Subscribe Now Subscribe Today
Research Article
 

Occurrence, Distribution and Characterization of Rice Yellow Mottle Virus Isolates Genus Sobemovirus in Southwest Nigeria



R.O. Onasanya, D.B. Olufolaji, A. Onasanya, Y. Sere, F.E. Nwilene, M. Wopereis and P. Kiepe
 
Facebook Twitter Digg Reddit Linkedin StumbleUpon E-mail
ABSTRACT

Rice Yellow Mottle Virus (RYMV) genus Sobemovirus is a highly variable pathogen that is very infectious to rice plant. This variability hinders rice breeding for durable resistance to the virus and effective deployment of improved cultivars in Southwest Nigeria. Disease surveys in 5 Southwest states (Lagos, Oyo, Ogun, Ekiti and Ondo) revealed RYMV disease incidence of between 15-70% in farmers’ fields and serological indexing confirmed 92% of collected leaf samples positive to RYMV with 24% from rice and 76% from weeds. The weed with 76% RYMV positive suggests being the main reservoir of RYMV in Southwest Nigeria. Biological test on collected fields leaf samples identified 3 groups (GroupA, GroupD and GroupE) of Resistance Breaking (RB) RYMV isolates and 2 groups (GroupB and GroupC) of normal isolates. Pathotyping 20 RYMV isolates against 10 differential varieties identified 17 isolates as Highly Pathogenic Isolates (HPI) and 3 as Mildly Pathogenic Isolates (MPI) while 4 rice varieties were Highly Resistant (HR), 2 were Moderately Resistant (MR) and 4 were susceptible. HPI isolates present in five states and MPI isolates in two states. Serological study using the same 20 RYMV isolates revealed two major Nigeria serogroup (NSg1 and NSg2) and four subgroups (NSg1a, NSg1b, NSg2a and NSg2b). NSg1a and NSg1b comprised both normal and RB isolates while NSg2a and NSg2b were typical of RB isolates only. This information would assist rice breeding programs to develop durable resistant cultivars to RYMV disease in Southwest Nigeria.

Services
Related Articles in ASCI
Search in Google Scholar
View Citation
Report Citation

 
  How to cite this article:

R.O. Onasanya, D.B. Olufolaji, A. Onasanya, Y. Sere, F.E. Nwilene, M. Wopereis and P. Kiepe, 2011. Occurrence, Distribution and Characterization of Rice Yellow Mottle Virus Isolates Genus Sobemovirus in Southwest Nigeria. Trends in Applied Sciences Research, 6: 1301-1323.

DOI: 10.3923/tasr.2011.1301.1323

URL: https://scialert.net/abstract/?doi=tasr.2011.1301.1323
 
Received: May 16, 2011; Accepted: August 30, 2011; Published: September 28, 2011



INTRODUCTION

Rice (Oryza spp.) is grown widely in many parts of the world. It is the major food source for about 40% of the world’s human population (Ortiz, 2011). Rice has become a major staple cereal in most countries of Africa especially West Africa where it accounted for more than 25% of the cereals consumed (Africa Focus, 2004). In Nigeria, the importance of rice in the diet of the people is steadily on the increase. The annual consumption of the staple for an average Nigerian is as high as 24.8 kg of rice which represents 9% of the total calorie intake (Akpokodje et al., 2001). In spite of the efforts made in increasing rice area under cultivation, yields remained very low, thus the production has not been able to meet the consumption level of the growing population. Rice production in Africa is seriously affected by diseases. Rice Yellow Mottle Virus (RYMV) constitutes a major constraint to rice production in Africa (Sere et al., 2008), particularly in the lowland and irrigated rice ecologies (Banwo et al., 2004). RYMV belongs to the genus Sobemovirus (Tamm and Truve, 2000). The virus which is indigenous to Africa is widely spread in almost all the West African countries including Nigeria (Banwo et al., 2004). RYMV is environmentally stable and highly infectious to rice (Banwo et al., 2004). The disease is characterized by mottle and yellowing symptoms of varying intensities depending on genotype and this could be mistaken for iron or nitrogen deficiency (Onasanya et al., 2006; Gnanamanickam, 2009). Gnanamanickam (2009) stated that infected plants had pale yellow mottle leaves, stunted, reduced tillering, non-synchronous flowering, poor panicle exertion, spikelet discoloration of grains which could be as a result of secondary infection by fungi and crinkling of new leaves. But in mechanically inoculated plants, the first symptoms are few yellow-green spots on the youngest leaves, although more resistant cultivars may show no distinctive symptoms (Gnanamanickam, 2009). Yield losses of between 4-90% have reported which depend on genotype and infection time (Onwughalu et al., 2010, 2011). RYMV is transmitted through mechanical contact and inoculations as well as by insect-vectors such as beetles and long-horned grasshoppers (Nwilene et al., 2009). It has been established that cows, donkeys and grass rats transmit the virus in irrigated rice fields (Sarra and Peters, 2003), however, the disease is not transmitted through seed or nematode (Abo et al., 2004). The virus has also been observed on some grasses, besides cultivated rice, including wild rices (Abo et al., 2000). RYMV came to limelight in Nigeria with the introduction of exotic rice varieties from Southeast Asia coupled with the introduction of cropping practices without dry season gaps (Abo et al., 2000). The disease has since become a limiting factor to rice production in Nigeria and rice is becoming increasingly important in Nigeria. For this reason, the government is investing heavily in the development of the domestic rice sector. However, the expensive efforts to increase rice production by the development of irrigation schemes where water and water management are available, allowing double cropping and promotion of productive varieties from Asia were hindered by the spread of RYMV (Banwo et al., 2004).

RYMV strains in the field differ in their pathogenicity (N’Guessan et al., 2000). The isolate variability of the virus accounts for the observation that rice variety resistant to RYMV in one location could be susceptible in another location. Therefore, there is the need to identify and characterize these strains biologically and serologically. Besides, the knowledge of the serological relationships between RYMV isolates is valuable in diagnostic work and may prove to be important in epidemiological studies and disease control. The existence of different RYMV strains in the field that are different in their pathogenicity is often a matter of considerable practical importance. Therefore reliable criteria are needed for distinguishing, identifying and pathotyping these strains. Screening for durable resistance need to take into consideration the existence of these different strains, as most often the breakdown in resistance is attributed to a poor prerelease challenge with appropriate pathogen population (Mekwatanakarn et al., 2000). In previous studies, RYMV isolates have been pathotyped in some West African countries (Onasanya et al., 2004, 2006) except Nigeria. Besides, the knowledge of the serological relationships between RYMV isolates is valuable in diagnostic work and may prove to be important in epidemiological studies and disease control. Also in some studies, African RYMV isolates were serotyped using double immunodiffusion gel assay (Sere et al., 2005). Phylogenetic analysis of some RYMV isolates based on sequences of the coat protein gene has been reported by Traore et al. (2005). However, because of relative expensiveness of sequencing many isolates of RYMV, few sequence data are available for phylogenetic analysis. Besides, few data are available on RYMV serodiversity, disease ecology and interactions between different RYMV strains in Southern Nigeria. However, Serological Differentiation Index (SDI) data has been reported using the phylogenetic analysis of plant viruses serological classification (Sere et al., 2007) but never been used for RYMV serodiversity in Southern Nigeria. For a better understanding of the RYMV pathogen population structure in Southern Nigeria, it will be very important to characterize this pathogen in order to reveal information on the diversity in RYMV pathogen population in terms of virulence, pathotypes, serotypes, cultivar resistance, disease epidemics and geographical distributions of pathogenic isolates. The present study aimed to assess RYMV disease occurrence and distribution, to characterize RYMV isolates serologically and biologically and to evaluate the RYMV population structure in terms of Resistance Breaking (RB) isolates in lowland and irrigated rice ecosystems in Southwest Nigeria. This approach will provide useful information on integrated management of RYMV disease for sustainable deployment of resistant varieties and development of suitable breeding strategies based on identification of donors for resistance to the Southern Nigeria RYMV isolates population.

MATERIALS AND METHODS

Research location: The laboratory and screen-house studies were carried out at Plant Pathology Unit, Africa Rice Center, Cotonou, Benin Republic. The RYMV disease survey and leaf sampling study was carried out in Southwest Nigeria with Africa Rice Center, Nigeria Station, Ibadan, Oyo State, Nigeria. All the research studies were conducted between April to December 2010.

RYMV disease survey and sampling: RYMV disease survey and sampling (Abo et al., 2002) was conducted in five states in South-west Nigeria where rice cultivation is predominant. The five states were Oyo, Ogun, Ondo, Ekiti and Lagos. Lowland and irrigated rice fields were visited to evaluate RYMV disease incidence in farmers’ fields. Leaf samples were collected from rice varieties that showed RYMV typical symptoms and also from weed in the surrounding rice fields. Collected leaf samples were stored in ice-box during collection and later transferred into freezers in the laboratory for analysis.

Serological tests on collected leaf samples: Enzyme-linked Immunosorbent Assay (ELISA) test using RYMV polyclonal antibody was carried out on the leaf samples collected from both rice varieties and weed on farmers’ fields to detect the virus. Indirect-antigen coated-plate Enzyme-linked Immunosorbent Assay (ACP-ELISA) was performed as described by Sere et al. (2007).

Biological test on collected leaf samples
RYMV propagation: All the RYMV leaf samples obtained both from rice varieties and weed during the survey were propagated on six rice varieties (two RYMV susceptible varieties and four RYMV resistant varieties) (Table 1) using method adopted by Onasanya et al. (2004).

Measurement of parameter: Plant height, chlorophyll was carried out by SPAD meter, disease incidence and severity were estimated at 21 Days after Inoculation (DAI) (Onasanya et al., 2004, 2006).

Table 1: Identity of rice varieties used for RYMV leaf sample propagation
Image for - Occurrence, Distribution and Characterization of Rice Yellow Mottle Virus Isolates Genus Sobemovirus in Southwest Nigeria

Table 2: List of Southwest RYMV isolates selected after biological test and were used for both serotyping and pathotyping studies
Image for - Occurrence, Distribution and Characterization of Rice Yellow Mottle Virus Isolates Genus Sobemovirus in Southwest Nigeria
*RB: Resistance breaking isolate; N: Normal isolate

Harvesting of RYMV isolates: Leaves with typical RYMV symptoms on susceptible IR 64 were harvested as isolate at 21 DAI after data collection and stored in freezer for use in serotyping and pathotyping analyses.

Pathotyping characterization analysis of different RYMV isolates
RYMV isolates: Twenty RYMV isolates (Table 2) harvested during biological test were used in the pathotyping study.

Experimental design: Randomized Complete Block Design (RCBD) with 3 replications was used. Twenty RYMV isolates (Table 2) were used to screen 10 rice varieties (Table 3) inside the screen house at Africa Rice Center (Africa Rice), Cotonou, Benin Republic. Two liters-plastic pots were used. Rice grains were pre-germinated in sterile Petri dishes under sterilization condition. One plastic pot per variety per isolate in three replications was used.

Table 3: Identity of rice varieties used for pathotyping characterization analysis of different RYMV isolates
Image for - Occurrence, Distribution and Characterization of Rice Yellow Mottle Virus Isolates Genus Sobemovirus in Southwest Nigeria

Inoculation of rice varieties: The ten young rice varieties were inoculated mechanically (Onasanya et al., 2004) with the selected isolates in the screen house 21 days after transplanting in 3 replicates. Another set of same ten young rice varieties in 3 replicates not inoculated were used as controls.

Measurement of parameter: Plant height, chlorophyll content (SPAD), disease incidence and severity at 21 and 42 Days after Inoculation (DAI) were estimated (Onasanya et al., 2004, 2006). Total yield was measured at maturity for both inoculated and control rice varieties.

Serotyping characterization analysis of different RYMV isolates
YMV isolates: The twenty RYMV isolates (Table 2) harvested during biological test used in pathotyping characterization study were also used for serotyping characterization analysis for result comparison purpose.

Polyclonal antibody used for serotyping: Twenty-six RYMV polyclonal antibodies (Table 4) were used for the serotyping characterization study. The polyclonal antibodies were obtained from Plant Pathology Unit, Africa Rice Center (Africa Rice), Cotonou, Benin.

ACP-ELISA: Indirect-antigen coated-plate enzyme-linked immunosorbent assay (ACP-ELISA) was performed as described by Sere et al. (2007).

Data analysis: Biological test and pathotyping characterization data analysis as well as Additive Main Effect and Multiplicative Interaction (AMMI) analysis were carried out using IRRISTAT version 4.3 (Zhu and Kuljaca, 2005; Ebdon and Gauch, 2002b).

In the serotyping characterization analysis, the Optical Density (OD) values from ACP-ELISA were transformed into a binary character matrix (“1” for a positive polyclonal antibody detection of each RYMV isolate and “0” for negative none detection of each RYMV isolate by a polyclonal antibody). Pairwise distance matrices were compiled by the numerical taxonomy system (NTSYS-pc 2.0) software (Rohlf, 2000) using the Jaccard coefficient of similarity (Ivchenko and Honov, 1998). Dendrogram was created by Unweighted Pair-group Method Arithmetic (UPGMA) cluster analysis (Jako et al., 2009).

Table 4: Identity of 26 RYMV polyclonal antibodies used for the RYMV isolates serotyping characterization study
Image for - Occurrence, Distribution and Characterization of Rice Yellow Mottle Virus Isolates Genus Sobemovirus in Southwest Nigeria

RESULTS

RYMV disease survey and sampling: RYMV disease survey and sampling were successfully carried out in five states (Ogun, Lagos, Oyo, Ondo and Ekiti) in Southwest Nigeria. A total of 50 RYMV leaf samples were collected from farmers’ fields in 6 localities in the five states in Nigeria (Table 5). Lowland and irrigated rice ecologies were covered during the survey. Out of the 50 RYMV leaf samples collected 14 were from cultivated rice varieties and 36 were from weeds. RYMV disease incidence was between 15-70% in farmers’ fields across the five states with highest disease incidence from Oyo state and the least disease incidence from Ekiti state.

Serological tests on collected leaf samples: The serological test conducted on 50 RYMV leaf samples was carried out successfully. The serological test using ACP-ELISA and RYMV polyclonal antibody was carried out to confirm the presence of RYMV in these leaf samples. Out of 50 leaf samples tested 46 (92%) were RYMV positive (Table 5). Out of these 46 (92%) tested positive to RYMV, 11 (24%) were from cultivated rice varieties and 35 (76%) were from weeds.

Biological test on collected leaf samples: The biological test was successfully conducted on all the RYMV leaf samples inside the screen-house. This comprised of the propagation of 50 RYMV leaf samples from Southwest Nigeria using 6 rice varieties and identification of resistance breaking RYMV isolates.

Table 5: RYMV leaf samples collected and RYMV indexing status
Image for - Occurrence, Distribution and Characterization of Rice Yellow Mottle Virus Isolates Genus Sobemovirus in Southwest Nigeria
*Number of leaf samples positive to RYMV in ELISA test

Table 6: List of RYMV isolates obtained after propagation and resistance breaking status
Image for - Occurrence, Distribution and Characterization of Rice Yellow Mottle Virus Isolates Genus Sobemovirus in Southwest Nigeria
*RB: Resistance breaking isolate, N: Normal isolate, +: Positive RYMV symptom, -: No symptom

From the study, out of 50 RYMV leaf samples propagated 15 RYMV isolates were recovered from which 4 were normal isolates and 11 were Resistance Breaking (RB) isolates (Table 6). Resistance breaking RYMV isolates were isolates that attacked RYMV resistant variety giving rise to a typical RYMV symptom. None of the RB isolates was able to attack Gigante and TOG5681. Using the six propagating rice hosts, the relationship and diversity among RB and Normal (N) RYMV isolates was revealed by AMMI cluster analysis (Fig. 1, 2). Out of 15 RYMV isolates analyzed, a total of 5 groups (GroupA, GroupB, GroupC, GroupD and GroupE) were obtained at 40% similarity coefficient (Fig. 1). RB RYMV isolates were clustered into 3 different groups (GroupA, GroupD and GroupE) while the normal RYMV isolates clustered into 2 different groups (GroupB and GroupC) (Fig. 1). The study was able to reveal that, normal RYMV isolate is different from resistance breaking RYMV isolate and diversity is higher among RB isolates than among the normal isolates.

Image for - Occurrence, Distribution and Characterization of Rice Yellow Mottle Virus Isolates Genus Sobemovirus in Southwest Nigeria
Fig. 1: Cluster showing relationship and diversity among Resistance Breaking (RB) and normal (N) RYMV isolates from Southwest Nigeria using six propagating rice hosts as revealed by AMMI analysis

Image for - Occurrence, Distribution and Characterization of Rice Yellow Mottle Virus Isolates Genus Sobemovirus in Southwest Nigeria
Fig. 2: Cluster showing relationship and diversity among two susceptible (S) and four resistant (R) in response to Resistance Breaking (RB) and Normal (N) RYMV isolates as revealed by AMMI analysis

Among the six propagating rice hosts used, some relationship and diversity among two Susceptible (S) and four Resistant (R) in response to RB and Normal (N) RYMV isolates were revealed by AMMI cluster analysis (Fig. 2). At 90 and 20% similarity coefficient, three clusters formed (high propagating reactive host, Hpr; low propagating reactive host, Lpr; none reactive host, Nr) that revealed the propagating characteristics of the six rice hosts (Fig. 2). The rice varieties IR64, Bouake189 and WAC 117 were characterized as High Propagating Reactive (Hpr) hosts, TOG 5672 as Low Propagating Reactive (Lpr) host and Gigante and TOG 5681 as None Reactive (Nr) host (Fig. 2). On the basis of High Propagating Reactive (Hpr) hosts, 20 RYMV isolates (Table 2) from Southwest Nigeria were selected and were used for both serotyping and pathotyping studies.

Pathotyping characterization analysis of different RYMV isolates: Considerable diversity was observed in the reactions of 10 rice genotypes to 20 RYMV isolates from 5 states in Southwest Nigeria in terms of chlorophyll reduction, height reduction, yield reductions, disease incidence and disease severity (Table 7, 8). On the basis of ANOVA results, there was significant different (p = 0.01) in variety by isolate interaction and variety by days after inoculation in terms of chlorophyll reduction, height reduction, yield reductions, disease incidence and disease severity, meaning that diverse interactions exist between RYMV isolates and rice varieties and RYMV disease development was not the same at 21 and 42 days after inoculation (Table 7, 8). Percentage chlorophyll reduction ranged between 14.4-39.9% (Table 9) while% height reduction was between 9.1-34.9% (Table 10). While disease incidence ranged between 11.3-60.4% (Table 11), disease severity was between 0.4-96.1% (Table 12) and (%) yield reduction was in the range of 35.7-91.7% (Table 13). According to AMMI analysis, all the 20 RYMV isolates were responsible mainly for unfavorable interactive conditions leading to significant chlorophyll reduction, height reduction, disease incidence, disease severity and yield reductions in all the rice cultivars (Fig. 3-5).

Table 7: Analysis of variance for percentage chlorophyll reduction, percentage height reduction, disease incidence and disease severity
Image for - Occurrence, Distribution and Characterization of Rice Yellow Mottle Virus Isolates Genus Sobemovirus in Southwest Nigeria
**: Significant at 1% level; *: Significant at 5% level; ns: Not significant, SPADR: Chlorophyll reduction; HR: Height reduction; DI: Disease incidence; SEV: Disease severity

Table 8: Analysis of variance for percentage yield reduction
Image for - Occurrence, Distribution and Characterization of Rice Yellow Mottle Virus Isolates Genus Sobemovirus in Southwest Nigeria
**: Significant at 1% level, *: Significant at 5% level

Table 9: Variety by isolate interaction means comparison for percentage chlorophyll reduction due to RYMV disease
Image for - Occurrence, Distribution and Characterization of Rice Yellow Mottle Virus Isolates Genus Sobemovirus in Southwest Nigeria
In a column under each D, means followed by a common letter are not significantly different at the 5% level by DMRT. D: Day after inoculation; D42 = 42 day after inoculation; D21 = 21 day after inoculation

Based on cluster dendrogram classification for isolates pathogenic and genotypes viral resistance levels, 17 RYMV isolates were classified as Highly Pathogenic Isolates (HPI) and 3 RYMV isolates were classified as Mildly Pathogenic Isolates (MPI) (Fig. 4) while 4 rice varieties Gigante, TOG5672, TOG5674, TOG5681) were Highly Resistant (HR), 2 rice varieties (TOG6691, WAC116) were Moderately Resistant (MR) and 4 rice varieties (BG90-1, Bouake189, WAC117, IR64) were susceptible (Fig. 3).

Table 10: Variety by isolate interaction means comparison for percentage height reduction due to RYMV disease
Image for - Occurrence, Distribution and Characterization of Rice Yellow Mottle Virus Isolates Genus Sobemovirus in Southwest Nigeria
In a column under each D, means followed by a common letter are not significantly different at the 5% level by DMRT. D: Day after inoculation; D42 = 42 day after inoculation; D21 = 21 day after inoculation
Table 11: Variety by isolate interaction means comparison for disease incidence due to RYMV disease
Image for - Occurrence, Distribution and Characterization of Rice Yellow Mottle Virus Isolates Genus Sobemovirus in Southwest Nigeria
In a column under each D, means followed by a common letter are not significantly different at the 5% level by DMRT. D: Day after inoculation; D42 = 42 day after inoculation; D21 = 21 day after inoculation

Table 12: Variety by isolate interaction means comparison for disease severity due to RYMV disease
Image for - Occurrence, Distribution and Characterization of Rice Yellow Mottle Virus Isolates Genus Sobemovirus in Southwest Nigeria
In a column under each D, means followed by a common letter are not significantly different at the 5% level by DMRT. D: Day after inoculation; D42 = 42 day after inoculation; D21 = 21 day after inoculation

The pathotyping study has also revealed the distribution, movement and population structure of RYMV isolates across the five Southwest states in Nigeria (Table 14).

Table 13: Variety by isolate interaction means comparison for percentage yield reduction due to RYMV disease
Image for - Occurrence, Distribution and Characterization of Rice Yellow Mottle Virus Isolates Genus Sobemovirus in Southwest Nigeria
In a column means followed by a common letter are not significantly different at the 5% level by DMRT

Table 14: Distribution of the RYMV isolates pathotypes across the five Southwest states in Nigeria
Image for - Occurrence, Distribution and Characterization of Rice Yellow Mottle Virus Isolates Genus Sobemovirus in Southwest Nigeria

Pathotype HPIa has 45% occurrence in three states (Ogun, Ekiti and Ondo), HPIb has 40% in three states (Lagos, Oyo and Ekiti) and MPI has 15% in two states (Oyo and Ekiti). Consequently HPI isolates were present in all the five states while MPI isolates were found only in two states (Oyo and Ekiti) (Table 14). At state level, Ogun and Ondo have only HPIa RYMV isolates, Lagos has only HPIb, Oyo has HPIb and MPI and Ekiti has HPIa, HPIb and MPI (Table 14).

Serotyping characterization analysis of different RYMV isolates: Serotyping characterization analysis of 20 RYMV isolates (Table 2) using 26 polyclonal antibodies (Table 4) in ACP-ELISA has been carried out. Serological relationship among 20 RYMV isolates from Southwest Nigeria has been revealed which comprised of two major serogroups (NSg1 and NSg2) and four subgroups (NSg1a, NSg1b, NSg2a and NSg2b) (Fig. 6). NSg1a and NSg1b serogroups comprised of both normal and RB RYMV isolates while NSg2a and NSg2b serogroups were typical of RB RYMV isolates only.

Image for - Occurrence, Distribution and Characterization of Rice Yellow Mottle Virus Isolates Genus Sobemovirus in Southwest Nigeria
Fig. 3: Cluster dendrogram showing classification of genotype (cultivar) level of resistance to environment (isolate) using Additive Main effects and Multiplicative Interaction (AMMI) analysis. HR: Highly resistant; MR: Moderately resistant; S: Susceptible

Table 15: Distribution of the RYMV isolates serogroups across the five Southwest states in Nigeria
Image for - Occurrence, Distribution and Characterization of Rice Yellow Mottle Virus Isolates Genus Sobemovirus in Southwest Nigeria

This serotyping study has further revealed the diversity-complex nature among the RB RYMV isolates from Southwest Nigeria and the possibility that some normal RYMV isolates seemed to possess RB characteristics. The serotyping study has also revealed the distribution, movement and population structure of RYMV isolates across the five Southwest states in Nigeria (Table 15). Serogroup NSg1a has 60% occurrence in four states (Lagos, Ogun, Ekiti and Ondo), NSg1b has 20% in three states (Oyo, Ekiti and Ondo), Nsg2a has 10% in two states (Oyo and Ondo) and NSg2b has 10% in one state (Ekiti). Consequently NSg1 isolates were present in all the five states while NSg2 isolates were found only in three states (Oyo, Ekiti and Ondo). At state level, Ogun and Lagos have only NSg1a RYMV isolates, Oyo has NSg1b and NSg2a, Ekiti has NSg1a, NSg1b and NSg2b and Ondo has NSg1a, NSg1b and NSg2a. The pathotyping study would therefore target the development of durable resistant rice varieties to Nsg1 and Nsg2 isolates serotypes and to determine any possible linkage between RYMV pathotype and serotype in Southwest Nigeria.

Image for - Occurrence, Distribution and Characterization of Rice Yellow Mottle Virus Isolates Genus Sobemovirus in Southwest Nigeria
Fig. 4: Cluster dendrogram showing classification of environment (isolate) pathogenic level to genotype (cultivar) using Additive Main effects and Multiplicative Interaction (AMMI) analysis

All the 26 polyclonal antibodies were separated into two major serogroups (PSg1 and PSg2) while PSg2 was further separated into three subgroups (Psg2a, Psg2b and PSg-2c) (Fig. 7). According to the composition of each serogroup, some polyclonal antibodies raised from isolates collected in different West African countries appeared to be similar. Besides, polyclonal antibodies produced from isolates collected in a same country were also different. Polyclonal antibodies belonging to PSg1, PSg2a, PSg2c and PSg-2b serogroups have diagnostic potential of 30, 55-65, 75-80 and 85-100%, respectively, for all the 20 RYMV isolates analyzed (Table 16).

Linkage between RYMV pathotype and serotype: At the state level, the identified RYMV NSg1a serotype in Ogun and Lagos are carrying HPIa and HPIb pathotype, respectively, Oyo with NSg1b and NSg2a serotypes formed HPIb and MPI pathotypes, all NSg1a, NSg1b and NSg2a serotypes in Ondo formed HPIa pathotype only and NSg1a and NSg1b serotypes in Ekiti were characterized as HPIa, HPIb and MPI (Table 17). Thus Ekiti has the highest number of serotypes with corresponding highest number of pathotypes (Table 17).

Image for - Occurrence, Distribution and Characterization of Rice Yellow Mottle Virus Isolates Genus Sobemovirus in Southwest Nigeria
Fig. 5: Genotype (cultivar) by environment (isolate) interaction effects on yield reduction using Additive Main effects and Multiplicative Interaction (AMMI) analysis

Table 16: Percentage diagnostic potential and diversity among 26 RYMV polyclonal antibodies
Image for - Occurrence, Distribution and Characterization of Rice Yellow Mottle Virus Isolates Genus Sobemovirus in Southwest Nigeria
Image for - Occurrence, Distribution and Characterization of Rice Yellow Mottle Virus Isolates Genus Sobemovirus in Southwest Nigeria

Table 17: Relationship between RYMV isolates serotype and pathotype population structure across five Southwest states in Nigeria
Image for - Occurrence, Distribution and Characterization of Rice Yellow Mottle Virus Isolates Genus Sobemovirus in Southwest Nigeria

Image for - Occurrence, Distribution and Characterization of Rice Yellow Mottle Virus Isolates Genus Sobemovirus in Southwest Nigeria
Fig. 6: Serological relationship among 20 RYMV isolates from Southwest Nigeria as revealed by 26 RYMV polyclonal antibodies in ACP-ELISA

DISCUSSION

Periodic disease survey and sampling as well as accurate serological indexing method are prerequisites into understanding the present status, movement and epidemiology of RYMV disease in upland, lowland and irrigated rice ecologies in Africa (Onasanya et al., 2004, 2006). In the current study, RYMV disease survey revealed RYMV disease incidence was between 15-70% in farmers’ fields across the five Southwest states in Nigeria with highest disease incidence from Oyo state and the least disease incidence from Ekiti state.

Image for - Occurrence, Distribution and Characterization of Rice Yellow Mottle Virus Isolates Genus Sobemovirus in Southwest Nigeria
Fig. 7: Serological relationship among 26 RYMV polyclonal antibodies in their reaction with 20 RYMV isolates from Southwest Nigeria in ACP-ELISA

Besides, serological indexing confirmed 92% of collected leaf samples were RYMV positive out of which 24% were from cultivated rice varieties and 76% were from weeds. The weed having the greater 76% RYMV positive by serological indexing suggests possibility of being the main reservoir of RYMV in Southwest Nigeria and may responsible for season-to-season source of RYMV inoculums and spread in farmers’ fields across rice ecologies (Onasanya et al., 2004, 2006). Previous study has revealed the importance of natural reservoir hosts in the persistence spread of RYMV under fields conditions (Abo et al., 2002).

RYMV is a variable virus with many pathological and serological variants and its unlimited number of pathological and virulence characters and lack of standardization of pathological conditions and virulence tests among different researchers have led to confusion and uncertainty in the characterization of this pathogen from rice (N’Guessan et al., 2000; Onasanya et al., 2004, 2006). Resistance Breaking (RB) RYMV isolates are isolates that attacked RYMV resistant variety giving rise to typical RYMV symptoms (Onasanya et al., 2006). The present study identified RB and normal RYMV isolates. Although this was the first time RB isolates identified in southwest Nigeria, it has been identified in the West and Central Africa (Hebrard et al., 2006; Traore et al., 2006). The study, however, revealed that normal RYMV isolate is different from RB RYMV isolate and diversity is higher among resistance breaking isolates than among the normal isolates in Southwest Nigeria.

The application and use of pathotyping methods to study distribution, movement and population structure of RYMV isolates has led to the identification of two pathotypes of RYMV isolates in Southwest Nigeria. The Additive Main Effect and Multiplicative Interaction (AMMI) analysis seemed effective in understanding and explaining complex Genotype by Environment (GE) interactions between the rice genotypes and RYMV pathotypes (Ebdon and Gauch, 2002a; Onasanya et al., 2004, 2006). Such interactions could generate complex data sets difficult to understand with Ordinary Analysis of Variance (ANOVA). In the current study, 20 RYMV isolates used covered major rice ecologies from five Southwest states in Nigeria leading to very high RYMV interactions among rice genotypes. The existence of HPI and MPI RYMV pathotypes obtained in this study have led to differential interactions among genotypes with heavy implications on the genotype resistance and yield stability. In previous studies, two virulent pathotypes of RYMV isolates have been known to exist in Mali and Cote d’Ivoire and these virulent pathotypes were present in different parts of the countries (Onasanya et al., 2004, 2006).

As revealed by this study, genotypes pathogenic resistance to HPI and MPI RYMV pathotypes first occurs at the level of the individual and involves physiological or behavioral tolerance or adaptability. Subsequent response to increasing viral pathogenicity may involve survival only of the better-adapted genotypes HPI pathotypes which consist of 17 isolates, could be described as possessing both stable and high level of virulence affecting genotypes resistance to RYMV across 5 Southwest states in Nigeria. Under different rice ecologies in Southwest Nigeria, four varieties (Gigante, TOG5672, TOG5674 and TOG5681) possessed heterogenous viral resistance characteristics making them to be more stable, adaptable and more resistant to stress induced by HPI pathotypes originated from different states. Genotypes that have adapted to endure variable isolates or strains infestations are more likely to tolerate an independent stress compared to those genotypes that are only adapted to a fixed isolate or strain (Ebdon and Gauch, 2002a, b).

As RYMV isolates population increases, there is probability that HPI pathotypes population will be more than that of MPI and possible interactions between these two pathotypes could lead to the emergence of new RB strains. The use of highly resistant varieties (Gigante, TOG5672, TOG5674 and TOG5681) will potentially reduce HPI and MPI pathotypes population and their interactions. There is probability that the four resistant varieties (Gigante, TOG5672, TOG5674 and TOG5681) obtained in this study will survive and evolve through combinations of genes present in the population since population resistance is enhanced by genes polymorphism that may result in short-term selection of more tolerant genotypes in stressful viral environments (Ebdon and Gauch, 2002a,b).

The classification of the 20 RYMV isolates into two main serogroups (NSg1 and NSg2) and four subgroups (NSg1a, NSg1b, NSg2a and NSg2b) indicates the existence and levels of serodiversity among RYMV isolates in Southwest Nigeria. The serodiversity patterns displayed by the two serogroups and four subgroups shown that they differed by specific combination of epitopes. This conformed to the earlier study of existence of several serotypes of RYMV isolates (N’Guessan et al., 2000; Sere et al., 2007). The serotyping study has further revealed the diversity-complex nature among the resistance breaking RYMV isolates from Southwest Nigeria and the possibility that some normal RYMV isolates seemed to possess resistance breaking characteristics. Besides, the serotyping study has also revealed the distribution, movement and population structure of RYMV isolates across the five Southwest states in Nigeria. Many isolates emanating from same locality, field and host were observed to be serologically different and this explains the fact that within a set of isolates of related strains in the same host plant, many possibilities of interaction exist (Onasanya et al., 2006). This possible isolate and host plant interaction varies between one locality to another thus account for diverse serological variability that exist among different isolates of RYMV in Southwest Nigeria. The serological similarities observed between isolates within the same and different states confirm the great cross-infection potential of RYMV transmitted under natural conditions by different insect vectors (Sere et al., 2007; Nwilene et al., 2009).

In this study, there were indications of localized micro variation among Southwest states isolates with the emergence of NSg2b serogroup in Ekiti and NSg2a serogroup in Ondo and Oyo that were not found among Ogun and Lagos isolates. This is practically important for various RYMV identifications and further strengthens the need for deployment of durable rice varieties in the region. Besides, serogroup NSg1a has 60% occurrence in four states (Lagos, Ogun, Ekiti and Ondo), NSg1b has 20% in three states (Oyo, Ekiti and Ondo), NSg2a has 10% in two states (Oyo and Ondo) while NSg2b has 10% in one state (Ekiti). Consequently NSg1 isolates were present in all the five states while NSg2 isolates were found only in three states (Oyo, Ekiti and Ondo). This indicates that isolates belonging to NSg1 serogroup are the most widely distributed in Southwest Nigeria and could be responsible for wide distribution RYMV infections of rice plants with up to 35.7-91.7% yield losses in the region. The evolution of NSg2 serogroup could be as a result of possible interaction and co-existence between NSg1a and NSg1b serotypes. It was suggested that, the successive transmission by beetles and other insects of NSg1a and NSg1b mixtures might have lead to interaction and co-existence among the serotypes from which NSg2 came into existence. It was hypothesized that such possibilities of interaction within a set of isolates of related strains might lead to frequent occurrence of mutants which might be responsible for the high level of serological variation among the isolates (Sere et al., 2005, 2007). More research involving the use of molecular techniques is needed to confirm if further sub-groupings would be appropriate, since there was a good correspondence between serological and molecular diversity of RYMV isolates (N’Guessan et al., 2000; Fargette et al., 2002).

One implication of our findings to the practical management of RYMV disease is that control measures will have to target different strains of the pathogen in different localities. Present results demonstrate that Serological Data Index (SDI) generated from ACP-ELISA has great potential for serological identification and classification of RYMV isolates in Southwest Nigeria. The specific distinction pattern of each isolate SDI and its phylogeny are consistent, repeatable and reliable (Sere et al., 2007). The definition of specific distinct pattern for each isolate or strain should be a simple and straightforward task. Obviously, for these distinctions to have a practical meaning for the rice breeder, specific distinct pattern for each isolate must be related to the degree of virulence present. For example, in the present study the identified RYMV NSg1a serotype in Ogun and Lagos were HPIa and HPIb pathotypes respectively, Oyo with NSg1b and NSg2a serotypes formed HPIb and MPI pathotypes, all NSg1a, NSg1b and NSg2a serotypes in Ondo formed HPIa pathotype only while NSg1a and NSg1b serotypes in Ekiti were characterized as HPIa, HPIb and MPI. Thus Ekiti has the highest number of serotypes with corresponding highest number of pathotypes. This was achieved by a systematic comparison of distinct serotyped isolates or strains contrasting to their degree of virulence to rice. A similar approach has been used to determine the serological relationships of RYMV isolates in Cote d’Ivoire (Sere et al., 2007). The phylogeny of RYMV isolates, using serological and pathological methods, should be useful for its surveillance in rice growing regions, in epidemiological studies to assess its identity and interaction as well as assist breeding programs aiming at the effective development of cultivars with durable resistant to RYMV.

CONCLUSION

RYMV is a variable virus with many pathological and serological variants. Periodic disease survey and sampling as well as accurate serological indexing method are prerequisites into understanding the present status, movement and epidemiology of RYMV disease in upland, lowland and irrigated rice ecologies in Southwest Nigeria. Two RYMV pathotypes and serotypes confirmed present in Southwest Nigeria. The serotyping and pathotyping studies have further revealed the diversity-complex nature among the resistance breaking RYMV isolates from Southwest Nigeria and the possibility that some normal RYMV isolates seemed to possess resistance breaking characteristics. Besides, the serotyping and pathotyping studies have also revealed the distribution, movement and population structure of RYMV isolates across the five Southwest states in Nigeria. The pathotyping study has been useful in the identification of four resistant rice varieties to RYMV disease in Southwest Nigeria. The phylogeny of RYMV isolates, using serological and pathological methods, should be useful for its surveillance in rice growing regions, in epidemiological studies to assess its identity and interaction as well as assist breeding programs aiming at the effective development of cultivars with durable resistant to RYMV disease.

ACKNOWLEDGMENT

We are very grateful to International Fund for Agricultural Research (IFAR) for financial support of this research work, the entire Africa Rice Center community and the staff of Plant Pathology Unit Africa Rice for their technical assistance.

REFERENCES

1:  Abo, M.E., M.D. Alegbejo, A.A. Sy and S.M. Misari, 2000. An overview of the mode of transmission, host plants and methods of detection of Rice yellow mottle virus. J. Sustain. Agric., 17: 19-36.
CrossRef  |  Direct Link  |  

2:  Abo, M.E., M.N. Ukwungwu and A. Onasanya, 2002. The distribution, incidence, natural reservoir hosts and insect vectors of Rice Yellow Mottle Virus (RYMV), genus Sobemovirus in Northern Nigeria. Tropicultura, 20: 198-202.
Direct Link  |  

3:  Abo, M.E., M.D. Alegbejo and A.A. Sy, 2004. Evidence of non-transmission of Rice yellow mottle virus through rice seed. Tropicultura, 22: 116-121.

4:  Africa Focus, 2004. Africa: Rice for the future. Africa Focus Bulletin, Feb. 4, 2004 (040204). http://www.africafocus.org/docs04/rice0401.php.

5:  Akpokodje, G., F. Lancon and O. Erenstein, 2001. Nigeria's rice economy: State of the art. Draft Report, WARDA-NISER, Collaborative study. http://pdf.dec.org/pdf_docs/Pnadb851.pdf.

6:  Banwo, O.O., M.D. Alegbejo and M.E. Abo, 2004. Rice yellow mottle virus genus Sobemovirus: A continental problem in Africa. Plant Prot. Sci., 39: 26-36.
Direct Link  |  

7:  Ebdon, J.S. and H.G. Gauch, 2002. Additive main effect and multiplicative interaction analysis of national turfgrass performance trials: II. Cultivar recommendations. Crop Sci., 42: 497-506.
Direct Link  |  

8:  Ebdon, J.S. and H.G. Gauch, 2002. AMMI analysis of national turfgrass performance trials. I. Interpretation of genotype by environment interaction. Crop Sci., 42: 489-496.

9:  Jako, E., E. Ari, P. Ittzes, A. Horvath and J. Podani, 2009. BOOL-AN: A method for comparative sequence analysis and phylogenetic reconstruction. Mol. Phylogenet. Evol., 52: 887-897.
CrossRef  |  Direct Link  |  

10:  Fargette, D., A. Pinel, H. Halimi, C. Brugidou, C. Fauquet and M. van Regenmortel, 2002. Comparison of molecular and immunological typing of the isolates of rice yellow mottle virus. Arch. Virol., 147: 583-596.
CrossRef  |  Direct Link  |  

11:  Gnanamanickam, S.S., 2009. Biological Control of Rice Diseases. Vol. 8, Springer, The Netherlands, pp: 13-42

12:  Hebrard, E., A. Pinel-Galzi, A. Bersoult, C. Sire and D. Fargette, 2006. Emergence of a resistance-breaking isolate of rice yellow mottle virus during serial inoculations is due to a single substitution in the genome-linked viral protein Vpg. J. Gen. Virol., 87: 1369-1373.
CrossRef  |  

13:  Ivchenko, G.I. and S.A. Honov, 1998. On the jaccard similarity test. J. Math. Sci., 88: 789-794.
CrossRef  |  Direct Link  |  

14:  Mekwatanakarn, P., W. Kositratana, M. Levy and R.S. Zeigler, 2000. Pathotype and a virulence gene diversity of Pyricularia grisea in Thailand as determined by rice lines near-isogenic for major resistance genes. Plant Dis., 84: 60-70.
Direct Link  |  

15:  N'Guessan, P., A. Pinel, M. Caruana, R. Frutos, A. Sy, A. Ghesquiere and D. Fargette, 2000. Evidence of the presence of two serotypes of rice yellow mottle Sobemovirus in Cote d'Ivoire. Eur. J. Plant Pathol., 106: 167-178.
CrossRef  |  Direct Link  |  

16:  Nwilene, F.E., A.K. Traore, A.N. Asidi, Y. Sere, A. Onasanya and M.E. Abo, 2009. New records of insect vectors of Rice Yellow Mottle Virus (RYMV) in Cote d'Ivoire, West Africa. J. Entomol., 6: 189-197.
CrossRef  |  Direct Link  |  

17:  Onasanya, A., Y. Sere, F. Nwilene, M.E. Abo and K. Akator, 2004. Reactions and resistance status of differential rice genotypes to Rice yellow mottle virus, genus Sobemovirus in Cote d'Ivoire. Asian J. Plant Sci., 3: 718-723.
CrossRef  |  Direct Link  |  

18:  Onasanya, A., Y. Sere, M. Sie, K. Akator, M. M. Coulibaly and A. Hamadoun, 2006. Existence of two pathotypes of rice yellow mottle virus, genus Sobemovirus, in Mali. Plant Pathol. J., 5: 368-372.
CrossRef  |  Direct Link  |  

19:  Onwughalu, J.T., M.E. Abo, J.K. Okoro, A. Onasanya and Y. Sere, 2010. The effect of rice yellow mottle virus infection on the performance of rice (Oryza sativa L.) relative to time of infection under screenhouse condition. J. Applied Sci., 10: 1341-1344.
CrossRef  |  Direct Link  |  

20:  Onwughalu, J.T., M.E. Abo, J.K. Okoro, A. Onasanya and Y. Sere, 2011. Rice yellow mottle virus infection and reproductive losses in rice (Oryza sativa Linn.). Trends Applied Sci. Res., 6: 182-189.
CrossRef  |  

21:  Ortiz, R., 2011. Agrobiodiversity management for climate change. CAB Int., 12: 189-211.
Direct Link  |  

22:  Rohlf, F.J., 2000. NTSys pc, Version 2.02, Exeter Software. Setauket, New York, USA.

23:  Sarra, S. and D. Peters, 2003. Rice yellow mottle virus is transmitted by cows, donkeys and grass rats in irrigated rice crops. Plant Dis., 87: 804-808.
Direct Link  |  

24:  Sere, Y., A. Onasanya, A.S. Afolabi and E.M. Abo, 2005. Evaluation and potential of double immunodifusion gel assay for serological characterization of Rice yellow mottle virus isolates in West Africa. Afr. J. Biotechnol., 4: 197-205.
Direct Link  |  

25:  Sere, Y., A. Onasanya, K. Akator, A. Afolabi and M.E. Abo, 2007. Serological differentiation indices and phylogenetic analysis ofRice yellow mottle virus isolates in cote d`Ivoire. J. Boil. Sci., 7: 1147-1154.
CrossRef  |  Direct Link  |  

26:  Sere, Y., F. Sorho, A. Onasanya, L. Jobe and S. Darboe et al., 2008. First report of in rice in the gambia rice yellow mottle virus. Plant Dis., 92: 316-316.
Direct Link  |  

27:  Tamm, T. and E. Truve, 2000. Sobemoviruses. J. Virol., 74: 6231-6241.

28:  Traore, O., F. Sorho, A. Pinel, Z. Abubakar and O. Banwo et al., 2005. Process of diversiofication and dispersion of rice yellow mottle virus inferred from large-scale and high-resolution phylogeographical studies. Mol. Ecol., 14: 2097-2110.
CrossRef  |  Direct Link  |  

29:  Traore, O., A. Pinel, E. Hebrard, M.Y.D. Gumedzoe, D. Fargette, A.S. Traore and G. Konate, 2006. Occurrence of resistance-breaking isolates of rice yellow mottle virus in West and central Africa. Plant Dis., 90: 259-263.
Direct Link  |  

30:  Zhu, X. and O. Kuljaca, 2005. A short preview of free statistical software packages for teaching statistics to industrial technology majors. J. Ind. Technol., 21: 1-6.
Direct Link  |  

©  2021 Science Alert. All Rights Reserved