Skip to main content
Log in

Combined study on genetic diversity of wheat genotypes using SNP marker and phenotypic reaction to Heterodera filipjevi

Genetic Resources and Crop Evolution Aims and scope Submit manuscript

Abstract

Wheat is the most important host for cereal cyst nematode, Heterodera filipjevi. The wild relatives of wheat have important sources of resistance genes to cereal nematodes. Phenotypic and genotypic evaluations have important implications for breeding programs, hence in this study information on the reaction of wheat genotypes to H. filipjevi and their genetic relationships are provided. A total of 223 wheat genotypes originating mostly from West Asia and North Africa (WANA countries) were evaluated against the H. filipjevi. Genetic diversity of 188 genotypes were assessed by using a 152 K single nucleotide polymorphism (SNP) chip. Data were analysed using generalized linear model, showed that there are significant differences at P ≤ 0.0001 among the tested genotypes. UPGMA clustering analysis clearly distinguished the genotypes into two main groups based on 840 SNP markers. The first group (A) consisted of 177 accessions containing multiple clusters, whilst the second group (B) with 11 accessions formed only a single cluster. The similarity coefficient between the accessions ranged from 0.30 and 0.99 with an average of 0.64. The present study demonstrated valuable source of resistance to the local population of H. filipjevi in a diverse range of bread wheat landraces that expand our knowledge towards promising perspective in development of resistant genotype in control strategies of cereal cyst nematode.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1

Similar content being viewed by others

References

  • Anonymous (2016) Manual protocols for Cereal Cyst Nematode, Root Lesion Nematode and Crown Rot’ employed by SBP Program CIMMYT—TURKEY. Prepared by: Soil Borne Pathogens Group—CIMMYT/Turkey

  • Balakhnina VP (1989) Resistance of varieties of Triticum durum Desf. and Triticum aestivum L. to the oat cyst nematode. In: Gel’mintologiya Segodnya: Problemy I Perspektivy. Tezisy Dokladov Nauchnoi Konferentsii, Moscow, 4–6 Apr 1989, Moscow, USSR, vol 2, pp 36–37

  • Batieno BJ, Souleymane O, Tignegre JB, Huynh BL, Kusi F, Poda SL, Close TJ, Roberts P, Danquah E, Ofori K, Ouedraogo TJ (2018) Single nucleotide polymorphism (SNP)-based genetic diversity in a set of Burkina Faso cowpea germplasm. Afr J Agric Res 13(19):978–987. https://doi.org/10.5897/AJAR2018.13121

    Article  Google Scholar 

  • Bhatta M, Morgounov A, Belamkar V, Poland J, Baenziger PS (2018) Unlocking the novel genetic diversity and population structure of synthetic Hexaploid wheat. BMC Genom 19(1):591. https://doi.org/10.1186/s12864-018-4969-2

    Article  Google Scholar 

  • Bishnoi SP, Bajaj H (2002) Response of resistant barley cultivars to the Indian populations of Heterodera avenae complex. Indian J Nematol 32:125–128

    Google Scholar 

  • Cobb NA (1918) Estimating the nema population of soil, with special reference to the sugar-beet and root-gall nemas, Heterodera schachtii Schmidt and Heterodera radicicola (Greef) Müller and with a description of Tylencholaimus aequalis n. sp. National Government Printing Office, Washington

    Google Scholar 

  • Cook R, Noel GR (2002) Cyst nematodes: Globodera and Heterodera species. In: Star JL, Cook R, Bridge J (eds) Plant resistance to parasitic nematodes. CAB International, Wallington, pp 71–105

    Chapter  Google Scholar 

  • Dhingani RM, Umrania VV, Tomar RS, Parakhia MV, Golakiya B (2015) Introduction to QTL mapping in plants. Ann Plant Sci 4(04):1072–1079

    Google Scholar 

  • Grosse E, Kohlmüller S (2004) Untersuchungen zur Verbreitung von Getreidezystennematoden nach einer neuen Differentialmethode. Mitteilungen Aus der Biologischen Bundesanstalt für Land- und Forstwirtschaft Berlin-Dahlem 396:563–564

    Google Scholar 

  • Hajihasani A, Maafi ZT, Nicol JM, Rezaee S (2010) Effect of the cereal cyst nematode, Heterodera filipjevi, on wheat in microplot trials. Nematology 12:357–363

    Article  Google Scholar 

  • Holgado R, Andersson S, Rowe JA, Magnusson C (2004) First record of Heterodera filipjevi in Norway. Nematol Mediterr 32:205–211

    Google Scholar 

  • Jehan T, Lakhanpaul S (2006) Single nucleotide polymorphism (SNP)–methods and applications in plant genetics: a review. Indian J Biotechnol 5:435–459

    CAS  Google Scholar 

  • Kabbaj H, Sall AT, Al-Abdallat A, Geleta M, Amri A, Filali-Maltouf A, Belkadi B, Ortiz R, Bassi FM (2017) Genetic diversity within a global panel of durum wheat (Triticum durum) landraces and modern germplasm reveals the history of alleles exchange. Front Plant Sci 8:1277

    Article  Google Scholar 

  • Kara K, Kanouni MR, Debbabi OS, Naceur MB (2017) Genetic diversity of bread wheat genotypes (Triticum Aestivum L.) revealed by agromorphological characteristics and microsatellite SSR markers. Int J Res Eng Technol 6:178–182

    Google Scholar 

  • Khan MK, Ozsensoy Y, Pandey A, Thomas G, Akkaya MS, Kayis SA, Hamurcu M, Gezgin S, Topal A, Hakki EE (2015) Genetic diversity and population structure of wheat in India and Turkey. AoB Plants 7:plv083. https://doi.org/10.1093/aobpla/plv083

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Khodadadi M, Fotokian MH, Miransari M (2011) Genetic diversity of wheat (Triticum aestivum L.) genotypes based on cluster and principal component analyses for breeding strategies. Aust J Crop Sci 5(1):17–24

    Google Scholar 

  • Madzhidow AR (1981) New species of Bidera filipjevi sp. nov. (Heteroderina: Tylenchida) from Tadzhikistan. Izvectija Akademii Nauk Tadzjikiskov SSR, Otdelenie Biologitseskich Nauk 2:40–44

    Google Scholar 

  • Mammadov J, Aggarwal R, Buyyarapu R, Kumpatla S (2012) SNP markers and their impact on plant breeding. Int. J Plant Genom 2012:728398. https://doi.org/10.1155/2012/728398

    Article  CAS  Google Scholar 

  • Mourad AMI, Sallam A, Belamkar V, Wegulo S, Bowden R, Jin Y, Mahdy E, Bakheit B, El-Wafaa AA, Poland J, Baenziger PS (2018) Genome-wide association study for identification and validation of novel SNP markers for Sr6 stem rust resistance gene in bread wheat. Front Plant Sci 9:380. https://doi.org/10.3389/fpls.2018.00380

    Article  PubMed  PubMed Central  Google Scholar 

  • Nicol JM, Bolat N, Şahin E, Tulek A, Yıldırım AF et al (2006) The cereal cyst nematode is causing economic damage on rain fed wheat production system of Turkey. Phytopathology 96:S169

    Google Scholar 

  • Nicol JM, Turner SJ, Coyne DL, Den Nijs L, Hockland S, Tahna Maafi Z (2011) Current nematode threats to world agriculture. In: Jones J, Gheysen G, Fenoll C (eds) Genomics and molecular genetics of plant-nematode interactions. Springer, Dordrecht, pp 21–23

    Chapter  Google Scholar 

  • Pariyar SR, Dababat AA, Sannemann W, Erginbas-Orakci G, Elashry A, Siddique S, Morgounov A, Leon J, Grundler FM (2016) Genome-wide association study in wheat identifies resistance to the cereal cyst nematode Heterodera filipjevi. Phytopathol 106(10):1128–1138. https://doi.org/10.1094/PHYTO-02-16-0054-FI

    Article  CAS  Google Scholar 

  • Rafalski A (2002) Applications of single nucleotide polymorphisms in crop genetics. Curr Opin Plant Biol 5:94–100

    Article  CAS  Google Scholar 

  • Ren J, Sun D, Chen L, You FM, Wang J, Peng Y, Nevo E, Sun D, Luo MC, Peng J (2013) Genetic diversity revealed by single nucleotide polymorphism markers in a worldwide germplasm collection of durum wheat. Int J Mol Sci 14:7061–7088. https://doi.org/10.3390/ijms14047061

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Riley IT, Nicol JM, Dababat AA (2009) Cereal cyst nematodes: status, research and outlook. In: Proceedings of the first workshop of the international cereal cyst nematode initiative, 21–23 Oct 2009, Antalya,Turkey. CIMMYT, Ankara

  • Rumpenhorst HJ, Elekçioğlu IH, Sturhan D, Öztürk G, Eneli S (1996) The cereal cyst nematode Heterodera filipjevi (Madzhidov) in Turkey. Nematol Mediterr 24:135–138

    Google Scholar 

  • Saghai-Maroof MA, Soliman K, Jorgensen RA, Allard RW (1984) Ribosomal DNA spacer-length polymorphisms in barley: Mendelian inheritance, chromosomal location, and population dynamics. PNAS 81:8014–8018

    Article  CAS  Google Scholar 

  • Sansaloni C, Petroli C, Jaccoud D, Carling J, Detering F, Grattapaglia D, Kilian A (2011) Diversity arrays technology (DArT) and next-generation sequencing combined: genome-wide, high throughput, highly informative genotyping for molecular breeding of Eucalyptus. BMC Proc 5:54

    Article  Google Scholar 

  • Schork N, Fallin D, Lanchbury J (2000) Single nucleotide polymorphisms and the future of genetic epidemiology. Clin Genet 58:250–264

    Article  CAS  Google Scholar 

  • Sharma P, Saini M, Gupta OP, Gupta N, Singh AK, Selvakumar R, Tiwari V, Sharma I (2013) Tracking of cereal cyst nematode resistance genes in wheat using diagnostic markers. J Wheat Res 5(1):35–40

    CAS  Google Scholar 

  • Shi A, Qin J, Mou B, Correll J, Weng Y, Brenner D (2017) Genetic diversity and population structure analysis of spinach by single-nucleotide polymorphisms identified through genotyping-by-sequencing. PLoS ONE 12(11):e0188745. https://doi.org/10.1371/journal.pone.0188745

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Smiley RW, Dababat AA, Iqbal S, Jones MGK, Tanha Maafi Z, Peng D, Subbotin SA, Waeyenberge L (2017) Cereal cyst nematodes: a complex and destructive group of Heterodera species. Plant Dis 101:1692–1720. https://doi.org/10.1094/PDIS-03-17-0355-FE

    Article  CAS  PubMed  Google Scholar 

  • Smiley RW, Yan GP, Handoo ZA (2008) First record of the cyst nematode Heterodera filipjevi on wheat in Oregon. Plant Dis 92:1136

    Article  CAS  Google Scholar 

  • Spanic V, Korzun V, Ebmeyer E (2016) Assessing genetic diversity of wheat genotypes from different origins by SNP markers. Cereal Res Commun 44(3):361–369. https://doi.org/10.1556/0806.44.2016.012

    Article  CAS  Google Scholar 

  • Sturhan D (1996) Occurrence of Heterodera flipjevi (Madzhidov, 1981) Stelter, 1984 in Iran. Pak J Nematol 14:89–93

    Google Scholar 

  • Subbotin SA, Sturhan D, Rumpenhorst HJ, Moens M (2003) Molecular and morphological characterisation of the Heterodera avenae species complex (Tylenchida: Heteroderidae). Nematology 5:515–538

    Article  CAS  Google Scholar 

  • Taranto F, D’Agostino N, Greco B, Cardi T, Tripodi P (2016) Genome-wide SNP discovery and population structure analysis in pepper (Capsicum annuum) using genotyping by sequencing. BMC Genom 17:943. https://doi.org/10.1186/s12864-016-3297-7

    Article  CAS  Google Scholar 

  • Tanha Maafi Z, Subbotin SA, Moens M (2003) Molecular identification of cyst forming nematodes (Heteroderidae) from Iran and a phylogeny based on ITS-rDNA sequences. Nematology 5:99–111

    Article  Google Scholar 

Website

  • FAOSTAT website, Food and Agriculture Organization of the United Nations. faostat.fao.org. Accessed on 2017

Download references

Acknowledgements

We would like to thank Farhad Saeidi Naeini from Nematology Research Department, Iranian Research Institute of Plant Protection for the help in statistical analyses.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Zahra Tanha Maafi.

Ethics declarations

Conflict of interest

The authors declare that they have no conflict of interest.

Human and animal rights

This research did not involve human participants or animals.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Majd Taheri, Z., Tanha Maafi, Z., Nazari, K. et al. Combined study on genetic diversity of wheat genotypes using SNP marker and phenotypic reaction to Heterodera filipjevi. Genet Resour Crop Evol 66, 1791–1811 (2019). https://doi.org/10.1007/s10722-019-00836-z

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10722-019-00836-z

Keywords

Navigation