Bioscience Methods 2026, Vol.17, No.1, 9-22 http://bioscipublisher.com/index.php/bm 9 Research Insight Open Access Application of Genome Editing in Pineapple Disease Resistance Breeding: CRISPR/Cas9 Strategies ChuchuLiu 1,2 , Zhonggang Li 2 1 Cuixi Academy of Biotechnology, Zhuji, 311800, Zhejiang, China 2 Hainan Institute of Tropical Agricultural Resources, Sanya, 572025, Hainan, China Corresponding author: chuchu.liu@cuixi.org Bioscience Methods, 2026, Vol.17, No.1 doi: 10.5376/bm.2026.17.0002 Received: 01 Dec., 2025 Accepted: 04 Jan., 2026 Published: 19 Jan., 2026 Copyright © 2026 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., 2026, Application of genome editing in pineapple disease resistance breeding: CRISPR/Cas9 strategies, Bioscience Methods, 17(1): 9-22 (doi: 10.5376/bm.2026.17.0002) Abstract The three main causes of yield loss in pineapple crops include heart rot and black rot and leaf spot. Breeding new types in the usual way takes many years. The crop maintains a restricted genetic diversity because it cannot produce self-pollination and requires extended periods for growth and testing. The research evaluates CRISPR/Cas9 as a fast method to introduce disease resistance. We show the main defense routes, such as SA, JA/ET, and MAPK. We implement editing approaches which have proven effective in different plant species. The main ways are: (i) change promoters or switch on defense genes; (ii) remove susceptibility genes and genes that decrease defense; (iii) modify control sites such as miRNA binding sites; and (iv) edit multiple genes simultaneously to build resistance. Some problems remain. The regeneration rate is low and edited plants can be mosaic and pineapple has high heterozygosity and off-target hits can occur. The solutions for this problem include tissue culture improvement and morphogenic regulator addition and nuclease precision enhancement and RNP delivery without DNA. Our approach consists of three phases which begin with omics-based target selection followed by DNA-free multiplex editing and end with field testing and compliance with transgene-free plant regulations. The described methods enable pineapples to develop robust and extensive resistance that can be used by breeders to create new plant lines. Keywords Pineapple (Ananas comosus); CRISPR/Cas9; Disease resistance; Susceptibility genes; Promoter editing; Multiplex editing; DNA-free delivery 1 Introduction The tropical fruit pineapple (Ananas comosus) gains its popularity from its enjoyable taste and nutritious value and its essential role in global trade because of its multiple industrial uses. Bananas and citrus fruits join mangoes as the world's leading tropical fruits according to global production statistics (Tripathy, 2024). The FAO reports that worldwide production exceeds 28 million tonnes each year according to Gunawardena and Lokupitiya (2024). The cultivation of this plant species occurs in approximately 90 nations which span across Asia and Africa and the Americas. The majority of these products originate from Costa Rica and the Philippines and Brazil and Thailand and Indonesia because these countries produce more than 70% of the world supply (Li et al., 2022). Costa Rica alone produces close to 2.9 million tonnes annually. The pineapple trade is valued at several billion US dollars (Ming et al., 2015) and people use it both as a fresh product and in processed items including juice and canned fruit and confectioneries and bromelain. Given its high economic and nutritional importance, considerable efforts have been devoted to cultivar improvement. The continuous emergence of diseases results in decreased agricultural output and interrupted market operations (Sapak et al., 2021). The creation of resistant crop varieties has become essential because fungal diseases now endanger agricultural production at an unprecedented level. The protection of harvests and farmer incomes and export markets requires immediate development of resistant crop varieties. Pineapple farming faces its most critical challenge from disease pressure which includes heart rot as one of its most damaging diseases. The disease starts with small water-soaked spots in plant cores which then quickly lead to decay of inner leaf tissue. It is typically caused by Phytophthora spp. The disease results from fungal infections by Phytophthora infestans and bacterial infections by Dickeya zeae which can lead to total plantation destruction
RkJQdWJsaXNoZXIy MjQ4ODYzNA==