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;
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