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
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