International Journal of Molecular Ecology and Conservation, 2025, Vol.15 http://ecoevopublisher.com/index.php/ijmec © 2025 EcoEvoPublisher, registered at the publishing platform that is operated by Sophia Publishing Group, founded in British Columbia of Canada. All Rights Reserved.
International Journal of Molecular Ecology and Conservation, 2025, Vol.15 http://ecoevopublisher.com/index.php/ijmec © 2025 EcoEvoPublisher, registered at the publishing platform that is operated by Sophia Publishing Group, founded in British Columbia of Canada. All Rights Reserved. EcoEvoPublisher is an international Open Access publishing platform that publishes scientific journals in the field of ecology and evolution registered at the publishing platform that is operated by Sophia Publishing Group (SPG), founded in British Columbia of Canada. Publisher EcoEvo Publisher Editedby Editorial Team of International Journal of Molecular Ecology and Conservation Email: edit@ijmec.ecoevopublisher.com Website: http://ecoevopublisher.com/index.php/ijmec Address: 11388 Stevenston Hwy, PO Box 96016, Richmond, V7A 5J5, British Columbia Canada International Journal of Molecular Ecology and Conservation (ISSN 1927-663X) is an open access, peer reviewed journal published online by EcoEvoPublisher. The journal is considering all the latest and outstanding research articles, letters and reviews in all aspects of molecular ecology and conservation, containing the contents of the ranges from the applied to the theoretical in molecular ecology and nature conservation, the policy and management with comprehensive and applicable information; the ecological bases for the conservation of ecosystems, species, genetic diversity, the restoration of ecosystems and habitats; as well as the expands the field of ecology and conservation work. All the articles published in International Journal of Molecular Ecology and Conservation 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. EcoEvoPublisher uses CrossCheck service to identify academic plagiarism through the world’s leading plagiarism prevention tool, iParadigms, and to protect the original authors’ copyrights.
International Journal of Molecular Ecology and Conservation (online), 2025, Vol. 15, No.1 ISSN 1927-663X https://ecoevopublisher.com/index.php/ijmec © 2025 EcoEvoPublisher, registered at the publishing platform that is operated by Sophia Publishing Group, founded in British Columbia of Canada. All Rights Reserved. Latest Content Domestication History and Adaptive Genomic Variations of Pineapple: From Wild to Cultivated Varieties Mengting Luo, Zhonggang Li International Journal of Molecular Ecology and Conservation, 2025, Vol. 15, No. 1, 1-8 Global Trade and Genetic Resource Flow of Durian: Ecological Analysis of Regional Variety Adaptation Chuchu Liu, Zhonggang Li International Journal of Molecular Ecology and Conservation, 2025, Vol. 15, No. 1, 9-18 The Role of Horizontal Gene Transfer and Structural Variation in the Adaptation of Goats to Diverse Environments Wei Liu, Jia Xuan International Journal of Molecular Ecology and Conservation, 2025, Vol. 15, No. 1, 19-29 Germplasm Flow and Regional Adaptation of Yellow Pitaya: The Role of Genetic Variation in Cultivation Expansion Zhonggang Li, Yeping Han International Journal of Molecular Ecology and Conservation, 2025, Vol. 15, No. 1, 30-43 Global Population Genomics of Chickens and Their Adaptation to Diverse Environments Jun Wang, Qibin Xu International Journal of Molecular Ecology and Conservation, 2025, Vol. 15, No. 1, 44-53
International Journal of Molecular Ecology and Conservation, 2025, Vol.15, No.1, 1-8 http://ecoevopublisher.com/index.php/ijmec 1 Research Insight Open Access Domestication History and Adaptive Genomic Variations of Pineapple: From Wild to Cultivated Varieties Mengting Luo 1,2 , Zhonggang Li 1 1 Cuixi Academy of Biotechnology, Zhuji, 311800, Zhejiang, China 2 Hainan Institute of Tropical Agricultural Resources, Tropical Animal and Plant Resources Research Center, Sanya, 572025, Hainan, China Corresponding author: menting.luo@jicat.org International Journal of Molecular Ecology and Conservation, 2025, Vol.15, No.1 doi: 10.5376/ijmec.2025.15.0001 Received: 21 Nov., 2024 Accepted: 28 Dec., 2024 Published: 08 Jan., 2025 Copyright © 2025 Luo and 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: Luo M.T., and Li Z.G., 2025, Domestication history and adaptive genomic variations of pineapple: from wild to cultivated varieties, International Journal of Molecular Ecology and Conservation, 15(1): 1-8 (doi: 10.5376/ijmec.2025.15.0001) Abstract This time, we studied the domestication process of pineapple (Ananas comosus) and the changes in its genes. This information helps us understand how it evolved step by step and can also help improve the quality of pineapples in the future. In the study, we focused on the changes that occurred in the genes of pineapples during domestication, especially some key mutations that can distinguish wild species from artificial species (that is, varieties grown by humans). We analyzed genomic data from different pineapple species and found signals related to domestication, such as larger fruits, more sugars, and enhanced stress resistance. We also found some interesting phenomena, such as some differences in the genetic composition between cultivated varieties, and introgression between genes. These make them more diverse. At the same time, we also found several genes that may be related to adaptability, such as those that can help pineapples resist drought or saline-alkali environments. Comparative analysis also made us see some things clearly, such as gene duplication and the disappearance of some specific genes, which may be the reasons for helping pineapples become more delicious or more resistant to the environment. Overall, our research reveals how pineapples have adapted to the environment step by step and become as delicious and easy to grow as they are now. These findings will be very helpful for future breeding and improving fruit quality and yield. Keywords Pineapple; Domestication; Genomic variations; Adaptive evolution; Genetic diversity 1 Introduction Pineapple (Ananas comosus) is one of the most important fruits in the world. Among tropical fruits, it ranks second only to bananas and mangoes (Zhou et al., 2015). Because it is grown and eaten in large quantities, especially in tropical regions, pineapple has high economic value (Ming et al., 2015). People have been growing pineapples for more than 6 000 years. There are many varieties on the market, such as "Smooth Cayenne", which is currently one of the most widely grown varieties in the world (Sanewski, 2018). However, wild genes are rarely introduced during modern breeding, so the genetic diversity of cultivated varieties is mostly accumulated through somatic mutations (Zhou et al., 2015; Sanewski, 2018). Why do we want to study the domestication of pineapples and the changes in their genes ? There are several reasons. For example, if we can understand the genetic basis of traits such as fiber content, sugar accumulation, and fruit ripening, we can breed higher-yield and better-quality varieties (Chen et al., 2019). For another example, in-depth research on pineapple's crassulacean acid metabolism (CAM) will help us understand how plants adapt to arid or semi-arid environments, which is very important for saving agricultural water (Ming et al., 2015; Zhu and Ming, 2019). In addition, genomic research also tells us that sexual reproduction and asexual reproduction actually coexist during the domestication of pineapples. In other words, pineapples are not domesticated in one step like some clonal crops, but have undergone a more complex process (VanBuren, 2018; Chen et al., 2019). The goal of this study is to understand how pineapples were domesticated step by step. We are particularly interested in the genetic differences between wild and artificial species. Next, we will analyze the possible effects of these genetic changes. The article first briefly reviews the domestication history of pineapples, then discusses
International Journal of Molecular Ecology and Conservation, 2025, Vol.15, No.1, 1-8 http://ecoevopublisher.com/index.php/ijmec 2 some of the key genetic variations and adaptation mechanisms currently known, and finally sees whether these findings can help with future breeding and how to use them in practice to make breeding more efficient. 2 Origin and Early Domestication of Pineapple 2.1 Wild ancestors and their geographical distribution It is now generally believed that the genus Ananas, including the cultivated pineapples we eat, originated from South America. Wild species such as Ananas comosus var. microstachys and Ananas parguazensis are mainly distributed in the northern Amazon region (d’Eeckenbrugge et al., 2018; VanBuren, 2018). These wild pineapples help us better understand the genetic characteristics of pineapples and how they evolved. Based on the distribution of these ancestral species, Guyana is likely to be the first place where pineapples were domesticated. The western Amazon may be another center, where pineapples have undergone genetic recombination brought about by sexual reproduction (d’Eeckenbrugge et al., 2018). 2.2 History of early cultivation by indigenous peoples Indigenous peoples in South America actually started to grow pineapples very early. According to archaeological and linguistic studies, they have been growing and eating pineapples in the Amazon basin and the coast of Peru for more than 3 000 years. In Central America, there is also a history of cultivation of about 2 500 years (d’Eeckenbrugge et al., 2018). These early cultivation activities show that pineapple was an important crop in the community at that time. 2.3 Archaeological and historical evidence of pineapple domestication Many archaeological discoveries and literature have proved that the domestication process of pineapple began as early as 6 000 years ago. Varieties such as “Smooth Cayenne”, which are still common today, were slowly cultivated at that time (Sanewski, 2018). In the process of pineapple domestication, sexual reproduction and asexual reproduction actually work together. This is different from our general view that clonal crops are “domesticated in one step” (VanBuren, 2018; Chen et al., 2019). In addition, historical data also mentioned that in the 16th century, Portuguese merchants brought pineapples from Brazil to tropical regions in Asia and Africa. This further shows that pineapples were widely planted and had a great influence at that time (d’Eeckenbrugge et al., 2018). 3 Morphological and Physiological Changes During Domestication 3.1 Key phenotypic differences between wild and cultivated varieties During the process of being domesticated by humans, the appearance and characteristics of pineapples have changed a lot. Compared with wild species, cultivated pineapples are usually larger, sweeter, and have fewer seeds. These characteristics were deliberately selected to make pineapples more delicious and easier to sell (Figure 1) (d’Eeckenbrugge et al., 2018; Chen et al., 2019). Most cultivated pineapples are now grown asexually. This ensures that good characteristics are passed down from generation to generation and are not easy to change (d’Eeckenbrugge et al., 2018). 3.2 Adaptability to different environments The reason why pineapples can grow in various environments, especially in arid areas, is mainly because of its special photosynthesis method. It uses a method called “crassulacean acid metabolism” (CAM). This method can save more water, so pineapples can grow well in semi-arid areas (Ming et al., 2015; Zhu and Ming, 2019). CAM photosynthesis is a "transformation" of the original C3 mode, which helps pineapples continue to grow even when water is scarce (Ming et al., 2015). In addition, in cultivated pineapples, the expression of some genes that control water transport (such as aquaporin genes) is different from that of wild species. These genes not only affect fruit development, but also allow pineapples to better adapt to different climates (Zhu and Ming, 2019). 4 Genomic Insights into Pineapple Domestication 4.1 Overview of genomic studies on pineapple Recently, scientists have done a lot of research on the pineapple genome. These studies have given us a better understanding of how pineapples were “domesticated” by humans. They measured the genes of several pineapple varieties, including Ananas comosus var. bracteatus and other common cultivated varieties. The study found that
International Journal of Molecular Ecology and Conservation, 2025, Vol.15, No.1, 1-8 http://ecoevopublisher.com/index.php/ijmec 3 some traits, such as pineapple fiber, sweetness, and ripening, are related to specific genes (Figure 1) (Chen et al., 2019). The study also pointed out that when people select seeds, whether through sexual reproduction or asexual reproduction, they have a great influence on pineapple traits. This also shows that the domestication process of pineapples cannot be completed in one step (VanBuren, 2018). Figure 1 Distribution of genomic features along the pineapple CB5 genome (Adopted from Chen et al., 2019) 4.2 Important genetic markers in domestication Researchers have found many single nucleotide polymorphism (SNP) markers. They are particularly useful in understanding the genetic diversity and domestication process of pineapples. These markers show that there are many duplications in the genes of cultivated varieties, as well as many somatic mutations. This shows that many changes in the appearance or traits of pineapples are actually due to these mutations, rather than complex breeding work (Zhou et al., 2015). In addition, scientists have also found genes related to “self-incompatibility”, which may also be selected during the domestication process (Chen et al., 2019). 4.3 Genetic comparison of wild species and cultivated species By comparing different genomes, the study found that the genetic diversity of cultivated pineapples is actually quite rich. This is because their ancestors came from different wild species and also experienced hybridization (VanBuren, 2018). However, although there are many types of cultivated pineapples, the genetic differences between them are not large. In other words, domestication has not reduced their genetic diversity too much (Gaut et al., 2018). This diversity may be related to the mixing of genes from wild species and the history of pineapple spread in different places (d’Eeckenbrugge et al., 2018). 5 Adaptive Genomic Variations in Pineapple 5.1 Key genes involved in stress tolerance Pineapple can adapt to drought, saline-alkali land and pests and diseases, which is related to some of its special gene mutations. Studies have found that there are 54 genes called WRKY in the pineapple genome. These genes will behave differently when facing various environmental pressures (Xie et al., 2018). They play a big role in improving pineapple's ability to adapt to difficult environments. Therefore, these genes are critical when breeding stress-resistant pineapple varieties. 5.2 Genetic basis of CAM photosynthesis Pineapple is a plant that uses CAM photosynthesis. Unlike ordinary C3 photosynthesis, CAM photosynthesis allows pineapples to live well in places with little water. Scientists have found that pineapples do not change the
International Journal of Molecular Ecology and Conservation, 2025, Vol.15, No.1, 1-8 http://ecoevopublisher.com/index.php/ijmec 4 way of photosynthesis by adding new genes, but by changing the use of existing genes, that is, changing their functions (Ming et al., 2015). This method allows pineapples to save water, which is very important for arid areas (Ming et al., 2015; Zhu and Ming, 2019). 5.3 How did pineapple’s disease resistance evolve? Pineapple's disease resistance also evolved over a long period of time. Some genes were gradually “eliminated” because they were not helpful in fighting diseases, and some repeated gene structures also appeared. For example, someone found a repeated “protease inhibitor” gene that may help pineapples resist pests (Chen et al., 2019). In addition, there are many types of genes such as WRKY, and there are complex interactions between them, which may also be one of the reasons why pineapples have enhanced disease resistance (Xie et al., 2018). 6 Population Genomics and Phylogenetics of Pineapple Varieties 6.1 Genetic relationships among different pineapple cultivars The genes of different pineapple varieties are quite different. Studies have found that there are two species and five variants in the genus Anine, and there is a clear genetic separation between them. But in many cultivated varieties, most of the differences in appearance and traits are due to somatic mutations, not the result of long-term breeding (VanBuren, 2018). Common varieties such as “Smooth Cayenne” and “Queen” have traces of ancient genes in their genes, as well as new genes that have been mixed in recently. This shows that the evolution and domestication process of pineapples is quite complicated (Chen et al., 2019). 6.2 New discoveries brought by whole genome research By measuring the whole genome of pineapples, such as the two varieties “F153” and “MD2”, scientists found that they did not experience ancient whole genome duplication events like some plants (Ming et al., 2015). In other words, the genes of pineapples are not changed through large-scale duplication. These studies also found many changes in gene structure that are useful for domestication, as well as some genes that may have been “selected”, which played a significant role in pineapple's adaptation to the environment (Figure 2) (Chen et al., 2019; Feng et al., 2024). Figure 2 Putative domestication sweep around a bromelain inhibitor gene that helps control fruit ripening (Adopted from Chen et al., 2019)
International Journal of Molecular Ecology and Conservation, 2025, Vol.15, No.1, 1-8 http://ecoevopublisher.com/index.php/ijmec 5 6.3 Gene exchange and hybridization in pineapple domestication Gene flow and hybridization are common in the evolution of pineapples. There have been a lot of mixing and hybridization between different pineapple species (VanBuren, 2018). Wild pineapples like A. macrodontes have also flowed into current cultivated varieties. This “hybridization” makes pineapple genes richer (d’Eeckenbrugge et al., 2018). These hybridization processes have helped people breed better pineapples, such as varieties with sweeter fruits and fewer diseases and pests. 7 Impact of Domestication on Pineapple Metabolomics and Flavor Compounds 7.1 Changes in sugar metabolism and fruit sweetness Domestication has caused significant changes in the sugar metabolism of pineapples. Simply put, the fruit has become sweeter, and sweetness is the key to whether people buy it or not. Researchers analyzed the genes of different pineapple varieties and found that the fruit becomes sweeter because sugar accumulates in the fruit. This sugar accumulation is related to the fruit ripening process and directly affects the sweetness (Chen et al., 2019; Feng et al., 2024). However, the genetic combination of pineapples is very complex, and its “heterozygosity” is very high. This brings diversity, but also brings a lot of difficulties to breeding work, such as it is not easy to control the sugar content (Sanewski, 2018). 7.2 Genetic basis of aroma The aroma is also very important for whether pineapples are delicious. These aromas come from a class of things called “volatile compounds”. Studies have found that the production of these compounds is related to certain specific genes. Scientists have found these key genes through genomic research (VanBuren, 2018; Chen et al., 2019). If you want to make pineapples more fragrant, these studies are particularly helpful for breeding. 7.3 The balance between flavor and nutrition Although domestication has made pineapples sweeter and more fragrant, it has also brought some “side effects”. When people choose sweet and fragrant varieties, they may ignore other nutrients that are good for the body. As a result, some originally beneficial substances have become less in the newly cultivated varieties (d’Eeckenbrugge et al., 2018; VanBuren, 2018). Therefore, when breeding in the future, we must consider not only the taste, but also pay attention to retaining the nutrition. 8 Case Study: Genomic and Agronomic Improvement of a Pineapple Cultivar Pineapple (Ananas comosus) is one of the common tropical fruits, and humans have been cultivating it for a long time. It originally came from South America and was domesticated about 6,000 years ago. Old varieties such as "Smooth Cayenne" are still widely planted in many countries (Sanewski, 2018). In the process of domesticating it, people used both sexual and asexual reproduction. And studies have found that the changes in pineapple traits are mainly the result of genetic diversity and somatic mutations (Zhou et al., 2015; VanBuren, 2018). Later, scientists began to study the genome of pineapples. They measured the genes of many varieties, such as “MD2” and “Queen”, and found that there are many important differences in the genes of these pineapples. These differences affect the sugar content, ripening speed, and fiber content of the fruit (Ming et al., 2015; Chen et al., 2019). In addition, these genetic studies have helped us understand an interesting phenomenon: pineapples have switched from C3 photosynthesis to CAM photosynthesis. This transformation makes it more water-efficient and easier to grow in dry areas (Ming et al., 2015; Zhu and Ming, 2019). “MD2” is a typical example of improved pineapple varieties. It is sweet and low in acid, and its taste is very popular. In order to make it better, scientists have made many breeding and genetic improvements to it (Chen et al., 2019; Feng et al., 2024). During the breeding process of this variety, many different gene backgrounds were added. The main method is breeding through somatic mutation and selection of good traits. This is done to cope with its complex gene combination and some repeated genetic content (Zhou et al., 2015; Sanewski, 2018). These research results are very helpful for future pineapple breeding. Now we have more comprehensive genetic data, as well as new breeding technologies such as marker-assisted selection and gene editing (Dhurve et al., 2021;
International Journal of Molecular Ecology and Conservation, 2025, Vol.15, No.1, 1-8 http://ecoevopublisher.com/index.php/ijmec 6 Feng et al., 2024). These tools can enable us to breed better pineapples that not only taste good, but are also more disease-resistant and adaptable to more complex weather. This way, pineapples can be grown more stably, profitably, and sustainably around the world. 9 Challenges and Future Directions in Pineapple Breeding 9.1 Genetic bottlenecks and loss of diversity During the domestication and breeding process of pineapples, a lot of “heterozygosity” has emerged, that is, the genes are very inconsistent. Although this situation can bring some diversity, it also makes breeding more difficult (Sanewski, 2018; VanBuren, 2018). At present, there are very few wild genes introduced into modern pineapple varieties, which makes its genetic base very narrow. It becomes difficult to add new traits or improve existing characteristics. This problem is called "genetic bottleneck", which is a major obstacle in breeding work. 9.2 Improving pineapple traits with CRISPR and other tools Now there are some new technologies, such as CRISPR and molecular marker-assisted breeding, which can help us solve the genetic problems mentioned above. These tools can directly modify the genes of pineapples and accurately add desired traits, such as making the fruit sweeter or enhancing disease resistance. Moreover, these methods do not require repeated hybridization and are much more efficient (Zhou et al., 2015; Sanewski, 2018). At the same time, scientists have also established a complete reference genome, which is like a “gene map” that can help us find the areas that need to be modified more accurately (Feng et al., 2024). 9.3 Breeding strategies for climate change and disease Now, climate change has affected agriculture. In order to make pineapples grow well in various climates, breeding goals have also begun to focus on “climate adaptability” and “disease resistance”. One way is to find good genes that can still be used from wild pineapples and old varieties. Another way is to use genomic technology to screen out disease-resistant traits and then use them in new varieties (Ming et al., 2015; Zhu and Ming, 2019). In addition, pineapples themselves have a special photosynthesis method called CAM, which can save more water. Scientists hope to make this ability work better through genetic adjustment (Ming et al., 2015). 10 Conclusion and Perspectives We are now learning more and more about the pineapple genome. These studies tell us one thing: the domestication process of pineapple is much more complicated than we originally thought. It not only relies on sexual reproduction (that is, breeding in the traditional sense), but also makes extensive use of asexual reproduction (such as propagation by rhizomes or cuttings). These two methods together determine the appearance of pineapples today. By analyzing genes, scientists have discovered some particularly important variations. These variations may be related to the sweetness, fragrance, ripening time, fiber content, and heat and drought resistance of the fruit. In other words, when people grow pineapples, they inadvertently “select” these good traits. Through genome research, we can look back and see: which genes have changed, why they have changed, and what results these changes have brought. Next, the research on the pineapple genome can be further deepened. For example, we still need to figure out which genes control fruit quality and which are related to disease and insect resistance, high temperature resistance, and water conservation. These are all of particular concern in breeding. At the same time, gene editing technologies such as CRISPR are also developing rapidly, which allows us to modify genes more accurately without spending many years on generation after generation. This could greatly speed up the process of breeding new varieties. However, to breed better, we need a larger genetic database. Although there is genetic data for some common varieties, such as “MD2” and “Queen”, it is still not enough. If more wild species and local varieties can be sequenced, more useful genetic information can be found. This will not only help us breed, but also help protect the diversity of varieties.
International Journal of Molecular Ecology and Conservation, 2025, Vol.15, No.1, 1-8 http://ecoevopublisher.com/index.php/ijmec 7 Finally, the results of these genetic studies are not just to make pineapples sweeter and more delicious. They can also help us solve bigger problems, such as challenges such as climate change, water shortages and increased pests and diseases. We can use this knowledge to breed stronger and more adaptable varieties to new environments. For example, improving water use efficiency can make pineapples grow in arid areas; enhancing disease resistance can reduce the use of pesticides. Doing so will not only benefit agricultural production itself, but also promote more environmentally friendly and sustainable agricultural development. Acknowledgments Thanks to Mai Rudi and Liang Qixue for their support and assistance in literature search and data analysis. Funding This study was supported by Hainan Institute of Tropical Agricultural Resources Funding (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 Chen L., VanBuren R., Paris M., Zhou H., Zhang X., Wai C., Yan H., Chen S., Alonge M., Ramakrishnan S., Liao Z., Liu J., Lin J., Yue J., Fatima M., Lin Z., Zhang J., Huang L., Wang H., Hwa T., Kao S., Choi J., Sharma A., Song J., Wang L., Yim W., Cushman J., Paull R., Matsumoto T., Qin Y., Wu Q., Wang J., Yu Q., Wu J., Zhang S., Boches P., Tung C., Wang M., d'Eeckenbrugge C., Sanewski G., Purugganan M., Schatz M., Bennetzen J., Lexer C., and Ming R., 2019, The bracteatus pineapple genome and domestication of clonally propagated crops, Nature Genetics, 51(10): 1549-1558. https://doi.org/10.1038/s41588-019-0506-8 D’Eeckenbrugge G., Duval M., and Leal F., 2018, The pineapple success story: from domestication to pantropical diffusion, Genetics and Genomics of Pineapple, 2018: 1-25. https://doi.org/10.1007/978-3-030-00614-3_1 Dhurve L., Kumar K., Bhaskar J., Sobhana A., Francies R., and Mathew D., 2021, Wide variability among the ‘Mauritius’ somaclones demonstrates somaclonal variation as a promising improvement strategy in pineapple (Ananas comosus L.), Plant Cell, Tissue and Organ Culture (PCTOC), 145: 701-705. https://doi.org/10.1007/s11240-021-02022-5 Feng J., Zhang W., Chen C., Liang Y., Li T., Wu Y., Liu H., Wu J., Lin W., Li J., He Y., He J., and Luan A., 2024, The pineapple reference genome: Telomere-to-telomere assembly, manually curated annotation, and comparative analysis, Journal of Integrative Plant Biology, 66(10): 2208-2225. https://doi.org/10.1111/jipb.13748 Gaut B., Seymour D., Liu Q., and Zhou Y., 2018, Demography and its effects on genomic variation in crop domestication, Nature Plants, 4(8): 512-520. https://doi.org/10.1038/s41477-018-0210-1 Hayati R., and Kasiamdari R., 2024, Genetic diversity of indonesian pineapple (Ananas comosus (L.) Merr.) cultivars based on ISSR markers, Pertanika Journal of Tropical Agricultural Science, 47(4): 1087-1100. https://doi.org/10.47836/pjtas.47.4.02 Jia P., Liu S., Lin W., Yu H., Zhang X., Xiao X., Sun W., Lu X., and Wu Q., 2024, Authenticity identification of F1 hybrid offspring and analysis of genetic diversity in pineapple, Agronomy, 14(7): 1490. https://doi.org/10.3390/agronomy14071490 Ming R., VanBuren R., Wai C., Tang H., Schatz M., Bowers J., Lyons E., Wang M., Chen J., Biggers E., Zhang J., Huang L., Zhang L., Miao W., Zhang J., Ye Z., Miao C., Lin Z., Wang H., Zhou H., Yim W., Priest H., Zheng C., Woodhouse M., Edger P., Guyot R., Guo H., Guo H., Zheng G., Singh R., Sharma A., Min X., Zheng Y., Lee H., Gurtowski J., Sedlazeck F., Harkess A., McKain M., Liao Z., Fang J., Liu J., Zhang X., Zhang Q., Hu W., Qin Y., Wang K., Chen L., Shirley N., Lin Y., Liu L., Hernandez A., Wright C., Bulone V., Tuskan G., Heath K., Zee F., Moore P., Sunkar R., Leebens-Mack J., Mockler T., Bennetzen J., Freeling M., Sankoff D., Paterson A., Zhu X., Yang X., Smith J., Cushman J., Paull R., and Yu Q., 2015, The pineapple genome and the evolution of CAM photosynthesis, Nature Genetics, 47(12): 1435-1442. https://doi.org/10.1038/ng.3435 Sanewski G., 2018, The history of pineapple improvement, Genetics and Genomics of Pineapple, 2018: 87-96. https://doi.org/10.1007/978-3-030-00614-3_7 VanBuren R., 2018, Genomic relationships, diversity, and domestication of ananas taxa, Genetics and Genomics of Pineapple, 2018: 259-272. https://doi.org/10.1007/978-3-030-00614-3_18 Xie T., Chen C., Li C., Liu J., Liu C., and He Y., 2018, Genome-wide investigation of WRKY gene family in pineapple: evolution and expression profiles during development and stress, BMC Genomics, 19: 1-18. https://doi.org/10.1186/s12864-018-4880-x Xu H., Yu Q., Shi Y., Hua X., Tang H., Yang L., Ming R., and Zhang J., 2018, PGD: pineapple genomics database, Horticulture Research, 5: 66. https://doi.org/10.1038/s41438-018-0078-2
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International Journal of Molecular Ecology and Conservation, 2025, Vol.15, No.1, 9-18 http://ecoevopublisher.com/index.php/ijmec 9 Case Study Open Access Global Trade and Genetic Resource Flow of Durian: Ecological Analysis of Regional Variety Adaptation ChuchuLiu 1,2 , Zhonggang Li 1 1 Cuixi Academy of Biotechnology, Zhuji, 311900, Zhejiang, China 2 Hainan Institute of Tropical Agricultural Resources, Sanya, 572025, Hainan, China Corresponding author: chuchu.liu@cuixi.org International Journal of Molecular Ecology and Conservation, 2025, Vol.15, No.1 doi: 10.5376/ijmec.2025.15.0002 Received: 08 Dec., 2024 Accepted: 12 Jan., 2025 Published: 20 Jan., 2025 Copyright © 2025 Liu and 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: Liu C.C., and Li Z.G., 2025, Global trade and genetic resource flow of durian: ecological analysis of regional variety adaptation, International Journal of Molecular Ecology and Conservation, 15(1): 9-18 (doi: 10.5376/ijmec.2025.15.0002) Abstract This study explores the global trade dynamics and genetic resource flow of durian, with a focus on the ecological adaptation of regional varieties. It examines major durian-producing and exporting countries, key importing markets, and trade regulations influencing durian distribution. Additionally, the study discusses the genetic diversity and exchange of durian germplasm, emphasizing the role of breeding programs and biotechnology in enhancing climate adaptation and disease resistance. From an ecological perspective, it assesses environmental factors affecting durian adaptation, including climate conditions, soil characteristics, and pest and disease management strategies. Through case studies, such as the expansion of Musang King in the Chinese market and the introduction of hybrid varieties in emerging markets, this study provides practical insights into the sustainability of durian cultivation. By integrating ecological analysis with market research, this study aims to support the long-term sustainability of durian production and trade while ensuring genetic diversity and environmental sustainability. Keywords Durian (Durio zibethinus L.); Global trade; Genetic resource flow; Variety adaptation; Ecological sustainability 1 Introduction Durian (Durio zibethinus L.), also known as Shaozi or civet fruit, is a tropical evergreen tree belonging to the Malvaceae family. Its leaves are slender and pointed at the front, and its flowers are light yellow and bloom in clusters. The fruit of durian is large, like a football, with a hard shell and covered with thorns. The flesh is composed of aril, which is yellowish in color, sticky, juicy, and tastes special. Because of its high nutrition and special taste, it is often called the “king of fruits”. The market price of durian has always been high, and the demand is also growing. This has led to the expansion of the planting scale of major durian producing countries such as Thailand, Malaysia, and Indonesia. Today, durian has become one of the most exported and profitable fruits in Southeast Asia. The demand for durian in the international market is also rising. This export-oriented planting method not only illustrates the economic potential of the durian industry, but also reflects the structural characteristics of Southeast Asian agriculture (Teh et al., 2017; Nawae et al., 2023). The taste of durian comes from its unique smell. Scientists have found that its pulp contains more than 50 volatile substances, most of which are sulfides, such as ethanethiol, methyl sulfide, dimethyl disulfide and trimethylamine (Aziz and Jalil, 2019). These ingredients work together to form the "stinky and fragrant" taste of durian. In order to meet market demand and increase production, many countries are also promoting new varieties and expanding the planting area of durian (Khaksar et al., 2024). Durian is also rich in nutrition and contains many active ingredients that are beneficial to the human body. For example, the calories per 100 grams of durian pulp are about 147 kcal, while apples only have 60 kcal. The energy of durian is about 2.4 times that of apples. In terms of carbohydrates, durian contains 28.3 grams per 100 grams, which is significantly higher than the 13.5 grams of apples and 10.2 grams of pears. Durian is also rich in minerals, especially potassium, which is high, with 261 mg of potassium per 100 grams. Potassium is very helpful in regulating the sodium-potassium balance in the body and can also help lower blood pressure. In addition, durian has a lot of dietary fiber, similar to apples, which can help intestinal peristalsis and facilitate defecation.
International Journal of Molecular Ecology and Conservation, 2025, Vol.15, No.1, 9-18 http://ecoevopublisher.com/index.php/ijmec 10 There are many types of durian, and different varieties are planted in different regions. These are the result of long-term artificial selection. Durian has a high genetic diversity, which makes it more adaptable to different climates and better resistant to pathogens such as palm phytophthora (Siew et al., 2018b; Lin et al., 2022; Numba, 2023). Now, scientists have analyzed the genes of durian varieties through some molecular marker technologies, such as SSR and RAPD, and found that there are obvious differences between different varieties. These research results also lay the foundation for future breeding and improvement. Further research also found that the genetic differences between durian varieties are the result of their adaptation to the environment in different regions (Songnuan et al., 2019). This study focuses on the global trade and genetic resource flows of durian, explores the ecological adaptability of varieties in different regions, focuses on analyzing the market structure of major durian producing and exporting countries, evaluates changes in demand in key import markets, and analyzes the diversity and exchange mechanism of durian germplasm resources from a genetic perspective, and discusses the role of breeding programs and biotechnology in improving durian climate adaptability and disease resistance. Through comprehensive ecological analysis and market research, this study hopes to provide scientific basis and policy recommendations for durian production, trade and germplasm resource protection, and promote the long-term sustainable development of the global durian industry. 2 Global Trade and Market Trends of Durian 2.1 Major durian-producing and exporting countries At present, Southeast Asia is still the world’s most important durian production area. Among them, Thailand, Malaysia and Vietnam are the three largest durian exporters. Thailand is the world’s largest durian exporter, accounting for more than 80% of the global market supply. As early as 2003, Thailand became the first country allowed by China to directly export durian. Thailand’s high-quality varieties such as “Monhong” are particularly popular, and once accounted for more than 90% of the Chinese market. Thailand's durian is mainly grown in the east and south, such as Monthong, Chanee and Kradumthong, which are the main export varieties. Thailand can maintain its leading position in the international market for a long time, mainly because it has a stable supply chain, government support policies, and a special trade agreement signed with China (Siew et al., 2018b; Nawae et al., 2023). In recent years, Vietnam’s durian industry has developed rapidly. In 2022, China officially approved Vietnam to export fresh durian, which greatly improved its market competitiveness. In 2024, drought and pests affected the production and quality of durian in Thailand, and Vietnam seized the opportunity to enter the market with cheaper transportation costs and prices. By October 2024, Vietnam has surpassed Thailand to become the largest supplier of durian to China. Durian in Vietnam is mainly grown in the central highlands and the Mekong Delta. Malaysia is also an important durian producer. However, its export volume is not as good as Thailand because it mainly exports high-end varieties such as Musang King and Black Thorn. Another reason is that most of Malaysia's durian can only be exported frozen due to plant quarantine restrictions. Recently, the Malaysian government has been expanding the planting area and improving post-harvest processing technology in the hope of improving export quality (Siew et al., 2018b). Indonesia and the Philippines are emerging durian producers, and their market share is slowly expanding. Indonesia has a large durian planting area, but most of it is only for domestic consumption. The Philippines signed a trade agreement with China in 2023 and began to export durian to the international market (Belgis et al., 2017). 2.2 Main trade routes and times of durian in China China now mainly imports durian from three countries: Thailand, Vietnam and the Philippines. In 2023, China's durian imports from Thailand accounted for 65.19% of the total import volume and 68.05% of the import value; durian imported from Vietnam accounted for 34.55% of the volume and 31.76% of the value (Zhou et al., 2021). Durian generally enters China through ports such as Guangzhou, Pingxiang, Guangxi, Kunming and Hekou. Among the 28 durian importing provinces in the country, Guangdong, Guangxi, Yunnan and Zhejiang all import
International Journal of Molecular Ecology and Conservation, 2025, Vol.15, No.1, 9-18 http://ecoevopublisher.com/index.php/ijmec 11 more than 100 000 tons. China does not export much durian, and currently there is only one export route, which is to export to Russia through Heilongjiang. The import time of durian is also obviously seasonal. The durian in Thailand generally matures from April to September each year, while in Vietnam it matures a little later, mainly from the end of July to October. Affected by the production seasons of these two countries, China’s durian import peaks are concentrated in the second and third quarters of each year. In 2023, the import volume in the second quarter accounted for 48.83% of the total annual volume, and the third quarter accounted for 31.71%. Since China's durian exports are still relatively small, the monthly export time fluctuates greatly and has not yet formed a stable trend (Aziz and Jalil, 2019). 2.3 Trade regulations and phytosanitary standards Durian must pass strict plant quarantine standards to be exported to other countries. Before export, durian needs to be pre-inspected, fumigated, and obtain relevant certification. These practices are to prevent the spread of pests and diseases. Exporting countries must also meet some international food safety standards, such as good agricultural practices (GAP), hazard analysis and critical control points (HACCP), and sanitary and phytosanitary measures (SPS) (Zhou et al., 2021). These standards ensure that durian remains safe and fresh during transportation. Scientists are now also using molecular markers and genetic fingerprinting to trace the origins of durian varieties. These technologies can verify the true identity of durian and help protect fair competition in the market (Lin et al., 2022). 3 Genetic Resource Flow and Durian Variety Exchange 3.1 Historical and contemporary genetic exchange The diversity of durian varieties is closely related to its cultivation and exchange in Southeast Asia. Durian has been spreading and developing in different regions for a long time, which also allows us to see many different varieties today. For example, Thailand’s very famous “Golden Pillow” durian (Thai: หมอนทอง, English: Monthong) has a very long history. Many commercial varieties currently circulating in the market, such as some durians in Malaysia and Indonesia, were actually first spread from Bangkok, Thailand (Aziz and Jalil, 2019). According to some data, as early as 1908, a Thai cookbook mentioned the extra-large durian produced in the Chinese community. This shows that the Golden Pillow variety has a planting history of at least more than 100 years, and it is likely that it was promoted by early Chinese through grafting (Nawae et al., 2023). 3.2 Genetic diversity and cross-breeding for adaptation The genetic diversity of durian is very important, which allows different varieties to adapt to various different growth environments. Researchers used molecular marker methods such as SSR (simple sequence repeats) and ISSR and found that there are great genetic differences between durian varieties in Malaysia and Indonesia (Siew et al., 2018a). Lin et al. (2022) analyzed 32 durian genotypes in Hainan. They used whole genome sequencing methods and RAD sequencing technology, and developed a set of SSR marker tools. These works laid the foundation for the protection of durian germplasm and breeding research. The study also used some analytical methods, such as genetic similarity (IBS), phylogenetic trees and principal component analysis, to divide the 32 genotypes into two groups. Many of the genotypes in the first group are repeated, while the genotypes in the second group have many common genetic characteristics with the first group. They also pointed out that the main varieties cultivated in Hainan include D24, D101, Musang King (MSW), Golden Red (JH), D163, HFH and NLX-5. They also developed more than 70 000 different SSR molecular markers. 3.3 Intellectual property rights and genetic resource protection Nowadays, there are more and more varieties of durian, and intellectual property protection is becoming more and more important. If durian clones, variants or cultivated varieties can be accurately registered and classified, it will help protect genetic resources and manage commercial interests (Siew et al., 2018b). With the development of molecular marker technology, such as SSR and ISSR, people can more clearly identify the origin of durian varieties. These tools not only help us protect resources, but also support the commercial development of varieties (Prakoso and Retnoningsih, 2021).
International Journal of Molecular Ecology and Conservation, 2025, Vol.15, No.1, 9-18 http://ecoevopublisher.com/index.php/ijmec 12 In recent years, the number of Chinese people eating durian has increased year by year, with an annual growth rate of more than 20%. However, more than 90% of durian in China is still imported. Now, domestic durian such as Hainan “tree-ripened” has begun to be promoted, indicating that domestic breeding technology has made a breakthrough. And the issue of intellectual property protection of these varieties has also received more and more attention. Durian is a tropical specialty fruit, and its varieties (such as Malaysia’s Musang King and Thailand's Golden Pillow) have obvious regional characteristics. According to the Convention on Biological Diversity (CBD), the genetic resources of durian belong to the country of origin; but if it is a new variety, the breeder can also own the variety rights. At this time, it is necessary to balance the relationship between resource ownership and innovative results. In China, new durian varieties can apply for exclusive rights under the Regulations on the Protection of New Plant Varieties, and the general protection period is 15 to 20 years. However, because durian breeding takes a long time and is asexually reproduced, it sometimes affects the recognition of the "uniqueness" of new varieties. If there are new breeding techniques or planting methods, invention patents can also be applied for. In addition, geographical indications and trademark protection such as "Hainan Tree-Ripe Durian" are also a key direction for brand building in the future. This requires the establishment of a strict quality control system to cooperate. 4 Ecological Adaptation of Durian in Different Regions 4.1 Environmental factors affecting durian growth Durian is a tropical fruit with high temperature requirements. It needs to grow in a high temperature climate throughout the year, and the average annual temperature should be between 22℃ and 30℃. During the fruiting period, if the temperature is below 20℃, the fruit may not develop well or even fall. Durian also needs sunlight. There must be 8 to 10 hours of sunlight every day to make the leaves grow lush, the flowers bloom well, and the fruits are plump and juicy. The strong and long sunlight in tropical areas creates good conditions for the growth of durian. Water is also very important for durian. It likes a humid climate, and the annual precipitation is preferably between 1000 and 3000 mm. The water requirements are different in different growth periods. In the seedling stage, the soil should be kept moist, but there should be no stagnant water, otherwise the roots will rot. In the flowering and fruiting period, there should be sufficient water, otherwise the flowers will fall easily and the fruits will not grow well. Different durian varieties also adapt to the environment differently. For example, the varieties Kradumthong, Monthong and Puangmanee show different adaptability, some are drought-tolerant and some are moisture-tolerant (Khaksar et al., 2024). In Hainan, China, the climate conditions are very similar to those in Southeast Asia. The annual average temperature is around 24°C, and the rainfall is relatively high, exceeding 1 500 mm. These conditions are very suitable for durian growth. The successful cultivation in Hainan also shows that as long as the climate is suitable, the right variety is selected and scientific management methods are adopted, durian can also be grown well in China (Figure 1) (Lin et al., 2022). 4.2 Regional adaptation of key durian varieties Durian is a tropical fruit, and different varieties have different adaptability to different environments. Temperature, humidity, light and precipitation will affect its performance. At present, most commercially cultivated durians are concentrated in Southeast Asia. Thailand's Golden Pillow (Monhong) is drought-tolerant and suitable for cultivation in the east and south. It can also be grown in Hainan, China and Xishuangbanna, Yunnan, but attention should be paid to cold protection in winter. Kanyao prefers well-drained soil and is suitable for the central plains of Thailand. Chanee is more tolerant to moisture and is suitable for rainy areas in southern Thailand. Malaysian Musang King prefers a high temperature and high humidity environment and is suitable for small-scale planting in Hainan and Xishuangbanna. Black Thorn is sensitive to temperature differences and is difficult to introduce; Red Prawn is more tolerant to moisture and is suitable for hot and humid areas such as Hainan and Guangdong in China. Vietnam's Ri6 variety is more drought-tolerant and can adapt to poor soils. It is suitable for
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