Karakter Molekuler Gen AB- FAR 1 Nematoda Aphelenchoides besseyi Asal Lima Varietas Padi

  • Fitrianingrum Kurniawati Department of Plant Protection, IPB University
  • Efi Toding Tondok Department of Plant Protection, IPB University
  • Yayi Munara Kusumah Department of Plant Protection, IPB University
  • Abdul Munif Department of Plant Protection, IPB University
Keywords: amplification, homology, pathogenicity, seed-transmitted, sequence analysis


Molecular Characters of AB-FAR Gene 1 of Aphelenchoides besseyi from Five Rice Varieties

Aphelenchoides besseyi is known as nematode species that causes seed-transmitted white shoot disease in rice. One important gene that has been reported to control the pathogenicity of A. besseyi is AB FAR-1. The study was conducted to determine the character of the AB FAR-1 gene of A. besseyi extracted from rice seeds. Nematode extraction was carried out using Baerman funnel method from the seeds of 5 rice varieties, i.e. “Ciherang”, “Inpari Sidenuk”, “Sintanur”, “Prime Hybrid” and “Pak Tiwi”. Total DNA extraction of nematodes was conducted using CTAB method, followed by amplification of the AB FAR-1 gene using specific primers FAR-F1/R1 and nucleotide sequence analysis. Specific DNA band of AB FAR-1 gene measuring 150 bp was successfully amplified from all nematode samples. Sequence analysis showed that the AB FAR-1 gene had the highest homology (92.5 – 100%) with the Genbank accession no. JQ686690.1, which is the AB FAR-1 gene of A. besseyi from China. Despite having high homology, there were some nucleotide differences in the AB FAR-1 gene samples of A. besseyi from "Ciherang", "Inpari Sidenuk" and "Prime Hybrid". Further phylogenetic tree analysis differentiated the AB FAR-1 A. besseyi gene into 2 groups, i.e.  group 1 consisting of the AB FAR-1 gene A. besseyi from China, "Sintanur", "Prime Hybrids" and "Pak Tiwi" and group 2 gene AB FAR-1 A. besseyi from "Ciherang", and "Inpari Sidenuk".


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Andreson R, Mols T, Remm M. 2008. Predicting failure rate of PCR in large genomes. Nucleic Acids Res. 36(11):e66. DOI: https://doi.org/10.1093/nar/gkn290.

Boyle B, Dallaire N, MacKay J. 2009. Evaluation of the impact of single nucleotide polymorphisms and primer mismatches on quantitative PCR. BMC Biotechnol 9:75. DOI: https://doi.org/10.1186/1472-6750-9-75.

Chalanska A, Labanowski G, Malewski T. 2011. Rapid microscopic and molecular method Aphelenchoides species identification. Comm Agric Appl Biol Sci. 76(3):399–402.

Cheng X, Xiang Y, Xie H, Xu LC, Xie FT, Zhang C, Li Y. 2013. Molecular characterization and functions of fatty acid and retinoid binding protein gene (Ab-far-1) in Aphelenchoides besseyi. PLoS One. 8(6):1–9. DOI: https://doi.org/10.1371/journal.pone.0066011.

Doyle JJ, Doyle JL. 1990. A rapid total DNA preparation procedure for fresh plant tissue. Focus. 12:13–15. DOI: https://doi.org/10.2307/2419362.

[EPPO] European and Mediterranean Plant Protection Organization. 2017. Aphelenchoides besseyi. EPPO Bull. 47(3):384–400. DOI: https://doi.org/10.1111/epp.12432.

Hidayat T, Pancoro A. 2008. Ulasan kajian filogenetika molekuler dan peranannya dalam menyediakan informasi dasar untuk meningkatkan kualitas sumber genetik anggrek. J ArgoBiogen. 4(1):35-40. DOI: https://doi.org/10.21082/jbio.v4n1.2008.p35-40.

Housley DJE, Zalewski ZA, Beckett SE, Venta PJ. 2006. Design factors that influence PCR amplification success of cross-species primers among 1147 mammalian primer pairs. BMC Genomics. 7(1):253. DOI: https://doi.org/10.1186/1471-2164-7-253.

Kemena C, Notredame C. 2009. Upcoming challenges for multiple sequence alignment methods in the high-throughput era. Bioinformatics 25(19):2455–2465. DOI: http://doi.org/10.1093/bioinformatics/btp452.

Mount DW. 2004. Bioinformatics: Sequence and Genome Analysis. New York (US): Cold Spring Harbor Laboratory.

Remeeus PM, Pelazza N. 2014. Detection of Aphelenchoides besseyi on Oryza sativa. Annexe to chapter 7: Seed Health Testing Methods. Switzerland (CH): ISTA.

Ye J, Coulouris G, Zaretskaya I, Cutcutache I, Rozen S, Madden TL. 2012. Primer-BLAST: A tool to design target-specific primers for polymerase chain reaction. BMC Bioinformatics 13:134. DOI: https://doi.org/10.1186/1471-2105-13-134.

Yuryev A, Huang J, Pohl M, Patch R, Watson F, Bell P, Donaldson M, Phillips MS, Boyce-Jacino MT. 2002. Predicting the success of primer extension genotyping assays using statistical modeling. Nucleic Acids Res. 30(23):e131. DOI: https://doi.org/10.1093/nar/gnf131.

How to Cite
Kurniawati, F., Tondok, E. T., Kusumah, Y. M., & Munif, A. (2021). Karakter Molekuler Gen AB- FAR 1 Nematoda Aphelenchoides besseyi Asal Lima Varietas Padi. Jurnal Fitopatologi Indonesia, 17(3), 121-130. https://doi.org/10.14692/jfi.17.3.121-130