Tree Genetics and Molecular Breeding 2024, Vol.14 http://genbreedpublisher.com/index.php/tgmb © 2024 GenBreed Publisher, registered at the publishing platform that is operated by Sophia Publishing Group, founded in British Columbia of Canada. All Rights Reserved.
Tree Genetics and Molecular Breeding 2024, Vol.14 http://genbreedpublisher.com/index.php/tgmb © 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 tree genetics and molecular breeding, trees genetic diversity and conservation genetics 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 Tree Genetics and Molecular Breeding Email: edit@tgmb.genbreedpublisher.com Website: http://genbreedpublisher.com/index.php/tgmb Address: 11388 Stevenston Hwy, PO Box 96016, Richmond, V7A 5J5, British Columbia Canada Tree Genetics and Molecular Breeding (ISSN 1927-5781) is an open access, peer reviewed journal published online by GenBreed Publisher. The journal publishes all the latest and outstanding research articles, letters and reviews in all aspects of tree genetics and molecular breeding, include studies in tree genetics and molecular breeding, include studies in crop/fruit/forest/ornamental/horticultural trees genetic diversity, conservation genetics, molecular genetics, evolutionary genetics, population genetics, physiology, biochemistry, transgene, genetic rule analysis, QTL analysis, vitro propagation; fruit/forest/ornamental/horticultural trees breeding studies and advanced breeding technologies. All the articles published in Tree Genetics and Molecular Breeding 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.
Tree Genetics and Molecular Breeding (online), 2024, Vol. 14 ISSN 1927-5781 http://genbreedpublisher.com/index.php/tgmb © 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 and Conservation Strategies of Apple Germplasm Resources JianxinLi Tree Genetics and Molecular Breeding, 2024, Vol. 14, No. 1, pp.1-7 Tropical Forest Mysteries: Unveiling the Global Consistency of Common Tree Species Patterns Josselynn X.Z. Feng Tree Genetics and Molecular Breeding, 2024, Vol. 14, No. 1, pp.8-11 Accelerating the Process of Tree Breeding: A Review and Progress of GWAS Applications in Forest Trees Chuchu Liu, Yuan Liu Tree Genetics and Molecular Breeding, 2024, Vol. 14, No. 1, pp.12-21 Agronomic Traits of Cassava and Their Genetic Bases: A Focus on Yield and Quality Improvements Zhongmei Hong, Wenzhong Huang Tree Genetics and Molecular Breeding, 2024, Vol. 14, No. 1, pp.22-31 CRISPR/Cas9 in Poplar Lignin Biosynthesis: Advances and Future Prospects Yongquan Lu Tree Genetics and Molecular Breeding, 2024, Vol. 14, No. 1, pp.32-42
Tree Genetics and Molecular Breeding 2024, Vol.14, No.1, 1-7 http://genbreedpublisher.com/index.php/tgmb 1 Research Article Open Access Genetic Diversity and Conservation Strategies of Apple Germplasm Resources JianxinLi Jiugu MolBreed SciTech Ltd., Zhuji, 311800, Zhejiang, China Corresponding email: 2397383131@qq.com Tree Genetics and Molecular Breeding, 2024, Vol.14, No.1 doi: 10.5376/tgmb.2024.14.0001 Received: 18 Dec., 2023 Accepted: 22 Jan., 2024 Published: 12 Feb., 2024 Copyright © 2024 Li, 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: Li J.X., 2024, Genetic diversity and conservation strategies of apple germplasm resources, Tree Genetics and Molecular Breeding, 14(1): 1-7 (doi: 10.5376/tgmb.2024.14.0001) Abstract Apples, as one of the globally significant fruit trees, possess a rich array of germplasm resources and extensive genetic diversity. This review aims to delve into the genetic diversity of apple germplasm resources and the associated conservation strategies. It begins by outlining the origin and evolutionary history of apples, then focuses on elucidating the significance of genetic diversity in the apple industry, as well as evaluating the effectiveness and challenges of current conservation strategies. Addressing the shortcomings of existing strategies, the review further explores improvement measures including diversity maintenance, genomics-based conservation methods, and ongoing monitoring and management. By providing a comprehensive discussion, this review seeks to offer a holistic understanding of conserving genetic diversity in apple germplasm resources, serving as a reference for future research and conservation efforts. Keywords Apple; Germplasm resources; Genetic diversity; Conservation strategies; DNA sequence analysis 1 Introduction The apple (Malus domestica) is one of the most important fruit trees in the world, not only providing people with a delicious fruit, it is also an important raw material for many foods and drinks, such as juices, jams and fruit wines (Bhargava and Bansal, 2021), but also plays an important role in the agricultural economy. In today's agricultural field, apple is not only a popular fruit, but also an extremely important genetic resource bank, the genetic diversity contained in this fruit, and its key role in the agricultural industry, has attracted extensive attention and research. As a kind of fruit widely cultivated all over the world, apple not only meets people's demand for fruit with its rich varieties and potential adaptability, but also is a treasure house of agricultural genetic resources. These resources contain a wide range of genetic characteristics, ranging from fruit color, form, quality, and plant adaptation to the environment. The diversity of apple germplasm resources is very important for breeding new varieties, crop improvement and maintaining ecosystem stability. The genetic diversity of apple is an important basis for its adaptation to various growing environments, stress resistance and quality improvement. In-depth understanding and utilization of this diversity will help to improve the resistance to pests and diseases of apple cultivars, adapt to different climatic conditions, and improve yield and quality (Basannagari and Kala, 2013). Genetic diversity also makes it possible to breed new, more competitive varieties. This study aims to explore the genetic diversity of apple germplasm resources, examine the importance of these resources to the development of the apple industry from different perspectives, and analyze the effectiveness and shortcomings of existing conservation strategies. At the same time, this study will also evaluate the existing conservation strategies and analyze their effectiveness and shortcomings, in order to provide useful references for improving and formulating more scientific conservation strategies in the future. Research on the genetic diversity of apple and its conservation strategies is crucial to the sustainability and improvement of agricultural production, and an in-depth understanding of the value of these resources and the limitations of existing conservation strategies will help researchers to better protect and utilize apple germplasm resources and promote the sustainable development of the apple industry.
Tree Genetics and Molecular Breeding 2024, Vol.14, No.1, 1-7 http://genbreedpublisher.com/index.php/tgmb 2 2 Genetic Diversity of Apple Germplasm Resources 2.1 The origin and evolution of apple The apple (Malus domestica), as an ancient and precious fruit, has gone through a long history of its origin and evolution, containing rich traces of cultural and human activities. The origin of apple can be traced back to Asia and Europe, where wild apple trees initially grew in the high mountains of Asia, forming the earliest apple gene pool (Figure 1) (Gao et al., 2015). Figure 1 The distribution of apples around the world (Adopted from Wang et al., 2018) Image caption: Malus sieversii in Central Asia, Malus sylvestris in Europe, and Malus orientalis in Caucasus were originally proposed to be ancestors of cultivated apple (Adopted from Wang et al., 2018) These wild apple trees not only gradually evolved diversity in their natural environment, but also became an important part of human agricultural civilization. Early human communities began to recognize the edible value of wild apples, and gradually formed the earliest artificial varieties through selective breeding and cultivation practices. This process is not only the domestication and improvement of plants, but also the product of the interaction between man and nature. With the expansion of cultural exchanges and trade, apples gradually spread to all parts of the world. The ancient trade and wars promoted the introduction of apples from Asia to Europe, and also gave birth to the traditions of apple cultivation in different regions. In this process, people through the continuous selection, breeding and reproduction to create a unique variety of apple. The origin and evolution of the apple is not only the subject of botany and genetics, but also a story throughout the history of human civilization. Woven into the story is the wisdom of the mutual domestication of man and nature, as well as the diversity formed through cultural exchange. A thorough understanding of the origin of apple will help people better understand the role of this fruit in human civilization, and also provide scientific basis for subsequent discussions on apple genetic diversity and conservation strategies. 2.2 Methods for determining genetic diversity The method of genetic diversity determination is very important for the conservation and utilization of apple germplasm resources. In exploring the genetic diversity of apple germplasm resources, scientists have adopted various methods. Among them, molecular marker technology is one of the most commonly used means to evaluate the genetic diversity of apple, by analyzing DNA or RNA sequences, such as random amplified polymorphic DNA (RAPD), simple repeat sequence (SSR), single nucleotide polymorphism (SNP), etc. It can reveal genetic differences and levels of diversity between different apple varieties (Ahmad et al., 2021). Morphological characteristics are also one of the important methods to evaluate the genetic diversity of apple, and researchers reveal the differences and variations among different varieties through quantitative and qualitative analysis of fruit morphology, leaf characteristics, tree structure, etc. Assessment of biological characteristics is also key to determining genetic diversity. The observation and recording of growth habits, flowering period, fruiting characteristics, etc., can provide information about differences between varieties, and then judge their genetic diversity.
Tree Genetics and Molecular Breeding 2024, Vol.14, No.1, 1-7 http://genbreedpublisher.com/index.php/tgmb 3 2.3 Classification and characteristics of germplasm resources of apple As an important fruit tree, apple has extensive and diverse germplasm resources, which show rich diversity in morphology, biological characteristics and genetic characteristics. The first is geographical classification, which refers to the classification of apple varieties according to their origin and distribution area. Apple varieties around the world can vary significantly in terms of growing environment, disease resistance and quality. For example, the Maras apple in Central Asia is considered to be the original wild species of apple, and apples from different countries and regions may also differ in fruit morphology and growth habits (Marconi et al., 2018). The second is genetic classification, which is based on the genetic characteristics and genotypes of apple varieties. The genetic background of different apple varieties determines the characteristics of disease resistance, fruit size, taste and maturity. Older varieties often have higher genetic diversity, which is important in breeding and conservation efforts. Another type of classification is based on fruit characteristics, such as size, color, shape and taste. This classification is often used to distinguish between different types of apples used for fresh food, for processing (making jams, juices, etc.), or for cooking purposes. Finally, there is the classification by use, which distinguishes apple varieties according to their different uses, including fresh food, processing or cooking purposes. Apple varieties used for different purposes may have significant differences in pulp texture, sugar content and taste. 3 Conservation Status of Germplasm Resources of Apple 3.1 Global apple resource bank and genetic resource conservation organization A number of apple resource banks and genetic resource conservation organizations have been established around the world to collect, preserve and study apple genetic resources and provide support for the protection and utilization of apple germplasm resources. The most well-known of these are Apple repositories located around the world, such as the National Apple Collection in the United States, the European Apple Varieties Database in Europe, and the Apple Repository in Asia. These repositories collect and preserve apple germplasm from all over the world, including wild, traditional and modern cultivars. They not only preserve rich genetic diversity, but also provide an important material basis for breeding and research (Shaziya et al., 2018). Apple Genetic Resources Conservation groups have also been established around the world, examples include the International Plant Genetic Resources Institute and the International Society for Horticultural Resources Science-Fruit Section. They promote the collection, evaluation and communication of apple genetic resources. Through collaboration and information sharing, these organizations contribute to the conservation, research and sustainable use of apple genetic resources worldwide. 3.2 Existing conservation measures and policies Some countries and regions have special laws and regulations to protect crop genetic resources, including apples. These policies include building germplasm banks, protecting wild species, encouraging the preservation of traditional varieties, and encouraging the exchange and sharing of plant genetic resources (Shaziya et al., 2018). Some governments and ngos have also developed special apple conservation programs to ensure the long-term conservation and sustainable use of genetic resources. Existing conservation measures and policies provide important support for the conservation and management of apple genetic resources and are widely implemented around the world. There are also a number of international cooperation mechanisms and agreements aimed at protecting plant genetic resources. For example, the International Plant Genetic Resources Treaty of the Food and Agriculture Organization of the United Nations (FAO) provides a framework and guidance for the conservation and sustainable use of plant genetic resources, facilitating resource sharing and exchange on a global scale. In addition to regulations and policies, scientific research institutions and agricultural organizations are also actively working on the conservation of apple genetic resources. These institutions are committed to the collection, preservation, research and utilization of apple germplasm resources, and promote the protection and utilization of apple diversity.
Tree Genetics and Molecular Breeding 2024, Vol.14, No.1, 1-7 http://genbreedpublisher.com/index.php/tgmb 4 3.3 Challenges and problems At present, a series of challenges and problems facing Apple genetic resources will directly affect its long-term protection, utilization and sustainable development. One of the major challenges is the loss and reduction of genetic diversity. Commercial cultivation, which favors a small number of superior varieties, has led to the marginalization and loss of many traditional or wild apple varieties, exacerbating the decline in genetic diversity, which may lead to a decline in the overall genetic performance of apple germplasm, weakening disease resistance, adaptability, and other important characteristics (Wang et al., 2019). Ecological pressure is also an important issue. Factors such as climate change, disease, insect pests and human activities have caused no small threat to the growing environment of apple, leading to the risk of endangered or even extinct apple genetic resources in some areas. The ongoing impact of these factors can cause lasting damage to the health and diversity of the apple population. There are also numerous management and conservation challenges. The collection, conservation and management of genetic resources are inadequate, there is a lack of comprehensive monitoring and evaluation mechanisms, and there is insufficient attention to long-term conservation and use. The trend of commercial cultivation may also lead to the neglect of diverse varieties, thus compromising the diversity and cultural inheritance of apple genetic resources. 4 Case Study 4.1 Apple genetic resource conservation program in the United States Many countries have set up conservation programs for Apple genetic resources, taking the United States as an example, the National Apple Collection is a typical apple genetic resource conservation program. This program, administered by the United States Department of Agriculture (USDA), aims to collect, preserve, and study apple germplasm from across the United States (Volk et al., 2023). The National Apple Collection is a research site located in Oregon, USA, that centrally preserves thousands of apple varieties and wild species from all over the country. These germplasm resources include traditional varieties, wild varieties and modern cultivated varieties, covering a rich genetic diversity. One of the goals of the program is to protect and preserve the diversity of apple genetic resources to ensure their long-term conservation. By collecting, labeling, describing and preserving these germplasm resources, the National Apple Collection provides a valuable resource for future breeding efforts. The program also focuses on research and evaluation of disease resistance, adaptability and quality characteristics of different varieties. These studies provide an important scientific basis for apple breeding and cultivation, and provide useful information and resources for farmers, horticultural enthusiasts and researchers. The National Apple Collection is a successful case that provides a feasible model and strategy for the protection and utilization of apple diversity through centralized management, conservation and research of apple genetic resources, and also provides useful experience and reference for the establishment of similar conservation programs in other parts of the world. 4.2 Background and objectives The National Apple Collection is a major apple genetic resource conservation program administered by the United States Department of Agriculture (USDA), which began in the 1940s against the backdrop of commercial cultivation that led to the gradual marginalization and loss of many traditional or wild apple varieties. Given this situation, it is particularly urgent and important to protect and maintain the diversity of apple genetic resources (Volk et al., 2023). The primary goal of this plan is to ensure the long-term preservation of apple's diversity. Through the collection, preservation and labeling of various apple varieties, the project centrally preserves the rich genetic diversity and provides an important resource for future apple breeding efforts. The project also focuses on the research and evaluation of the characteristics of apple varieties, including disease resistance, adaptability and quality
Tree Genetics and Molecular Breeding 2024, Vol.14, No.1, 1-7 http://genbreedpublisher.com/index.php/tgmb 5 characteristics. These studies provide important information and reference for apple scientific research and industrial development, and help to choose more adaptable and better quality apple varieties to enhance the competitiveness and sustainable development of the industry. The goals and motivations behind the National Apple Collection highlight the importance attached to the conservation of apple genetic resources. Through the centralized management, conservation and research of apple germplasm resources, the project provides a useful framework and strategy for the conservation and utilization of apple diversity, providing a solid foundation for scientific research and industrial development. 4.3 Effectiveness evaluation and challenge The National Apple Collection Program has achieved some results in the conservation of apple genetic resources, but it also faces some evaluation and challenges. In terms of effectiveness evaluation, the program has successfully collected and preserved a large number of apple germplasm resources from all over the United States, ensuring the long-term preservation and utilization of these resources. This includes traditional, wild and modern cultivars, providing a rich resource base for conservation of genetic diversity and future breeding (Volk et al., 2023). At the same time, the research and evaluation of apple variety characteristics also provide important information and support for scientific research and industrial development. However, the national apple collection program also faces some challenges. One of these is the challenge of resource management and maintenance. Long-term conservation and management of large amounts of apple genetic resources requires ongoing financial, human and technical support, and maintaining the quality and integrity of these resources requires constant updating and maintenance, which poses challenges for sustainable operation of the repository. Another challenge is the question of adaptability and applicability. Although a large number of apple variety resources have been collected, how to effectively use these resources in breeding and actual industries to meet market needs and challenges is still a problem that needs to be solved. In-depth study of the characteristics of different varieties and effective docking with the industry are the key to promote the application of these resources. 5 Improvement Measures of Protection Policy 5.1 Diversity maintenance and introduction of new germplasm Conservation of diversity and introduction of new germplasm are important for the conservation and development of apple genetic resources. Diversity conservation involves the protection and preservation of existing apple varieties, as well as the continuous maintenance of genetic diversity. This means protecting traditional and wild varieties from the pressures of commercial cultivation and ensuring that the diversity of apple germplasm is not lost. At the same time, it also includes maintaining and enhancing the diversity of existing varieties through innovative and scientific methods to enhance their disease resistance and adaptability, ensuring their growth and yield in different environments (Papp et al., 2020). The introduction of new germplasm is to enrich the apple genetic resources. This may involve the exploration and collection of wild apples in search of new varieties with unique disease resistance, good taste or adaptability. The introduction of new germplasm also includes scientific breeding and genetic improvement research work, through mating or genetic improvement, new genotypes are introduced into existing varieties to improve their characteristics and quality. 5.2 A genomics-based approach to conservation The genomics-based conservation approach brings new possibilities and prospects for the conservation and management of apple genetic resources. This approach utilizes advanced genomics techniques and molecular biology tools to contribute to a more comprehensive and in-depth understanding of the genetic relationships and diversity among apple varieties (Buiteveld et al., 2021).
Tree Genetics and Molecular Breeding 2024, Vol.14, No.1, 1-7 http://genbreedpublisher.com/index.php/tgmb 6 Genomics technologies can provide a high throughput of genetic information to help identify and verify genetic differences and characteristics between different breeds. Through genomic analysis of apple genetic resources, we can accurately identify and describe the genetic relationships, genetic diversity and their differences at the genome level among different varieties. This will contribute to a better understanding of the structure and characteristics of apple genetic resources and help select suitable varieties for breeding and conservation efforts. The genomics-based conservation method can also promote the digitization and informatization of apple genetic resources. By establishing the genomic database of apple germplasm resources, researchers can integrate and manage a large amount of genetic information to facilitate the long-term preservation and utilization of resources. This digital approach to management also facilitates the sharing and exchange of resources and promotes cooperation and collaboration on a global scale. 5.3 Continuous monitoring and management Continuous monitoring and management makes an important contribution to the conservation of apple genetic resources. This approach involves long-term tracking and management of apple varieties and their diversity, with the aim of ensuring timely conservation and utilization of these resources. Continuous monitoring involves regular surveys and assessments of apple germplasm resources in different regions to understand their quantity, distribution and status (Gepts, 2006). This monitoring can help identify threatened varieties and take timely measures for protection and conservation, and the ongoing management of apple resources also includes the collection, preservation, classification and digital management of genetic resources to ensure the integrity and sustainability of resources. Continuous monitoring and management methods also help to identify new varieties and potentially good resources. Through regular investigation and research, new apple varieties with disease resistance, adaptability and other excellent characteristics can be discovered, providing new resources and possibilities for the apple industry and breeding work. However, the ongoing monitoring and management approach faces some challenges due to financial, technical and human resource constraints, as well as the issue of sustained investment and attention to long-term monitoring and management. In addition, the monitoring and management of apple resources on a global scale also requires international cooperation and information sharing, which is also a problem that needs to be solved. 6 Summary and Prospect As an important species of fruit trees, the genetic diversity and conservation strategies of apple germplasm resources have attracted much attention. The diversity of apple genetic resources has been well understood by the existing research results. This diversity is not only reflected in morphological characteristics, but also in disease resistance, adaptability, taste characteristics and so on. Full recognition of these diversity provides an important genetic basis for the long-term development of the apple industry. In order to protect and make full use of these valuable genetic resources, researchers have adopted a series of conservation strategies. The establishment of germplasm bank, the formulation of relevant laws and regulations, the research based on genomics and the continuous monitoring and management have provided a solid foundation for the long-term conservation and rational utilization of apple genetic resources. However, there are still some challenges and issues to be addressed in the future. With the increasing impact of environmental change and globalization, apple resources may face more pressure and threats, which requires more targeted protection measures. Digital and information management needs more perfect system and technical support to better manage and use these resources. The conservation and utilization of traditional and wild species, which often have rich genetic diversity and special adaptability, also need more attention and research. In subsequent studies, researchers need to dig deeper into the potential of apple genetic resources, through genomics-based research methods, to better understand the genetic relationships and characteristics between different varieties, and provide a more scientific basis for breeding and protection. At the same time, strengthening
Tree Genetics and Molecular Breeding 2024, Vol.14, No.1, 1-7 http://genbreedpublisher.com/index.php/tgmb 7 international cooperation and information sharing can promote the protection and exchange of apple resources worldwide. In addition, follow-up research can also strengthen the research and protection of traditional varieties and wild varieties, and tap their genetic potential, which is of great significance to the sustainable development of the apple industry. Acknowledgments The author would like to appreciate the two anonymous peer reviewers for their suggestions on the manuscript. Conflict of Interest Disclosure The author affirms that this research was conducted without any commercial or financial relationships that could be construed as a potential conflict of interest. References Ahmad R., Anjum M.A., Naz S., and Balal R.M., 2021, Applications of molecular markers in fruit crops for breeding programs-A Review, Phyton., 90(1): 17-34. https://doi.org/10.32604/phyton.2020.011680 Basannagari B., and Kala C.P., 2013, Climate change and apple farming in Indian Himalayas: a study of local perceptions and responses, PLoS One, 8(10): e77976. Bhargava A., and Bansal A., 2021, Classification and grading of multiple varieties of apple fruit, Food Anal. Methods, 14: 1359-1368. https://doi.org/10.1007/s12161-021-01970-0 Buiteveld J., Putten H.J.K., Kodde L., Laros I., Tumino G., Howard N.P., van de Weg E., and Smulders M.J.M., 2021, Advanced genebank management of genetic resources of European wild apple, Malus sylvestris, using genome-wide SNP array data, Tree Genetics & Genomes, 17: 32. Gao Y., Liu F., Wang K., Wang D., Gong X., Liu L., Richards C.M., Henk A.D., and Volk G.M., 2015, Genetic diversity of Malus cultivars and wild relatives in the Chinese National Repository of Apple Germplasm Resources, Tree Genetics & Genomes, 11: 106. https://doi.org/10.1007/s11295-015-0913-7 Gepts P., 2006, Plant genetic resources conservation and utilization: the accomplishments and future of a societal insurance policy, Crop Science, 46(5): 2278-2292. Marconi G., Ferradini N., Russi L., Concezzi L., Veronesi F., and Albertini E., 2018, Genetic characterization of the apple germplasm collection in central Italy: The value of local varieties, Front Plant Sci., 9: 1460. Papp D., Gao L., Thapa R., Olmstead D., and Khan A., 2020, Field apple scab susceptibility of a diverse Malus germplasm collection identifies potential sources of resistance for apple breeding, CABI Agriculture and Bioscience, 1: 16. https://doi.org/10.1186/s43170-020-00017-4 Shaziya H., Bhat K.M., Aarifa J., Sheikh M., Ahmad W.S., Din K.M.U., and Bisati I.A., 2018, Managing genetic resources in temperate fruit crops, Economic Affairs, 63(4): 987-996. https://doi.org/10.30954/0424-2513.4.2018.23 Volk G.M., Carver D., Irish B.M., Marek L., Frances A., Greene S., Khoury C.K., Bamberg J., del Rio A., Warburton M.L., and Bretting P.K., 2023, Safeguarding plant genetic resources in the United States during global climate change, Crop Science, 63(4): 2274-2296. Wang N., Jiang S., Zhang Z., Fang H., Xu H., Wang Y., and Chen X., 2018, Malus sieversii: the origin, flavonoid synthesis mechanism, and breeding of red-skinned and red-fleshed apples, Hortic. Res., 5: 70. https://doi.org/10.1038/s41438-018-0084-4 Wang N., Zhang J., Yu L., Zou Q., Guo Z.W., Mao Z.L., Wang Y.C., Jiang S.H., Fang H.C., Xu H.F., Su M.Y., Zhang Z.Y., Feng S.Q., Chen X.L., Wang Z.G., Jiang Z.T., Dong M.X., Xu Y.H., Li J.M., Mao Z.Q., and Chen X.S., 2019, Progress on the resource breeding of kernel fruits II : Progress on the germplasm resources, quality development and genetic breeding of apple in China, Zhiwu Yichuan Ziyuan Xuebao (Journal of Plant Genetic Resources), 20(4): 801-812.
Tree Genetics and Molecular Breeding 2024, Vol.14, No.1, 8-11 http://genbreedpublisher.com/index.php/tgmb 8 Scientific Review Open Access Tropical Forest Mysteries: Unveiling the Global Consistency of Common Tree Species Patterns Josselynn X.Z. Feng Hainan Institute of Tropical Agricultural Resources, Sanya, 572024, Hainan, China Corresponding email: josselynn.editor@gmail.com Tree Genetics and Molecular Breeding, 2024, Vol.14, No.1 doi: 10.5376/tgmb.2024.14.0002 Received: 23 Dec., 2023 Accepted: 25 Jan., 2024 Published: 15 Feb., 2024 Copyright © 2024 Feng, 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: Feng J.X.Z., 2024, Tropical forest mysteries: unveiling the global consistency of common tree species patterns, Tree Genetics and Molecular Breeding, 14(1): 8-11 (doi: 10.5376/tgmb.2024.14.0002) The paper titled "Consistent patterns of common species across tropical tree communities" was published in the journal Nature on January 10, 2024, by authors Declan L.M. Cooper, Simon L.Lewis, Martin J.P. Sullivan, and others, are from the Department of Geography, University College London, London, UK; the Centre for Biodiversity and Environment Research, Department of Genetics, Evolution and Environment, University College London, London, UK; and the School of Geography, University of Leeds, Leeds, UK. The research presents a comprehensive study on the abundance patterns of common tree species across old-growth tropical forests in Africa, Amazonia, and Southeast Asia. Using inventory data of over a million trees, the study estimates that a small percentage of species account for half of the tropical trees in these regions. Despite differences in biogeographic history, a consistent pattern of species abundance distribution is observed across continents, suggesting universal mechanisms of tree community assembly. 1 Experimental Data Analysis The study's key results are derived from analyzing inventory data of 1 003 805 trees across 1 568 locations. Rarefaction analysis and resampling techniques are used to standardize sampling and assess species abundance patterns. The analysis shows that, consistently across continents, approximately 2.2%-2.3% of species comprise 50% of tropical trees. These findings are visualized through figures such as location maps of inventory plots and rarefaction curves, indicating a notable consistency in the proportion of common species across diverse tropical forests. Based on Figure 1, the study seems to have analyzed 1 568 plots across different tropical forest regions, with the plots marked by dots and categorized by continental areas. The dark green dots represent plots from the Amazonia, Africa, and Southeast Asia regions—these are areas to which the study's findings are extrapolated. The light green areas depict 'tropical and subtropical moist broadleaf forests', which is the biome the study considers as closed canopy tropical forests. This distribution of plots suggests a comprehensive geographic coverage within the specified tropical forest biome, potentially providing a diverse set of data points for the study. Figure 2 illustrates the relationship between sample size and biodiversity metrics in tropical tree communities by using rarefaction curves. It compares the number of hyperdominants, total species, hyperdominant percentage, and Fisher's α values across tropical Africa (magenta), Amazonia (cyan), and Southeast Asia (blue). As the sample size increases, indicated by the number of stems, there is a general rise in the number of hyperdominants and total species, which tends to plateau, suggesting a threshold of biodiversity in these regions. The hyperdominant percentage decreases with more samples, possibly indicating that hyperdominance is more apparent in smaller samples. The Fisher's α, a measure of diversity, shows a variable increase. The shaded areas denote 95% confidence intervals, giving a visual representation of the reliability of the data across resampling iterations. The curves emphasize the importance of sample size in estimating biodiversity and the dominance of certain species within these ecosystems.
Tree Genetics and Molecular Breeding 2024, Vol.14, No.1, 8-11 http://genbreedpublisher.com/index.php/tgmb 9 Figure 1 Location of the 1 568 plots, tropical forest regions, and tropical forest biome extent used in the study Figure 2 Rarefaction curves showing the effect of increasing sample size on the number of hyperdominants, total species, hyperdominant percentage and fitted values of Fisher's α in tropical tree communities Table 1 presents a comparative analysis of tree species hyperdominance in tropical forests across Africa, Amazonia, and Southeast Asia, standardized to a common sample size of 77 587 trees. Africa has the lowest number of hyperdominants (77) and total species (1 132), whereas Amazonia exhibits the highest in both categories, with 174 hyperdominants and 2 656 total species. Southeast Asia is comparable to Amazonia in species richness but slightly less in hyperdominance. Hyperdominant percentages are fairly similar across regions, ranging from 6.79% in Africa to around 6.60% in Amazonia and 6.65% in Southeast Asia. Fisher's α, a diversity index, is notably higher in Amazonia (525) and Southeast Asia (526) compared to Africa (191), suggesting greater species diversity in the Amazonian and Southeast Asian forests relative to African forests at this sample size. Figure 3 depicts the dominance-diversity relationship in tropical forests of Amazonia, Africa, and Southeast Asia by showing the dominant proportion of total species required to account for various dominance thresholds (10% to 90%) of the total number of stems. The circles indicate data rarefied to the Southeast Asia dataset size, while diamonds represent extrapolated regional scale data. It shows that for a lower dominance threshold, a small percentage of total species is sufficient to account for the given percentage of stems. As the dominance threshold increases, the proportion of species required to meet the threshold also increases, with the highest variability observed at extreme dominance thresholds, particularly in the Amazon. The plot highlights notable differences in species dominance between rarefied and extrapolated data, suggesting that dominance patterns may differ significantly when projected across larger scales. This also underscores the variation in species dominance among different tropical regions, with Southeast Asia showing a narrower confidence interval, indicating more consistent results across samples.
Tree Genetics and Molecular Breeding 2024, Vol.14, No.1, 8-11 http://genbreedpublisher.com/index.php/tgmb 10 Table 1 Tree species hyperdominance results for African, Amazonian and Southeast Asian tropical forests, resampled to the common sample size of 77 587 trees Figure 3 The minimum percentage of total species required to account for given dominance thresholds of the total number of stems when this varies from 10% to 90% Table 2 presents extrapolated data on hyperdominance in tree species across tropical forests of Africa, Amazonia, and Southeast Asia at a regional scale. Africa is reported to have 104 hyperdominant species, with a total species count of 4 638, and the hyperdominant percentage is the lowest at 2.23%. Amazonia has the highest number of hyperdominants at 299 and the greatest species richness with 13 826 species, yet its hyperdominant percentage is slightly lower than Africa's at 2.16%. Southeast Asia has 278 hyperdominants with a total of 11 963 species, and the highest hyperdominant percentage among the three regions at 2.32%. The combined total shows 681 hyperdominants out of 30 427 species across the regions, resulting in a hyperdominant percentage of 2.24%. Prediction intervals in brackets provide an estimate of uncertainty, accounting for the variability in the data and the potential error in extrapolation methods used. This table suggests that while Amazonia is the most species-rich, Southeast Asia has a slightly higher proportion of hyperdominants relative to its species count. Table 2 Extrapolated tree species hyperdominance results for African, Amazonian, Southeast Asian tropical forests at the regional scale 2 Analysis of Research Findings The study uncovers a surprisingly consistent pattern of common tree species across the world's most biodiverse ecosystems. This consistency holds true despite varying climatic, biogeographic, and anthropogenic factors across
Tree Genetics and Molecular Breeding 2024, Vol.14, No.1, 8-11 http://genbreedpublisher.com/index.php/tgmb 11 the studied regions. The identified common species offer a manageable subset for targeted ecological research, suggesting that understanding these species' roles could significantly advance our knowledge of tropical forest ecology, productivity, and responses to environmental changes. 3 Evaluation of the Research The research provides a groundbreaking perspective on tropical forest biodiversity by highlighting the significance of common species in understanding complex ecological dynamics. The methodology, encompassing comprehensive data analysis and innovative approaches to data standardization, sets a high standard for ecological studies. However, the reliance on existing inventory data and the variability in plot sizes and species identification precision may introduce limitations to the study's generalizability. 4 Conclusions This study challenges the traditional focus on the vast species richness of tropical forests by demonstrating the disproportionate importance of a relatively small number of common species. The findings advocate for a shift in conservation and research priorities towards these common species to enhance our understanding of tropical forests' ecological and functional dynamics. 5 Access the Full Text Cooper D.L.M., Lewis S.L., Sullivan M.J.P. et al. Consistent patterns of common species across tropical tree communities. Nature 625, 728-734 (2024). https://doi.org/10.1038/s41586-023-06820-z. Acknowledgments The author expresses sincere gratitude to Nature magazine for its open access policy, which allows free access, reading, commentary, and sharing of the outstanding paper "Healey, A.L., Garsmeur, O., Lovell, J.T. et al. The complex polyploid genome architecture of sugarcane." This initiative not only broadens the channels for disseminating scientific knowledge but also provides a valuable academic resource for researchers, students, and science enthusiasts worldwide. Nature magazine, through its philosophy of openness and sharing, has significantly advanced the development of science and deepened the public's understanding and interest in scientific research, for which the author expresses sincere appreciation and gratitude. Conflict of Interest Disclosure The author affirms that this research was conducted without any commercial or financial relationships that could be construed as a potential conflict of interest.
Tree Genetics and Molecular Breeding 2024, Vol.14, No.1, 12-21 http://genbreedpublisher.com/index.php/tgmb 12 Review and Progress Open Access Accelerating the Process of Tree Breeding: A Review and Progress of GWAS Applications in Forest Trees LiuChuchu1 , LiuYuan2 1 Institute of Life Science, Jiyang College of Zhejiang A&F University, Zhuji, 311800, Zhejiang, China 2 Modern Agricultural Research Center, Cuixi Academy of Biotechnology, Zhuji, 311800, Zhejiang, China Corresponding email: natashaccliu2023@gmail.com Tree Genetics and Molecular Breeding, 2024, Vol.14, No.1 doi: 10.5376/tgmb.2024.14.0003 Received: 03 Jan., 2024 Accepted: 05 Feb., 2024 Published: 17 Feb., 2024 Copyright © 2024 Liu and Liu, 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: Liu C.C., and Liu Y., 2024, Accelerating the process of tree breeding: a review and progress of GWAS applications in forest trees, Tree Genetics and Molecular Breeding, 14(1): 12-21 (doi: 10.5376/tgmb.2024.14.0003) Abstract This study reviews and prospects the application of Genome-wide Association Studies (GWAS) in forest tree breeding. With the rapid development of molecular biology and genomics, GWAS has become an essential tool for deciphering the relationship between genetic variation and trait expression in trees. This research introduces the basic principles and methods of GWAS technology and discusses its successful application in the field of plant breeding, showcasing the potential of GWAS in identifying genetic markers related to important agronomic traits such as crop yield, quality, and disease resistance. The study focuses on the special considerations and challenges of GWAS in tree breeding, including the long lifespan of trees, their large genomes, and genetic diversity, and elucidates the application of GWAS in identifying genetic markers related to important traits in trees, using actual case studies. The application of GWAS in tree breeding not only improves the efficiency and accuracy of breeding but also provides new strategies and methods for protecting genetic resources and adapting to environmental changes. Keywords Genome-wide Association Studies (GWAS); Forest trees; Breeding process; Genetic markers; Technical challenges 1 Introduction Tree breeding, a science deeply rooted in human history, has become the core of modern forestry research. Since ancient times, trees have provided indispensable resources for humans, such as timber and pulp, and played a crucial role in maintaining global ecological balance and biodiversity (Ahmar et al., 2021). In terms of coping with climate change, protecting soil and water sources, and maintaining a balanced biosphere, the role of trees is not to be underestimated. However, with the rapid changes in the global environment and the increasing human demand for forest products, tree breeding is facing unprecedented challenges. Traditional tree breeding methods, such as selective breeding, controlled hybridization, and grafting, rely on long-term selection and hybridization experiments, but are limited by the long lifespan of trees and their genetic diversity (Whetten et al., 2023). These methods are inefficient in improving tree quality, adaptability, and stress resistance, making it difficult to rapidly adapt to environmental changes and market demands. To overcome these limitations, modern genetic technologies, especially Genome-wide Association Studies (GWAS), have provided new perspectives for tree breeding. GWAS utilizes high-throughput sequencing techniques to analyze genomic variations and explore their associations with specific traits in trees, revealing the genetic factors influencing these traits. This method has achieved significant results in elucidating the genetic basis of crops and human diseases. For example, in crops, GWAS has been successfully applied to genetic improvement of wheat, rice, and corn. In wheat, through GWAS analysis, researchers have successfully identified multiple genetic markers associated with important traits such as yield, quality, and stress resistance (Saini et al., 2022). In human diseases, the application of GWAS has also made significant progress, identifying many important gene variations associated with diseases such as diabetes, cardiovascular diseases, and cancer (Mills and Rahal, 2020). The application of GWAS in tree breeding is also becoming increasingly widespread, particularly in the genetic improvement of trees, showing great potential. Breeders can use GWAS to identify genetic markers associated with important traits such as growth rate, wood quality, and disease resistance, thereby accelerating the breeding process and cultivating tree species with stronger adaptability, faster growth, and better disease resistance (Sawitri et al., 2020).
Tree Genetics and Molecular Breeding 2024, Vol.14, No.1, 12-21 http://genbreedpublisher.com/index.php/tgmb 13 This study will delve into the application of GWAS in tree breeding, reviewing its developmental history in tree genetics research, analyzing current achievements and challenges, and prospecting future directions. As global environmental changes and the demand for sustainable forestry increase, integrating traditional breeding techniques with modern molecular biology methods to develop tree species that are more adaptable to environmental changes and more economically valuable is becoming increasingly important. Through this comprehensive overview, not only can scientific researchers gain a comprehensive perspective on tree breeding and GWAS applications, but forestry managers and policymakers can also obtain practical references to promote the development of sustainable forestry and the rational utilization of forest resources. Furthermore, this study emphasizes the potential of GWAS in addressing the protection and sustainable utilization of tree genetic diversity. As the impact of global climate change on forest ecosystems intensifies, developing tree species with stronger resistance to adverse environments has become crucial. The application of GWAS technology provides new avenues for identifying and cultivating these tree species. This not only helps to improve the productivity and economic value of trees but also plays a crucial role in maintaining biodiversity and a healthy ecosystem. The role and potential of GWAS in tree breeding cannot be underestimated. It not only complements traditional breeding methods but also holds significant importance for improving the efficiency and adaptability of tree breeding, protecting genetic diversity, and promoting sustainable forestry development in the new era. With the advancement of science and technology, future tree breeding will continue to progress toward higher efficiency and sustainability based on the integration of traditional experience and modern biotechnology. 2 History and Current Status of Tree Breeding As a science, tree breeding has a long and rich history. From initial selective breeding to modern gene editing, tree breeding has undergone a transformation from experience to science. Over centuries, the core goal of tree breeding has always been to improve the productivity, adaptability, and disease resistance of trees. Nevertheless, with rapid global environmental changes and the increasing human demand, tree breeding is facing unprecedented challenges and opportunities. 2.1 Review of traditional tree breeding methods The history of tree breeding can be traced back several centuries, when the methods were mainly based on natural selection and human selection. In natural selection, the tree species best adapted to the environment naturally propagated. Human selection, on the other hand, involved the selection of specific traits in trees for breeding, such as selecting trees with fast growth and good wood quality. Although simple, these methods were often limited by the long lifespan of trees and their complex genetic backgrounds. In the early 20th century, with the development of Mendelian genetics principles, tree breeding began to incorporate scientific hybridization experiments, including controlled hybridization to combine the desirable traits of different tree species, such as combining the fast growth of one species with the disease resistance of another (He et al., 2023). Other methods included population selection, grafting, and propagation techniques for tree improvement and breeding. 2.2 Application of modern biotechnology in tree breeding Entering the 21st century, advances in genomics and bioinformatics have provided new perspectives for tree breeding. With the rapid development of molecular biology and genetic engineering technologies, modern biotechnology has become an important tool for tree breeding. Techniques such as marker-assisted selection (MAS), genome editing (e.g., CRISPR-Cas9), and tissue culture have enabled breeders to manipulate and improve the genetic traits of trees more precisely and efficiently. For example, through MAS, breeders can identify and select individuals carrying beneficial genetic traits at the seedling stage, greatly shortening the breeding cycle (Hasan et al., 2021). Genome editing techniques provide the possibility of precisely modifying target genes at the molecular level, offering new avenues for creating tree species with specific traits.
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