Molecular characterization of Iranian isolates of Alfalfa mosaic virus based on movement protein gene

Document Type : Research Paper


1 : Department of plant protection, college of Agriculture, Shahid Bahonar university of Kerman

2 Department of Plant Pathology, Shahid Bahonar University of Kerman

3 Associate professor, Department of Plant Pathology, College of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran

4 Department of Plant Pathology, College of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran


Alfalfa mosaic virus (AMV) is one of the most important plant viruses that has a wide host range and economically is a destructive virus in the world and Iran. The aim of this research is to study the MP gene of Iranian AMV isolates and its application in the phylogenetical analysis and compare it with the CP gene.
Materials and methods
During 2014 to 2017, a number of plant samples including alfalfa and weeds were collected from alfalfa fields in six Iranian provinces. ELISA test using polyclonal antibodies and RT-PCR were employed to check the AMV infection of the samples. Among the AMV infected samples, 20 isolates including 17 from alfalfa and three wild species including Sonchus oleraceus L., Chenopodium amaranticolor L. and Plantago ovate L. were chosen for phylogenetical analysis based on the sequence of the MP gene.
Phylogenetic analysis based on the nucleotide sequence of movement protein (MP) gene of AMV including Iranian (n=20) and GenBank isolates (n=15) showed that all isolates are divided into two group I and II and each group is also divided into two subgroups A and B. The majority of Iranian isolates were placed in group II. All abroad and two Iranian isolates (Accession numbers: KX535454 and KX535456) were placed in subgroup IA, and subgroup IB is limited to three Iranian isolates (Accession numbers: KX535460, KX535458 and KX535462). Whereas based on the part of the nucleotide sequence of the MP gene (468nt), most of Iranian isolates, together with one Spanish isolate (JQ691163) were clustered in a new subgroup (IIB).
According to the results of this study, it seems that the MP gene can be used to analyze the phylogenetic relationships between AMV isolates. Since the origin of AMV is from Far-East and central Asia and due to the host variability of the virus in these regions, AMV probably has a high genetic diversity in Iran.


Bergua M, Luis- Artega M, Escriu F (2014) Genetic diversity, reassortment, and recombination in Alfalfa mosaic virus population in Spain. Phytopathol 104 (11), 1241-1250.
Clark MF, Adams SAN (1997) Characteristics of microplates method of enzyme-linked-immunosorbent assay for detection of plant viruses. J Gen Virol 34, 475-483.
Crill P, Hagedorn DJ, Hanson EW (1970). Incidence and effect of AMV on alfalfa. Phytopathol 60, 1432-1435.
Edwardson JR, Christie RG (1997) Virus infecting peppers and others solanaceous crops (volume I). Agricultural Experiment Station, University of Florida.
Garcia-Arenal F, Fraile A, Malpica JM (2001) Variability and genetic structure of plant virus populations. Annu Rev Phytopathol 39, 157-186.
Guyader S, Ducray DG (2002) Sequence analysis of Potato leaf roll virus isolates reveals genetic stability, major evolutionary events and differential selection pressure between overlapping reading frame products. J Gen Virol 83, 1799–1807.
Hall TA (1999) BioEdit: A User-Friendly Biological Sequence Alignment Editor and Analysis Program for Windows 95/98/NT. Nucleic Acids Symp Ser 41, 95-98.
Hull R (1969) Alfalfa mosaic virus. Adv Virus Res 15, 365 – 433.
Jaspars EMJ, Bos JF (1980) Alfalfa Mosaic virus. CMI/ AAB. DPV No. 229.
Kimura M (1980) A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleic sequences. J Mol Evol 16,111-120.
King AMQ, Adams MJ, Carestens EB, Lefkowitz EJ (2012) Virus taxonomy classification and nomenclature of viruses. Ninth report of international committee on taxonomy of viruses. Elsevier Academic Press. 1327pp.
Li WH (1993) Unbiased estimation of the rates of synonymous and nonsynonymous substitution. J Mol Evol 36, 96–99.
Libardo P, Rozas J (2009) DnaSP V5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25, 1451–1452.
Mangeli F, Massumi H, Alipour F et al. (2019) Molecular and partial biological characterization of the coat protein sequences of Iranian alfalfa mosaic virus isolates. J Plant Pathol 101, 735–742.
Miczynski KA, Hiruki C (1987) Effect of Alfalfa mosaic virus on the yield and regeneration of alfalfa at different growth temperature. Can J Plant Pathol 9, 49- 55.
Muhire BM, Varsani A, Martin DP (2014) SDT: a virus classification tool based on pairwise sequence alignment and identity calculation. PLoS ONE 9, e108277.
Ouibrahim L, Caranta C (2013) Exploitation of natural genetic diversity to study plant-virus interactions: what can we learn from Arabidopsis thaliana? Mol plant Pathol 14(8), 844-854.
Pamilo P, Bianchi NO (1993) Evolution of the Zfx and Zfy genes: rates and independence between the genes. Mol Biol Evol 10, 271–281.
Parrella G, Acanfora N, Orilio A F, Navas-Castillo J (2011) Complete nucleotide sequence of a Spanish isolate of Alfalfa mosaic virus: evidence for additional genetic variability. Arch Virol 156, 1049-1052.
Sharifi M, Massumi H, Heydarnejad J et al. (2008) Analysis of the biological and molecular variability of Watermelon mosaic virus isolates from Iran. Virus Genes 37, 304-313.
Smith K M (1972). A textbook of Plant Virus Diseases, 3rd ed., Academic Press, New York.
Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) MEGA6: Molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30, 2725-2729.
Tian YP, Liu JL, Zhang CL, Liu YY, Wang B, Li XD, Valkonen JPT (2011) Genetic diversity of Potato virus Y infecting tobacco crops in China. Phytopathol 101(3), 377-387.
Trucco VN, Breuil SD, Bejerman N, Lenardon S, Giolitti F (2014) Complete nucleotide sequence of Alfalfa mosaic virus isolated from alfalfa (Medicago sativa L.) in Argentina. Virus Genes 48, 562–565.
Tu JC, Holmes TM (1980). Effect of Alfalfa mosaic virus infection on nodulation, forage yield, forage protein and overwintering of alfalfa. Phytopathol 97, 1- 9.
Westgate JM (1908) Alfalfa. Washington: U.S. Department of Agriculture. P.5. Retrieved July 2013.
Weimer JL (1931). Alfalfa mosaic virus. Phytopathol 21, 122 - 123.
Yang Z, Nielsen R (2000) Estimating synonymous and non-synonymous substitution rates under realistic evolutionary models. Mol Biol Evol 17, 32-43.
Yoon JY, Joa JH, San Choi K, Do KS, Lim HC, Chung BN (2014) Genetic diversity of a natural population of Apple stem pitting virus isolated from apple in Korea. Plant Pathol J 30(2), 195-199.