Application of Low Molecular Peptide-Based Biomarkers for the Rapid Identification of Echinochloa Species

Authors

  • Sung Yung Yoo Institute of Ecological Phytochemistry/Department of Plant Life and Environmental Science, Hankyong National University, The Republic of Korea
  • So Hyun Park Institute of Ecological Phytochemistry/Department of Plant Life and Environmental Science, Hankyong National University, The Republic of Korea
  • Jae Ho An Department of Civil, Safety and Environmental Engineering, Hankyong National University, The Republic of Korea
  • Tae Wankim Institute of Ecological Phytochemistry/Department of Plant Life and Environmental Science, Hankyong National University, The Republic of Korea

Keywords:

Barnyard grass, Echinochloa crus-galli, low molecular peptide biomarker, proteomic profiling, SELDI-TOF

Abstract

The objective of the present study was to determine the low molecular peptides in Echinochloa seeds as biomarkers for classification. Some peptide-based biomarkers for the classification of Echinochloa species were identified using SELDI-TOF, a mass spectrometry (MS) technique. Proteomic profiling using SELDI-TOF MS techniques could be a useful and powerful tool to discover peptide biomarkers and to discriminate and classify Echinochloa species, especially under 20 kDa. In 12 Echinochloa species, a total of 72 peptides were significantly detected on strong anion exchanger (CM10) and weak cation exchanger (Q10) arrays. Sixteen peptides on CM10 and 12 peptides on Q10 were selected as peptide biomarkers. The hierarchical heat map analysis of the peptide-based biomarkers indicated that Echinochloa species were classified into two groups and then more precisely subdivided. One major cluster group included early barnyard grass (ECOR), large barnyard grass (ECREC), jungle ricegrass (ECOLON), meadow barnyard grass (EPRAT), and barnyard grass (ECHCG). Hairless barnyard grass (ECGL), cockspur (ECRCR), awned billion-dollar grass (ECFRAW), awnless billion-dollar grass (ECFRAWL), awnless barnyard grass (EMITIS), awnless Japanese barnyard millet (EESCAWL), and awned Japanese barnyard millet (EESCAW) belonged to the other group.

Downloads

Download data is not yet available.

References

Agrawal G K, Jwa N S, Jung Y H, Kim S T, Kim D W, Cho K, Shibato J, Rakwal R (2013). Rice proteomic analysis: sample preparation for protein identification. In: Rice Protocols). Springer, 151-184.

Altop E K, Mennan H (2011). Genetic and morphologic diversity of Echinochloa crus-galli populations from different origins. Phytoparasitica 39: 93-102. Baginsky S (2009). Plant proteomics: concepts, applications, and novel strategies for data interpretation. Mass spectrometry reviews 28: 93-120.

Bradford M M (1976). Rapid and Sensitive Method for Quantitation of Microgram Quantities of Protein Utilizing Principle of Protein-Dye Binding. Analytical Biochemistry 72: 248-254.

Branlard G, Dardevet M, Saccomano R, Lagoutte F, Gourdon J (2001). Genetic diversity of wheat storage proteins and bread wheat quality. In: Wheat in a global environment). Springer, 157-169.

Damalas C A, Dhima K V, Eleftherohorinos I G (2008). Morphological and physiological variation among species of the genus Echinochloa in Northern Greece. Weed science 56: 416- 423.

Ehara K, Abe S (1950). Classification of the forms of Japanese barnyard millet. In: Proceedings of the Crop Science Society of Japan). 245-246.

Im I, Guh J, Lee Y (1989). Weed-Ecological Classification of the Collected Barnyardgrass [Echinochloa crus-galli (L.) Beauv.] in Korea-II. Classification of collected barnyardgrass in growth pattern by multivariate clustering. Korean Journal of Weed Science 9: 1-15.

Issaq H J, Veenstra T D, Conrads T P, Felschow D (2002). The SELDI-TOF MS approach to

proteomics: protein profiling and biomarker identification. Biochemical and biophysical research mmunications 292: 587-592.

Lee J Y, Kim J Y, Park G W, Cheon M H, Kwon K H, Ahn Y H, Moon M H, Lee H J, Paik Y K, Yoo J S (2011). Targeted Mass Spectrometric Approach for Biomarker Discovery and Validation with Nonglycosylated Tryptic Peptides from N-linked Glycoproteins in Human Plasma. Molecular & Cellular Proteomics 10. Lopez-Martinez N, Salva A P, Finch R P, Marshall G, De Prado R (1999). Molecular markers indicate intraspecific variation in the control of Echinochloa spp. with quinclorac. Weed science, 310-315.

Mæland Nilsen M, Uleberg K E, Janssen E A, Baak J, Andersen O K, Hjelle A (2011). From SELDI-TOF MS to protein identification by on-chip elution. Journal of proteomics 74: 2995- 2998.

Moon B C, Oh S M, DiTomaso J M, Fischer A, Kwon Y W (2004). Morphological classification of Echinochloa species collected in rice paddy fields of California, US. Korean Journal of Weed Science 24: 213-220.

Nozawa S, Takahashi M, Nakai H, Sato Y I (2006). Difference in SSR variations between Japanese barnyard millet (Echinochloa esculenta) and its wild relative E. crus-galli. Breeding Science 56: 335-340.

Parani M, Rajesh K, Lakshmi M, Parducci L, Szmidt A E, Parida A (2001). Species identification in seven small millet species using polymerase chain reaction-restriction fragment length polymorphism of trn S-psb C gene region. Genome 44: 495-499.

Park S J, Lee Y H, Nam Y J, Baik B K, Kim T W (2013). Peptide-Based Biomarker Discovery for Identification of Rice Cultivars using Surface Enhanced Laser Desorption/Ionization Time-of-Flight Mass pectrometry. Crop Science 53: 987-995.

Randall R P (2002) A global compendium of weeds. R G and F J Richardson, Melbourne, Victoria. 906, abstr.

Ruiz-Santaella J, Bastida F, Franco A, De Prado R (2006). Morphological and molecular characterization of different Echinochloa spp. and Oryza sativa populations. Journal of agricultural and food chemistry 54: 1166-1172.

Schudoma C, Steinfath M, Sprenger H, van Dongen J T, Hincha D, Zuther E, Geigenberger P, Kopka J, Köhl K, Walther D (2012). Conducting Molecular Biomarker Discovery Studies in Plants. In: High-Throughput Phenotyping in Plants). Springer, 127-150.

Seibert V, Wiesner A, Buschmann T, Meuer J (2004). Surface-enhanced laser desorption ionization time-of-flight mass spectrometry (SELDI TOF-MS) and ProteinChip® technology in proteomics research. Pathology-Research and Practice 200, 83-94.

Smith J, Seaton J, Osuji P, Daguiar P, Chesney P, Mcbean M, Haynes A, Harding C, Cumberbatch N (1991). Dry-Matter and Crude Protein Yields of Echinochloa-Pyramidalis on Coastal Clay Soil of Guyana. Turrialba 41: 69-75.

Sood S, Khulbe R K, Gupta A K, Agrawal P K, Upadhyaya H D, Bhatt J C (2015). Barnyard millet–a potential food and feed crop of future. Plant Breeding 134: 135-147.

Tabacchi M., Mantegazza R., Spada A. and Ferrero A. (2009). Morphological traits and molecular markers for classification of Echinochloa species from Italian rice fields.

Thathola A, Srivastava S (2002). Physicochemical properties and nutritional traits of millet‐ based weaning food suitable for infants of the Kumaon hills, Northern India. Asia Pacific journal of clinical nutrition 11: 28-32.

van Wijk K J (2001). Challenges and prospects of plant proteomics. Plant Physiol 126: 501-508.

Wallace J G, Upadhyaya H D, Vetriventhan M, Buckler E S, Tom Hash C, Ramu P (2015). The genetic makeup of a global barnyard millet germplasm collection. The Plant Genome 8.

Zhong L, Taylor D L, Whittington R J (2010). Proteomic profiling of ovine serum by SELDITOF MS: optimisation, reproducibility and feasibility of biomarker discovery using routinely collected samples. Comparative immunology, microbiology and infectious diseases 33: 47-63.

Downloads

Published

2019-02-28

How to Cite

Yoo, S. Y., Park, S. H., An, J. H., & Wankim, T. (2019). Application of Low Molecular Peptide-Based Biomarkers for the Rapid Identification of Echinochloa Species. International Journal For Research In Agricultural And Food Science, 5(2), 17–39. Retrieved from https://gnpublication.org/index.php/afs/article/view/825

Issue

Vol. 5 No. 2 (2019): International Journal For Research In Agricultural And Food Science (ISSN: 2208-2719)

Section

Articles

License

Copyright (c) 2019 International Journal For Research In Agricultural And Food Science (ISSN: 2208-2719)

Creative Commons License

This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.

In consideration of the journal, Green Publication taking action in reviewing and editing our manuscript, the authors undersigned hereby transfer, assign, or otherwise convey all copyright ownership to the Editorial Office of the Green Publication in the event that such work is published in the journal. Such conveyance covers any product that may derive from the published journal, whether print or electronic. Green Publication shall have the right to register copyright to the Article in its name as claimant, whether separately
or as part of the journal issue or other medium in which the Article is included.

By signing this Agreement, the author(s), and in the case of a Work Made For Hire, the employer, jointly and severally represent and warrant that the Article is original with the author(s) and does not infringe any copyright or violate any other right of any third parties, and that the Article has not been published elsewhere, and is not being considered for publication elsewhere in any form, except as provided herein. Each author’s signature should appear below. The signing author(s) (and, in