Plant Gene and Trait 2025, Vol.16, No.1, 1-14 http://genbreedpublisher.com/index.php/pgt 8 overexpression of the AcWRKY31 gene may increase the sensitivity of plants to drought and salt stress, showing the complexity of plant stress response mechanisms (Huang et al., 2022; Macioszek et al., 2024). Another key gene family is the DREB transcription factor family, which plays a core role in plant response to stress by regulating the activity of specific DNA elements. They are currently considered an important target for improving the stress tolerance of future pineapple varieties, providing a theoretical basis and technical direction for breeding new varieties that are more adaptable to drought, salinity, high temperature or low temperature environments (Chai et al., 2020). 6.2 Contributions to improved pest and pathogen resistance Pineapple growers have long faced serious pests and diseases, with mealybugs, nematodes and root rot being the main threats to yield. Fortunately, some wild pineapple species - Ananas bracteatu and Ananas ananassoides - are naturally resistant to mealybugs. These resistance traits have been introduced into commercial breeding, and breeders hope to cultivate stronger varieties through genetic improvement, while reducing the use of pesticides and maintaining or even increasing yield levels. In the Caribbean, the Red Spanish variety is well known for its natural defense mechanism. Its thick skin and fibrous leaves are structural features that help to keep out nematodes (Charles et al., 2025). Similarly, traditional local varieties from Brazil and Colombia show strong resistance to root rot, and their genetic resources are now being used to improve the resistance of major cultivated varieties. With the rapid development of genomics technology, breeders have more efficient tools to accelerate the process of disease-resistant breeding. Macioszek et al. (2024) pointed out that enhancing the expression of the AcWRKY31 gene can effectively improve pineapple’s resistance to mealybugs. The plant calcium-dependent protein kinase (CDPK) gene has also been identified as a key regulatory factor in responding to pathogen infection and is an important target with potential in future disease-resistant breeding (Zhang et al., 2020). 7 Case Study 7.1 Identification and diversity of pineapple germplasm based on SNP markers Globally, with the widespread planting of pineapples as economic fruit trees, countries have continuously introduced and improved cultivars, forming a complex germplasm flow network. How to accurately identify the genetic background of many pineapple varieties and clarify the relationship between different varieties is one of the basic tasks of modern breeding and resource protection. Zhou et al. (2015) developed 58 stable SNP molecular markers for 94 pineapple materials from different sources for rapid identification of germplasm resources. The study specifically analyzed the differences between two materials HANA 96 and HANA 97 in the ‘Cayenne 7898’ group. Although the two are very similar in appearance, their flesh color is obviously different: one is white and the other is dark yellow (Figure 2). This somatic mutation was successfully identified by SNP markers, indicating that molecular methods can accurately track small variations in asexually propagated crops. This method provides a practical tool for variety management, germplasm protection and pineapple breeding. 7.2 Global germplasm flow promotes pineapple variety diversification and modern cultivation system optimization The global exchange of pineapple germplasm resources has provided an important impetus for the cultivation of new varieties and the optimization of cultivation systems. A typical case is the study of the Japanese variety “Yugafu”. Nashima et al. (2022) used haplotype-resolved genome sequencing methods to deeply analyze the genetic background of the variety and identify key genes related to leaf morphology and flesh color. This information was used in molecular marker-assisted selection (MAS) to guide more precise breeding strategies. The study also confirmed that “Yugafu” was bred from the hybrid of the two parents “Cream pineapple” and “HI101”.
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