Bioscience Methods 2026, Vol.17, No.1, 9-22 http://bioscipublisher.com/index.php/bm 10 during major outbreaks (Sapak et al., 2021). Leaf spot which also goes by the names black spot or yellow spot represents a significant issue that usually results fromPenicillium funiculosum fungal infections. The pathogen causes damage to photosynthesis and creates harm to fruits while simultaneously degrading their quality (Serrato-Diaz et al., 2023). The postharvest black rot disease which Ceratocystis paradoxa causes damages crops at the same level by entering through fruit injuries to create a soft decay with foul odor (Hubert et al., 2014). The diseases affect pineapple cultivation throughout every pineapple-producing region worldwide. Phytophthora nicotianae-induced heart rot has been documented in Latin America Asia and Africa after heavy rainfall events (Ratti et al., 2018). Black rot has spread so widely that in some regions it has been designated a quarantine concern. Brazilian agricultural production faces major losses because fusariosis and black spot diseases continue to be major agricultural threats. The control strategies for disease management include disease-free seedlings and strict field hygiene and fungicides or antibiotics and quick removal of infected plants but these methods are not always effective (Sapak et al., 2021). The continued presence of these pathogens shows that breeding programs need to establish long-term resistance as their primary goal. Traditional breeding approaches, including hybridization and mutation breeding, have achieved only limited progress in improving pineapple resistance. The main challenge arises from the limited genetic diversity of commercial cultivars including 'Smooth Cayenne' and 'MD2' (Li et al., 2022). The limited availability of useful resistance genes exists because plant breeding operations face additional challenges due to the biological characteristics of the crop. Pineapple requires 2~3 years from planting to fruiting and because it is both self-incompatible and highly heterozygous, progeny populations show broad genetic variation that makes selection challenging. The execution of long-term field tests which extend across multiple years results in both high expenses and prolonged testing periods. The advancement of new crop varieties through chance seedlings and somaclonal variants has led to some progress yet the rate of improvement continues to be sluggish. Mutation breeding produces new traits but the process of screening big populations is time-consuming and unwanted genetic changes frequently emerge (Serrato-Diaz et al., 2023). The development of new hybrid cultivars requires 15–20 years but pathogens can adapt their resistance in less than this timeframe which creates a continuous challenge for plant breeders. In this context, CRISPR/Cas9 genome-editing technology represents a promising alternative. The system employs guide RNA together with Cas9 protein to generate precise double-strand breaks at predetermined positions in the genome. The plant cell fixes these breaks through its built-in cellular mechanisms which lead to minor genetic changes that result in gene inactivation (Guo et al., 2023). Scientists employ this method to disable disease-producing genes which makes plants more vulnerable to disease while maintaining their important agricultural characteristics (Wan et al., 2020). CRISPR technology enables scientists to evaluate edited lines within a single breeding cycle which results in faster breeding processes. The method allows scientists to turn on defense genes according to Han et al. (2025) and Rivera-Toro et al. (2025) or to edit multiple targets at once by using multiplexing approaches (Li et al., 2025; Oliva et al., 2019). Research studies show that CRISPR technology demonstrates potential for creating long-term disease resistance according to Langner et al. (2018), and its successful application in other crops strongly suggests that pineapple may also benefit from this technology. This study explores how CRISPR/Cas9 can help build disease-resistant pineapple. It reviews the pineapple genome and key defense routes, takes lessons from other crops, and puts forward editing plans for heart rot, black rot, and leaf spot. It also points out problems such as low transformation efficiency and off-target edits, and suggests possible fixes. The aim is to give clear scientific guidance for accurate breeding and to support lasting disease control and higher yields in tropical fruit crops. 2 Pineapple Genome and Disease-Related Gene Resources 2.1 Pineapple genome sequencing and annotation progress In the past ten years, research has made big progress in understanding the pineapple genome. This provides a base for using genome editing. The first draft genome of pineapple (‘F153’) was published in 2015 (Ming et al., 2015).
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