Nucleotide sequence diversities of Chitinase and PR1 genes from Theobroma cacao cv. MCC 02 and Sulawesi 1
##plugins.themes.bootstrap3.article.sidebar##
Issue
Section
Articles
This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.
##plugins.themes.bootstrap3.article.main##
Abstract
Abstract. Setiowati A, Ardie SW, Santoso TJ, Sudarsono. 2024. Nucleotide sequence diversities of Chitinase and PR1 genes from Theobroma cacao cv. MCC 02 and Sulawesi 1. Biodiversitas 25: 1-13. Cocoa (Theobroma cacao) faces vascular streak dieback (VSD) disease caused by Ceratobasidium theobromae, so disease control strategies are necessary, such as developing disease-resistant cocoa cultivars. Characterization of Chitinase (Chi) and Pathogenesis Related Protein 1 (PR1) could be the starting point for such purposes. This research aimed to characterize Chi-like and PR1-like genes from cocoa cv. MCC 02 (VSD resistant) and Sulawesi 1 (SUL 1, susceptible). The Chi-like and PR1-like amplicons were generated from cocoa cultivars, and sequencing of the amplicons generated 858 bp (Chi-like) and 569 bp (PR1-like). The multiple sequence alignment (MSA) of seven Chi-like fragments from two cocoa clones identifies four non-synonymous and two synonymous SNPs. The MSA of seven PR1-like fragments from two cocoa clones identifies three non-synonymous and two synonymous SNPs in the PR1-like coding and two SNPs in the 3’-non-coding regions. Phylogenetic tree construction among four TcChi-like accessions and 36 accessions from the NCBI Database indicates that all cocoa Chi-like genes are clustered in Clade II, separated from Chi-like of other species that belong to Clade I or Clade III. Phylogenetic tree construction among 24 accessions of PR1-like sequences from various plant species indicates that the cocoa PR1-like gene sequences are more closely related to Herrania umbratica and Theobroma grandiflorum.
##plugins.themes.bootstrap3.article.details##
References
Agung MB, Budiarsa IM, Suwastika IN. 2016. Analisa “In Silico” Gen Kakao (Theobroma cacao L.) yang Terlibat dalam Sistem Ketahanan Terhadap Hama dan Penyakit. Nat Sci J Sci Technol. 5(2). doi:10.22487/25411969.2016.v5.i2.6710.
Augustin NP, Prasetyo E, Santoso SI. 2022. ANALISIS DAYA SAING DAN TREND EKSPOR KAKAO INDONESIA KE LIMA NEGARA TUJUAN TAHUN 2010-2019. 6:442–455. https://doi.org/10.21776/ub.jepa.2022.006.02.10.
Allegre M, Argout X, Boccara M, Fouet O, Roguet Y, Bérard A, Thévenin JM, Chauveau A, Rivallan R, Clement D, et al. 2012. Discovery and mapping of a new expressed sequence tag-single nucleotide polymorphism and simple sequence repeat panel for large-scale genetic studies and breeding of Theobroma cacao L. DNA Res. 19(1):23–35. doi:10.1093/dnares/dsr039.
Anwar M, Nurjanah S, Rahayu WP. 2022. Basic Local Alignment Search Tool. Bioinformatics. 7(11):407–452. doi:10.1201/9781003226611-8.
Broglie K, Chet I, Holliday M, Cressman R, Biddle P, Knowlton S, Mauvais CJ, Broglic R. 1991. Transgenic plants with enhanced resistance to fungal pathogen. Rhizoctonaia solani Sci. 254 SRC-(3):1194–1197.
Budiman LF, Apriyanto A, Pancoro A, Sudarsono S. 2019. Illegitimacy Testing of Elaeis guineensis Population Based on Simple Sequence Repeat Markers. AGRIVITA, Journal of Agricultural Science 41 (3), 504-512. https://doi.org/10.17503/agrivita.v41i3.1969
Carranza MS, Zapata YP, Gallego G, Rodríguez JN, Carriel JM, Rosero NC, Jara SM, Muñoz JE. 2020. Genetic diversity of ecuadorian cocoa from the germplasm bank of tenguel-guayas ecuador based in snp’s. Bioagro. 32(2):75–86.
Central Bureau of Statistics. 2020. Indonesian Cocoa Statistics. Central Agency Statistics, Jakarta.
Carta LK, Li S. 2019. PCR amplification of a long rDNA segment with one primer pair in agriculturally important nematodes. J Nematol. 51(1):1–8. doi:10.21307/jofnem-2019-026.
Clausen PTLC. 2023. Scaling neighbor-joining to one million taxa with dynamic and heuristic neighbor-joining. Bioinformatics. 39(1):1–5. doi:10.1093/bioinformatics/btac774.
Darojat MR, Ardhie SW, Oktavia F, Sudarsono S. 2023. New leaf fall disease in rubber-pathogen characterization and rubber clone resistance evaluation using detached leaf assay. Biodiversitas Journal of Biological Diversity 24 (4): 1935-1945. https://doi.org/10.13057/biodiv/d240401
Davidson R, Campo AM del. 2020. Combinatorial and Computational Investigations of Neighbor-Joining Bias. Front Genet. 11 October. doi:10.3389/fgene.2020.584785.
De Wever J, Everaert H, Coppieters F, Rottiers H, Dewettinck K, Lefever S, Messens K. 2019. The development of a novel SNP genotyping assay to differentiate cacao clones. Sci Rep. 9(1):1–10. doi:10.1038/s41598-019-45884-8.
Defitri Y. 2017. Penyakit busuk buah tanaman kakao (theobroma cacao l. ) serta persentase serangannya di desa betung kecamatan kumpeh ilir kabupaten muaro jambi. J Media Pertan. 2(2):98. doi:10.33087/jagro.v2i2.41.
Defitri Y. 2019. Intensitas beberapa penyakit utama pada tanaman kakao (theobroma cacao, l. )di desa betung kecamatan kumpeh ilir. J Media Pertan. 4(2):81. doi:10.33087/jagro.v4i2.86.
Dewi IS, Arisanti Y, Purwoko BS, Hariyadi H, Syukur M. 2016. Keragaman Genetik Beberapa Genotipe Jarak Pagar (Jatropha curcas L.) Berdaya Hasil Tinggi Berdasarkan Karakter Morfologi, Agronomi, dan Isozim. J AgroBiogen. 9(1):28. doi:10.21082/jbio.v9n1.2013.p28-38.
Dukariya G, Kumar A. 2020. Distribution and Biotechnological Applications of Chitinase: A Review. Int J Biochem Biophys. 8(2):17–29. doi:10.13189/ijbb.2020.080201.
Elina J, Sukma D, Giyanto, Sudarsono. 2017. Isolasi dan Karakterisasi Gen Pto Asal 20 Aksesi Anggrek Phalaenopsis (Isolation and Characterization of Pto Gene from 20 Phalaenopsis Orchid Genotypes). Jurnal Agronomi Indonesia 45 (2), 204-211. https://doi.org/10.24831/jai.v45i2.12905
Fang LJ, Qin RL, Liu Z, Liu CR, Gai YP, Ji XL. 2019. Expression and functional analysis of a PR-1 Gene, MuPR1, involved in disease resistance response in mulberry (Morus multicaulis). J Plant Interact. 14(1):376–385. doi:10.1080/17429145.2019.1640295.
Farhanandi BW, Indah NK. 2022. Karakteristik Morfologi dan Anatomi Tanaman Kakao (Theobroma cacao L.) yang Tumbuh pada Ketinggian Berbeda. LenteraBio Berk Ilm Biol. 11(2):310–325. doi:10.26740/lenterabio.v11n2.p310-325.
Farid M, Nasaruddin, Anshori MF, Ridwan I, Israil S. 2021. Fruit trait-based evaluation of diallel crossing compatibility of six elite clones of cocoa. Sabrao J Breed Genet. 53(1):15–26.
Gutiérrez OA, Martinez K, Zhang D, Livingstone DS, Turnbull CJ, Motamayor JC. 2021. Selecting SNP markers reflecting population origin for cacao (Theobroma cacao L.) germplasm identification. Beverage Plant Res. 1(1):1–9. doi:10.48130/bpr-2021-0015.
Hamdi I, Lakani I. 2021. Tingkat Keparahan Penyakit Vascular Streak Dieback (Ceratobasidium theobromae) pada Tanaman Kakao (Theobroma cacao L .) setelah Pemberian Perlakuan Infus Akar. J Agrotekbis. 9(1):188–196.
Han Z, Xiong D, Schneiter R, Tian C. 2023. The function of plant PR1 and other members of the CAP protein superfamily in plant–pathogen interactions. Mol Plant Pathol. March. doi:10.1111/mpp.13320.
Hatta ANNL, Sukma D, Maskromo I, Sudarsono S. 2023. Validated SNAP markers based on the CYP P450 87 A3 gene in coconut (Cocos nucifera) are associated with yearly stem height increase. Biodiversitas Journal of Biological Diversity 24 (5): 2503-2512. https://doi.org/10.13057/biodiv/d240501
Henkrar F, UDUPA S. 2021. Marker Assisted Selection in Plant Breeding?: Future Opportunities. January.
Jehan T, Lakhanpaul S. 2006. Single nucleotide polymorphism (SNP) - methods and applications in plant genetics: A review. Indian J Biotechnol. 5(4):435–459.
Katsura Y, Stanley CE, Kumar S, Nei M. 2017. The reliability and stability of an inferred phylogenetic tree from empirical data. Mol Biol Evol. 34(3):718–723. doi:10.1093/molbev/msw272.
Kumar M, Brar A, Yadav M, Chawade A, Vivekanand V, Pareek N. 2018. Chitinases—Potential candidates for enhanced plant resistance towards fungal pathogens. Agric. 8(7):1–12. doi:10.3390/agriculture8070088.
Livingstone DS, Motamayor JC, Schnell RJ, Cariaga K, Freeman B, Meerow AW, Brown JS, Kuhn DN. 2011. Development of single nucleotide polymorphism markers in Theobroma cacao and comparison to simple sequence repeat markers for genotyping of Cameroon clones. Mol Breed. 27(1):93–106. doi:10.1007/s11032-010-9416-2.
Lukman L, Dinarti D, Siregar UJ, Turjaman M, Sudarsono S. 2022. Characterization and identification of agarwood-producing plants (Aquilaria spp.) from North Aceh, Indonesia, based on morphological and molecular markers. Biodiversitas Journal of Biological Diversity 23 (9), 4861-4871. https://doi.org/10.13057/biodiv/d230955
Mathur R, Jha AK. 2020. Encyclopedia of Animal Cognition and Behavior. Encycl Anim Cogn Behav. December. doi:10.1007/978-3-319-47829-6.
Maximova SN, Marelli JP, Young A, Pishak S, Verica JA, Guiltinan MJ. 2006. Over-expression of a cacao class I chitinase gene in Theobroma cacao L. enhances resistance against the pathogen, Colletotrichum gloeosporioides. Planta. 224(4):740–749. doi:10.1007/s00425-005-0188-6.
McMahon PJ, Susilo AW, Parawansa AK, Bryceson SR, Nurlaila, Mulia S, Saftar A, Purwantara A, bin Purung H, Lambert S, et al. 2018. Testing local cacao selections in Sulawesi for resistance to vascular streak dieback. Crop Prot. 109 January 2016:24–32. doi:10.1016/j.cropro.2018.02.026.
Nurlaila N, Rosmana A, Dewi VS. 2020. The capability of Trichoderma asperellum in suppressing vascular streak diseases on five different cocoa clones. IOP Conf Ser Earth Environ Sci. 486(1). doi:10.1088/1755-1315/486/1/012158.
Oktavia F, Kuswanhadi K, Dinarty D, Widodo W, Sudarsono S. 2017. Genetic diversity and population structure of IRRDB 1981 and Wickham rubber germplasm based on EST-SSR. AGRIVITA, Journal of Agricultural Science 39 (3), 239-251. http://doi.org/10.17503/agrivita.v39i3.881
Pesik A, Efendi D, Novarianto H, Dinarti D, Sudarsono S. 2017. Development of SNAP markers based on nucleotide variability of WRKY genes in coconut and their validation using multiplex PCR. Biodiversitas 18 (2), 465-475. https://doi.org/10.13057/biodiv/d180204
Pratiwi RS, Susanto TE, Wardani KAY, Sutrisno A. 2015. Enzim Kitinase dan Aplikasi di Bidang Industri?: Kajian Pustaka. J Pangan dan Agroindustri. 3(3):878–887. https://jpa.ub.ac.id/index.php/jpa/article/view/209.
Prihatini R, Dinarti D, Sutanto A, Sudarsono S. 2023. Sex-linked Single Nucleotide Polymorphism (SNP) identification and molecular marker development of salacca (Salacca zalacca (Gaertn.) Voss). Biodiversitas Journal of Biological Diversity 24 (2): 704-712. https://doi.org/10.13057/biodiv/d240207
Punja ZK, Zhang YY. 1993. Plant chitinases and their roles in resistance to fungal diseases. J Nematol. 25(4):526–40. http://www.ncbi.nlm.nih.gov/pubmed/19279806%0Ahttp://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC2619419.
Purwakasih DB, Achyar A. 2021. Desain primer dan PCR In Silico untuk deteksi Shigella sp. pada sampel air minum isi ulang. J Serambi Biol. 6(1):1–6. http://www.ncbi.nlm.nih.gov.
Purwoko D, Cartealy IC, Tajuddin T, Dinarti D, Sudarsono S. 2019. SSR identification and marker development for sago palm based on NGS genome data. Breeding Science 69 (1), 1-10. https://doi.org/10.1270/jsbbs.18061
Rahayu MS, Setiawan A, Maskromo I, Purwito A, Sudarsono S. 2022. Genetic diversity analysis of Puan Kalianda kopyor coconuts (Cocos nucifera) from South Lampung, Indonesia based on SSR markers. Biodiversitas Journal of Biological Diversity 23 (1), 205-211. https://doi.org/10.13057/biodiv/d230126
Ramstein GP, Buckler ES. 2022. Prediction of evolutionary constraint by genomic annotations improves functional prioritization of genomic variants in maize. Genome Biol. 23(1):1–26. doi:10.1186/s13059-022-02747-2.
Rangkuti AB, Mawarni A, Rangkuti RR. 2022. Phylogenetic reconstruction of tree species on the University of North Sumatra Campus, based on the rbcL gene. IOP Conf Ser Earth Environ Sci. 1115(1):11–16. doi:10.1088/1755-1315/1115/1/012030.
Raynalta E, Elina J, Sudarsono S, Sukma D. 2018. Clonal Fidelity of Micro-propagated Phalaenopsis Plantlets Based on Assessment Using Eighteen Ph-Pto SNAP Marker Loci. AGRIVITA, Journal of Agricultural Science 40 (3), 390-402. http://doi.org/10.17503/agrivita.v40i3.1493
Rinawati DY, Reflinur R, Dinarti D, Sudarsono S. 2021. Genetic diversity of sugar palm (Arenga pinnata) derived from nine regions in Indonesia based on SSR markers. Biodiversitas Journal of Biological Diversity 22 (9), 3749-3755. https://doi.org/10.13057/biodiv/d220919
Rosmana A, Taufik M, Asman A, Jayanti NJ, Hakkar AA. 2019. Dynamic of vascular streak dieback disease incidence on susceptible cacao treated with composted plant residues and trichoderma asperellum in field. Agronomy. 9(10). doi:10.3390/agronomy9100650.
Rubiyo. 2013. Inovasi Teknologi Perbaikan Bahan Tanam Kakao di Indonesia. Bul RISTRI. 4(3):199–214.
Rubiyo, Purwantara A, Sudarsono. 2010. Aktivitas Kitinase dan Peroksidase , Kerapatan Stomata Serta Ketahanan Kakao Terhadap Penyakit Busuk Buah. Pelita Perkeb. 26(2):104–114.
Sari IA, Susilo AW. 2011. Indikasi Pengaruh Xenia pada Tanaman Kakao ( Theobroma cacao L .). Pelita Perkeb. 27(90):181–190.
Santos C dos, Franco OL. 2023. Pathogenesis-Related Proteins (PRs) with Enzyme Activity Activating Plant Defense Responses. Plants. 12(11):1–13. doi:10.3390/plants12112226.
Syamsidi A, Aanisah N, Fiqram R, Jultri I Al. 2021. Primer Design and Analysis for Detection of mecA gene. J Trop Pharm Chem. 5(3):245–253. doi:10.25026/jtpc.v5i3.297.
Tasma IM. 2017. Aplikasi Teknologi DNA untuk Akselerasi Program Pemuliaan Ketahanan Tanaman Kakao terhadap Hama dan Penyakit Utama. J Penelit dan Pengemb Pertan. 35(4):155. doi:10.21082/jp3.v35n4.2016.p155-166.
Taufik M, Asniah A, Botek M, M R, Tasrif A. 2021. Role of Cocoa Clones and Endophyte Fungi in controlling VSD Disease in the Field. Crop - J Plant Prot. 4(1):27. doi:10.24198/cropsaver.v4i1.33087.
Tomkowiak A, Bocianowski J, Kwiatek M, Kowalczewski P?. 2020. Dependence of the heterosis effect on genetic distance, determined using various molecular markers. Open Life Sci. 15(1):1–11. doi:10.1515/biol-2020-0001.
Trisno J, Reflin R, Martinius M. 2016. Vascular Streak Dieback: Penyakit Baru Tanaman Kakao di Sumatera Barat. J Fitopatol Indones. 12(4):142. doi:10.14692/jfi.12.4.142.
Wicaksono INA, Rubiyo R, Sukma D, Sudarsono S. 2017. Analisis Keragaman Genetik 28 Nomor Koleksi Kakao (Theobroma cacao L.) Berdasarkan Marka SSR. Jurnal Tanaman Industri dan Penyegar 4 (1), 13-22. https://doi.org/10.21082/jtidp.v4n1.2017.p13-22
Widiyani DP, Hartono JSS, Mispandi L. 2022. Inventory of superior cocoa ( Theobroma cacoa L .) clones in Gedong Tataan sub-district Pesawaran. November:83–88.
Xin Y, Wang D, Han S, Li S, Gong N, Fan Y, Ji X. 2022. Characterization of the Chitinase Gene Family in Mulberry (Morus notabilis) and MnChi18 Involved in Resistance to Botrytis cinerea. Genes (Basel). 13(1). doi:10.3390/genes13010098.
Yurnaliza, Esyanti RR, Susanto A, Aryantha INP. 2017. The chitinase activity of oil palm (Elaeis guineensis Jacq.) roots against fungal endophytes and pathogenic Ganoderma boninense. Plant Omics. 10(5):247–251. doi:10.21475/poj.10.05.17.pne853.
Zakariyya F, Yuliasmara F. 2015. Top Grafting Performance of Some Cocoa (Theobroma cacao L.) Clones as Affected by Scion Budwood Number. Pelita Perkeb (a Coffee Cocoa Res Journal). 31(3):163–174. doi:10.22302/iccri.jur.pelitaperkebunan.v31i3.198.
Zhang HL, Jiang K, Jiang ZL, Lou H, Meng XJ. 2014. Significance of PR-1 proteins in infected plants. Adv Mater Res. 893 February 2014:482–487. doi:10.4028/www.scientific.net/AMR.893.482.
Zhao Z, Xie X, Liu W, Huang J, Tan J, Yu H, Zong W, Tang J, Zhao Y, Xue Y, et al. 2022. STI PCR: An efficient method for amplification and de novo synthesis of long DNA sequences. Mol Plant. 15(4):620–629. doi:10.1016/j.molp.2021.12.018.