Development of a Multiplex PCR Assay to Detect Neofusicoccum parvum and Botryosphaeria dothidea in Walnut.
Journal
Current microbiology
ISSN: 1432-0991
Titre abrégé: Curr Microbiol
Pays: United States
ID NLM: 7808448
Informations de publication
Date de publication:
29 Oct 2024
29 Oct 2024
Historique:
received:
10
07
2024
accepted:
12
10
2024
medline:
30
10
2024
pubmed:
30
10
2024
entrez:
30
10
2024
Statut:
epublish
Résumé
In walnut orchards, frequent symptoms of cankers and dieback (fruit blight, twig and branch cankers up to tree death) are caused by different agents, in particular by Botryosphaeriaceae, primarily Neofusicoccum parvum and Botryosphaeria dothidea. This study aimed at developing a sensitive, rapid, specific and internally controlled multiplex PCR assay for the detection of these species. The ability of the multiplex PCR, with an internal inhibition control (i.e. E. coli DNA), to specifically and successfully detect members of the two targeted species was validated using 11 different isolates for each fungal target (inclusivity) and 20 tree-associated fungal species different from B. dothidea or N. parvum (exclusivity). Applicability to plant materials was further investigated and showed an absence of amplification for asymptomatic husk or twig samples while the amplification profiles of symptomatic tissues ranged from no amplification to amplification of both species, in correlation with the observed fungal contamination level. In conclusion, we developed a rapid diagnostic tool for simultaneous detection of two major fungal pathogens of walnut. Although this protocol was tailored for walnut husks and twigs, applicability to any plant sample contaminated by these pathogens can be considered.
Identifiants
pubmed: 39472323
doi: 10.1007/s00284-024-03954-9
pii: 10.1007/s00284-024-03954-9
doi:
Substances chimiques
DNA, Fungal
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
432Subventions
Organisme : Ministère de l'Agriculture, de l'Agroalimentaire et de la Forêt
ID : CASDAR RT 2020_CARIBOU
Organisme : Ministère de l'Education Nationale, de l'Enseignement Superieur et de la Recherche
ID : 2020 CDE Grant
Organisme : Région Bretagne
ID : 2020 ARED grant #1797
Informations de copyright
© 2024. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.
Références
FAOSTAT (2021) The Food and Agriculture Organization Corporate Statistical Database.
Voulgaridis V., Vassiliou VG. (2005) The walnut wood and its utilisation to high value products. Acta Horticulturae 69–81
Moral J, Morgan D, Trapero A, Michailides TJ (2019) Ecology and epidemiology of diseases of nut crops and olives caused by Botryosphaeriaceae fungi in California and Spain. Plant Dis 103:1809–1827. https://doi.org/10.1094/PDIS-03-19-0622-FE
doi: 10.1094/PDIS-03-19-0622-FE
pubmed: 31232653
Laloum Y, Verhaegue A, Moronvalle A, Masson C, Hebrard MN, Picot A, Pensec F, Belair M (2022) Élancer la recherche pour cerner le dépérissement du noyer. Infos_ctifl 386:48–58
López-Moral A, Lovera M, Raya MDC, Cortés-Cosano N, Arquero O, Trapero A, Agustí-Brisach C (2020) Etiology of branch dieback and shoot blight of English walnut caused by Botryosphaeriaceae and Diaporthe species in Southern Spain. Plant Dis 104:533–550. https://doi.org/10.1094/PDIS-03-19-0545-RE
doi: 10.1094/PDIS-03-19-0545-RE
pubmed: 31746696
Yildiz A, Benlioglu S, Benlioglu K, Korkom Y (2022) Occurrence of twig blight and branch dieback of walnut caused by Botryosphaeriaceae species in Turkey. J Plant Dis Prot 129:687–693. https://doi.org/10.1007/s41348-022-00591-x
doi: 10.1007/s41348-022-00591-x
Michailides TJ, Morgan DP, Felts D, Phillimore J (2002) First report of Botryosphaeria rhodina causing shoot blight of pistachio in California. Plant Dis 86:1273. https://doi.org/10.1094/PDIS.2002.86.11.1273C
doi: 10.1094/PDIS.2002.86.11.1273C
pubmed: 30818488
McDonald V, Lynch S, Eskalen A (2009) First report of Neofusicoccum australe, N. luteum, and N. parvum associated with avocado branch canker in California. Plant Dis 93:967. https://doi.org/10.1094/PDIS-93-9-0967B
doi: 10.1094/PDIS-93-9-0967B
pubmed: 30754556
Xu C, Zhang H, Chi F, Ji ZR, Dong QL, Cao KQ, Zhou ZS (2016) Species-specific PCR-based assays for identification and detection of Botryosphaeriaceae species causing stem blight on blueberry in China. J Integr Agric 15:573–579. https://doi.org/10.1016/S2095-3119(15)61177-7
doi: 10.1016/S2095-3119(15)61177-7
Holland LA, Trouillas FP, Nouri MT, Lawrence DP, Crespo M, Doll DA, Duncan RA, Holtz BA, Culumber CM, Yaghmour MA, Niederholzer FJA, Lightle DM, Jarvis-Shean KS, Gordon PE, Fichtner EJ (2021) Fungal pathogens associated with canker diseases of almond in California. Plant Dis 105:346–360. https://doi.org/10.1094/PDIS-10-19-2128-RE
doi: 10.1094/PDIS-10-19-2128-RE
pubmed: 32757731
Aiello D, Guarnaccia V, Costanzo MB, Leonardi GR, Epifani F, Perrone G, Polizzi G (2022) Woody canker and shoot blight caused by Botryosphaeriaceae and Diaporthaceae on mango and litchi in Italy. Horticulturae 8:330. https://doi.org/10.3390/horticulturae8040330
doi: 10.3390/horticulturae8040330
Díaz GA, Valdez A, Halleen F, Ferrada E, Lolas M, Latorre BA (2022) Characterization and pathogenicity of Diplodia, Lasiodiplodia, and Neofusicoccum species causing Botryosphaeria canker and dieback of apple trees in central Chile. Plant Dis 106:925–937. https://doi.org/10.1094/PDIS-06-21-1291-RE
doi: 10.1094/PDIS-06-21-1291-RE
pubmed: 34664980
Kenfaoui J, Radouane N, Mennani M, Tahiri A, El Ghadraoui L, Belabess Z, Fontaine F, El Hamss H, Amiri S, Lahlali R, Barka EA (2022) A panoramic view on grapevine trunk diseases threats: case of Eutypa dieback, Botryosphaeria dieback, and Esca disease. Journal of Fungi 8:595. https://doi.org/10.3390/jof8060595
doi: 10.3390/jof8060595
pubmed: 35736078
pmcid: 9224927
Vučković N, Vico I, Duduk B, Duduk N (2022) Diversity of Botryosphaeriaceae and Diaporthe species associated with postharvest apple fruit decay in Serbia. Phytopathology 112:929–943. https://doi.org/10.1094/PHYTO-07-21-0304-R
doi: 10.1094/PHYTO-07-21-0304-R
pubmed: 34664974
Su Y-Y, Qi Y-L, Cai L (2012) Induction of sporulation in plant pathogenic fungi. Mycology 3:195–200
doi: 10.1080/21501203.2012.719042
Slippers B, Boissin E, Phillips AJL, Groenewald JZ, Lombard L, Wingfield MJ, Postma A, Burgess T, Crous PW (2013) Phylogenetic lineages in the Botryosphaeriales: a systematic and evolutionary framework. Stud Mycol 76:31–49. https://doi.org/10.3114/sim0020
doi: 10.3114/sim0020
pubmed: 24302789
pmcid: 3825231
Massart S, Nagy C, Jijakli MH (2014) Development of the simultaneous detection of Ralstonia solanacearum race 3 and Clavibacter michiganensis subsp. sepedonicus in potato tubers by a multiplex real-time PCR assay. Eur J Plant Pathol 138:29–37. https://doi.org/10.1007/s10658-013-0294-4
doi: 10.1007/s10658-013-0294-4
Nechwatal J, Theil S (2022) A rapid DNA extraction method for the detection of Clavibacter sepedonicus and Ralstonia solanacearum in potato samples in a multiplex PCR test. EPPO Bulletin 52:712–717. https://doi.org/10.1111/epp.12893
doi: 10.1111/epp.12893
Chen S, Cao Y, Li T, Wu X (2015) Simultaneous detection of three wheat pathogenic fungal species by multiplex PCR. Phytoparasitica 43:449–460. https://doi.org/10.1007/s12600-014-0442-1
doi: 10.1007/s12600-014-0442-1
Silva-Campos M, Nadiminti P, Cahill D (2022) Rapid and accurate detection of Gnomoniopsis smithogilvyi the causal agent of chestnut rot, through an internally controlled multiplex PCR Assay. Pathogens 11:907. https://doi.org/10.3390/pathogens11080907
doi: 10.3390/pathogens11080907
pubmed: 36015028
pmcid: 9415963
Masek A, Latos-Brozio M, Chrzescijanska E, Podsedek A (2019) Polyphenolic profile and antioxidant activity of Juglans regia L. leaves and husk extracts. Forests. 10:988. https://doi.org/10.3390/f10110988
doi: 10.3390/f10110988
Sambrook J, Russell DW (2001) Molecular cloning: a laboratory manual. CSHL Press
Brygoo Y, Gautier AA (2007) Polymorphisme moléculaire des souches de Fusarium isolées sur épis de blé et de maïs en France - Récoltes 2003 et 2004. Mycotoxines fusariennes des céréales - Arcachon
White T, Bruns T, Lee S, Taylor J (1990) Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Pcr Protocols: a Guide to Methods and Applications,. pp 315–322
Carbone I, Kohn LM (1999) A method for designing primer sets for speciation studies in filamentous ascomycetes. Mycologia 91:553–556. https://doi.org/10.1080/00275514.1999.12061051
doi: 10.1080/00275514.1999.12061051
Glass NL, Donaldson GC (1995) Development of primer sets designed for use with the PCR to amplify conserved genes from filamentous ascomycetes. Appl Environ Microbiol 61:1323–1330
doi: 10.1128/aem.61.4.1323-1330.1995
pubmed: 7747954
pmcid: 167388
Katoh K, Rozewicki J, Yamada KD (2019) MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization. Brief Bioinform 20:1160–1166. https://doi.org/10.1093/bib/bbx108
doi: 10.1093/bib/bbx108
pubmed: 28968734
Kuraku S, Zmasek CM, Nishimura O, Katoh K (2013) aLeaves facilitates on-demand exploration of metazoan gene family trees on MAFFT sequence alignment server with enhanced interactivity. Nucl Acids Res 41:W22-28. https://doi.org/10.1093/nar/gkt389
doi: 10.1093/nar/gkt389
pubmed: 23677614
pmcid: 3692103
Talavera G, Castresana J (2007) Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst Biol 56:564–577. https://doi.org/10.1080/10635150701472164
doi: 10.1080/10635150701472164
pubmed: 17654362
Castresana J (2000) Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 17:540–552. https://doi.org/10.1093/oxfordjournals.molbev.a026334
doi: 10.1093/oxfordjournals.molbev.a026334
pubmed: 10742046
Swofford D (2002) PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods). Version 4.0b10
Kumar S, Stecher G, Li M, Knyaz C, Tamura K (2018) MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 35:1547–1549. https://doi.org/10.1093/molbev/msy096
doi: 10.1093/molbev/msy096
pubmed: 29722887
pmcid: 5967553
Bouckaert R, Vaughan TG, Barido-Sottani J, Duchêne S, Fourment M, Gavryushkina A, Heled J, Jones G, Kühnert D, De Maio N, Matschiner M, Mendes FK, Müller NF, Ogilvie HA, du Plessis L, Popinga A, Rambaut A, Rasmussen D, Siveroni I, Suchard MA, Wu CH, Xie D, Zhang C, Stadler T, Drummond AJ (2019) BEAST 2.5: an advanced software platform for Bayesian evolutionary analysis. PLOS Comput Biol 15:e1006650. https://doi.org/10.1371/journal.pcbi.1006650
doi: 10.1371/journal.pcbi.1006650
pubmed: 30958812
pmcid: 6472827
Rambaut A, Drummond AJ, Xie D, Baele G, Suchard MA (2018) Posterior summarization in Bayesian phylogenetics using Tracer 1.7. Syst Biol 67:901–904. https://doi.org/10.1093/sysbio/syy032
doi: 10.1093/sysbio/syy032
pubmed: 29718447
pmcid: 6101584
Hodcroft E, TreeCollapserCL4. http://emmahodcroft.com/TreeCollapseCL.html
Ni HF, Yang HR, Chen RS, Hung TH, Liou RF (2012) A nested multiplex PCR for species-specific identification and detection of Botryosphaeriaceae species on mango. Eur J Plant Pathol 133:819–828. https://doi.org/10.1007/s10658-012-0003-8
doi: 10.1007/s10658-012-0003-8
Weisburg WG, Barns SM, Pelletier DA, Lane DJ (1991) 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 173:697–703. https://doi.org/10.1128/jb.173.2.697-703.1991
doi: 10.1128/jb.173.2.697-703.1991
pubmed: 1987160
pmcid: 207061
Iradukunda L, Wang Y-P, Nkurikiyimfura O, Wang T, Yang LN, Zhan J (2022) Establishment and application of a multiplex PCR assay for the rapid detection of Rhizoctonia solani anastomosis group (AG)-3PT, the pathogen causing potato black scurf and stem canker. Pathogens 11:627. https://doi.org/10.3390/pathogens11060627
doi: 10.3390/pathogens11060627
pubmed: 35745481
pmcid: 9228993