Analysis of Resistance to Fungal Pathogen Hemileia Vastatrix of Liberica Coffee Based on Functional Marker
Coffee Leaf Rust (CLR) disease caused by fungal pathogen Hemileia vastatrix is one of devastated diseases in coffee plants. Disease RGA (resistance gene analog) primer pair CARF 005 has been reported for leaf rust-resistant screening in Arabica coffee and has never been reported in Liberica coffee. Previously, Liberoid Meranti 1 and 2 (Lim 1 and Lim 2) from Meranti Islands Indonesia were officially published by the government as CLR resistant cultivars and adaptive to peat soil. Our study aimed to analyze the resistance of Liberica coffee plants based on functional primer CARF 005. We sampled healthy plants of three Liberica genotypes (Lim 1, Lim 2, Bengkalis) in commercial farmer fields. DNA was extracted from young leaves, amplified and sequenced using CARF 005 primers. All samples generated DNA band about 400 bp. In addition, nucleotide sequences are similar to Arabica putative disease resistance gene. All the three sequences contain NB-ARC conserved domain which contribute to pathogenic-resistant trait. The regions also contain one motif sequence of P-loop/Walker-A domain. Our result confirmed that DNA fragments amplified by CARF 005 are linked to RGA region and eventually we suggested that CARF 005 can be used to identify resistance to CLR in Liberica. It will particularly contribute for supporting Liberica breeding program and conservation of Liberica germplasm
Alkimim, E. R., E. T. Caixeta, T. V. Sousa, A. A. Pereira, A. C. B. de Oliveira, L. Zambolim and N. S. Sakiyama. 2017. Marker-assisted selection provides arabica coffee with genes from other Coffea species targeting on multiple resistance to rust and coffee berry disease. Molecular Breeding, 37: 1-10.
Almeida, D. P. d., I. S. L. Castro, T. A. d. O. Mendes, D. R. Alves, G. D. Barka, P. R. R. M. Barreiros, L. Zambolim, N. S. Sakiyama and E. T. Caixeta. 2021. Receptor-Like Kinase (RLK) as a candidate gene conferring resistance to Hemileia vastatrix in coffee. Scientia Agricola, 78: e20200023.
Alvarenga, S. M., E. T. Caixeta, B. Hufnagel, F. Thiebaut, E. Maciel-Zambolim, L. Zambolim and N. S. Sakiyama. 2011. Molecular markers from coffee genome expressed sequences potentially involved in resistance to rust. Pesquisa agropecuária brasileira, 46: 890-98.
Alvarenga, S. M., E. T. Caixeta, B. Hufnagel, F. Thiebaut, E. Maciel-Zambolim, L. Zambolimand and N. S. Sakiyama. 2010. In silico identification of coffee genome expressed sequences potentially associated with resistance to diseases. Genetics and Molecular Biology, 33: 795-806.
Barka, G. D., E. T. Caixeta, S. S. Ferreira and L. Zambolim. 2020. In silico guided structural and functional analysis of genes with potential involvement in resistance to coffee leaf rust: A functional marker based approach. PLoS One, 15: e0222747.
Cao, H., Y. Yang, Z. Pei, W. Zhang, D. Ge, Y. Sha, W. Zhang, K. Fu, Y. Liu and Y. Chen. 2013. Intellectualized identifying and precision controlsystem for horticultural crop diseases based on small unmanned aerial vehicle. Computer and Computing Technologies in Agriculture VI: 6th IFIP WG 5.14 International Conference, CCTA 2012, Zhangjiajie, China.
de Araújo, A. C., F. C. D. A. Fonseca, M. G. Cotta, G. S. C. Alves and R. N. G. Miller. 2019. Plant NLR receptor proteins and their potential in the development of durable genetic resistance to biotic stresses. Biotechnology Research and Innovation, 3: 80-94.
Dodds, P. N. and J. P. Rathjen. 2010. Plant immunity: Towards an integrated view of plant–pathogen interactions. Nature Reviews Genetics, 11: 539-48.
Harni, R., E. Taufiq and B. Martono. 2015. Ketahanan pohon induk kopi liberika terhadap penyakit karat daun (Hemileia vastatrix B. et Br.) di Kepulauan Meranti. Jurnal tanaman Industri dan penyegar, 2: 35-42.
Jibat, M. 2020. Review on resistance breeding methods of coffee leaf rust in Ethiopia. International Journal of Research in Agriculture and Forestry, 7: 32-41.
Jones, J. D. and J. L. Dangl. 2006. The plant immune system. Nature, 444: 323-29.
Kim, J., C. J. Lim, B.-W. Lee, J.-P. Choi, S.-K. Oh, R. Ahmad, S.-Y. Kwon, J. Ahn and C.-G. Hur. 2012. A genome-wide comparison of NB-LRR type of resistance gene analogs (RGA) in the plant kingdom. Molecules and cells, 33: 385-92.
Kumar, S., G. Stecher and K. Tamura. 2016. MEGA7: Molecular evolutionary genetics analysis version 7.0 for bigger datasets. Molecular biology and evolution, 33: 1870-74.
Lee, H.-A. and S.-I. Yeom. 2015. Plant NB-LRR proteins: Tightly regulated sensors in a complex manner. Briefings in functional genomics, 14: 233-42.
Martanti, D., U. Widyastuti, Y. S. Poerba and R. Megia. 2015. Identification of gene candidate of nucleotide binding site (NBS) from banana Musa acuminata Colla var Malaccensis (Riddl.) Nasution and Musa, AAA, Cavendish sub-group. Pakistan Journal of Biological Sciences, 18: 99-106.
Maryani, S. and D. Novriadhy. 2022. The potency of Coffea liberica to remediate peat soil after fires in the musi-belida peat hydrological unity, Indonesia. IOP Conference Series: Earth and Environmental Science.
McCook, S. and J. Vandermeer. 2015. The big rust and the red queen: Long-term perspectives on coffee rust research. Phytopathology, 105: 1164-73.
Noir, S., M.-C. Combes, F. Anthony and P. Lashermes. 2001. Origin, diversity and evolution of NBS-type disease-resistance gene homologues in coffee trees (Coffea L.). Molecular Genetics and Genomics, 265: 654-62.
Pestana, K. N., A. S. Capucho, E. T. Caixeta, D. P. de Almeida, E. M. Zambolim, C. D. Cruz, L. Zambolim, A. A. Pereira, A. C. B. de Oliveira and N. S. Sakiyama. 2015. Inheritance study and linkage mapping of resistance loci to Hemileia vastatrix in Híbrido de Timor UFV 443-03. Tree Genetics and Genomes, 11: 1-13.
Prasetyo, P., R. Hidayat and H. Purnomo. 2019. Budidaya Kopi Liberika di lahan gambutCenter for International Forestry Research. Bogor, Indonesia. pp. 3-6.
Santos, M. d. L., M. L. V. de Resende, B. A. dos Santos Ciscon, N. C. Freitas, M. H. d. B. Pereira, T. Reichel and S. M. Mathioni. 2022. LysM receptors in Coffea arabica: Identification, characterization, and gene expression in response to Hemileia vastatrix. PLoS One, 17: e0258838.
Silva, M. d. C., L. Guerra-Guimarães, I. Diniz, A. Loureiro, H. Azinheira, A. P. Pereira, S. Tavares, D. Batista and V. Várzea. 2022. An overview of the mechanisms involved in Coffee-Hemileia vastatrix interactions: Plant and pathogen perspectives. Agronomy, 12: 326.
Steele, J. F., R. K. Hughes and M. J. Banfield. 2019. Structural and biochemical studies of an NB-ARC domain from a plant NLR immune receptor. PLoS One, 14: e0221226.
Talhinhas, P., D. Batista, I. Diniz, A. Vieira, D. N. Silva, A. Loureiro, S. Tavares, A. P. Pereira, H. G. Azinheira and L. Guerra‐Guimarães. 2017. The coffee leaf rust pathogen Hemileia vastatrix: one and a half centuries around the tropics. Molecular plant pathology, 18: 1039.
Van Ghelder, C., G. J. Parent, P. Rigault, J. Prunier, I. Giguère, S. Caron, J. Stival Sena, A. Deslauriers, J. Bousquet and D. Esmenjaud. 2019. The large repertoire of conifer NLR resistance genes includes drought responsive and highly diversified RNLs. Scientific Reports, 9: 1-13.
Van Ooijen, G., G. Mayr, M. M. Kasiem, M. Albrecht, B. J. Cornelissen and F. L. Takken. 2008. Structure–function analysis of the NB-ARC domain of plant disease resistance proteins. Journal of experimental botany, 59: 1383-97.
Zimmer, E. A. and J. Wen. 2015. Using nuclear gene data for plant phylogenetics: Progress and prospects II. Next‐gen approaches. Journal of Systematics and Evolution, 53: 371-79.
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