Detection of ColletotrichumSpecies Causing Anthracnose of Chili by Polymerase Chain reaction

Received: 21-01-2019

Accepted: 19-02-2019

DOI:

Views

5

Downloads

1

Issue: Vol. 16 No. 12 (2018)

Section:

NÔNG HỌC

How to Cite:

Hung, N., Cuong, H., & Lam, H. (2024). Detection of ColletotrichumSpecies Causing Anthracnose of Chili by Polymerase Chain reaction. Vietnam Journal of Agricultural Sciences, 16(12), 1025–1038. http://testtapchi.vnua.edu.vn/index.php/vjasvn/article/view/528

Detection of ColletotrichumSpecies Causing Anthracnose of Chili by Polymerase Chain reaction

Nguyen Duy Hung (*) 1 , Ha Viet Cuong 2 , Hoang Chung Lam 1

  • 1 Viện nghiên cứu Rau quả
  • 2 Khoa Nông học,Học viện Nông nghiệp Việt Nam

    • Keywords

    Colletotrichum, chili, specific primerdesign, diagnosis, PCR

    Abstract


    Anthracnose caused by Colletotrichumspp. is one of the most destructive diseases of chili in Vietnam and worldwide. Identifying Colletotrichumspecies that cause anthracnosebased on morphological characteristics often causes confusion. The objective of the study was to design specific primer pairs for rapid and accurate diagnosis of Colletotrichumfungus causing anthracnose by PCR(polymerase chain reaction). In the study, based on the Internal TranscribedSpacer (ITS) region and the intergenic region of apn2 and MAT1-2-1genes (ApMat) four specific primer pairs were designed. Four species,i.e.C. truncatum, C. fructicola, C. gloeosporioides sensu strictoandC. siamensethat cause chili anthracnose in the Red River Delta and some other provinceswere detected.The study also showed that a modified rapid extraction protocol using NaOH was highly effective to prepare DNA samples from Colletotrichumcultures for PCR reaction. PCR analyses using the newly designed specific primers on 52 chili Colletotrichumisolates collected from 13 provinces, mainly the Red River Delta, revealedC. siamenseas the most abundant species (51.9%of total isolates), followed by C. fructicola(21.2%), C. truncatum(15.4%), and C. gloeosporioidessensu stricto (9.6%).

    References

    Cannon P.F., Damm U., Johnston P.R. & Weir B.S. (2012). Colletotrichum-current status and future directions. Studies in Mycology, 73: 181-213.

    De Silva D.D., Ades P.K., Crous P.W. & Taylor P.W.J. (2017). Colletotrichumspecies associated with chili anthracnose in Australia. Plant pathology, 66(2): 254-267.

    Diao Y.Z., Zhang C., Liu F., Wang W.Z., Liu L., Cai L. & Liu X.L. (2017). Colletotrichumspecies causing anthracnose disease of chili in China. Persoonia: Molecular Phylogeny and Evolution of Fungi, 38: 20.

    Dieffenbach C.W., Lowe T.M., & Dveksler G.S. (1993). General concepts for PCR primer design. PCR Methods Appl, 3(3): S30-S37.

    Don L.D., Van T.T., Phuong VyT.T. & KieuP.T.M. (2007). Colletotrichumspp. Attacking on Chilli Pepper Growing inVietnam. Country Report In:Oh D.G., KimK.T.(Eds.), Abstracts of the First International Symposium on Chilli Anthracnose National Horticultural Research Institute, Rural Development of Administration, Republic of Korea, p. 24.

    Doyle J.J. & Doyle J.L. (1987). A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochemical Bulletin,19: 11-15.

    Hyde K., Cai L., McKenzie E., Yang Y., Zhang J. & Prihastuti H. (2009). Colletotrichum: a catalogue of confusion. Fungal Diversity, 39: 1-12.

    Imjit N., Rattanakreetakul C. & Pongpisutta R. (2012). Polymerase chain reaction based detection of Chilli anthracnose disease. In I International Conference on Postharvest Pest and Disease Management in Exporting Horticultural Crops-PPDM2012 973,pp. 199-206

    JudelsonH. (2006). Guidelines For Designing Primers. Primer Guidelines, 10(6): 1-5.

    Kamle M., Pandey B.K., Kumar P. & KumarM. (2013). A Species-Specific PCR based Assay for rapid detection of mango anthracnose pathogen Colletotrichumgloeosporioides Penz and Sacc. J. Plant Pathol. Microbiol., 4(184): 10-4172.

    Ko T.W.K., McKenzie E.H.C., Bahkali A.H., To-anun C., Chukeatirote E., Promputtha I., Ahmed K., Wikee S., Chamyuang S. & Hyde K.D. (2011). The need for re-inventory of Thai phytopathogens. Chiang Mai Journal of Science,38: 625-637.

    Larkin M.A., Blackshields G., Brown N.P., Chenna R., McGettigan P.A., McWilliam H. &Thompson J.D. (2007). Clustal W and Clustal X version 2.0. bioinformatics, 23(21): 2947-2948.

    Liu F., Wang M., Damm U., Crous P.W., & Cai L. (2016). Species boundaries in plant pathogenic fungi: a Colletotrichumcase study. BMC evolutionary biology, 16(1): 81.

    Liu F., Weir B.S., Damm U., Crous P.W., Wang Y., Liu B.& Cai L. (2015). Unravelling Colletotrichumspecies associated with Camellia: employing ApMat and GS loci to resolve species in the C. gloeosporioides complex. Persoonia: Molecular Phylogeny and Evolution of Fungi, 35:63.

    Mongkolporn O., Montri P., Supakaew T. & Taylor P. W. (2010). Differential Reactions on Mature Green and Ripe Chili Fruit Infected byThree Colletotrichumspp. Plant Disease, 94: 306-310.

    Ngô Bích Hảo (1992). Bệnh thán thư hại ớt, Tạp chí Bảo vệ thực vật, 124(4): 15-17.

    Nguyễn Duy Hưng, Hà Viết Cường, Hoàng Chúng Lằm, Nguyễn Đức Huy (2017). Xác định nấm Colletotrichumgây bệnh thán thư ớt ở đồng bằng sông Hồng. Tạp chí khoa học công nghệ nông nghiệp Việt Nam, 12(85): 87-93.

    Osmundson T.W., Eyre C.A., Hayden K.M., Dhillon J. & Garbelotto M.M. (2013). Back to basics: an evaluation of NaOH and alternative rapid DNA extraction protocols for DNA barcoding, genotyping, and disease diagnostics from fungal and oomycete samples. Molecular ecology resources, 13(1): 66-74.

    Peres N., Souza N., Peever T. & Timmer L. (2004). Benomyl sensitivity of isolates of Colletotrichumacutatumand C. gloeosporioidesfrom citrus. Plant Disease, 88: 125-130.

    Prihastuti H., CaiL., Chen H., McKenzie E.H.C. & Hyde K.D. (2009). Characterization of Colletotrichumspecies associated with coffee berries in northern Thailand. Fungal Diversity, 39(1): 89-109.

    Ranathunge N.P., Mongkolporn O., Ford R. & Taylor P.W.J. (2012). ColletotrichumtruncatumPathosystem on Capsicumspp: infection, colonization and defence mechanisms. Australasian Plant Pathology, 41(5): 463-473.

    RychlikW. (1993). Selection of primers for polymerase chain reaction. In PCR Protocols. Humana Press, Totowa, NJ., pp. 31-40.

    Rychlik W.J.S.W., Spencer W.J. & Rhoads R.E. (1990). Optimization of the annealing temperature for DNA amplification in vitro. Nucleic acids research, 18(21): 6409-6412.

    Sharma G. & ShenoyB.D. (2013). Colletotrichumfructicolaand C. siamenseare involved in chilli anthracnose in India. Archives Of Phytopathology And Plant Protection,47: 1179-1194.

    Shi A., Kantartzi S.K., Mmbaga M.T., Chen P., Mrema F. & Nnodu E. (2008). PCR-based markers for detection of Colletotrichumacutatum and C.gloeosporioidesin flowering dogwood (Cornusflorida). Australasian Plant Pathology, 37(1): 65-68.

    Silva D.N., TalhinhasP.,Várzea V., Cai L., Paulo O.S. & BatistaD. (2012). Application of the Apn2/MAT locus to improve the systematics of the Colletotrichumgloeosporioidescomplex: an example from coffee (Coffeaspp.) hosts. Mycologia, 104(2): 396-409.

    Srinivasan M., Kothandaraman S.V., Vaikuntavasan P. & Rethinasamy V. (2014). Development of conventional and real-time PCR protocols for specific and sensitive detection of Colletotrichum capsiciin chilli (Capsicum annuumL.). Phytoparasitica, 42(4): 437-444.

    Suwannarat S., SteinkellnerS., SongkumarnP.& SangchoteS. (2017). Diversity of Colletotrichumspp. isolated from chili pepper fruit exhibiting symptoms of anthracnose in Thailand. Mycological Progress, 16(7): 677-686.

    ThanP.P., Prihastuti H., Phoulivong S., TaylorP.W. & HydeK.D. (2008). Chilli anthracnose disease caused by Colletotrichumspecies. Journal of Zhejiang University Science B,9: 764-778.

    Torres-Calzada C., Tapia-Tussell R., Quijano-Ramayo A., Martin-Mex R., Rojas-Herrera R., Higuera-Ciapara I. & Perez-BritoD. (2011). A species-specific polymerase chain reaction assay for rapid and sensitive detection of Colletotrichumcapsici. Molecular biotechnology, 49(1): 48-55.

    Udayanga D., Manamgoda D.S., Liu X., Chukeatirote E. & Hyde K.D. (2013). What are the common anthracnose pathogens of tropical fruits? Fungal Diversity, 61(1):165-179.

    Wang H., Qi M. & Cutler A.J. (1993). A simple method of preparing plant samples for PCR. Nucleic acids research, 21(17): 4153.

    Weir B.S., Johnston P.R. & DammU. (2012). The Colletotrichumgloeosporioidesspecies complex.Studies in Mycology 73: 115-180

    Yao J., Lan C., Huang P. & YuD. (2018). PCR detection of Colletotrichumgloeosporioidesin Psidium guajava. Australasian Plant Pathology, 47(1): 95-100.