The production of chili pepper (Capsicum annuum L.) is hindered by several biotic factors even though striding progresses were made in genetic improvement in the last two decades. Among the advancements were the fast-track genetic improvement of disease-resistant varieties by the use of marker-assisted selection (MAS) and the conventional breeding-based introgression of major resistance genes. Marker development, marker-based identification and fine mapping have revealed a large number of resistance genes, from which cloning of some candidate genes demonstrated the applicability and versatility of map-based cloning for disease resistance. In some of the recent fine mapping of disease resistance QTLs, closely linked DNA markers were identified, which in turn resulted in the rapid introgression of target gene(s) into breeding lines. Also, progresses were made on the characterization and map-based cloning of resistance genes conferring broad-spectrum resistance. As the number of identified and characterized resistance genes and the DNA markers linked to resistance genes are steadily generated, the development of multiple/durable resistance to major chili pepper diseases is accelerated by MAS. In the present review, the development of molecular markers, marker-based mapping of genes conferring resistance to ten major chili pepper diseases were discussed, focusing on the recent advancements in major and QTL-spanning resistance gene mapping. The review provides up-to-date insights into the development of DNA markers linked to disease resistance genes and the cloning of resistance genes, which are all so crucial in pepper breeding for disease resistance.

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• Effects of a Coal-derived Soil Amendment on Plant Growth of Sweet Pepper (Capsicum annuum) and Rhizosphere Microbial Communities
  Xing-Feng Huang, Paul H. Fallgren, Kenneth F. Reardon, Song Jin
  Journal of Soil Science and Plant Nutrition.2026; 26(1): 2799.     CrossRef
• Integrating Hybrid and Molecular Breeding as Approaches in Vegetable Breeding Strategies
  Janko Červenski, Srđan Zec, Gordana Tamindžić, Dragana Miljaković, Jelena Marinković, Boris Adamović, Đorđe Vojnović, Aleksandra Ilić
  Horticulturae.2026; 12(6): 666.     CrossRef
• Molecular and genomic insights into viral resistance in Capsicum spp.: pathogenesis, defense mechanisms, and breeding innovations
  Jayabalan Shilpha, Won-Hee Kang
  Frontiers in Plant Science.2025;[Epub]     CrossRef
• Fine mapping of the Chilli veinal mottle virus resistance 4 (cvr4) gene in pepper (Capsicum annuum L.)
  Joung-Ho Lee, Jung-Min Kim, Jin-Kyung Kwon, Byoung-Cheorl Kang
  Theoretical and Applied Genetics.2025;[Epub]     CrossRef
• Wild-type and resistance-breaking strains of tomato spotted wilt virus differentially upregulate the immunosuppressive epoxyoctadecamonoenoic acid biosynthesis of its insect vector, Frankliniella occidentalis
  Niayesh Shahmohammadi, Falguni Khan, Donghee Lee, Daehong Lee, Yonggyun Kim
  Journal of General Virology .2025;[Epub]     CrossRef
• Development of SNP Markers for ms3 Gene of Genetic Male Sterility in Pepper (Capsicum annuum L.)
  Soeun Lee, Bora Geum, Jundae Lee
  Korean Journal of Breeding Science.2025; 57(4): 391.     CrossRef
• Cleaved Amplified Polymorphic Sequence Markers in Horticultural Crops: Current Status and Future Perspectives
  Krishnanand P. Kulkarni, Richmond K. Appiah, Umesh K. Reddy, Kalpalatha Melmaiee
  Agronomy.2024; 14(11): 2598.     CrossRef
• The landscape of sequence variations between resistant and susceptible hot peppers to predict functional candidate genes against bacterial wilt disease
  Ji-Su Kwon, Junesung Lee, Jayabalan Shilpha, Hakgi Jang, Won-Hee Kang
  BMC Plant Biology.2024;[Epub]     CrossRef
• Phenotypical and molecular characterization of new pepper genotypes resistant to Chili pepper mild mottle virus firstly detected in Europe and other tobamoviruses
  Mikel Ojinaga, Ana Aragones, Mónica Hernández, Santiago Larregla
  Scientia Horticulturae.2024; 330: 113074.     CrossRef
• Assessment of elite pepper breeding lines using molecular markers
  Ercan Ekbiç, Ceylan Özlem Okay
  Plant Biotechnology Reports.2024; 18(4): 515.     CrossRef
• Current knowledge and breeding strategies for management of aphid-transmitted viruses of pepper (Capsicum spp.) in Africa
  Herbaud P. F. Zohoungbogbo, Fabrice Vihou, Enoch G. Achigan-Dako, Derek W. Barchenger
  Frontiers in Plant Science.2024;[Epub]     CrossRef
• Comparison of effectiveness of molecular markers linked to Me1 and N genes in pepper (Capsicum annuum L.) (Solanales: Solanaceae)
  Gülsüm Uysal, Zübeyir Devran
  Turkish Journal of Entomology.2024; 48(2): 239.     CrossRef
• Pepper mild mottle virus: a formidable foe of capsicum production—a review
  Nidhi Kumari, Vivek Sharma, Priyankaben Patel, P. N. Sharma
  Frontiers in Virology.2023;[Epub]     CrossRef
• Development and Application of a Cleaved Amplified Polymorphic Sequence Marker (Phyto) Linked to the Pc5.1 Locus Conferring Resistance to Phytophthora capsici in Pepper (Capsicum annuum L.)
  Giacomo Bongiorno, Annamaria Di Noia, Simona Ciancaleoni, Gianpiero Marconi, Vincenzo Cassibba, Emidio Albertini
  Plants.2023; 12(15): 2757.     CrossRef
• QTL Mapping for Resistance to Bacterial Wilt Caused by Two Isolates of Ralstonia solanacearum in Chili Pepper (Capsicum annuum L.)
  Saeyoung Lee, Nidhi Chakma, Sunjeong Joung, Je Min Lee, Jundae Lee
  Plants.2022; 11(12): 1551.     CrossRef
• A multiplex RT-PCR assay for detection of emergent pepper Tsw resistance-breaking variants of tomato spotted wilt virus in South Korea
  Sun-Jung Kwon, Young-Eun Cho, Hee-Seong Byun, Hae-Ryun Kwak, Jang-Kyun Seo
  Molecular and Cellular Probes.2022; 61: 101792.     CrossRef
• Advances in S gene targeted genome-editing and its applicability to disease resistance breeding in selected Solanaceae crop plants
  Geleta Dugassa Barka, Jundae Lee
  Bioengineered.2022; 13(6): 14646.     CrossRef
• Genomic regions and candidate genes linked with Phytophthora capsici root rot resistance in chile pepper (Capsicum annuum L.)
  Dennis N. Lozada, Guillermo Nunez, Phillip Lujan, Srijana Dura, Danise Coon, Derek W. Barchenger, Soumaila Sanogo, Paul W. Bosland
  BMC Plant Biology.2021;[Epub]     CrossRef
• Resistance-Breaking Tomato Spotted Wilt Virus Variant that Recently Occurred in Pepper in South Korea is a Genetic Reassortant
  Sun-Jung Kwon, Young-Eun Cho, Oh-Hun Kwon, Hyung-Gon Kang, Jang-Kyun Seo
  Plant Disease.2021; 105(10): 2771.     CrossRef
• Identification of QTLs Controlling α-Glucosidase Inhibitory Activity in Pepper (Capsicum annuum L.) Leaf and Fruit Using Genotyping-by-Sequencing Analysis
  Doie Park, Geleta Dugassa Barka, Eun-Young Yang, Myeong-Cheoul Cho, Jae Bok Yoon, Jundae Lee
  Genes.2020; 11(10): 1116.     CrossRef