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Molecular Characterization of Cereal Yellow Dwarf Virus-RPV in Grasses in European Part of Turkey

Molecular Characterization of Cereal Yellow Dwarf Virus-RPV in Grasses in European Part of Turkey Agriculture (Poľnohospodárstvo), 66, 2020 (4): 161 − 170 Original paper DOI: 10.2478/agri-2020-0015 MOLECULAR CHARACTERIZATION OF CEREAL YELLOW DWARF VIRUS-RPV IN GRASSES IN EUROPEAN PART OF TURKEY 1* 1 1 2 Havva IlbağI , Ahmet Çıtır , AdnAn KArA , myem Uys er Al Namık Kemal University, Tekirdağ, Turkey Selçuk University, Konya,Turkey ılBAğ ı, h. – Çıtır, a. − KaRa, a. − UYSal, M.: Molecular characterization of cereal yellow dwarf virus-RPv in grasses in european part of Turkey. agriculture (Poľnohospodárstvo), vol. 66, no. 4, pp. 161 – 170. Yellow dwarf viruses (YDvs) are economically destructive viral diseases of cereal crops, which cause the reduction of yield and quality of grains. Cereal yellow dwarf virus-RPV (CYDv -RPv) is one of the most serious virus species of YDvs. These virus diseases cause epidemics in cereal fields in some periods of the year in Turkey depending on potential reservoir natural hosts that play a significant role in epidemiology. This study was conducted to investigate the presence and prevalence of CYDv -RPv in grasses and volunteer cereal host plants including 33 species from Poaceae, asteraceae, Juncaceae, Gerani- aceae, Cyperaceae, and Rubiaceae families in the Trakya region of Turkey. a total of 584 symptomatic grass and volunteer cereal leaf samples exhibiting yellowing, reddening, irregular necrotic patches and dwarfing symptoms were collected from Trakya and tested by ElISa and RT-PCR methods. The screening tests showed that 55 out of 584 grass samples were infect- ed with CYDv -RPv in grasses from the Poaceae family, while none of the other families had no infection. The incidence of CYDv -RPv was detected at a rate of 9.42%. Transmission experiments using the aphid species Rhopalosiphum padi l . showed that CYDv -RPv was transmitted persistently from symptomatic intact grasses such as Avena sterilis, Lolium perenne and Phleum exratum to barley cv. barbaros seedlings. PCR products of five Turkish RPv grass isolates were sequenced and compared with eleven known CYDv -RPv isolates in the Genbank⁄ EMbl databases. Compared nucleotide and amino acid sequences of CYDv -RPv isolates showed that the identities ranged from 40.38 − 95.86 % to 14.04 − 93.38%, respectively. In this study, 19 grass species from the Poaceae family and two volunteer cereal host plants were determined as natural reservoir hosts of CYDv -RPv in the cereal growing areas of Turkey. Key words: CYDv -RPv , polerovirus, grasses, molecular diversity The Trakya region is one of the most important viruses (YDvs) considerably reduced the yield and cereal growing areas in Turkey. almost one million quality of cereal crops in Trakya. High incidence ha of arable land, which covers 65% of the region, rates of YDvs causing severe infections and epi- has been allocated to field crops and cereal pro- demics on cereals have been reported periodical- duction. With the effects of global climate change ly in Turkey. Early sown susceptible winter wheat in recent years, increasing temperatures have grad- cultivars were especially affected by the highest ually caused prevailing pest and diseases. besides incidences of YDvs (Ilbağı et al. 2005; Ilbağı et the very damaging fungal pathogens, Yellow dwarf al. 2013). Moreover, bYDvs or CYDv infections Havva Ilbağı (*Corresponding author), ahmet Çıtır, adnan Kara, Department of Plant Protection, Faculty of agriculture, Namık Kemal University, Tekirdağ, Turkey. E-mail: hilbagi@nku.edu.tr Meryem Uysal, Department of Plant Protection, Faculty of agriculture, Selçuk University, Konya,Turkey © 2020 authors. This is an open access article licensed under the Creative Commons attribution-NonComercial-NoDerivs license (http://creativecommons.org/licenses/by-nc-nd/4.0/). 161 Agriculture (Poľnohospodárstvo), 66, 2020 (4): 161 − 170 caused up to 80% yield losses on cereal crops by ence in these agroecosystems (Power & Gray 1995). reducing the number of tillers per plant, number a list of 96 annual, 2 biannual and 111 perennial of seeds per tiller, and seed weights as reported by Poaceae weed hosts worldwide were compiled by McKirdy et al. (2002) and Perry et al. (2000). Sim- D’arcy (1995). In the subsequent years, the grass ilarly, Miller & Rasochova (1997) and Pike (1990) hosts of YDvs were reported in different countries determined average yield losses between 11% and by Garrett et al. (2004) in the USa, Pokorny (2006) 33% and sometimes up to 80% in the wheat fields. in the Czech Republic, bisnieks et al. (2004) in lat - YDvs are the most destructive virus diseases on ce- via and Sweden, bakardjeiva et al. (2006) in bul- real crops comprising a complex virus group. There garia. Previously, sporadic infections of bYDv in are currently 10 recognized YDv species within the wheat fields were investigated in the western part family Luteoviridae (adams et al. 2014), consisting of Turkey by bremer & Raatikainen (1975). Since of Barley yellow dwarf viruses (bYDvs), Cereal 1999 the year in the Trakya region, YDvs have be- yellow dwarf viruses (CYDvs), and Maize yellow come epidemics in the cereal fields, as reported by dwarf virus-RMV (MYDv -RMv). Five species Ilbağı et al. (2013). In addition to the Trakya region, have been assigned to the genus Luteovirus (bY- YDv infections were determined in 15 other cereal Dv -Kerll, bYDv -KerIII, bYDv -Mav , bYDv -PaS growing provinces of Turkey (Pocsai et al. 2003). and bYDv -Pav), three species have been assigned later, Ilbağı (2006) identified common reed (Phrag- to the genus Poleovirus (CYDv -RPv , CYDv -RPS, mites communis Trin) as a perennial natural weed and MYDv -RMv), and two have not yet been as- host of bYDv -Pav ; however, CYDv -RPv was not signed any genus (bYDv -GPv and bYDv -SGv). detected in the reed. Following this study, birdseed 30 nm in YDvs have isometric particles of 25 − (Phalaris canariensis l.) was also determined as diameter and ss(+) RNa genome of approximately the most susceptible host of both bYDv -Pav and 5,600 nucleotides (Rochow & Duffus 1981). There CYDv -RPv in Tekirdağ (Ilbağı et al. 2008). late - are six open reading frames (ORFs) in the genome, ly, dicotyledonous weed hosts of bYDv -Pav and which are numbered 1 – 6 in the members of Lu- Mav such as Juncus compressus Jacq. and Gera- teovirus and 0 – 5 in the members of Polerovirus nium dissectum l. were reported in Trakya, Turkey (Miller et al. 2002). These viruses are phloem-li- (Ilbağı et al. 2019). Güncan & Karaca (2018) sug- mited and are transmitted in a persistent circulati- gested effective weed control for potential reser- ve manner by over 25 aphid vectors. among them, voir sources of YDvs, as well as competition with Rhopalosiphum padi l. and Rhopalosiphum maidis cultivated cereals for plant nutrients and water. Del Fitch are the most common and efficient ones (Smith blanco et al. (2014) reported in barley two major & Plumb 1981). The bird cherry-oat aphid, Rho- QTls for CYDv tolerance from cultivar Madre Sel- palosiphum padi l., is a frequent vector of bYDv va on chromosomes 2H and 7H, four minor QTls species (Halbert & v oegtlin 1995). Çalı & Yurdakul from line butta 12 on chromosomes 3H, 4H, and 2H (1996) identified four more aphid species as the vec- with potential value to improve barley tolerance to tor of bYDvs in four provinces of Central anatolia CYDv -RPv . Moreover, balaji et al. (2003) suggest- in Turkey. Seven aphid species in the wheat fields ed determining bYDv and CYDv by using RT-qP- of Tekirdağ province in Trakya were identified by CR for rapid and sensitive diagnosis. v incent et al. Özder & Toros (1999). The mechanisms associat- (1991) identified nucleotide sequence and genome ed with YDv infections in the field conditions are organization of RPv serotypes. also, Zammurrad complex and influenced by many factors. The wild et al. (2014) indicated the high similarity of CP se- grasses, perennial pasture grasses, and volunteer quences of RPv isolates from different geographical cereals play a significant role as inoculum sources regions. Recently, Singh et al. (2019) identified CY - of virus and vector reservoirs during summer and Dv -RPvs in wheat samples by deep sequencing and throughout the growing seasons (McKirdy & Jones determined they should be grouped separately from 1997). because of the direct interactions between bYDvs in phylogenetic analysis. the viruses, aphid vectors, and cereal host plants, it The aim of this study was to investigate the pres- is also important to investigate the grass hosts pres- ence and prevalence of CYDv -RPv in natural grass 162 Agriculture (Poľnohospodárstvo), 66, 2020 (4): 161 − 170 hosts in the Trakya region. In order to determine the planted grasses. Five days of post-inoculation, the aphids were killed by spraying insecticide and the phylogenetic relationship of the Turkish five grass plants were maintained in insect-proof greenhouse RPv isolates, the PCR products were sequenced, conditions till the plants exhibited viral symptoms. and partial nucleotide and amino acid sequences of RPv were compared with published sequences of Serological test other RPv isolates available in the Genbank (ben- a total of 584 grass and volunteer cereal leaf son et al. 2013) and EMbl (Stoesser et al. 2000) samples, 30 intact grass samples and 50 indicator databases. plant leaves obtained from aphid transmission, were tested by ElISa Reagent Set for Cereal yellow dwarf virus-RPv (bioReba aG, Reinach, Switzer - mA terıAl And methOds land) for the presence of CYDv -RPv by Double antibody Sandwich Enzyme-linked Immunosor - Survey studies and sampling bent assays (DaS-ElISa) as described by Clark Extensive survey studies were conducted in the and adams (1977). cereal growing areas of the Trakya region, Turkey. Nucleic acid isolation and cDNA synthesis a total of 584 grasses and volunteer cereal leaf sam- all the samples of this work to investigate CY - ples exhibiting yellowing, reddening, stripe mosaic, Dv -RPv were subjected to the isolation of the viral irregular necrotic patches and dwarfing symptoms nucleic acids by employing the total nucleic acid ex- were collected from the border of cereal fields in traction method based on Trizol as described by Por- Edirne, Kırklareli, and Tekirdag provinces of Tra- tillo et al. (2006). First-strand cDNa was synthesized kya. Moreover, 30 intact grass plants representing tm from total isolated RNa by using a Revertaid each species were collected to determine aphid trans- First Strand cDNa Synthesis Kit (Fermentas, v il- missions and herbariums. nius, lithuania). In each reaction, 0.5 µg RNa sam- ple and 20 pmol of Reverse complementary primer Aphid transmission of CYDv -RPv designed by Deb & anderson (2007) Thirty symptomatic intact grass plants with col- were used and processed according to the manufac- onized aphids were transplanted into 5 l pots filled turer’s instructions. with a mixture of sterile soil, sand and compost (1:1:1) and were kept alive in greenhouse conditions RT-PCR amplifications (21 ± 5°C, l16: D8). apterous aphid colonies free The primer pairs RPv -l (5’-a TGTTGTaC- from their parasites were collected and examined CGCTTGa TCCaC-3’), RPv -R (5’-GCGaaC - for diagnosis under a Stereomicroscope (Olympus Ca TTGCCa TTG-3’) as designed by Deb & ander - SZ51). They were cultured on potted healthy wheat son (2007) were used for the amplification of coat (cv. Pehlivan, and atilla 12) and barley (cv. bar - protein region of CYDv -RPv . The amplified frag- baros) plants grown under greenhouse conditions. ments were 400 bp long. The PCR reaction for RPv barley (cv. barbaros) was selected as the indicator consisted of 3 µl 10x reaction buffer, 2 µl MgCl plant for RPv . Five seeds were sown into 500 ml (25 mM), 1 μl dNTP (10 mM), 0.5 µl for each pri- pots filled with a sterilized mixture of soil, sand, mer, 0.3 µl Tag DNa polymerase enzyme (MbI and compost (1:1:1). aphid transmissions were Fermentas), 2 µl cDNa and 15.7 µl RNase free performed as suggested by Du et al. (2007). Using water. The amplification protocol for RPv was as a camel hairbrush, apteral individuals were collect- follows: initial denaturation step at 94°C for 2 min, ed in petri dishes and placed on each transplanted followed by 40 cycles at 94°C for 30 sec, 60°C for grass and left to feed for 72 h for the acquisition of 45 sec, 72°C for 1 min and the final extension step at RPv viral particles. For inoculation, 1 pot contain- 72°C for 10 min in a thermal cycler. PCR products were analyzed by electrophoresis in 1.5% agarose ing 5 barley plants at the 2-leaf stage was allocated gel, stained with ethidium bromide, and viewed un- and 5 viruliferous aphids were placed on per each der Uv illumination in a gel documentation system plant, saving 1 healthy barley plant in each pot as (v ilber lourmet, Marne la v allee Cedex 1, France). control. This procedure was repeated for all trans- 163 Agriculture (Poľnohospodárstvo), 66, 2020 (4): 161 −170 Sequencing of PCR products which also was examined for the presence of RPv . For sequence analysis, PCR products were pu- However, one grass, A. sterilis was a common grass rified from agarose gels using QIaquick Gel Ex- in the cereal fields and grassland in Trakya. Similar - traction Kit (Qiagen N.v ., v enlo, Netherlands) ly, the most of those species were reported as com- in accordance with the manufacturer’s protocol petitive grasses in Turkey’s cereal fields by Güncan and sequenced by RefGen biotechnology (Mid- & Karaca (2018). among the aphid species known dle East Technical University (ODTU), ankara, to transmit CYDv -RPv (Halbert & v oegtlin 1995), Turkey). Obtained nucleotide and deduced amino only R. padi has been recorded in the Trakya region acid sequences were aligned with bioedit Program was used for the aphid transmission tests in this (version 7.2.5; https://bioedit.software.informer. study. These findings confirmed the observations com/7.2, Hall 1999). The alignments were used as obtained by Çalı and Yurdakul (1996) that deter- input data to construct phylogenetic trees with the mined aphid vectors in Central anatolia, and R. padi neighbor-joining distance method implemented in were identified as common aphid vectors in cereal the Mega X program (Kumar et al. 2018). Pairwise fields in Tekirdag province of Trakya by Ozder and sequence comparisons were calculated with the Toros (1999). During the survey studies, R. padi bioEdit Program. The distance matrix for the neigh- were observed to colonize particularly on A. sterilis bor-joining the analysis was calculated using the and be locally abundant and also on other grass spe- Kimura two-parameter model (Kimura 1980). boot- cies such as L. perenne, P. exaratum, P. austrialis strap analysis with 1,000 replicates was performed and A. fatua grasses. Such 30 symptomatic intact to assess the robustness of the branches. grasses with aphid colonies were used for the aphid transmission tests of RPv as shown in Table 1. aphid transmission test results showed that apterous RESUl TS aND DISCUSSION Rhopalosiphum padi l. transmitted CYDv -RPv from A. steriles. L. perenne and P. exaratum symp- The present survey study included three prov- tomatic intact grasses to barley (cv. barbaros) seed- inces of Trakya and resulted in the collection of 584 lings. according to ElISa and RT-PCR test results, symptomatic grass and volunteer cereal leaf sam- 28 out of 50 indicator plants were found positive for ples from 33 species belonging to the Poaceae, as- RPv . Thus, the intact grass species found to be in- teraceae, Juncaceae, Geraniaceae, Cyperaceae, and fected by RPv is among those observed to be the Rubiaceae families. Such wild grasses exhibiting preferred hosts of R. padi. However, A. sterilis could yellowing, reddening, stripe mosaic, irregular ne- have an otherwise greater attractivity for the aphid crotic patches and dwarfing symptoms were exam - vectors than other grass species. This could be ex- ined for the presence of CYDv -RPv by ElISa and plained that R. padi prefers more to feed and main- RT-PCR methods, and the transmission experiments tain on this grass than in other grass species. The were performed using aphid vector R. padi l. to screening test results revealed that 55 (9.42%) out of confirm the RPv infections. During survey studies, 584 samples were infected with CYDv -RPv , as the most common grasses in Trakya were detected shown in Table 2. according to this, 19 grass species to be Avena sterilis, Phragmites austrialis, Horde- and two volunteer cereal samples were found infect- um spp., Bromus spp., Lolium spp. in the family of ed with RPv . The results of this study showed that Poaceae, which showed typical YDv symptoms in- over-summering and over-wintering grasses were fected naturally. Moreover, except for Poaceae potential natural wild grass hosts of CYDv -RPv in grasses, the other weeds such as Gastridium ventri- the cereal fields of Trakya. Moreover, the infection cosum, Galium aparine l., Cynodon dactylon, Dac- rates of Avena sterilis and Lolium rigidum were tylis glomerate, Sonchus asper, Juncus compressus, more significant among the tested grass species than Geranium dissectum, Dasypyrum villosum, Lactuca RPv’s alternative potential reservoir hosts. Thus, serriola, Carex divisa and Taeniatherum caput-me- our results revealed that the presence of significant dusa showing systemic symptoms were common in reservoir grasses of RPv in Trakya. Similarly, the border of the cereal fields and in grassland, McKirdy and Jones (1997) and Power and Gray 164 Agriculture (Poľnohospodárstvo), 66, 2020 (4): 161 − 170 (1995) reported the wild grasses, perennial pasture a widespread perennial grass as a natural reservoir grasses, and volunteer cereals are the crucial reser- host of YDvs. However, Ilbağı (2006) reported that voir plant hosts of YDvs, which are important to P. communis Trin was not infected with RPv but know the direct interactions among the viruses, was found bYDv -Pav in Tekirdağ province of aphid vectors and host plants in the ecological sys- Trakya. v irus detection tests were confirmed by tem. also, the previous findings in the Trakya region direct sequencing of the PCR products in order to reported by Ilbağı et al. (2013) revealed Bromus complete the molecular characterization of CYDv - sterilis, Bromus arvensis, Poa trivialis and Sorghum RPv . The partial sequences belonged to five grass halepense were also the significant grass hosts of isolates originated from Tekirdağ (isolate TR-2 YDvs in the cereal growing areas of Trakya. Never - RPv , Genbank code KR005847; isolate TR-6 RPv , theless, the results concerning twelve virus-free KT923457), Edirne (isolate TR-3 RPv , KT923454; weed species including Gastridium ventricosum, isolate TR-4 RPv , KT923455), and Kirklareli (iso- Galium aparine l., Cynodon dactylon, Dactylis late TR-5 RPv , KT923456). The obtained nucleo- glomerate, Sonchus asper, Juncus compressus, Ely- tide sequences were aligned and compared with 11 mus repens, Geranium dissectum, Dasypyrum villo- accessions available in Genbank⁄EMbl database. sum, Lactuca serriola, Carex divisa and Taenia- Multiple sequence alignments and pairwise se- therum caput-medusa were not found as alternative quence comparisons were performed using bioedit reservoir hosts of RPv as indicated in Table 2. ad- software, as shown in Table 3. Sequence analysis ditionally, C. dactylon and D. glomerate weed spe- among the studied five Turkish isolates of grasses cies were identified as reservoir hosts of bYDv -Pav indicated that the intragroup percentage of nucleo- by D’arcy (1995). afterward, such grasses like tide identities were 93.93 − 98.62%. The lowest Echinochloa crus-galli, Seteria pumila, and Phalar- level of identity was 93.93% between isolate TR-2 is canariensis were identified as the sources of RPv and TR-3 RPv , TR-6 RPv isolates, and also YDvs in the Czech Republic (Pokorny 2006). also, between TR-3 RPv and TR-6 RPv isolates, while Elymus repens, Avena fatua, and Sorghum halep- the highest level of identity was 98.62% between ense as grass hosts of YDvs were reported in TR-4 RPv and TR-5 RPv isolate. The comparison bulgaria (bakardjieva et al. 2006). Thus, our results of the known RPv isolates with five Turkish isolates confirm their findings related to S. halepense, A. fat- revealed that lowest identity was 40.38% between ua as grass hosts of RPv . The present results also TR-3 RPv and isolate NY RPv and the highest was showed that P. australis was found as an over-sum- 95.86% between TR-2 RPv and 44P4b04-RPv mering and over-wintering host of RPv . Similarly, from the USa. amino acid multiple sequence align - Ilbağı et al. (2013) cited that P. australis was ments revealed that the lowest identity of five Turk- T a b l e 1 Intact grass plants used in aphid transmission experiments Province Intact grass species No. of intact grasses Edirne Avena sterilis l. 5 Edirne Phragmites australis (Cav.) Trin. ex Steudel 4 Kirklareli Phleum exaratum Hochst. ex Griseb. 3 Kirklareli Avena fatua l. 3 Kirklareli Avena sterilis l. 3 Tekirdağ Avena sterilis l. 5 Tekirdağ Lolium perenne l. 4 Tekirdağ A vena fatua l. 3 165 Agriculture (Poľnohospodárstvo), 66, 2020 (4): 161 −170 T a b l e 2 The incidence rate of the naturally infected grass species in the Trakya region of Turkey Number of RPv Name of grass species Family name Number of samples infected samples Avena fatua l. Poaceae 20 2 Avena sterilis l. Poaceae 60 11 Aegilops triuncialis l. Poaceae 2 1 Alopecurus myosuroides Huds. Poaceae 7 2 Apera spica venti (l.) P. beauv. Poaceae 4 1 Avena barbata l. Poaceae 20 1 Avena sativa l. (voluntary) Poaceae 31 2 Bromus sterilis l. Poaceae 32 2 Bromus arvensis l. Poaceae 17 3 Bromus hordeceaus l. Poaceae 29 3 Bromus tomentellus l. Poaceae 20 1 Hordeum bulbosum l. Poaceae 10 1 Hordeum murinum l. Poaceae 34 3 Lolium rigidum Gaudin Poaceae 35 9 Lolium perenne l. Poaceae 15 1 Phleum exaratum (Sali) aschers and Graebn. Poaceae 25 3 Phragmites australis (Cav.) Trin. ex Steudel Poaceae 57 2 Poa trivialis l. Poaceae 23 1 Sorghum halepense (l.) Pers. Poaceae 24 3 Echinocloa cruss-galli (l.) P.b Poaceae 23 1 Triticum aestivum l. (voluntary) Poaceae 2 2 Elymus repens (l.) Gould Poaceae 15 − Juncus compressus Jacq. Juncaceae 3 − Gastridium ventricosum (Gouan) Schinz & Thell Poaceae 3 − Galium aparine l. Rubiaceae 13 − Cynodon dactylon (l.) Pers. Poaceae 16 − Dactylis glomerata l. Poaceae 9 − Sonchus asper (l.) Hill asteraceae 4 − Dasypyrum villosum (l.) Cand. Poaceae 9 − Carex divisa Huds. Cyperaceae 1 − Geranium dissectum l. Geraniaceae 17 − Taeniatherum caput-medusa (l.) Nevski Poaceae 2 − Lactuca serriola l. asteraceae 2 − 33 6 584 55 Rate of virus infections [%] 9.42 166 Agriculture (Poľnohospodárstvo), 66, 2020 (4): 161 −170 T a b l e 3 Percentage of nucleotide (above the diagonal) and amino acid (below the diagonal) sequence identity of partial sequencing region among studied RPv isolates RPv isolate 44P4b04 05P1b02 O1 ny PK 05YC3 TR-v an Mardin117 005RPv MI-RPv NY-RPv TR-2 TR-3 TR-4 TR-5 TR-6 names 44P4b04 80.16 41.32 41.32 42.14 40.77 42.42 42.69 41.59 41.87 41.59 95.86 93.66 92.28 93.11 95.04 05P1b02 61.15 41.32 41.04 41.87 40.77 41.04 41.04 41.32 41.87 41.32 80.44 80.99 82.09 82.92 82.92 O1 16.62 13.22 98.86 94.60 88.35 96.31 95.17 98.59 98.59 98.30 41.87 41.87 42.42 41.87 42.14 ny 15.70 13.22 96.65 94.60 87.78 96.31 95.17 98.02 97.46 98.87 41.87 40.38 42.42 41.87 41.59 PK 15.70 13.22 90.90 90.90 86.93 94.33 95.17 93.80 93.80 94.08 42.42 41.67 42.42 42.42 42.14 05YC3 15.70 14.87 76.03 74.38 73.55 86.96 86.93 87.60 87.04 87.32 41.04 41.59 41.87 41.87 41.32 TR-v an 17.35 12 39 91.73 91.73 89.25 73.55 97.73 96.61 95.49 96.33 42.42 42.42 42.69 42.14 42.42 Mardin117 17.35 12 39 90.90 90.90 90.90 75.20 95.86 94.92 94.36 94.64 42.42 42.42 42.97 42.42 42.42 005RPv 16.52 13.22 96.69 95.04 89.25 74.38 93.38 90.90 98.87 99.15 42.14 42.14 42.69 42.14 41.87 MI-RPv 16.52 13.22 97.52 94.21 88.42 73.55 90.90 88.42 97.52 98.59 42.42 42.42 42.97 42.42 42.69 NY-RPv 16.52 13.22 95.86 97.52 90.08 73.55 92.56 90.08 97.52 96.69 42.14 42.14 42.69 42.14 41.87 TR-2 93.38 63.63 15.70 14.87 14.87 14.87 16.52 16.52 15.70 15.70 15.70 93.93 94.21 94.49 93.93 TR-3 86.77 63.63 15.70 14.87 15.70 17.35 16.52 16.52 15.70 15.70 15.70 85.95 95.04 95.86 93.93 TR-4 83.47 66.11 14.87 14 04 14.87 16.52 15.72 15.70 14.87 14.87 14.87 87.60 90.82 98.62 94.76 TR-5 82.29 66.11 14.87 14 04 14.87 16.52 15.70 15.70 14.87 14.87 14.87 86.77 92.56 97.52 95.59 TR-6 85.12 68.59 15.70 14.87 15.70 16.52 16.52 16.52 15.70 15.70 15.70 86.77 87.60 90.90 91.73 Agriculture (Poľnohospodárstvo), 66, 2020 (4): 161 −170 Figure 1. Constructed phylogenetic tree based on partial nucleotide sequencing results of PCR products from 5 Turkish RPv isola- tes and nucleotide sequences of 11 RPv isolates from the Genbank database. ish isolates was 14.04% between TR-4 RPv , TR-5 v incent et al. (1991) determined that the sequence RPv and isolate NY-RPv while the highest was similarity and genome relationship of RPv serotype 93.38% between TR-2 RPv and isolate 44P4b04- was more closely related to bWYv and PlR v , RPv from the USa. The intragroup percentage of which typically infect dicotyledonous hosts, than to amino acid identities of five Turkish grass RPv iso- Pav serotypes of bYDv . This study constitutes the lates was 85.95% between TR-2 RPv and TR-3 first study revealing the molecular characterization RPv while the highest was 97.52% between TR4- of RPv Turkish isolates on grass species. The re- RPv and TR-5 RPv isolates. Similar high identity sults will increase the genetic composition and tax- (99.95%) had the Pakistan RPv isolate with two onomical relationship within different host isolates RPv isolates from the USa belonging to different of YDvs in Turkey. geographical regions as determined by Zamurrad et al. (2014). Phylogenetic tree of nucleotide sequen- ces of five Turkish RPv isolates revealed two major CONClUSIONS groups as shown in Figure 1. Thus, the phylogenetic analysis indicated five Turkish RPv grass isolates YDvs cause economically important virus dis- clustered into the same group with two RPv isolates eases of cereal crops worldwide. CYDv -RPv is from the USa. These two RPv isolates included one of the most serious virus species within them. two ancestral recombination events for some isola- This study was conducted to investigate the pres- tes, as described by Robertson and French (2007). ence and prevalence of CYDv -RPv in reservoir also, Sigh et al. (2019) indicated that CYDv -RPv grasses and volunteer cereal host plants exhibiting had several recombination events, which are distinct yellowing, reddening, and dwarfing symptoms in from the commonly detected bYDvs. Similarly, Turkey’s Trakya region. The screening tests showed 168 Agriculture (Poľnohospodárstvo), 66, 2020 (4): 161 − 170 10.1007/s00705-003-0242-2. that grasses in the family Poaceae were infected ClaRK, M.F. − aDaMS, a.N. 1977. Characteristics of the with CYDv -RPv as natural reservoir hosts in the Microplate method of enzyme-linked immunosorbent as- cereal growing areas in Trakya. The incidence of say for the detection of plant viruses. In Journal of General Virology, vol. 34, pp.475 − 483. DOI: 10.1099/0022-1317- RPv was at a rate of 9.42% in tested 584 symptom- 34-3-475. atic grass samples. Transmission experiments using ÇalI, S. – YURDaKUl, S. 1996. Investigation on virus dis- th eases of wheat in Central anatolia. In Book of Abstracts, 5 the aphid species Rhopalosiphum padi l. showed International Wheat Conference. June10−14, ankara, Tur - that CYDv -RPv was transmitted persistently from key, p. 120. ISbN:07923-4727-7. symptomatic intact grasses such as Avena sterilis, D’aRCY, C.J. 1995. Symptomatology and host range of bar - ley yellow dwarf. In D’aRCY, C.J − bURNET, P.a. (Eds.), Lolium perenne and Phleum exratum to barley cv. Barley yellow dwarf 40 years of progress. St Paul, MN- barbaros seedlings. PCR products of five Turkish USa: aPS Press, pp. 9 − 28. ISbN:0890541671. DEb, M. ‒ aNDERSON, J.M. 2007. Development of a multi - grass RPv isolates were sequenced and compared plexed PCR detection method for barley and cereal yellow with eleven known RPv isolates in the Genbank. dwarf viruses, wheat spindle streak virus, wheat streak mo- a phylogenetic tree of nucleotide sequences of five saic virus and soil-borne wheat mosaic virus. In Journal of Virological Methods, vol. 148, pp. 17 − 24. 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POCSaI, E. ‒ CITIR, a. ‒ IlbaGI, H. ‒ KÖKlÜ, G. ‒ KOR- ZaMURRaD, M. – SHaHID, H. – KaMRaN, S. – Ul KUT, K. ‒ MURÁNYI, I. ‒ vIDa G. 2003. Incidence of HaQUE, I. – KaUSaR, S. 2014. Phylogenetic analysis of barley yellow dwarf viruses, cereal yellow dwarf virus coat protein gene of CYDv -RPv strain from wheat. In Ad- and wheat dwarf virus in cereal growing areas of Turkey. vancements in Life Sciences, vol. 2, no. 1, pp. 16 − 22. DOI: In Agriculture (Poľnohospodárstvo), vol. 49, no. 11, pp. www.als-journal.com/214-14. 583 − 591. Received: September 9, 2020 POKORNY, R. 2006. Occurrence of viruses of the family luteo- accepted: December 14, 2020 viridae on maize and some annual weed grasses in the Czech http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Agriculture de Gruyter

Molecular Characterization of Cereal Yellow Dwarf Virus-RPV in Grasses in European Part of Turkey

Agriculture , Volume 66 (4): 10 – Dec 1, 2020

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Abstract

Agriculture (Poľnohospodárstvo), 66, 2020 (4): 161 − 170 Original paper DOI: 10.2478/agri-2020-0015 MOLECULAR CHARACTERIZATION OF CEREAL YELLOW DWARF VIRUS-RPV IN GRASSES IN EUROPEAN PART OF TURKEY 1* 1 1 2 Havva IlbağI , Ahmet Çıtır , AdnAn KArA , myem Uys er Al Namık Kemal University, Tekirdağ, Turkey Selçuk University, Konya,Turkey ılBAğ ı, h. – Çıtır, a. − KaRa, a. − UYSal, M.: Molecular characterization of cereal yellow dwarf virus-RPv in grasses in european part of Turkey. agriculture (Poľnohospodárstvo), vol. 66, no. 4, pp. 161 – 170. Yellow dwarf viruses (YDvs) are economically destructive viral diseases of cereal crops, which cause the reduction of yield and quality of grains. Cereal yellow dwarf virus-RPV (CYDv -RPv) is one of the most serious virus species of YDvs. These virus diseases cause epidemics in cereal fields in some periods of the year in Turkey depending on potential reservoir natural hosts that play a significant role in epidemiology. This study was conducted to investigate the presence and prevalence of CYDv -RPv in grasses and volunteer cereal host plants including 33 species from Poaceae, asteraceae, Juncaceae, Gerani- aceae, Cyperaceae, and Rubiaceae families in the Trakya region of Turkey. a total of 584 symptomatic grass and volunteer cereal leaf samples exhibiting yellowing, reddening, irregular necrotic patches and dwarfing symptoms were collected from Trakya and tested by ElISa and RT-PCR methods. The screening tests showed that 55 out of 584 grass samples were infect- ed with CYDv -RPv in grasses from the Poaceae family, while none of the other families had no infection. The incidence of CYDv -RPv was detected at a rate of 9.42%. Transmission experiments using the aphid species Rhopalosiphum padi l . showed that CYDv -RPv was transmitted persistently from symptomatic intact grasses such as Avena sterilis, Lolium perenne and Phleum exratum to barley cv. barbaros seedlings. PCR products of five Turkish RPv grass isolates were sequenced and compared with eleven known CYDv -RPv isolates in the Genbank⁄ EMbl databases. Compared nucleotide and amino acid sequences of CYDv -RPv isolates showed that the identities ranged from 40.38 − 95.86 % to 14.04 − 93.38%, respectively. In this study, 19 grass species from the Poaceae family and two volunteer cereal host plants were determined as natural reservoir hosts of CYDv -RPv in the cereal growing areas of Turkey. Key words: CYDv -RPv , polerovirus, grasses, molecular diversity The Trakya region is one of the most important viruses (YDvs) considerably reduced the yield and cereal growing areas in Turkey. almost one million quality of cereal crops in Trakya. High incidence ha of arable land, which covers 65% of the region, rates of YDvs causing severe infections and epi- has been allocated to field crops and cereal pro- demics on cereals have been reported periodical- duction. With the effects of global climate change ly in Turkey. Early sown susceptible winter wheat in recent years, increasing temperatures have grad- cultivars were especially affected by the highest ually caused prevailing pest and diseases. besides incidences of YDvs (Ilbağı et al. 2005; Ilbağı et the very damaging fungal pathogens, Yellow dwarf al. 2013). Moreover, bYDvs or CYDv infections Havva Ilbağı (*Corresponding author), ahmet Çıtır, adnan Kara, Department of Plant Protection, Faculty of agriculture, Namık Kemal University, Tekirdağ, Turkey. E-mail: hilbagi@nku.edu.tr Meryem Uysal, Department of Plant Protection, Faculty of agriculture, Selçuk University, Konya,Turkey © 2020 authors. This is an open access article licensed under the Creative Commons attribution-NonComercial-NoDerivs license (http://creativecommons.org/licenses/by-nc-nd/4.0/). 161 Agriculture (Poľnohospodárstvo), 66, 2020 (4): 161 − 170 caused up to 80% yield losses on cereal crops by ence in these agroecosystems (Power & Gray 1995). reducing the number of tillers per plant, number a list of 96 annual, 2 biannual and 111 perennial of seeds per tiller, and seed weights as reported by Poaceae weed hosts worldwide were compiled by McKirdy et al. (2002) and Perry et al. (2000). Sim- D’arcy (1995). In the subsequent years, the grass ilarly, Miller & Rasochova (1997) and Pike (1990) hosts of YDvs were reported in different countries determined average yield losses between 11% and by Garrett et al. (2004) in the USa, Pokorny (2006) 33% and sometimes up to 80% in the wheat fields. in the Czech Republic, bisnieks et al. (2004) in lat - YDvs are the most destructive virus diseases on ce- via and Sweden, bakardjeiva et al. (2006) in bul- real crops comprising a complex virus group. There garia. Previously, sporadic infections of bYDv in are currently 10 recognized YDv species within the wheat fields were investigated in the western part family Luteoviridae (adams et al. 2014), consisting of Turkey by bremer & Raatikainen (1975). Since of Barley yellow dwarf viruses (bYDvs), Cereal 1999 the year in the Trakya region, YDvs have be- yellow dwarf viruses (CYDvs), and Maize yellow come epidemics in the cereal fields, as reported by dwarf virus-RMV (MYDv -RMv). Five species Ilbağı et al. (2013). In addition to the Trakya region, have been assigned to the genus Luteovirus (bY- YDv infections were determined in 15 other cereal Dv -Kerll, bYDv -KerIII, bYDv -Mav , bYDv -PaS growing provinces of Turkey (Pocsai et al. 2003). and bYDv -Pav), three species have been assigned later, Ilbağı (2006) identified common reed (Phrag- to the genus Poleovirus (CYDv -RPv , CYDv -RPS, mites communis Trin) as a perennial natural weed and MYDv -RMv), and two have not yet been as- host of bYDv -Pav ; however, CYDv -RPv was not signed any genus (bYDv -GPv and bYDv -SGv). detected in the reed. Following this study, birdseed 30 nm in YDvs have isometric particles of 25 − (Phalaris canariensis l.) was also determined as diameter and ss(+) RNa genome of approximately the most susceptible host of both bYDv -Pav and 5,600 nucleotides (Rochow & Duffus 1981). There CYDv -RPv in Tekirdağ (Ilbağı et al. 2008). late - are six open reading frames (ORFs) in the genome, ly, dicotyledonous weed hosts of bYDv -Pav and which are numbered 1 – 6 in the members of Lu- Mav such as Juncus compressus Jacq. and Gera- teovirus and 0 – 5 in the members of Polerovirus nium dissectum l. were reported in Trakya, Turkey (Miller et al. 2002). These viruses are phloem-li- (Ilbağı et al. 2019). Güncan & Karaca (2018) sug- mited and are transmitted in a persistent circulati- gested effective weed control for potential reser- ve manner by over 25 aphid vectors. among them, voir sources of YDvs, as well as competition with Rhopalosiphum padi l. and Rhopalosiphum maidis cultivated cereals for plant nutrients and water. Del Fitch are the most common and efficient ones (Smith blanco et al. (2014) reported in barley two major & Plumb 1981). The bird cherry-oat aphid, Rho- QTls for CYDv tolerance from cultivar Madre Sel- palosiphum padi l., is a frequent vector of bYDv va on chromosomes 2H and 7H, four minor QTls species (Halbert & v oegtlin 1995). Çalı & Yurdakul from line butta 12 on chromosomes 3H, 4H, and 2H (1996) identified four more aphid species as the vec- with potential value to improve barley tolerance to tor of bYDvs in four provinces of Central anatolia CYDv -RPv . Moreover, balaji et al. (2003) suggest- in Turkey. Seven aphid species in the wheat fields ed determining bYDv and CYDv by using RT-qP- of Tekirdağ province in Trakya were identified by CR for rapid and sensitive diagnosis. v incent et al. Özder & Toros (1999). The mechanisms associat- (1991) identified nucleotide sequence and genome ed with YDv infections in the field conditions are organization of RPv serotypes. also, Zammurrad complex and influenced by many factors. The wild et al. (2014) indicated the high similarity of CP se- grasses, perennial pasture grasses, and volunteer quences of RPv isolates from different geographical cereals play a significant role as inoculum sources regions. Recently, Singh et al. (2019) identified CY - of virus and vector reservoirs during summer and Dv -RPvs in wheat samples by deep sequencing and throughout the growing seasons (McKirdy & Jones determined they should be grouped separately from 1997). because of the direct interactions between bYDvs in phylogenetic analysis. the viruses, aphid vectors, and cereal host plants, it The aim of this study was to investigate the pres- is also important to investigate the grass hosts pres- ence and prevalence of CYDv -RPv in natural grass 162 Agriculture (Poľnohospodárstvo), 66, 2020 (4): 161 − 170 hosts in the Trakya region. In order to determine the planted grasses. Five days of post-inoculation, the aphids were killed by spraying insecticide and the phylogenetic relationship of the Turkish five grass plants were maintained in insect-proof greenhouse RPv isolates, the PCR products were sequenced, conditions till the plants exhibited viral symptoms. and partial nucleotide and amino acid sequences of RPv were compared with published sequences of Serological test other RPv isolates available in the Genbank (ben- a total of 584 grass and volunteer cereal leaf son et al. 2013) and EMbl (Stoesser et al. 2000) samples, 30 intact grass samples and 50 indicator databases. plant leaves obtained from aphid transmission, were tested by ElISa Reagent Set for Cereal yellow dwarf virus-RPv (bioReba aG, Reinach, Switzer - mA terıAl And methOds land) for the presence of CYDv -RPv by Double antibody Sandwich Enzyme-linked Immunosor - Survey studies and sampling bent assays (DaS-ElISa) as described by Clark Extensive survey studies were conducted in the and adams (1977). cereal growing areas of the Trakya region, Turkey. Nucleic acid isolation and cDNA synthesis a total of 584 grasses and volunteer cereal leaf sam- all the samples of this work to investigate CY - ples exhibiting yellowing, reddening, stripe mosaic, Dv -RPv were subjected to the isolation of the viral irregular necrotic patches and dwarfing symptoms nucleic acids by employing the total nucleic acid ex- were collected from the border of cereal fields in traction method based on Trizol as described by Por- Edirne, Kırklareli, and Tekirdag provinces of Tra- tillo et al. (2006). First-strand cDNa was synthesized kya. Moreover, 30 intact grass plants representing tm from total isolated RNa by using a Revertaid each species were collected to determine aphid trans- First Strand cDNa Synthesis Kit (Fermentas, v il- missions and herbariums. nius, lithuania). In each reaction, 0.5 µg RNa sam- ple and 20 pmol of Reverse complementary primer Aphid transmission of CYDv -RPv designed by Deb & anderson (2007) Thirty symptomatic intact grass plants with col- were used and processed according to the manufac- onized aphids were transplanted into 5 l pots filled turer’s instructions. with a mixture of sterile soil, sand and compost (1:1:1) and were kept alive in greenhouse conditions RT-PCR amplifications (21 ± 5°C, l16: D8). apterous aphid colonies free The primer pairs RPv -l (5’-a TGTTGTaC- from their parasites were collected and examined CGCTTGa TCCaC-3’), RPv -R (5’-GCGaaC - for diagnosis under a Stereomicroscope (Olympus Ca TTGCCa TTG-3’) as designed by Deb & ander - SZ51). They were cultured on potted healthy wheat son (2007) were used for the amplification of coat (cv. Pehlivan, and atilla 12) and barley (cv. bar - protein region of CYDv -RPv . The amplified frag- baros) plants grown under greenhouse conditions. ments were 400 bp long. The PCR reaction for RPv barley (cv. barbaros) was selected as the indicator consisted of 3 µl 10x reaction buffer, 2 µl MgCl plant for RPv . Five seeds were sown into 500 ml (25 mM), 1 μl dNTP (10 mM), 0.5 µl for each pri- pots filled with a sterilized mixture of soil, sand, mer, 0.3 µl Tag DNa polymerase enzyme (MbI and compost (1:1:1). aphid transmissions were Fermentas), 2 µl cDNa and 15.7 µl RNase free performed as suggested by Du et al. (2007). Using water. The amplification protocol for RPv was as a camel hairbrush, apteral individuals were collect- follows: initial denaturation step at 94°C for 2 min, ed in petri dishes and placed on each transplanted followed by 40 cycles at 94°C for 30 sec, 60°C for grass and left to feed for 72 h for the acquisition of 45 sec, 72°C for 1 min and the final extension step at RPv viral particles. For inoculation, 1 pot contain- 72°C for 10 min in a thermal cycler. PCR products were analyzed by electrophoresis in 1.5% agarose ing 5 barley plants at the 2-leaf stage was allocated gel, stained with ethidium bromide, and viewed un- and 5 viruliferous aphids were placed on per each der Uv illumination in a gel documentation system plant, saving 1 healthy barley plant in each pot as (v ilber lourmet, Marne la v allee Cedex 1, France). control. This procedure was repeated for all trans- 163 Agriculture (Poľnohospodárstvo), 66, 2020 (4): 161 −170 Sequencing of PCR products which also was examined for the presence of RPv . For sequence analysis, PCR products were pu- However, one grass, A. sterilis was a common grass rified from agarose gels using QIaquick Gel Ex- in the cereal fields and grassland in Trakya. Similar - traction Kit (Qiagen N.v ., v enlo, Netherlands) ly, the most of those species were reported as com- in accordance with the manufacturer’s protocol petitive grasses in Turkey’s cereal fields by Güncan and sequenced by RefGen biotechnology (Mid- & Karaca (2018). among the aphid species known dle East Technical University (ODTU), ankara, to transmit CYDv -RPv (Halbert & v oegtlin 1995), Turkey). Obtained nucleotide and deduced amino only R. padi has been recorded in the Trakya region acid sequences were aligned with bioedit Program was used for the aphid transmission tests in this (version 7.2.5; https://bioedit.software.informer. study. These findings confirmed the observations com/7.2, Hall 1999). The alignments were used as obtained by Çalı and Yurdakul (1996) that deter- input data to construct phylogenetic trees with the mined aphid vectors in Central anatolia, and R. padi neighbor-joining distance method implemented in were identified as common aphid vectors in cereal the Mega X program (Kumar et al. 2018). Pairwise fields in Tekirdag province of Trakya by Ozder and sequence comparisons were calculated with the Toros (1999). During the survey studies, R. padi bioEdit Program. The distance matrix for the neigh- were observed to colonize particularly on A. sterilis bor-joining the analysis was calculated using the and be locally abundant and also on other grass spe- Kimura two-parameter model (Kimura 1980). boot- cies such as L. perenne, P. exaratum, P. austrialis strap analysis with 1,000 replicates was performed and A. fatua grasses. Such 30 symptomatic intact to assess the robustness of the branches. grasses with aphid colonies were used for the aphid transmission tests of RPv as shown in Table 1. aphid transmission test results showed that apterous RESUl TS aND DISCUSSION Rhopalosiphum padi l. transmitted CYDv -RPv from A. steriles. L. perenne and P. exaratum symp- The present survey study included three prov- tomatic intact grasses to barley (cv. barbaros) seed- inces of Trakya and resulted in the collection of 584 lings. according to ElISa and RT-PCR test results, symptomatic grass and volunteer cereal leaf sam- 28 out of 50 indicator plants were found positive for ples from 33 species belonging to the Poaceae, as- RPv . Thus, the intact grass species found to be in- teraceae, Juncaceae, Geraniaceae, Cyperaceae, and fected by RPv is among those observed to be the Rubiaceae families. Such wild grasses exhibiting preferred hosts of R. padi. However, A. sterilis could yellowing, reddening, stripe mosaic, irregular ne- have an otherwise greater attractivity for the aphid crotic patches and dwarfing symptoms were exam - vectors than other grass species. This could be ex- ined for the presence of CYDv -RPv by ElISa and plained that R. padi prefers more to feed and main- RT-PCR methods, and the transmission experiments tain on this grass than in other grass species. The were performed using aphid vector R. padi l. to screening test results revealed that 55 (9.42%) out of confirm the RPv infections. During survey studies, 584 samples were infected with CYDv -RPv , as the most common grasses in Trakya were detected shown in Table 2. according to this, 19 grass species to be Avena sterilis, Phragmites austrialis, Horde- and two volunteer cereal samples were found infect- um spp., Bromus spp., Lolium spp. in the family of ed with RPv . The results of this study showed that Poaceae, which showed typical YDv symptoms in- over-summering and over-wintering grasses were fected naturally. Moreover, except for Poaceae potential natural wild grass hosts of CYDv -RPv in grasses, the other weeds such as Gastridium ventri- the cereal fields of Trakya. Moreover, the infection cosum, Galium aparine l., Cynodon dactylon, Dac- rates of Avena sterilis and Lolium rigidum were tylis glomerate, Sonchus asper, Juncus compressus, more significant among the tested grass species than Geranium dissectum, Dasypyrum villosum, Lactuca RPv’s alternative potential reservoir hosts. Thus, serriola, Carex divisa and Taeniatherum caput-me- our results revealed that the presence of significant dusa showing systemic symptoms were common in reservoir grasses of RPv in Trakya. Similarly, the border of the cereal fields and in grassland, McKirdy and Jones (1997) and Power and Gray 164 Agriculture (Poľnohospodárstvo), 66, 2020 (4): 161 − 170 (1995) reported the wild grasses, perennial pasture a widespread perennial grass as a natural reservoir grasses, and volunteer cereals are the crucial reser- host of YDvs. However, Ilbağı (2006) reported that voir plant hosts of YDvs, which are important to P. communis Trin was not infected with RPv but know the direct interactions among the viruses, was found bYDv -Pav in Tekirdağ province of aphid vectors and host plants in the ecological sys- Trakya. v irus detection tests were confirmed by tem. also, the previous findings in the Trakya region direct sequencing of the PCR products in order to reported by Ilbağı et al. (2013) revealed Bromus complete the molecular characterization of CYDv - sterilis, Bromus arvensis, Poa trivialis and Sorghum RPv . The partial sequences belonged to five grass halepense were also the significant grass hosts of isolates originated from Tekirdağ (isolate TR-2 YDvs in the cereal growing areas of Trakya. Never - RPv , Genbank code KR005847; isolate TR-6 RPv , theless, the results concerning twelve virus-free KT923457), Edirne (isolate TR-3 RPv , KT923454; weed species including Gastridium ventricosum, isolate TR-4 RPv , KT923455), and Kirklareli (iso- Galium aparine l., Cynodon dactylon, Dactylis late TR-5 RPv , KT923456). The obtained nucleo- glomerate, Sonchus asper, Juncus compressus, Ely- tide sequences were aligned and compared with 11 mus repens, Geranium dissectum, Dasypyrum villo- accessions available in Genbank⁄EMbl database. sum, Lactuca serriola, Carex divisa and Taenia- Multiple sequence alignments and pairwise se- therum caput-medusa were not found as alternative quence comparisons were performed using bioedit reservoir hosts of RPv as indicated in Table 2. ad- software, as shown in Table 3. Sequence analysis ditionally, C. dactylon and D. glomerate weed spe- among the studied five Turkish isolates of grasses cies were identified as reservoir hosts of bYDv -Pav indicated that the intragroup percentage of nucleo- by D’arcy (1995). afterward, such grasses like tide identities were 93.93 − 98.62%. The lowest Echinochloa crus-galli, Seteria pumila, and Phalar- level of identity was 93.93% between isolate TR-2 is canariensis were identified as the sources of RPv and TR-3 RPv , TR-6 RPv isolates, and also YDvs in the Czech Republic (Pokorny 2006). also, between TR-3 RPv and TR-6 RPv isolates, while Elymus repens, Avena fatua, and Sorghum halep- the highest level of identity was 98.62% between ense as grass hosts of YDvs were reported in TR-4 RPv and TR-5 RPv isolate. The comparison bulgaria (bakardjieva et al. 2006). Thus, our results of the known RPv isolates with five Turkish isolates confirm their findings related to S. halepense, A. fat- revealed that lowest identity was 40.38% between ua as grass hosts of RPv . The present results also TR-3 RPv and isolate NY RPv and the highest was showed that P. australis was found as an over-sum- 95.86% between TR-2 RPv and 44P4b04-RPv mering and over-wintering host of RPv . Similarly, from the USa. amino acid multiple sequence align - Ilbağı et al. (2013) cited that P. australis was ments revealed that the lowest identity of five Turk- T a b l e 1 Intact grass plants used in aphid transmission experiments Province Intact grass species No. of intact grasses Edirne Avena sterilis l. 5 Edirne Phragmites australis (Cav.) Trin. ex Steudel 4 Kirklareli Phleum exaratum Hochst. ex Griseb. 3 Kirklareli Avena fatua l. 3 Kirklareli Avena sterilis l. 3 Tekirdağ Avena sterilis l. 5 Tekirdağ Lolium perenne l. 4 Tekirdağ A vena fatua l. 3 165 Agriculture (Poľnohospodárstvo), 66, 2020 (4): 161 −170 T a b l e 2 The incidence rate of the naturally infected grass species in the Trakya region of Turkey Number of RPv Name of grass species Family name Number of samples infected samples Avena fatua l. Poaceae 20 2 Avena sterilis l. Poaceae 60 11 Aegilops triuncialis l. Poaceae 2 1 Alopecurus myosuroides Huds. Poaceae 7 2 Apera spica venti (l.) P. beauv. Poaceae 4 1 Avena barbata l. Poaceae 20 1 Avena sativa l. (voluntary) Poaceae 31 2 Bromus sterilis l. Poaceae 32 2 Bromus arvensis l. Poaceae 17 3 Bromus hordeceaus l. Poaceae 29 3 Bromus tomentellus l. Poaceae 20 1 Hordeum bulbosum l. Poaceae 10 1 Hordeum murinum l. Poaceae 34 3 Lolium rigidum Gaudin Poaceae 35 9 Lolium perenne l. Poaceae 15 1 Phleum exaratum (Sali) aschers and Graebn. Poaceae 25 3 Phragmites australis (Cav.) Trin. ex Steudel Poaceae 57 2 Poa trivialis l. Poaceae 23 1 Sorghum halepense (l.) Pers. Poaceae 24 3 Echinocloa cruss-galli (l.) P.b Poaceae 23 1 Triticum aestivum l. (voluntary) Poaceae 2 2 Elymus repens (l.) Gould Poaceae 15 − Juncus compressus Jacq. Juncaceae 3 − Gastridium ventricosum (Gouan) Schinz & Thell Poaceae 3 − Galium aparine l. Rubiaceae 13 − Cynodon dactylon (l.) Pers. Poaceae 16 − Dactylis glomerata l. Poaceae 9 − Sonchus asper (l.) Hill asteraceae 4 − Dasypyrum villosum (l.) Cand. Poaceae 9 − Carex divisa Huds. Cyperaceae 1 − Geranium dissectum l. Geraniaceae 17 − Taeniatherum caput-medusa (l.) Nevski Poaceae 2 − Lactuca serriola l. asteraceae 2 − 33 6 584 55 Rate of virus infections [%] 9.42 166 Agriculture (Poľnohospodárstvo), 66, 2020 (4): 161 −170 T a b l e 3 Percentage of nucleotide (above the diagonal) and amino acid (below the diagonal) sequence identity of partial sequencing region among studied RPv isolates RPv isolate 44P4b04 05P1b02 O1 ny PK 05YC3 TR-v an Mardin117 005RPv MI-RPv NY-RPv TR-2 TR-3 TR-4 TR-5 TR-6 names 44P4b04 80.16 41.32 41.32 42.14 40.77 42.42 42.69 41.59 41.87 41.59 95.86 93.66 92.28 93.11 95.04 05P1b02 61.15 41.32 41.04 41.87 40.77 41.04 41.04 41.32 41.87 41.32 80.44 80.99 82.09 82.92 82.92 O1 16.62 13.22 98.86 94.60 88.35 96.31 95.17 98.59 98.59 98.30 41.87 41.87 42.42 41.87 42.14 ny 15.70 13.22 96.65 94.60 87.78 96.31 95.17 98.02 97.46 98.87 41.87 40.38 42.42 41.87 41.59 PK 15.70 13.22 90.90 90.90 86.93 94.33 95.17 93.80 93.80 94.08 42.42 41.67 42.42 42.42 42.14 05YC3 15.70 14.87 76.03 74.38 73.55 86.96 86.93 87.60 87.04 87.32 41.04 41.59 41.87 41.87 41.32 TR-v an 17.35 12 39 91.73 91.73 89.25 73.55 97.73 96.61 95.49 96.33 42.42 42.42 42.69 42.14 42.42 Mardin117 17.35 12 39 90.90 90.90 90.90 75.20 95.86 94.92 94.36 94.64 42.42 42.42 42.97 42.42 42.42 005RPv 16.52 13.22 96.69 95.04 89.25 74.38 93.38 90.90 98.87 99.15 42.14 42.14 42.69 42.14 41.87 MI-RPv 16.52 13.22 97.52 94.21 88.42 73.55 90.90 88.42 97.52 98.59 42.42 42.42 42.97 42.42 42.69 NY-RPv 16.52 13.22 95.86 97.52 90.08 73.55 92.56 90.08 97.52 96.69 42.14 42.14 42.69 42.14 41.87 TR-2 93.38 63.63 15.70 14.87 14.87 14.87 16.52 16.52 15.70 15.70 15.70 93.93 94.21 94.49 93.93 TR-3 86.77 63.63 15.70 14.87 15.70 17.35 16.52 16.52 15.70 15.70 15.70 85.95 95.04 95.86 93.93 TR-4 83.47 66.11 14.87 14 04 14.87 16.52 15.72 15.70 14.87 14.87 14.87 87.60 90.82 98.62 94.76 TR-5 82.29 66.11 14.87 14 04 14.87 16.52 15.70 15.70 14.87 14.87 14.87 86.77 92.56 97.52 95.59 TR-6 85.12 68.59 15.70 14.87 15.70 16.52 16.52 16.52 15.70 15.70 15.70 86.77 87.60 90.90 91.73 Agriculture (Poľnohospodárstvo), 66, 2020 (4): 161 −170 Figure 1. Constructed phylogenetic tree based on partial nucleotide sequencing results of PCR products from 5 Turkish RPv isola- tes and nucleotide sequences of 11 RPv isolates from the Genbank database. ish isolates was 14.04% between TR-4 RPv , TR-5 v incent et al. (1991) determined that the sequence RPv and isolate NY-RPv while the highest was similarity and genome relationship of RPv serotype 93.38% between TR-2 RPv and isolate 44P4b04- was more closely related to bWYv and PlR v , RPv from the USa. The intragroup percentage of which typically infect dicotyledonous hosts, than to amino acid identities of five Turkish grass RPv iso- Pav serotypes of bYDv . This study constitutes the lates was 85.95% between TR-2 RPv and TR-3 first study revealing the molecular characterization RPv while the highest was 97.52% between TR4- of RPv Turkish isolates on grass species. The re- RPv and TR-5 RPv isolates. Similar high identity sults will increase the genetic composition and tax- (99.95%) had the Pakistan RPv isolate with two onomical relationship within different host isolates RPv isolates from the USa belonging to different of YDvs in Turkey. geographical regions as determined by Zamurrad et al. (2014). Phylogenetic tree of nucleotide sequen- ces of five Turkish RPv isolates revealed two major CONClUSIONS groups as shown in Figure 1. Thus, the phylogenetic analysis indicated five Turkish RPv grass isolates YDvs cause economically important virus dis- clustered into the same group with two RPv isolates eases of cereal crops worldwide. CYDv -RPv is from the USa. These two RPv isolates included one of the most serious virus species within them. two ancestral recombination events for some isola- This study was conducted to investigate the pres- tes, as described by Robertson and French (2007). ence and prevalence of CYDv -RPv in reservoir also, Sigh et al. (2019) indicated that CYDv -RPv grasses and volunteer cereal host plants exhibiting had several recombination events, which are distinct yellowing, reddening, and dwarfing symptoms in from the commonly detected bYDvs. Similarly, Turkey’s Trakya region. The screening tests showed 168 Agriculture (Poľnohospodárstvo), 66, 2020 (4): 161 − 170 10.1007/s00705-003-0242-2. that grasses in the family Poaceae were infected ClaRK, M.F. − aDaMS, a.N. 1977. Characteristics of the with CYDv -RPv as natural reservoir hosts in the Microplate method of enzyme-linked immunosorbent as- cereal growing areas in Trakya. The incidence of say for the detection of plant viruses. In Journal of General Virology, vol. 34, pp.475 − 483. DOI: 10.1099/0022-1317- RPv was at a rate of 9.42% in tested 584 symptom- 34-3-475. atic grass samples. Transmission experiments using ÇalI, S. – YURDaKUl, S. 1996. Investigation on virus dis- th eases of wheat in Central anatolia. 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Agriculturede Gruyter

Published: Dec 1, 2020

Keywords: CYDV-RPV; polerovirus; grasses; molecular diversity

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