Journal of
General and Molecular Virology

  • Abbreviation: J. Gen. Mol. Virol.
  • Language: English
  • ISSN: 2141-6648
  • DOI: 10.5897/JGMV
  • Start Year: 2009
  • Published Articles: 37

Full Length Research Paper

Genetic diversity of rice yellow mottle virus from Niger Office and Selingue Development Rural Office in Mali

Samaké Salimatou
  • Samaké Salimatou
  • Laboratory of Research in Microbiology and Microbial Biotechnology, Faculty of Sciences and Techniques, University of Sciences, Techniques and Technologies, Bamako, BP E3206, Mali.
  • Google Scholar
Traoré Diakaridia
  • Traoré Diakaridia
  • Laboratory of Research in Microbiology and Microbial Biotechnology, Faculty of Sciences and Techniques, University of Sciences, Techniques and Technologies, Bamako, BP E3206, Mali.
  • Google Scholar
Goita Oumarou
  • Goita Oumarou
  • Institute of Rural Economy, Bamako, BP E 438, Mali.
  • Google Scholar
Sarra Soungalo
  • Sarra Soungalo
  • Institute of Rural Economy, Bamako, BP E 438, Mali.
  • Google Scholar
Dao Sognan
  • Dao Sognan
  • Laboratory of Research in Microbiology and Microbial Biotechnology, Faculty of Sciences and Techniques, University of Sciences, Techniques and Technologies, Bamako, BP E3206, Mali.
  • Google Scholar
Doumbia Bakaye
  • Doumbia Bakaye
  • Laboratory of Research in Microbiology and Microbial Biotechnology, Faculty of Sciences and Techniques, University of Sciences, Techniques and Technologies, Bamako, BP E3206, Mali.
  • Google Scholar
Amadou Hamadoun Babana
  • Amadou Hamadoun Babana
  • Laboratory of Research in Microbiology and Microbial Biotechnology, Faculty of Sciences and Techniques, University of Sciences, Techniques and Technologies, Bamako, BP E3206, Mali.
  • Google Scholar

  •  Received: 10 October 2018
  •  Accepted: 12 December 2018
  •  Published: 31 December 2018


Virus is the most constraint of rice production in West Africa. Genetic diversity of rice yellow mottle virus (RYMV) was assessed in two rice growing areas of Mali. Forty-three (43) infected rice leaf samples were collected from five locations within the Niger Office and Selingue Development Rural Office rice’s growing areas. The infected samples were confirmed by Reverse Transcriptase Polymerase Chain Reaction (RT-PCR) using primers pair Prymv1 and Prymv2. A total of twenty-six RYMV isolates were obtained and classified into two genotypes A and B with Prymv1 and one genotype with Prymv2. Sequencing of the cDNA fragments with Prymv2 shared isolates into three distinct groups I, II and III. Most of the isolates were under Group I whereas isolates from the Selingue Development Rural Office area and Moussa-Were (Niger Office) area constituted respectively Groups II and III. This study provided baseline data for monitoring the genetic diversity of rice yellow mottle virus in the two rice-growing areas of Mali which could contribute to strategies development for the disease control.


Key words: Genetic diversity, reverse transcriptase polymerase chain reaction (RT-PCR), rice yellow mottle virus (RYMV), sequencing, Mali.


Yellow mottle disease of rice is caused by a virus that belongs to the group sobemovirus (Hull and Fargette, 2005) and is endemic to only the African continent (IRD, 2014). This disease is more severe in irrigated rice-growing areas located in sub-Sahara Africa and the most damaging disease in rice cultivation (APCAM, 2004; IRD, 2014; Sere et al., 2013). It was first recorded on IET 2911 and  BG 90-2   varieties   in  1991  at  Kogoni  Agricultural Research Sub-Station and Niger Office rice growing area in the Niono sector in Mali (Anonymous, 1992). The incidence of the disease varied from 64 to 100% in Niger Office zone (WARDA, 2000) and 25 to 80% in Selingue Development Rural Office depending on the date of infection and the susceptibility of rice cultivars (APCAM, 2004). Most rice cultivars are susceptible to this virus (APCAM, 2004). Some  varieties  such as Gigante (Oryza
sativa) and Tog series (Oryza glaberrima) showed natural resistance (Thottappilly and Rossell, 1993; Ndjiondjop et al., 1999; Pidon, 2016). In rice, the resistance against this virus is governed by three genes which are rymv1-2 (O. sativa), rymv1-3 and rymv1-4 (O. glaberrima) (Thiemele et al., 2010). Other developed resistant varieties like Moroberekan, Faro 11 and IR47686-15-1-1 (Soko et al., 2015; Amancho et al., 2009), WITA9 and WAT316 (Michel et al., 2008) showed some level of susceptibility to few virus isolates.
Emergence of the virulent pathotypes capable of overcoming one or two resistance alleles has often occurred (Hebrad et al., 2018; Pidon et al., 2017; Pinel-Galzi et al., 2016). A hypervirulent pathotype was discovered in West and Central Africa by Hebrad et al. (2018). Knowledge and mapping of viral diversity are important to reduce disease incidences through improvement of local varieties susceptible to rice yellow mottle virus (RYMV). The diversity of RYMV strains has been well documented in Africa (Pinel-Galzi et al., 2015; Trovào et al., 2015; Hubert et al., 2017; Longue et al., 2017). In Mali, there is little information on the diversity of rice yellow mottle virus. RT-PCR and sequencing are the most appropriate tools for assessing the genetic variability of rice yellow mottle virus in Mali since it is RNA virus. In this study, we assessed the genetic diversity of 26 Rice Yellow Mottle Virus (RYMV), isolated from rice leaves collected in Niger Office and Selingue Development Rural Office rice growing areas in Mali.


Sampling was done from rice fields (Niono 7, Koyan N'peguena and Moussa Were) at the Niger Office and Selingue Development Rural Office (Selingue). A total of forty-three (43) leaves samples, suspected to be infected by rice yellow mottle virus, were collected which was composed of nineteen from Niono 7, eighteen from Moussa-Were, one from Koyan, two from N'peguena and three from Selingue. In each study area, diseased rice samples were collected at tillering in the four corners and the middle of each infected parcel, by harvesting leaves bearing typical yellow mottle symptoms. All samples were stored in ice for analysis at the Microbiology and Biotechnology Research Laboratory at the Faculty of Sciences and Techniques at the University of Sciences, Techniques and Technologies of Bamako (USTTB).
Identification of rice yellow mottle virus by RT-PCR
Extraction of total viral RNA
RNA was extracted from leaf samples using the Qiagen RNeasy Mini Kit Promega. The concentration of different RNA was measured in ng/μl using Biophotometer Eppendorf.
Amplification by RT-PCR
Samples   were   amplified  by  Reverse  Transcriptase-Polymerase Chain Reaction (RT-PCR) with two specific primer pairs PRymv1 (F: 5'-TGCCAATACCTATCTCCACCA-3'; R: 5'-TCACCTCTAGCGTTTGGTACG- 3’) and PRymv2 (F: 5'-CCCGCAGGACCATACTAACGA-3'; R: 5'-GGGCTTCGTCACCTCTAGC-3') in addition to the reagents of the Access Kit RT-PCR system according to manufacture instructions. The mixture was distributed in PCR Flat Cap 0.2 ml BIOLOGIX tubes with a negative control (mixed without RNA) and amplified using the Applied Biosystems thermocycler based on the following programs : reverse transcription at 48°C for 45 min, inactivation of Reverse transcription (RT) at 94°C for 2 min, denaturation at 94°C for 30 s, hybridization at 61°C for 1 min, elongation at 68°C for 2 min, final extension at 68°C for 7 min and 4°C for conservation forever. The denaturation, hybridization and elongation steps were repeated in 45 times.
Electrophoresis of RT-PCR products
RT-PCR products were run on Agarose D1 Low EEO 2% (w/v) gel which was prepared with a solution of TBE (Tris, Borate, EDTA) and mixed with 30 μl of 10% ethidium bromide (1 mg/ml). The gel products were visualized under Ultra-Violet (UV) rays and photographed with the Gel Documentation System E-BoX.
All positive samples identified with Prymv2 primer pair were directly sent at Inqaba biotec (South Africa) for sequencing.
Data analysis
The size of amplified cDNA fragments was determined in base pair (bp) with the E-cap software in comparison with the standard 50 bp DNA Step Ladder Marker Cat # G4521 for Prymv2 primer and with the Bench standard 100 bp DNA Step Ladder marker Cat # G8291 for Prymv1 primer. Sequence alignment was performed with the MEGA.7 software. Phylogenetic tree was constructed from the genetic distance between RYMV isolates with MEGA.7 software (Dao et al., 2018; Kumar et al., 2016).



The forty-three (43) suspected infected rice leaf samples collected from the different was confirmed by RT-PCR using primer pairs Prymv1 and Prymv2. Twenty-six out of 43 samples were amplified between 250 and 1100 bp. The amplified samples from Prymv2 primer pair were purified and sequenced. Variability was observed among the forty-three (43) samples with 60% of RYMV infected rice samples identified by both primers. Additional two migration profile, A and B, were obtained with Prymv1. Profile A was formed from a band of 300 bp and profile B from three bands of 300, 500 and 1100 pb (Figure 1). These two profiles corresponded to two (2) isolates of rice yellow mottle virus which were identified at Niger Office area whilst isolate A was identified only at Selingue Development Rural Office area. Isolate A was the most predominant with 96% out of the whole isolate while genotype B consisted of only VE7 isolate.
All  the   twenty-six   (26)   isolates   showed    a   single  migration pattern composed of a single band of approximately 250 bp with Prymv2 (Figure 2).
Information on positive samples is recorded in Table 1. Fifty-eight percent (58%) or 23 samples from the Niger Office area as well as the 3 samples from the Selingue Development Rural Office positively confirmed the presence of the disease which was previously reported by WARDA (2000) and APCAM (2004).
This information indicates the persistence of the disease in these different rice growing areas for about thirty years. The number of groups revealed by Prymv1 is similar to that of N'Guessan et al. (2001) who  worked  on 9 isolates from Mali by immunological and molecular characterization. Similarly, Onasanya et al. (2006) revealed the existence of two pathogenic groups on 10 strains of RYMV in Mali by greenhouse screening. However, Sere et al. (2005) found three groups with isolates collected in Mali using serological analysis. Alkali et al. (2015) and Issaka et al. (2012) generated three groups using also serological technic with isolates collected from the northern of Nigeria and Niger. Isolates from Central Africa Republic were classified into three distinct pathogenic profiles by mechanical inoculation of six   rice  cultivars (Longue  et   al.,  2018).  According   to Sérémé (2009), these different groups are related to the proteins involved in the mechanism of "silencing" to circumvent the defense system of the plant. This information reported intra- and inter-regional variability of RYMV. The sequencing of the RT-PCR products using Prymv2, showed a high nucleotide variability of the envelope protein gene of the isolates (Figure 3). The order of nucleotide sequences allowed knowing more information on the genetic diversity of the isolates.
According to similarity level, the study samples were classified into major groups: I, II and III (Figure 4). Group I, with two clusters (I1 and I2), was composed of genotypes from Niono 7, Moussa-Were (Niger Office area) and those from Selingue. This group constituted 95% of isolates from Niger Office rice growing area and more than 85% of total study’s materials. Isolate VE7, which was genotype B with Prymv1, showed high similarity with isolates VE1, VE2, VE3, VE5, VE7, VE8, VE11, VE31, VE32 and VE34 under cluster I1 in accordance with the results of Prymv2 cDNA fragment sequencing. This indicates a strong phylogenetic similarity  between   the   isolates,   although   they   were collected from different localities. This result was aligned with those from Adego et al. (2017) founding diversity of isolates within the same S4 group in western Kenya by serological and molecular typing. Groups II and III were respectively composed of isolates from Selingue and Moussa Were. No virus was detected on N'peguena and Koyan samples. Results from current study revealed genetical and regional diversities of RYMV isolates collected from different locations of Niger Office (Niono 7, Koyan N'peguena and Moussa Were) and Selingue Development Rural Office (Selingue) rice’s growing areas. Abubakar et al. (2003) reported relationships between genetic and geographical distances of rice yellow mottle virus strains. The three isolates from Selingue located about 395 km away from the Niger Office area showed genetic dissimilarity with respect to all isolates. However, one isolate (VE43) from this group was classified in Group I and the other two (VE41 and VE42) in Group II. According to Abubakar et al. (2003), the greater the geographical distance, the higher the genetic distance. Classification of the virus based on the nature  of   the   proteins    predicts    the    complexity   to overcome it. Due to frequent genetic mutations, microorganisms have the ability to adapt and grow within the new environments which facilitates their emergence at any time and becoming more virulent or more contagious (Hubert et al., 2017; Herzog, 2016). Virulent pathotypes overcoming one or two resistance alleles have been reported (Longue et al., 2018; Hebrad et al., 2018; Pidon et al., 2017; Pinel-Galzi et al., 2016). N'Guessan et al. (2001) obtained two strains of RYMV at 6% divergence in nucleotide sequence of the capsid gene showing no difference in term of pathogenicity. According to Hubert et al. (2017), knowledge about the genetic diversity of RYMV is based on a limited number of protein sequences in the envelope. The results obtained in the current study provide basic information for monitoring the evolution of yellow mottle virus genetic diversity within rice-growing areas in Mali.


Rice yellow mottle virus is present within the most growing areas of rice in Mali (Niger Office and Selingue Development Rural Office). High genetic dissimilarity was noticed from different areas based on several genotypes showing genetic variability related to geographical distance. There is therefore a complication to control this disease. Information generated on the variability of the RYMV capsid gene sequences is a good starting point of database creation for RYMV in Mali with a goal to set up a disease control program.


The authors have not declared any conflict of interests.



The author’s greatly appreciated the National Committee for Agricultural Research in Mali for funding this work. Also, Microbiology and Biotechnology Research Laboratory of the Faculty of Sciences and Techniques, Niger Office and Selingue Development Rural Office are thanked for providing facilities to conduct the work.


Abubakar Z, Ali F, Pinel A, Traore O, N'Guessan P, Notteghem JL, Kimmins F, Konate G Fargette D (2003). Phylogeography of Rice yellow mottle virus in Africa. Journal of General Virology 84:733-743.


Adego AK, Were HK, Muoma J, Mukoye B, Hebrad E, Poulicard N, Fargette D (2017). Current Status of Rice Yellow Mottle Disease in Mottle Disease in Western Kenya. Researchjournali's. Journal of Agriculture 4(9):1-12.


Alkali G, Alegbejo MD, Kashina BD, Banwo OO (2015). Analysis of serological variability and hierarchical distribution of rice yellow mottle sobemovirus isolates in northern Nigeria. International Letters of Natural Sciences 37:1-9.


Amancho NA, Kouassi NK, Diallo HA, Bouet A, Sangare A, Kouadio JY (2009). The Report of Highly Resistance-breaking isolates of Rice yellow mottle virus in Cote d'ivoire. African Journal of Plant Science and Biotechnology 3(1):44-50.


Anonymous (1992). Analytical Reports Irrigated Rice Program IER-CRRA-Niono-Mali. P 155.


Assemblée Permanente des Chambres d'Agriculture du Mali (APCAM) (2004). Six-monthly newsletter and network liaison Rice. P 12.


Dao S, Timbine, H, Goita O, Traore D (2018). Genetic Variability Assessment in Irrigated Rice (Oryza sativa and Oryza glaberrima) by PCR-SSR in Mali. International Journal of Genetics and Genomics 6(2):22-29.


Hebrad E, Pinel-Galzi A, Oludare A, Poulicard N, Aribi J, Fabre S, Siluée D (2018). Identification of a hypervirulent pathotype of Rice yellow mottle virus: A threat to genetic resistance deployment in West-Central Africa. Phytopathology 108(2):299-307.


Herzog J (2016). Emerging viruses: presentation of the Schmallenberg virus discovered in farm animals and analysis of its progression in Europe and France. An example of an emerging success. State Diploma of Doctor in Pharmacy pp. 1-151.


Hubert J, Lyimo HJ, Luzi-Kihupi A (2017). Geographical variation, distribution and diversity of Rice yellow mottle virus phylotypes in Tanzania. American Journal of Plant Sciences 8(06):1264.


Hull S, Fargette D (2005). Sobemovirus. In Virus Taxonomy: Eighth report of the international committee on taxonomy of viruses. Elsevier pp. 885-890.


Institut de Recherche pour le Développement (IRD) (2014). Rice Yellow Mottle Virus: Diversity, Pathogenesis, Evaluation and Deployment of rice varieties resistant to this pathogen LMI Patho-bios Observatory of phytopathogenic agents in West Africa P 1.


Issaka S, Onasanya A, Basso A, Shoro F, Haougui A, Sido AY, Ake S, Fargette D, Sere Y (2012). Existence of several pathotypes among Rice yellow mottle virus (RYMV) isolates collected in Niger Republic. Trends in Applied Science Research 7(1):32-45.


Kumar S, Stecher G, Tamura K (2016). MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Molecular biology and evolution 33(7):1870-1874.


Longue SRD, Pinel-Galzi A, Zinga I, Semballa S, Fargette D, Barro N (2017). Genetic diversity and molecular epidemiology of Rice yellow mottle virus in Central African Republic. International Journal of Virology 13:80-89.


Longue RDS, Traore VSE, Zinga I, Asante MD, Bouda Z, Neya JB, Traore O (2018). Pathogenicity of rice yellow mottle virus and screening of rice accessions from the Central African Republic. Virology Journal 15(1):6.


Michel Z, Hilaire KT, Mongomakée K, Souley I (2008). Screening rice (Oryza sativa L.) varieties for resistance to rice yellow mottle virus. Scientific Research and Essays 3(9):416-424.


Ndjiondjop MN, Albar L, Fargette D, Fauquet C, Ghesquière A (1999). The Genetic basis of high resistance to rice yellow mottle virus (RYMV) in cultivars of two cultivated rice species. Plant Disease 83(10).


N'Guessan P, Pinel A, Sy AA, Ghesquièere A, Fargette D (2001). Distribution, pathogenicity, and interactions of two strains of Rice yellow mottle virus in forested and savanna zones of West Africa. Plant Disease 85:59-64.


Onasanya A, Sere Y, Sie M, Akator K, Coulibaly MM, Hamadoun A (2006). Existence of Two Pathotypes of Rice Kellov mottle virus. Plant Pathology Journal 5(3):368-372.


Pidon H, Ghesquiere A, Cheron S, Issaka S, Hebrad E, Sabot F, Kolade O, Silue D, Albar L (2017). Fine mapping of RYMV3: A new resistance gene to Rice yellow mottle virus from Oryza glaberrima. Theoretical and Applied Genetics 130:807-818.


Pidon H (2016). Diversity of genetic basis of rice yellow mottle virus (RYMV) resistance in the African rice species Oryza glaberrima (Doctoral dissertation, Montpellier University) pp. 1-172.


Pinel-Galzi A, Dubreuil-Tranchant C, Héebrard E, Mariac C, Ghesquièere A, Albar L (2016). Mutations in Rice yellow mottle virus polyprotein P2a involved in RYMV2 gene resistance breakdown. Frontiers in Plant Science 7:1779.


Pinel-Galzi A, Traorée O, Séerée Y, Héebrard E, Fargette D (2015). The biogeography of viral emergence: Rice yellow mottle virus as a case study. Current Opinion in Virology 10:7-13.


Sere Y, Fargette D, Abo M E, Wydra K, Bimerew M, Onasanya A, Akator SK (2013). Managing the Major Diseases of Rice in Africa. Realizing Africa's Rice Promise 17:213-228.


Sere Y, Onasanya A, Afolabi AS, Abo ME (2005). Evaluation and potential of double immunodifusion gel essay for serological characterization of Rice yellow mottle virus isolates in West Africa. African Journal of Biotechnology 4(2):197-205.


Sérémé D (2009). The suppressor protein P1 of yellow variegated rice and quack grass (Imperata cylindrica) viruses: Diversity, functional study and applications in biotechnology. State Thesis in Science of the University of Ouagadougou, Burkina Faso.


Soko DF, Siena LAC, Kochi V, Gogbeu SJ, Sere Y, Ake S (2015). Assessment of the susceptibility and resistance level of Africarice differential rice varieties to eight isolates of Gagnoa yellow rice variegation (RYMV) (Côte d'Ivoire). Journal of Animal and Plant Sciences 26(3):4138-4149.


Thiemele DE, Boisnard A, Ndjiondjop MN, Chéeron S, Séerée Y, Akée S, Ghesquièere A, Albar L (2010). Identification of a second major resistance gene to Rice yellow mottle virus, RYMV2, in the African cultivated rice species, O. glaberrima. TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik 121(1):169-179.


Thottappilly G, Rossel H (1993). Evaluation of resistance to Rice yellow mottle virus in Oryza species. Indian Journal of Virology 9(1):65-73.


Trovào NS, Baele G, Vrancken B, Bielejec F, Suchard MA, Fargette D, Lemey P (2015). Host ecology determines the dispersal patterns of a plant virus. Virus Evolution 1(1):vev016.


West Africa Rice Devlopment Association (WARDA) (2000). Rice yellow mottle virus; WARDA Annual Report pp. 27-37.