Tree Genetics and Molecular Breeding 2025, Vol.15 http://genbreedpublisher.com/index.php/tgmb © 2025 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 2025, Vol.15 http://genbreedpublisher.com/index.php/tgmb © 2025 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 Edited by 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), 2025, Vol. 15 ISSN 1927-5781 http://genbreedpublisher.com/index.php/tgmb © 2025 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 Basis of Tree Size and Fruit Yield in Durian Roles of Auxin and Cytokinin Signaling Pathways Zhonggang Li, Mengting Luo Tree Genetics and Molecular Breeding, 2025, Vol. 15, No. 1, 1-8 Genetic Diversity Analysis and Superior Gene Mining of Sapindus mukorossi Germplasm Resources Jie Zhang Tree Genetics and Molecular Breeding, 2025, Vol. 15, No. 1, 9-17 Harnessing Genetic Diversity for Kiwifruit Breeding: Opportunities and Challenges Dandan Huang Tree Genetics and Molecular Breeding, 2025, Vol. 15, No. 1, 18-24 Revitalizing Bamboo Shoot Industry in Ninghai Mountainous Areas: Challenges and Strategic Practices Leijie Hu Tree Genetics and Molecular Breeding, 2025, Vol. 15, No. 1, 25-32 High-Density Tea Planting: A Case Study in Commercial Tea Gardens Jiayao Zhou Tree Genetics and Molecular Breeding, 2025, Vol. 15, No. 1, 33-43
Tree Genetics and Molecular Breeding 2025, Vol.15, No.1, 1-8 http://genbreedpublisher.com/index.php/tgmb 1 Research Insight Open Access Genetic Basis of Tree Size and Fruit Yield in Durian Roles of Auxin and Cytokinin Signaling Pathways Zhonggang Li 1, Mengting Luo 1,2 1 Tropical Medicinal Plant Research Center, Hainan Institute of Tropical Agricultural Resources, Sanya, 572025, Hainan, China 2 Modern Agricultural Research Center, Cuixi Academy of Biotechnology, Zhuji, 311800, Zhejiang, China Corresponding email: menting.luo@cuixi.org Tree Genetics and Molecular Breeding, 2025, Vol.15, No.1 doi: 10.5376/tgmb.2025.15.0001 Received: 18 Dec., 2024 Accepted: 20 Jan., 2025 Published: 28 Jan., 2025 Copyright © 2025 Li and Luo, 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 Z.G., and Luo M.T., 2025, Genetic basis of tree size and fruit yield in durian roles of auxin and cytokinin signaling pathways, Tree Genetics and Molecular Breeding, 15(1): 1-8 (doi: 10.5376/tgmb.2025.15.0001) Abstract Durian (Durio zibethinus), widely known as the “King of Fruits”, holds significant economic and cultural value across Southeast Asia. The size of its trees and fruit yield are critical agronomic traits, directly affecting cultivation efficiency and commercial viability. Despite their importance, the genetic underpinnings of these traits remain insufficiently understood. This study explores the influence of auxin and cytokinin signaling pathways in shaping durian tree architecture and determining fruit productivity. Auxin primarily regulates apical dominance and cell elongation, influencing overall tree morphology, while cytokinin drives branch differentiation and canopy expansion. During fruit development, auxin plays a crucial role in fruit set and expansion, whereas cytokinin modulates fruit number and size by controlling cell division rates. The balance between these two plant hormones is essential for optimizing durian growth and yield. Advancements in molecular breeding technologies, such as genetic modification and marker-assisted selection, present new opportunities for durian productivity enhancement. Understanding the intricate interactions between auxin and cytokinin at the genetic level will not only deepen our comprehension of durian growth and fruiting but also provide valuable insights for precision breeding and improved orchard management. Keywords Durian (Durio zibethinus); Auxin signaling pathway; Cytokinin regulation; Tree architecture; Fruit yield optimization 1 Introduction Durian (Durio zibethinus), known as the “King of Fruits”, is a highly valuable tropical fruit crop cultivated primarily in Southeast Asia. Its economic significance is driven by increasing global demand, yet its cultivation is challenged by long juvenile phases, variable fruit yields, and large tree size, which complicates orchard management. Understanding the genetic basis of tree size and fruit yield in durian is crucial for improving productivity and optimizing breeding strategies. Among the key regulators of plant growth and fruit production, plant hormones- particularly auxin and cytokinin- play fundamental roles in shaping tree architecture and determining fruit yield potential. Recent advances in molecular biology and genomics provide new opportunities to explore the genetic mechanisms underlying auxin and cytokinin signaling in durian, offering insights for targeted breeding and cultivation improvements (Khaksar and Sirikantaramas, 2020). Tree size and fruit yield are critical agronomic traits that significantly impact durian cultivation and commercial viability. Durian trees are naturally large, with some varieties reaching heights of over 40 meters, making harvesting and maintenance labor-intensive (Immanen et al., 2016). Reducing tree size through genetic or agronomic interventions can enhance orchard efficiency, enabling higher planting densities and improved resource utilization. Additionally, fruit yield varies widely among cultivars and environmental conditions, affecting profitability. Optimizing yield-related traits through genetic improvement can help stabilize fruit production and meet market demands. Therefore, understanding the genetic factors that regulate tree growth and fruit set is essential for enhancing durian cultivation efficiency (Iqbal et al., 2021). Plant hormones are key regulators of growth and development, orchestrating various physiological processes that shape tree morphology and fruit characteristics. Among them, auxin and cytokinin are central to the regulation of vegetative growth and reproductive development. Auxin influences apical dominance, root formation, and fruit initiation, while cytokinin controls cell division, shoot branching, and sink-source dynamics (Khaksar et al., 2019).
Tree Genetics and Molecular Breeding 2025, Vol.15, No.1, 1-8 http://genbreedpublisher.com/index.php/tgmb 2 The interplay between these hormones determines the overall architecture of the durian tree, affecting branching patterns, canopy density, and ultimately fruit-bearing capacity. In fruit development, auxin promotes ovary expansion and fruit set, while cytokinin plays a role in nutrient allocation and fruit size determination. A deeper understanding of auxin and cytokinin interactions will provide new insights into improving tree growth regulation and optimizing fruit yield in durian (Suntichaikamolkul et al., 2021). Despite the recognized importance of auxin and cytokinin in plant growth, their specific regulatory mechanisms in durian remain largely unexplored. This research aims to investigate the genetic basis of tree size and fruit yield by focusing on auxin and cytokinin signaling pathways. By identifying key genes involved in hormonal regulation, we can develop strategies to modulate tree architecture and improve yield efficiency. Recent advances in durian genomics, transcriptomics, and functional studies provide an opportunity to dissect the molecular interactions between auxin and cytokinin, leading to potential applications in precision breeding. This research will contribute to a better understanding of durian’s growth dynamics and offer new approaches to optimizing its cultivation through genetic and hormonal interventions. 2 Genetic Regulation of Tree Size in Durian 2.1 Key genes involved in tree height and canopy development The genetic factors controlling durian tree size are linked to several key genes that influence height and canopy growth. While specific genes directly affecting tree height in durian remain under investigation, transcription factors such as Dof proteins, known for their role in various plant growth processes, present promising candidates. These proteins regulate auxin biosynthesis, which is essential for plant development and plays a key role in determining tree size (He et al., 2018). 2.2 Influence of auxin signaling pathway on tree morphology Auxin is a crucial plant hormone that significantly affects tree morphology, including height and canopy structure. In durian, auxin signaling is mediated by auxin response factors (ARFs), such as DzARF2A, which have been identified for their role in fruit ripening via ethylene biosynthesis regulation (Liu et al., 2018a). Although auxin’s direct effects on durian tree morphology remain unclear, its well-documented influence on plant growth suggests it plays an important role in shaping tree structure (Liu et al., 2018b). 2.3 Role of cytokinin in shoot differentiation and growth Cytokinin is another essential phytohormone that regulates shoot differentiation and overall tree growth. While specific data on cytokinin’s role in durian tree development is limited, its well-established function in promoting cell division and shoot formation in other plants highlights its significance in determining tree architecture (He and Yamamuro, 2022). The dynamic interaction between cytokinin and auxin is critical for balancing root and shoot growth, ultimately influencing tree size and productivity. 2.4 Interaction between auxin and cytokinin in tree development The interplay between auxin and cytokinin is a fundamental aspect of plant development, affecting multiple growth processes. In durian, auxin-ethylene crosstalk, regulated by DzARF2A, demonstrates the complex hormonal interactions that drive growth and structural changes. Although specific auxin-cytokinin interactions in durian tree development remain underexplored, their well-established synergistic and antagonistic relationships in other plant species suggest that similar regulatory mechanisms may influence durian tree morphology (Reyes-Olalde et al., 2017). Understanding these interactions will provide valuable insights for optimizing durian tree architecture and improving orchard management strategies. 3 Genetic Control of Fruit Yield in Durian 3.1 Genetic regulatory mechanisms affecting flowering and fruiting The regulation of flowering and fruiting in durian is influenced by complex interactions between plant hormones and transcription factors. Auxin response factors (ARFs) play a critical role in fruit development and ripening by acting as key regulators in hormone-dependent pathways, impacting fruit size, yield, and quality. Additionally, MADS-box transcription factors are involved in modulating cytokinin levels, which are essential for fruit growth
Tree Genetics and Molecular Breeding 2025, Vol.15, No.1, 1-8 http://genbreedpublisher.com/index.php/tgmb 3 and development. These genetic regulators collectively influence flowering timing and fruit production, ultimately shaping yield outcomes (Zhao et al., 2023). The weight of a durian fruit is determined by multiple components, including pulp, peel, and seed (Figure 1) (Khaksar et al., 2024). Figure 1 Images of durian (Durio zibethinus L.) fruit: peduncle, peel (husk), aril (pulp), locules, and seed (Adopted from Khaksar et al., 2024) 3.2 Role of auxin in fruit set and expansion Auxin is a primary hormone governing fruit set and expansion. It promotes both cell division and enlargement, which are vital processes in early fruit development. In durian, auxin levels rise during post-harvest ripening, indicating its role in enhancing fruit size and quality through ethylene biosynthesis regulation. Auxin also interacts with gibberellic acid (GA) to further support fruit enlargement by coordinating cell growth and expansion. Its impact on fruit size has been observed in various plant species, where it influences endoreduplication-related cell expansion, leading to larger fruit (Su et al., 2014). 3.3 Influence of cytokinin on fruit number and size Cytokinin also plays a key role in determining fruit number and size. It regulates cell division and expansion, both of which contribute to overall fruit growth (Li et al., 2024). However, cytokinin levels must be carefully balanced, as excessive amounts can negatively impact cell expansion and hinder fruit development. In durian, cytokinin signaling likely interacts with other hormonal pathways to influence fruit yield, similar to other species where cytokinin oxidase/dehydrogenase (CKX) genes regulate fruit size (Di Marzo et al., 2020). 3.4 Potential genetic markers for high-yield durian varieties Identifying genetic markers associated with high-yield durian varieties can enhance breeding programs. Auxin response factors, such as DzARF2A, have been identified as potential markers due to their role in regulating ethylene biosynthesis and fruit ripening. Additionally, genes involved in cytokinin degradation, such as CKX, may serve as useful markers for selecting varieties with optimal fruit size and yield. Incorporating these genetic markers into breeding strategies could lead to the development of durian varieties with improved fruit yield and quality (Zhao et al., 2021). 4 Synergistic Role of Auxin and Cytokinin in Durian Growth and Yield 4.1 Hormonal balance in tree growth regulation Maintaining a balance between auxin and cytokinin is essential for durian tree growth. Auxin promotes cell elongation and division, while cytokinin regulates cell differentiation and organ formation. Their interaction helps coordinate tree growth, with auxin driving shoot and root elongation and cytokinin stimulating new shoot formation (Sharif et al., 2022). A well-maintained hormonal balance supports tree structure and health, ultimately influencing fruit production (Teh et al., 2017).
Tree Genetics and Molecular Breeding 2025, Vol.15, No.1, 1-8 http://genbreedpublisher.com/index.php/tgmb 4 4.2 Synergistic and antagonistic effects during fruit development Auxin and cytokinin interact in both cooperative and opposing ways during fruit development. Auxin plays a central role in the early stages, driving cell division and expansion, which are critical for fruit set and growth (Huang and Hong, 2024). Cytokinin becomes more influential in later stages, affecting nutrient distribution and fruit maturation. The relationship between these hormones is complex- auxin enhances ethylene biosynthesis, which accelerates ripening, as seen in the fast-ripening durian cultivar Chanee (Figure 2) (Hurny et al., 2020; Suntichaikamolkul et al., 2021). While auxin speeds up ripening, cytokinin is more involved in maintaining fruit quality and size. Figure 2 Fruit morphology during fruit development (Adopted from Suntichaikamolkul et al., 2021) Image caption: (A) whole fruit. (B) peeled fruit. (C) Arils across five developmental and ripening stages. Stage abbreviations: IM1, immature 1; IM2, immature 2; M, mature; MR, mid-ripe; R, ripe (Adopted from Suntichaikamolkul et al., 2021) 4.3 Environmental and genotypic effects on hormonal regulation Both environmental factors and genetic variations play a role in the hormonal regulation of durian growth and yield. Different durian cultivars display variations in auxin and cytokinin levels, influencing their growth and fruiting patterns (Fenn and Giovannoni, 2020). For instance, the Chanee cultivar has higher auxin levels during ripening compared to Monthong, contributing to its faster ripening process. Environmental elements such as temperature, sunlight, and soil conditions also impact hormone activity, ultimately affecting tree growth and fruit yield. Understanding these genetic and environmental influences is crucial for refining durian cultivation practices and boosting production efficiency (Cao et al., 2020). 5 Applications in Durian Breeding and Agricultural Production 5.1 Genetic improvement strategies for optimizing tree structure and yield Understanding the roles of auxin and cytokinin in durian growth offers opportunities to enhance breeding strategies. Identifying key auxin response factors (ARFs), such as DzARF2A, which regulate ethylene biosynthesis, allows for targeted genetic modifications to improve fruit ripening and overall yield (Khaksar et al.,
Tree Genetics and Molecular Breeding 2025, Vol.15, No.1, 1-8 http://genbreedpublisher.com/index.php/tgmb 5 2024). Selecting cultivars with elevated DzARF2A expression could lead to varieties that ripen more quickly and produce higher yields, as observed in the fast-ripening Chanee compared to the slower-ripening Monthong. Additionally, the differential expression of Dof transcription factors (DzDofs) during fruit development suggests potential targets for enhancing auxin biosynthesis and fruit yield (Nawae et al., 2023). 5.2 Application of hormonal regulation techniques in yield enhancement Modulating key phytohormones, including auxin and ethylene, provides another approach to increasing durian yields. The upregulation of DzARF2A and its role in activating ethylene biosynthesis genes highlight the potential of applying exogenous auxin to accelerate fruit ripening and enhance production (Husin et al., 2018). This technique could be particularly effective in fast-ripening cultivars like Chanee, where higher auxin levels correlate with increased DzARF2A expression. Similarly, enhancing DzDof2.2 expression, which is associated with auxin biosynthesis, may further boost auxin levels and initiate the ethylene response earlier, potentially improving fruit yield and consistency (Santoso et al., 2017). 5.3 Future prospects for molecular breeding in durian The integration of genomic and transcriptomic data is paving the way for advanced molecular breeding in durian. The identification of regulatory genes such as DzARF2A and DzDof2.2, both of which play essential roles in auxin and ethylene signaling, provides opportunities for developing improved durian cultivars with enhanced fruit quality and yield (Huang, 2024). With advancements in gene-editing tools like CRISPR/Cas9, targeted modifications to these genes could lead to varieties with optimized ripening characteristics and greater resistance to environmental stress. As research continues to uncover the genetic foundations of tree size and fruit yield, breeders will be better equipped to cultivate high-yielding, resilient durian varieties suited to both producer needs and consumer preferences (Huy et al., 2023). 6 Future Research Directions 6.1 Further elucidation of auxin and cytokinin regulatory networks in durian Auxin and cytokinin play essential roles in durian tree development and fruit ripening, but their precise regulatory mechanisms remain insufficiently understood. Research has linked auxin response factors (ARFs), particularly DzARF2A, to ethylene biosynthesis, which accelerates ripening in some cultivars. Future studies should focus on mapping the complete auxin and cytokinin signaling pathways and their interactions, which could reveal new targets for genetic improvement aimed at optimizing fruit yield and quality (Lin, 2020). 6.2 Advances in durian genomics and precision breeding technologies The identification of key transcription factors, such as DzDofs, associated with auxin biosynthesis and cultivar-specific ripening characteristics, underscores the potential of genomic research in durian breeding. With developments in genomic tools like CRISPR/Cas9, researchers have the opportunity to create improved durian varieties with enhanced traits (Cheng et al., 2021). Future efforts should focus on integrating genomic data with phenotypic traits to refine breeding strategies, ultimately leading to cultivars with higher yields and improved fruit quality (Tang et al., 2024). 6.3 Strategies for enhancing durian yield and quality by hormonal balance regulation Achieving a balance between auxin and cytokinin is crucial for maximizing durian fruit yield and quality. Auxin-ethylene crosstalk, as demonstrated by the role of DzARF2A in ethylene biosynthesis regulation, offers a framework for adjusting hormonal pathways to control ripening and enhance fruit development (Desta and Amare, 2021). Future research should explore genetic and agronomic techniques to fine-tune hormonal levels, aiming for an optimal balance that improves yield consistency while preserving fruit quality (Ngoc et al., 2024). 7 Concluding Remarks The genetic factors influencing durian tree size and fruit yield are closely tied to hormonal signaling pathways, particularly those involving auxin and cytokinin. Auxin plays a fundamental role in fruit ripening, as indicated by the identification of auxin response factors (ARFs) that regulate ethylene biosynthesis, a key hormone in the ripening of climacteric fruits. Specifically, DzARF2A has been found to upregulate ethylene biosynthetic genes,
Tree Genetics and Molecular Breeding 2025, Vol.15, No.1, 1-8 http://genbreedpublisher.com/index.php/tgmb 6 leading to a faster ripening process in cultivars such as Chanee compared to the slower-ripening Monthong. Additionally, the involvement of Dof transcription factors, particularly DzDof2.2, in auxin biosynthesis further supports the link between auxin and ethylene in fruit ripening. Despite recent progress in understanding the hormonal regulation of fruit ripening in durian, there are still several knowledge gaps. The exact mechanisms through which auxin and cytokinin interact to regulate tree size and fruit yield remain unclear. Additionally, the variation in hormone responses among different cultivars suggests a more complex genetic basis that requires further exploration. The interplay of other phytohormones with auxin and cytokinin in shaping these traits also warrants more investigation. Furthermore, environmental factors influencing hormonal pathways in durian need to be studied in greater detail to optimize fruit production and quality. Gaining deeper insights into the hormonal regulation of durian growth and fruiting presents significant opportunities for improving cultivation practices and breeding strategies. By targeting genes such as DzARF2A and DzDof2.2, it may be possible to enhance fruit yield and accelerate ripening in commercial durian varieties. This could contribute to the development of new cultivars with traits like faster ripening and larger fruit size, aligning with market demands. Moreover, understanding hormonal interactions could guide breeding programs aimed at enhancing stress resilience and refining growth conditions for durian trees, ultimately supporting more efficient and sustainable production. Acknowledgments We sincerely thank Mr. Rudi Mai and Mr. Qixue Liang for their valuable assistance in data organization and verification, which greatly helped us improve the manuscript. We also extend our heartfelt gratitude to the two anonymous peer reviewers for their comprehensive and insightful evaluation and valuable comments on the manuscript. Funding This study was supported by the Research and Training Fund of the Hainan Institute of Tropical Agricultural Resources (Project No. H2025-02). 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 Cao J., Li G., Qu D., Li X., and Wang Y., 2020, Into the seed: auxin controls seed development and grain yield, International Journal of Molecular Sciences, 21(5): 1662. https://doi.org/10.3390/ijms21051662 Cheng B., Jiang Y., and Cao C., 2021, Balance rice yield and eating quality by changing the traditional nitrogen management for sustainable production in China, Journal of Cleaner Production, 312: 127793. https://doi.org/10.1016/j.jclepro.2021.127793 Desta B., and Amare G., 2021, Paclobutrazol as a plant growth regulator, Chemical and Biological Technologies in Agriculture, 8: 1. https://doi.org/10.1186/s40538-020-00199-z Di Marzo M., Herrera-Ubaldo H., Caporali E., Novák O., Strnad M., BalanzàV., Ezquer I., Mendes M., De Folter S., and Colombo L., 2020, SEEDSTICK controls Arabidopsis fruit size by regulating cytokinin levels and FRUITFULL, Cell Reports, 30(8): 2846-2857. https://doi.org/10.1016/j.celrep.2020.01.101 Fenn M., and Giovannoni J., 2020, Phytohormones in fruit development and maturation, The Plant Journal, 105(2): 446-458. https://doi.org/10.1111/tpj.15112 He H., and Yamamuro C., 2022, Interplays between auxin and GA signaling coordinate early fruit development, Horticulture Research, 9: uhab078. https://doi.org/10.1093/hr/uhab078 He Q., Yang L., Hu W., Zhang J., and Xing Y., 2018, Overexpression of an auxin receptor OsAFB6 significantly enhanced grain yield by increasing cytokinin and decreasing auxin concentrations in rice panicle, Scientific Reports, 8: 14051. https://doi.org/10.1038/s41598-018-32450-x Huang D.D., 2024, CRISPR/Cas9 genome editing in legumes: opportunities for functional genomics and breeding, Legume Genomics and Genetics, 15(4): 199-209. https://doi.org/10.5376/lgg.2024.15.0020 Huang W.Z., and Hong Z.M., 2024, Marker-assisted selection in cassava: from theory to practice, Plant Gene and Trait, 15(1): 33-43. https://doi.org/10.5376/pgt.2024.15.0005
Tree Genetics and Molecular Breeding 2025, Vol.15, No.1, 1-8 http://genbreedpublisher.com/index.php/tgmb 7 Hurny A., Cuesta C., Cavallari N., Ötvös K., Duclercq J., Dokládal L., Montesinos J., GallemíM., SemerádováH., Rauter T., Stenzel I., Persiau G., Benade F., Bhalearo R., SýkorováE., Gorzsás A., Sechet J., Mouille G., Heilmann I., De Jaeger G., Ludwig-Müller J., and BenkováE., 2020, SYNERGISTIC ON AUXIN AND CYTOKININ 1 positively regulates growth and attenuates soil pathogen resistance, Nature Communications, 11: 2170. https://doi.org/10.1038/s41467-020-15895-5 Husin N., Rahman S., Karunakaran R., and Bhore S., 2018, A review on the nutritional, medicinal, molecular and genome attributes of Durian (Durio zibethinus L.), the King of fruits in Malaysia, Bioinformation, 14: 265-270. https://doi.org/10.6026/97320630014265 Huy T., Hoan N., Thi N., and Khang D., 2023, Advancements in genetic diversity and genome characteristics of durians (Durio spp.), Annual Research and Review in Biology, 38(5): 12-23. https://doi.org/10.9734/arrb/2023/v38i530584 Immanen J., Nieminen K., Smolander O., Kojima M., Serra J., Koskinen P., Zhang J., Elo A., Mähönen A., Street N., Bhalerao R., Paulin L., Auvinen P., Sakakibara H., and Helariutta Y., 2016, Cytokinin and auxin display distinct but interconnected distribution and signaling profiles to stimulate cambial activity, Current Biology, 26: 1990-1997. https://doi.org/10.1016/j.cub.2016.05.053 Iqbal Z., Iqbal M., Sangpong L., Khaksar G., Sirikantaramas S., and Buaboocha T., 2021, Comprehensive genome-wide analysis of calmodulin-binding transcription activator (CAMTA) in Durio zibethinus and identification of fruit ripening-associated DzCAMTAs, BMC Genomics, 22: 743. https://doi.org/10.1186/s12864-021-08022-1 Khaksar G., and Sirikantaramas S., 2020, Auxin response factor 2A is part of the regulatory network mediating fruit ripening through auxin-ethylene crosstalk in durian, Frontiers in Plant Science, 11: 543747. https://doi.org/10.3389/fpls.2020.543747 Khaksar G., Kasemcholathan S., and Sirikantaramas S., 2024, Durian (Durio zibethinus L.): nutritional composition, pharmacological implications, value-added products, and omics-based investigations, Horticulturae, 10(4): 342. https://doi.org/10.3390/horticulturae10040342 Khaksar G., Sangchay W., Pinsorn P., Sangpong L., and Sirikantaramas S., 2019, Genome-wide analysis of the Dof gene family in durian reveals fruit ripening-associated and cultivar-dependent Dof transcription factors, Scientific Reports, 9: 12109. https://doi.org/10.1038/s41598-019-48601-7 Li B., Bao R., Shi Y., Grierson D., and Chen K., 2024, Auxin response factors: important keys for understanding regulatory mechanisms of fleshy fruit development and ripening, Horticulture Research, 11(10): uhae209. https://doi.org/10.1093/hr/uhae209 Lin W., 2020, Designed manipulation of the brassinosteroid signal to enhance crop yield, Frontiers in Plant Science, 11: 854. https://doi.org/10.3389/fpls.2020.00854 Liu M., Ma Z., Zheng T., Wang J., Huang L., Sun W., Zhang Y., Jin W., Zhan J., Cai Y., Tang Y., Wu Q., Tang Z., Bu T., Li C., Chen H., and Zhao G., 2018b, The potential role of auxin and abscisic acid balance and FtARF2 in the final size determination of Tartary buckwheat fruit, International Journal of Molecular Sciences, 19(9): 2755. https://doi.org/10.3390/ijms19092755 Liu S., Zhang Y., Feng Q., Qin L., Pan C., Lamin-Samu A., and Lu G., 2018a, Tomato AUXIN RESPONSE FACTOR 5 regulates fruit set and development via the mediation of auxin and gibberellin signaling, Scientific Reports, 8: 2971. https://doi.org/10.1038/s41598-018-21315-y Nawae W., Naktang C., Charoensri S., U-Thoomporn S., Narong N., Chusri O., Tangphatsornruang S., and Pootakham W., 2023, Resequencing of durian genomes reveals large genetic variations among different cultivars, Frontiers in Plant Science, 14: 1137077. https://doi.org/10.3389/fpls.2023.1137077 Ngoc N., Dang L., Ly L., Thao P., and Hung N., 2024, Use of the diagnosis and recommendation integrated system (DRIS) for determining the nutritional balance of durian cultivated in the Vietnamese Mekong delta, Horticulturae, 10(6): 561. https://doi.org/10.3390/horticulturae10060561 Reyes-Olalde J., Zúñiga-Mayo V., Serwatowska J., Montes R., Lozano-Sotomayor P., Herrera-Ubaldo H., González-Aguilera K., Ballester P., Ripoll J., Ezquer I., Paolo D., Heyl A., Colombo L., Yanofsky M., Ferrándiz C., Marsch-Martínez N., and De Folter S., 2017, The bHLH transcription factor SPATULA enables cytokinin signaling, and both activate auxin biosynthesis and transport genes at the medial domain of the gynoecium, PLoS Genetics, 13(4): e1006726. https://doi.org/10.1371/journal.pgen.1006726 Santoso P., Pancoro A., Suhandono S., and Aryantha I., 2017, Development of simple-sequence repeats markers from durian (Durio zibethinus Murr. cultv. Matahari) genomic library, Agrivita: Journal of Agricultural Science, 39: 257-265. https://doi.org/10.17503/agrivita.v39i3.1171 Sharif R., Su L., Chen X., and Qi X., 2022, Hormonal interactions underlying parthenocarpic fruit formation in horticultural crops, Horticulture Research, 9: uhab024. https://doi.org/10.1093/hr/uhab024 Su L., Bassa C., Audran C., Mila I., Chéniclet C., Chevalier C., Bouzayen M., Roustan J., and Chervin C., 2014, The auxin Sl-IAA17 transcriptional repressor controls fruit size via the regulation of endoreduplication-related cell expansion, Plant and Cell Physiology, 55(11): 1969-1976. https://doi.org/10.1093/pcp/pcu124
Tree Genetics and Molecular Breeding 2025, Vol.15, No.1, 1-8 http://genbreedpublisher.com/index.php/tgmb 8 Suntichaikamolkul N., Sangpong L., Schaller H., and Sirikantaramas S., 2021, Genome-wide identification and expression profiling of durian CYPome related to fruit ripening, PLoS One, 16(11): e0260665. https://doi.org/10.1371/journal.pone.0260665 Tang R., Wei S., Tang J., Aridas N., and Talip M., 2024, A method for durian precise fertilization based on improved radial basis neural network algorithm, Frontiers in Plant Science, 15: 1387977. https://doi.org/10.3389/fpls.2024.1387977 Teh B., Lim K., Yong C., Ng C., Rao S., Rajasegaran V., Lim W., Ong C., Chan K., Cheng V., Soh P., Swarup S., Rozen S., Nagarajan N., and Tan P., 2017, The draft genome of tropical fruit durian (Durio zibethinus), Nature Genetics, 49: 1633-1641. https://doi.org/10.1038/ng.3972 Zhao X., Muhammad N., Zhao Z., Yin K., Liu Z., Wang L., Luo Z., Wang L., and Liu M., 2021, Molecular regulation of fruit size in horticultural plants: a review, Scientia Horticulturae, 288: 110353. https://doi.org/10.1016/j.scienta.2021.110353 Zhao X., Zhao Z., Cheng S., Wang L., Luo Z., Ai C., Liu Z., Liu P., Wang L., Wang J., Liu M., Li Y., and Liu M., 2023, ZjWRKY23 and ZjWRKY40 promote fruit size enlargement by targeting and downregulating cytokinin oxidase/dehydrogenase 5 expression in Chinese jujube, Journal of Agricultural and Food Chemistry, 71(46): 18046-18058. https://doi.org/10.1021/acs.jafc.3c04377
Tree Genetics and Molecular Breeding 2025, Vol.15, No.1, 9-17 http://genbreedpublisher.com/index.php/tgmb 9 Research Insight Open Access Genetic Diversity Analysis and Superior Gene Mining of Sapindus mukorossi Germplasm Resources Jie Zhang Institute of Life Sciences, Jiyang Colloge of Zhejiang A&F University, Zhuji, 311800, Zhejiang, China Corresponding email: jie.zhang@jicat.org Tree Genetics and Molecular Breeding, 2025, Vol.15, No.1 doi: 10.5376/tgmb.2025.15.0002 Received: 23 Dec., 2024 Accepted: 25 Jan., 2025 Published: 01 Feb., 2025 Copyright © 2025 Zhang, 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 J., 2025, Genetic diversity analysis and superior gene mining of Sapindus mukorossi germplasm resources, Tree Genetics and Molecular Breeding, 15(1): 9-17 (doi: 10.5376/tgmb.2025.15.0001) Abstract This study conducted a relatively comprehensive analysis of the germplasm resources of Sapindus mukorossi, examined its genetic diversity, explored the structure among different populations and their evolutionary relationships, identified some functional genes related to saponin content and stress resistance, and evaluated the performance of superior germplasm in different ecological environments. This study also confirmed through the association analysis of genotypes and phenotypes which genes might affect saponin content and stress resistance. This study reveals the diversity of Sapindus mukorossi germplasm and the genetic basis behind these good traits, aiming to provide a theoretical basis for future molecular breeding. Keywords Sapindus mukorossi; Genetic diversity; Superior genes; Saponin content; Molecular markers 1 Introduction Sapindus mukorossi (also known as the soap nut tree) is an economic tree species with many uses. The fact that its fruit contains natural saponins makes it very popular in industries such as laundry, medicine and cosmetics (Upadhyay and Singh, 2012; Li et al., 2013; Wei et al., 2020; Sochacki and Vogt, 2022). Zhao et al. (2019) believed that if the germplasm resources of Sapindus mukorossi have rich genetic diversity, it is helpful for its protection and laying a good foundation for subsequent development and utilization. Understanding these genetic differences is useful for breeders to select varieties with high saponin content and strong stress resistance and to expand its application in industry (Chang et al., 2021). Gao et al. (2023) proposed that the fruit saponin content of Sapindus mukorossi is high, and its economic value is highly valued. The improvement of economic traits is inseparable from the rich genetic diversity in germplasm resources. Mahar et al. (2011b) and Xue et al. ’s research in 2022 found that Sapindus mukorossi populations in different regions showed significant differences, with the highest genetic diversity in the southwest region. This is beneficial for the adaptation and survival of the species itself and providing more options for subsequent breeding (Sun et al., 2018a; Liu et al., 2022). Understanding the genetic diversity of Sapindus mukorossi can provide a scientific basis for breeding high-quality varieties and is a key step in improving economic benefits. Sun et al. (2018b) and Liu et al. (2021) demonstrated that by identifying genes related to high saponin content or stress resistance, molecular breeding methods can be utilized to cultivate stronger and more productive Sapindus mukorossi. This genetic information is very useful for the screening of high-quality germplasm and the breeding of good varieties suitable for various environments (Mahar et al., 2011a; Xue et al., 2022). This study will analyze the genetic diversity of Sapindus mukorossi, identify the dominant genes suitable for breeding, understand its genetic structure and variation, and also provide a reference for formulating more scientific protection and utilization strategies. This study will also explore the practical application of molecular markers in germplasm screening, laying the foundation for the future promotion of molecular-assisted breeding techniques in Sapindus mukorossi.
Tree Genetics and Molecular Breeding 2025, Vol.15, No.1, 9-17 http://genbreedpublisher.com/index.php/tgmb 10 2 Distribution and Ecological Characteristics of Sapindus mukorossi Germplasm Resources 2.1 Distribution of Sapindus mukorossi germplasm resources Sapindus mukorossi is mainly distributed in the subtropical and tropical regions of Asia. It is relatively adaptable to warm climates and diverse ecological environments and can grow widely in these areas (Sun et al., 2017; Liu et al., 2021b; Liu et al., 2021c). S. mukorossi is the most widely distributed species in the Sapindus genus, concentrated in the central and eastern regions of China. S. delavayi is mainly distributed in southwestern China, while S. rarak is mainly found in Southeast Asia (Figure 1). Liu et al. (2021d) and Wang et al. (2020) hold that the ability of Sapindus mukorossi to adapt to different environmental changes is also one of the reasons why it can survive in multiple regions. Figure 1 Spatial distribution of occurrence records of S. mukorossi, S. delavayi, and S. rarak (Adopted from Liu et al., 2021d) The main production areas of Sapindus mukorossi in China include provinces such as Fujian, Zhejiang and Guizhou. These places have a warm climate and belong to the climate type between the temperate and tropical zones. The precipitation is generally medium to high, and the soil is relatively fertile. The pH value is mostly between 5.6 and 7.6. This soil condition is very suitable for the growth of Sapindus mukorossi (Liu et al., 2021b; Liu et al., 2021c). Liu et al. (2021c) also found that the soil moisture content in these areas was generally between 40 and 140 millimeters, providing a good water basis for the normal growth and yield of Sapindus mukorossi. 2.2 Phenotypic diversity of Sapindus mukorossi germplasm The germplasm resources of Sapindus mukorossi vary greatly in appearance and traits. Different varieties have obvious differences in tree height, leaf size and fruit weight (Sun et al., 2017; Gao et al., 2018; Wang et al., 2020). The size and saponin content of fruits vary greatly, which is very important for breeding work because better varieties need to be selected for promotion and cultivation during breeding (Liu et al., 2021b; Liu et al., 2022; Song et al., 2023). The research by Liu et al. (2021b) showed that the saponin content in the fruit of Sapindus mukorossi varied between 4.14% and 27.04%, and the oil content in the seeds ranged from 26.15% to 44.69%. Sun et al. (2017) and Liu et al. (2021b) hold that this difference is mainly influenced by both genes and the external environment. It is crucial to accurately assess these traits before breeding Sapindus mukorossi varieties with high yield and good quality.
Tree Genetics and Molecular Breeding 2025, Vol.15, No.1, 9-17 http://genbreedpublisher.com/index.php/tgmb 11 2.3 Impact of ecological factors on genetic diversity Climatic conditions such as temperature and precipitation can affect the growth performance and adaptability of plants, leading to genetic differentiation in Sapindus mukorossi populations in different regions (Diao et al., 2014; Liu et al., 2021d; Wang et al., 2022). Liu et al. (2021b) and Liu et al. (2021c) hold that the pH value and moisture content of the soil can affect the growth status of Sapindus mukorossi, and these differences are also directly related to the genetic variations of populations in different regions. Sun et al. (2018) and Liu et al. (2022) found that geographical isolation is equally important and it may cause long-term differentiation among populations in different regions. 3 Methods and Techniques for Genetic Diversity Analysis 3.1 Research materials and sampling strategy The studies of Mahar et al. (2011), Ba (2014), and Liu et al. (2022) all found that Sapindus plants are distributed in many places (such as China, India, etc.), and there are significant genetic differences among the populations in these regions. Extensive sampling is beneficial for breeders and conservationists to better grasp germplasm resources and lay the foundation for subsequent selection and breeding as well as resource conservation. Liu et al. (2021a) demonstrated that the phenotypic trait data of Sapindus mukorossi were collected through agricultural morphology methods, and the assessment contents included the size of the fruit, the oil content in the seeds, and the saponin level in the fruit, etc. These traits will be recorded first, and then the outstanding germplasm resources will be identified through correlation analysis and principal component analysis. Sun et al. (2018a) found that the research would also take into account the phenotypic plasticity and adaptability of Sapindus mukorossi, as these factors would also affect its economic value. 3.2 Application of molecular marker technologies SSR and SNP markers can detect very subtle genetic differences when analyzing the genetic diversity of Sapindus mukorossi. SSR markers are often used to evaluate the genetic diversity and population structure of Sapindus mukorossi. Studies have found that they can reveal obvious intraspecific and interspecific variations. Sun et al. (2018b) and Liu et al. (2022) hold that the advantages of such markers lie in their codominant nature, large amount of information, high polymorphism, and suitability for studying kinship and genetic diversity. High-throughput sequencing technology can be used to obtain more comprehensive genetic information. It is useful for in-depth understanding of the changes in the entire genome, identifying those candidate genes related to agronomic traits, and revealing the evolutionary history of the Sapindus mukorossi. Xue et al. (2022) demonstrated that the introduction of high-throughput sequencing can provide a more detailed analysis of genetic differences among germplasm resources and more accurately select superior materials suitable for breeding. 3.3 Methods for evaluating genetic diversity Statistical indicators such as the Shannon index and the Nei index are beneficial for understanding the genetic differences within and between populations. The Shannon information index is often used to measure the genetic diversity of different populations. The research of Mahar et al. (2011b) shows that Sapindus mukorossi in different geographical regions has significant changes in polymorphism and genetic differences. Sun et al. (2018a) found that the Nei genetic diversity index is often used to quantitatively assess the degree of variation and has been used to analyze the diversity parameters of Sapindus plants in some studies based on ISSR markers. Methods such as UPGMA cluster analysis and Dice genetic similarity coefficient are often used to analyze the genetic similarity and distance between germplasms. Mahar et al. (2011b) and Ba (2014) found that UPGMA clustering can divide different populations into several groups based on genetic distance, and the results are often related to geographical distribution. That is to say, populations from similar areas are more likely to be classified into one category. These analytical methods are very useful for understanding the genetic relationships and differences among different germplasm resources.
Tree Genetics and Molecular Breeding 2025, Vol.15, No.1, 9-17 http://genbreedpublisher.com/index.php/tgmb 12 3.4 Population structure and evolutionary analysis Sun et al. (2018b) found that PCA can represent complex genetic data in the form of images, allowing the genetic differences between different populations to be visually observed, and also analyze whether these differences are related to ecological and environmental factors. Liu et al. (2022) indicated that the Fst value is used to measure the degree of genetic differentiation among different populations, and the higher the value, the greater the difference between populations. ISSR markers are widely used in the genetic analysis of Sapindus plants. They can effectively distinguish the genetic structure among different species and populations and reveal obvious genotype differences and evolutionary directions (Sun et al., 2018a; Sun et al., 2018b). Xue et al. (2022) demonstrated that these research results are helpful for understanding the evolutionary process and environmental adaptability of Sapindus mukorossi, as well as enabling breeders to identify superior germplasms with greater utilization value. 4 Mining and Functional Analysis of Superior Genes in Sapindus mukorossi 4.1 Functional genes related to saponin content The chromosome-level genome of Sapindus mukorossi has been assembled, providing a complete reference framework for identifying genes related to saponin synthesis. In the 2022 study by Xue et al., genomic data revealed that the Sapindus mukorossi contains many genes related to plant defense, growth and development, and these genes are very likely to include the key parts that control saponin synthesis. Liu et al. (2021a) and Xue et al. (2022) conducted gene expression analysis on germplasm with high saponin content using RNA-Seq technology and identified the core genes that might regulate saponin synthesis. This method is beneficial for a better understanding of the genetic basis of saponin content and also provides technical support for screening high-quality germplasm with higher saponin yield. 4.2 Genes related to stress resistance Identifying genes related to drought resistance, salt tolerance, heat tolerance and other stress resistance is crucial for breeding Sapindus mukorossi varieties with strong adaptability. Xue et al. (2022) have identified a number of candidate genes that may be involved in plant defense responses through genome-wide analysis. These genes may be crucial in enhancing plants' resistance to adverse environments. Studies have screened and verified the expression of candidate genes in Sapindus mukorossi germplasm with strong stress resistance, and found that these genes do have potential in enhancing the tolerance of plants to external environmental stress, highlighting the importance of genetic diversity and also indicating the key role of certain specific genes in adapting to different adverse conditions (Mahar et al., 2011; Ba, 2014; Sun et al., 2018b). 4.3 Validation technologies for functional genes RT-qPCR can quantify the expression of a certain target gene and verify whether it is really related to important economic traits such as saponin content or stress resistance. Sun et al. (2018a) and Xue et al. (2022) argued that these target genes are often preliminarily screened out in genome-wide analysis or selective dissection studies, and RT-qPCR is used to confirm whether these genes do play a role in key traits. Mahar et al. (2011a) and Xue et al. (2022) found that gene editing technology can precisely modify specific loci in the genome and knockout a gene involved in saponin synthesis or stress resistance pathways, thereby directly verifying its role in plant traits. The combined use of gene editing technology and traditional breeding methods can accelerate the breeding process of high-yield and stress-resistant Sapindus mukorossi varieties and enhance their commercial utilization and environmental adaptability. 4.4 Candidate gene association analysis Candidate gene association analysis is to obtain genotype data through molecular markers, and then conduct association analysis on these data with phenotypic traits such as saponin content and stress resistance in fruits. Sun et al. (2018a) and Liu et al. (2021a) demonstrated that in this way, genetic loci related to key economic traits can be identified, which is beneficial for locating the genes that play a role and providing a genetic basis for breeding work.
Tree Genetics and Molecular Breeding 2025, Vol.15, No.1, 9-17 http://genbreedpublisher.com/index.php/tgmb 13 Combining association analysis and genetic diversity assessment can help understand the extent to which certain genes influence the target traits. The research by Mahar et al. (2011b) and Sun et al. (2018a) utilized ISSR markers to identify loci related to saponin synthesis and other economic traits, revealing the genetic mechanisms behind these traits. By understanding these genetic factors, breeders can formulate more targeted strategies, focusing on enhancing key indicators such as saponin content and stress resistance of Sapindus mukorossi, and promoting its application value in biodiesel, pharmaceutical development and biochemical engineering fields. 5 Screening and Evaluation of Superior Germplasm in Sapindus mukorossi 5.1 Comprehensive trait evaluation indicators Xue et al. (2022) found that Sapindus mukorossi exhibits distinct biological characteristics from flowering to fruiting. Detailed records of its morphology and growth habits provide a solid foundation for subsequent breeding, cultivation, and medicinal development (Figure 2). Sun et al. (2018a) and Liu et al. (2022) indicated that germplasms with high saponin content have attracted attention due to their applications in biodiesel and the pharmaceutical fields, and the high content of oil in seeds is related to the production efficiency of biodiesel. Mahar et al. (2011b) and Sun et al. (2018b) hold that the stress resistance ability that can grow in various environments is an important factor in evaluating the quality of germplasm, and it is related to the sustainable planting performance in different ecological areas. Figure 2 Representative photographs of S. mukorossi (Adopted from Xue et al., 2022) Image caption: a Mature S. mukorossi tree in its natural habitat. b Flowers. c, d Fruits. Bar =1 cm (Adopted from Xue et al., 2022)
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