Development and characterisation of SSR markers in the potato rot nematode Ditylenchus destructor
In: NematologySearch for other papers by Jukui Ma in
Current site
Google Scholar
Search for other papers by Jingwei Chen in
Current site
Google Scholar
Search for other papers by Chengling Zhang in
Current site
Google Scholar
Search for other papers by Dongjing Yang in
Current site
Google Scholar
Search for other papers by Wei Tang in
Current site
Google Scholar
Search for other papers by Fangyuan Gao in
Current site
Google Scholar
Search for other papers by Yiping Xie in
Current site
Google Scholar
Search for other papers by Houjun Sun in
Current site
Google Scholar
Summary
The potato rot nematode, Ditylenchus destructor, causes serious disease limiting the production of many crops. This disease usually decreases sweet potato yield by 20-50%, and in heavily infested fields the crop may be completely lost. Although the nematode has economic importance in China, its transmission route and genetic diversity are unknown. In this study, a collection of 1761 contigs of the D. destructor genome was mined for simple sequence repeat (SSR) markers, which resulted in the identification of 9745 SSRs. A total of 150 pairs of SSR primers were further developed and used for validation of the amplification rate and assessment of the polymorphism. Nine SSR markers were finally identified and analysed using 96 individual specimens of D. destructor sampled from four provinces in China. These loci were found to be moderately polymorphic with 2-8 alleles per locus. The observed and expected heterozygosity across the four populations ranged from 0.000 to 0.833 and from 0.000 to 0.666, respectively. This is the first report of the development and characterisation of genomic SSR markers in D. destructor. Our study demonstrated the obvious gene differentiation among different populations of D. destructor in China. This suggests that D. destructor in China may have been introduced from multiple origins. Much more work is needed on this species to identify patterns of spread, and the microsatellite loci we develop here should be useful in many regions for modelling range expansion, studying the evolution of resistance, and increasing the effectiveness of pest management strategies.
Purchase
Buy instant access (PDF download and unlimited online access):
Institutional Login
Log in with Open Athens, Shibboleth, or your institutional credentials
Personal login
Log in with your brill.com account
-
Alenda, C., Montarry, J. & Grenier, E. (2014). Human influence on the dispersal and genetic structure of French Globodera tabacum populations. Infection, Genetics and Evolution 27, 309-317. DOI: 10.1016/j.meegid.2014.07.027
-
Amiri, S., Subbotin, S.A. & Moens, M. (2002). Identification of the beet cyst nematode Heterodera schachtii by PCR. European Journal of Plant Pathology 108, 497-506. DOI: 10.1023/A:1019974101225
-
Basson, S., De Waele, D. & Meyer, A.J. (1992). Effect of host plant age on population development and pathogenicity of Ditylenchus destructor on peanut. Journal of Nematology 24, 310-314.
-
Beier, S., Thiel, T., Münch, T., Scholz, U. & Mascher, M. (2017). MISA-web: a web server for microsatellite prediction. Bioinformatics 33, 2583-2585. DOI: 10.1093/bioinformatics/btx198
-
Boucher, A.C., Mimee, B., Montarry, J., Bardou-Valette, S., Bélair, G., Moffett, P. & Grenier, E. (2013). Genetic diversity of the golden potato cyst nematode Globodera rostochiensis and determination of the origin of populations in Quebec, Canada. Molecular Phylogenetics and Evolution 69, 75-82. DOI: 10.1016/j.ympev.2013.05.020
-
Earl, D.A. & von Holdt, B.M. (2012). STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conservation Genetics Resources 4, 359-361. DOI: 10.1007/s12686-011-9548-7
-
Goodey, J.B. (1952). The influence of the host on the dimensions of the plant parasitic nematode, Ditylenchus destructor. Annals of Applied Biology 39, 468-474.
-
Goudet, J. (1995). FSTAT (version 1.2): a computer program to calculate F-statistics. Journal of Heredity 86, 485-486.
-
Huang, J., Qi, L.J., Wang, J.C., Li, H.M., Song, S.Y., Wang, H.B. & Lin, M.S. (2009). Morphological and genetic analysis on different populations of Ditylenchus destructor. Acta Phytopathologica Sinica 39, 125-131.
-
Jeger, M., Bragard, C., Caffier, D., Candresse, T., Chatzivassiliou, E., Dehnen-Schmutz, K., Gilioli, G., Gregoire, J., Miret, J.A.J., Rafoss, T. et al. (2016). Risk to plant health of Ditylenchus destructor for the EU territory. EFSA Journal 14, 4602. DOI: 10.2903/j.efsa.2016.4602
-
Kalinowski, S.T. & Taper, M.L. (2006). Maximum likelihood estimation of the frequency of null alleles at microsatellite loci. Conservation Genetics 7, 991-995. DOI: 10.1007/s10592-006-9134-9
-
Kim, J., Kim, T., Lee, Y.C., Chun, J.Y., Kern, E.M., Jung, J. & Park, J.K. (2016). Characterization of 15 microsatellite loci and genetic analysis of Heterodera schachtii (Nematoda: Heteroderidae) in South Korea. Biochemical Systematics and Ecology 64, 97-104. DOI: 10.1016/j.bse.2015.11.013
-
Ma, J.K., Zhang, C.L., Yang, D.J. & Xie, Y.P. (2021). [Development and application of recombinase polymerase amplification assay for rapid detection of Ditylenchus destructor.] Southwest China Journal of Agricultural Sciences 34, 293-298.
-
Mallez, S., Castagnone, C., Espada, M., Vieira, P., Eisenback, J.D., Mota, M., Guillemaud, T. & Castagnone-Sereno, P. (2013). First insights into the genetic diversity of the pinewood nematode in its native area using new polymorphic microsatellite loci. PLoS ONE 8, e59165. DOI: 10.1371/journal.pone.0059165
-
Mallez, S., Castagnone, C., Espada, M., Vieira, P., Eisenback, J.D., Harrell, M., Mota, M., Aikawa, T., Akiba, M. et al. (2015). Worldwide invasion routes of the pinewood nematode: what can we infer from population genetics analyses? Biological Invasions 17, 1199-1213. DOI: 10.1007/s10530-014-0788-9
-
Marshall, T.C., Slate, J., Kruuk, L.E.B. & Pemberton, J.M. (1998). Statistical confidence for likelihood-based paternity inference in natural populations. Molecular Ecology 7, 639-655. DOI: 10.1046/j.1365-294x.1998.00374.x
-
Metzgar, D., Bytof, J. & Wills, C. (2000). Selection against frameshift mutations limits microsatellite expansion in coding DNA. Genome Research 10, 72-80.
-
Montarry, J., Jan, P.-L., Gracianne, C., Overall, A.D.J., Bardou-Valette, S., Olivier, E., Fournet, S., Grenier, E. & Petit, E.J. (2015). Heterozygote deficits in cyst plant-parasitic nematodes: possible causes and consequences. Molecular Ecology 24, 1654-1667. DOI: 10.1111/mec.13142
-
Mulet, K., Fargette, M., Richaud, M., Genson, G. & Castagnone-Sereno, P. (2011). Isolation of microsatellites from an enriched genomic library of the plant-parasitic nematode Meloidogyne incognita and their detection in other root-knot nematode species. European Journal of Plant Pathology 129, 501-505. DOI: 10.1007/s10658-010-9721-y
-
O’Bannon, J.H. & Esser, R.P. (1987). Regulatory perspectives in nematology. In: Veech, J.A. & Dickson, D.W. (Eds). Vistas in nematology. Hyattsville, MD, USA, Society of Nematologists, pp. 38-46.
-
Peakall, R. & Smouse, P.E. (2006). genalex 6: genetic analysis in Excel. Population genetic software for teaching and research. Molecular Ecology Notes 6, 288-295. DOI: 10.1111/j.1471-8286.2005.01155.x
-
Picard, D., Plantard, O., Scurrah, M. & Mugniéry, D. (2004). Inbreeding and population structure of the potato cyst nematode (Globodera pallida) in its native area (Peru). Molecular Ecology 13, 2899-2908. DOI: 10.1111/j.1365-294X.2004.02275.x
-
Plantard, O. & Porte, C. (2004). Population genetic structure of the sugar beet cyst nematode Heterodera schachtii: a gonochoristic and amphimictic species with highly inbred but weakly differentiated populations. Molecular Ecology 13, 33-41. DOI: 10.1046/j.1365-294x.2003.02023.x
-
Pritchard, J.K., Stephens, M. & Donnelly, P. (2000). Inference of population structure using multilocus genotype data. Genetics 155, 945-959. DOI: 10.1093/genetics/155.2.945
-
Raymond, M. & Rousset, F. (1995). GENEPOP (version 1.2): population genetics software for exact tests and ecumenicism. Journal of Heredity 86, 248-249. DOI: 10.1093/oxfordjournals.jhered.a111573
-
Rice, W.R. (1989). Analyzing tables of statistical tests. Evolution 43, 223-225. DOI: 10.1111/j.1558-5646.1989.tb04220.x
-
Selkoe, K.A. & Toonen, R.J. (2006). Microsatellites for ecologists: a practical guide to using and evaluating microsatellite markers. Ecology Letters 9, 615-629. DOI: 10.1111/j.1461-0248.2006.00889.x
-
Silva, A.T.D., Penna, J.C., Goulart, L.R., Santos, M.A.D. & Arantes, N.E. (2000). Genetic variability among and within races of Heterodera glycines ichinohe assessed by RAPD markers. Genetics and Molecular Biology 23, 223-229. DOI: 10.1590/S1415-47572000000200014
-
Singh, S.K., Hodda, M., Ash, G.J. & Banks, N.C. (2013). Plant-parasitic nematodes as invasive species: characteristics, uncertainty and biosecurity implications. Annals of Applied Biology 163, 323-350. DOI: 10.1111/aab.12065
-
Tamura, K., Stecher, G., Peterson, D., Filipski, A. & Kumar, S. (2013). MEGA6: molecular evolutionary genetics analysis version 6.0. Molecular Biology and Evolution 30, 2725-2729. DOI: 10.1093/molbev/mst197
-
Van Oosterhout, C., Hutchinson, W.F., Wills, D.P. & Shipley, P. (2004). MICRO-CHECKER: software for identifying and correcting genotyping errors in microsatellite data. Molecular Ecology Notes 4, 535-538. DOI: 10.1111/j.1471-8286.2004.00684.x
-
Villate, L., Esmenjaud, D., Coedel, S. & Plantard, O. (2009). Development of nine polymorphic microsatellite markers for the phytoparasitic nematode Xiphinema index, the vector of the grapevine fanleaf virus. Molecular Ecology Resources 9, 229-232. DOI: 10.1111/j.1755-0998.2008.02411.x
-
Wan, F., Peng, D.-L., Yang, Y.-W. & He, Y.-Q. (2008). [Species specific molecular diagnosis of Ditylenchus destructor populations occurring in China.] Acta Phytopathologica Sinica 38, 263-270.
-
Wang, G., Li, E.F., Mao, Z.C. & Xie, B.Y. (2015a). Development of polymorphic microsatellites for Meloidogyne incognita, through screening predicted microsatellite loci based on genome sequence. Russian Journal of Genetics 51, 116-120. DOI: 10.7868/s0016675815010130
-
Wang, H.M., Zhao, H.H., Zhao, C.Z. & Chu, D. (2014). EST-SSR markers from Heterodera glycines Ichinohe. Russian Journal of Genetics 50, 1117-1119. DOI: 10.7868/s0016675814100154
-
Wang, H.M., Zhao, H. & Chu, D. (2015b). Genetic structure analysis of populations of the soybean cyst nematode, Heterodera glycines, from north China. Nematology 17, 591-600. DOI: 10.1163/15685411-00002893
-
Wang, X., Ma, J., Liu, H., Liu, R. & Li, H. (2018). Development and characterization of EST-derived SSR markers in the cereal cyst nematode Heterodera avenae. European Journal of Plant Pathology 150, 105-113. DOI: 10.1007/s10658-017-1256-z
-
Weir, B.S. & Cockerham, C.C. (1984). Estimating F-statistics for the analysis of population structure. Evolution 38, 1358-1370. DOI: 10.1111/j.1558-5646.1984.tb05657.x
-
Xie, Y.Z., Yin, Q.H., Dai, Q.W. & Qiu, R.L. (2004). [Inheritance and breeding for resistance to sweetpotato nematodes.] Journal of Plant Genetic Resources 5, 393-396. DOI: 10.13430/j.cnki.jpgr.2004.04.020
-
Xu, J.R., Wu, X.Q., Lu, Y. & Ye, J.R. (2014). [Development of simple sequence repeats base on pine wood nematode (Bursaphelenchus xylophilus) genome sequence.] Journal of Nanjing Forestry University (Natural Sciences Edition) 38, 36-42. DOI: 10.3969/j.issn.1000-2006.2014.02.008
-
Xu, Z., Zhao, Y.-Q., Yang, D.-J., Sun, H.-J., Zhang, C.-L. & Xie, Y.-P. (2015). Attractant and repellent effects of sweet potato root exudates on the potato rot nematode, Ditylenchus destructor. Nematology 17, 117-124. DOI: 10.1163/15685411-00002856
-
Yu, H.Y., Peng, D.L., Hu, X.Q. & Huang, W.K. (2009). Molecular cloning and sequences analysis of 28S rDNA-D2/D3 regions of Ditylenchus destructor on sweet potato in China. Acta Phytopathologica Sinica 39, 254-261. DOI: 10.13926/j.cnki.apps.2009.03.004
-
Zane, L., Bargelloni, L. & Patarnello, T. (2002). Strategies for microsatellite isolation: a review. Molecular Ecology 11, 1-16. DOI: 10.1046/j.0962-1083.2001.01418.x
-
Zhang, S.L., Li, H.X., Xu, P.G., Liu, Y.G., Yu, H.T. & Liu, X. (2019). Isolation and identification of Ditylenchus destructor from Heilongjiang. Acta Phytopathologica Sinica 49, 756-762. DOI: 10.13926/j.cnki.apps.000403
-
Zheng, J.S., Peng, D.H., Chen, L., Liu, H.L., Chen, F., Xu, M.C., Ju, S.Y., Ruan, L.F. & Sun, M. (2016). The Ditylenchus destructor genome provides new insights into the evolution of plant parasitic nematodes. Proceedings of the Royal Society B: Biological Sciences 283, 20160942. DOI: 10.1098/rspb.2016.0942
| All Time | Past 365 days | Past 30 Days | |
|---|---|---|---|
| Abstract Views | 427 | 215 | 36 |
| Full Text Views | 29 | 1 | 0 |
| PDF Views & Downloads | 40 | 2 | 0 |
Development and characterisation of SSR markers in the potato rot nematode Ditylenchus destructor
In: NematologySearch for other papers by Jukui Ma in
Current site
Google Scholar
PubMed
Search for other papers by Jingwei Chen in
Current site
Google Scholar
PubMed
Search for other papers by Chengling Zhang in
Current site
Google Scholar
PubMed
Search for other papers by Dongjing Yang in
Current site
Google Scholar
PubMed
Search for other papers by Wei Tang in
Current site
Google Scholar
PubMed
Search for other papers by Fangyuan Gao in
Current site
Google Scholar
PubMed
Search for other papers by Yiping Xie in
Current site
Google Scholar
PubMed
Search for other papers by Houjun Sun in
Current site
Google Scholar
PubMed
Summary
The potato rot nematode, Ditylenchus destructor, causes serious disease limiting the production of many crops. This disease usually decreases sweet potato yield by 20-50%, and in heavily infested fields the crop may be completely lost. Although the nematode has economic importance in China, its transmission route and genetic diversity are unknown. In this study, a collection of 1761 contigs of the D. destructor genome was mined for simple sequence repeat (SSR) markers, which resulted in the identification of 9745 SSRs. A total of 150 pairs of SSR primers were further developed and used for validation of the amplification rate and assessment of the polymorphism. Nine SSR markers were finally identified and analysed using 96 individual specimens of D. destructor sampled from four provinces in China. These loci were found to be moderately polymorphic with 2-8 alleles per locus. The observed and expected heterozygosity across the four populations ranged from 0.000 to 0.833 and from 0.000 to 0.666, respectively. This is the first report of the development and characterisation of genomic SSR markers in D. destructor. Our study demonstrated the obvious gene differentiation among different populations of D. destructor in China. This suggests that D. destructor in China may have been introduced from multiple origins. Much more work is needed on this species to identify patterns of spread, and the microsatellite loci we develop here should be useful in many regions for modelling range expansion, studying the evolution of resistance, and increasing the effectiveness of pest management strategies.
| All Time | Past 365 days | Past 30 Days | |
|---|---|---|---|
| Abstract Views | 427 | 215 | 36 |
| Full Text Views | 29 | 1 | 0 |
| PDF Views & Downloads | 40 | 2 | 0 |
