecious plants, such as Eucommia ulmoides, have distinct male and female individuals, each producing only one type of reproductive organ. This separation of sexes can complicate breeding programs and commercial cultivation, as the sex of the plants cannot be determined until they reach reproductive maturity (Wang et al., 2011). The genetic mechanisms underlying sex determination in dioecious plants are complex and often involve sex-specific gene expression and chromosomal differences. In E. ulmoides, sex determination is likely genetically controlled, with specific genes and molecular markers associated with male and female plants (Wang and Zhang, 2017; Wang et al., 2020; Du et al., 2023). 2.3 Previous research on sex-specific markers in dioecious species Several studies have focused on identifying sex-specific markers in Eucommia ulmoides to facilitate early sex determination. For instance, a male-specific Amplified Fragment Length Polymorphism (AFLP) marker was developed and converted into a Sequence Characterized Amplified Region (SCAR) marker, which can be used for early sexual identification (Wang et al., 2011). Comparative transcriptome analyses have identified differentially expressed genes (DEGs) between male and female plants, including genes related to sex determination and sexually dimorphic traits (Wang and Zhang, 2017). Additionally, double-digest restriction site-associated DNA sequencing (ddRAD-seq) has been used to identify male-specific loci, with one locus, MSL4, being highly conserved and stable across male individuals (Wang et al., 2020). Random Amplified Polymorphic DNA (RAPD) markers have also been linked to sex determination, with a specific marker exclusive to pistillate plants (Xu et al., 2004; You et al., 2023). 2.4 Identified research gaps Despite the progress made in identifying sex-specific markers in Eucommia ulmoides, several research gaps remain. The genetic mechanisms of sex determination and differentiation in E. ulmoides are not fully understood, and further studies are needed to elucidate these processes. Additionally, while several sex-specific markers have been identified, their practical application in breeding programs and commercial cultivation requires further validation and optimization (Xu et al., 2004; Wang et al., 2011; Wang et al., 2020). There is also a need for more comprehensive genomic and transcriptomic analyses to identify additional sex-associated genes and markers, which could provide deeper insights into the molecular regulation of sex in E. ulmoides (Figure 1) (Wang and Zhang, 2017; Du et al., 2023; Zhang et al., 2023).
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