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Molecular characterisation of Alfalfa mosaic virus isolates in potato from the Tokat province, Türkiye

Year 2022, Volume: 35 Issue: 2, 75 - 81, 02.08.2022
https://doi.org/10.29136/mediterranean.1045447

Abstract

The Alfalfa mosaic virus (AMV) was detected in potato fields in the Tokat province. The coat protein (CP) sequences of AMV isolates from the Tokat province were determined and compared with sequences of reference AMV isolates from GenBank. Total nucleic acid (TNA) was extracted from plants with positive results according to serological test results. Then, reverse-transcription polymerase chain reaction (RT-PCR) was performed using primer pair specific to partial the coat protein region, and positive PCR products were sent for sequence analysis in both directions. Two Turkish AMV isolates (AMV-PN3-5 and AMV-PN3-6) had a 96-99% nt homology amongst themselves, according to nucleotides (nt) sequence analysis. Based on the phylogenetic tree obtained from 24 AMV isolates from GenBank for both sequences, the two Turkish AMV isolates were clustered in subgroup I containing Iranian, Canadian, Turkish, Korean, and Serbian isolates, at the nucleotide level. Sequence comparison showed that these two isolates of AMV shared 96% to 99.7% sequence similarity with the twenty-six reported isolates of AMV obtained from GenBank. This is the first report on the genetic variability of AMV isolates infecting potato crops in the Tokat province.

References

  • Abdel Aleem EE, Taha RM, Fattouh FA (2018) Biodiversity and full genome sequence of potato viruses Alfalfa mosaic virus and potato leaf roll virus in Egypt. Zeitschrift für Naturforschung C Journal of biosciences 73(11-12): 423-438.
  • Al-Saleh, MA, Amer MA, AL-Shahwan IM, Abdalla OA, Shakeel MT (2014) Molecular characterization of two alfalfa mosaic virus isolates infecting potato crop in central region of Saudi Arabia. International Journal of Agriculture and Biology 16: 976-980.
  • Arlı-Sökmen M, Mennan H, Sevik MA, Ecevit O (2005) Occurrence of viruses in field-grown pepper crops and some of their reservoir weeds hosts in Samsun, Turkey. Phytoparasitica 33(4): 347-358.
  • Astruc N, Marcos JF, Macquaire G, Candresse T, Pallas V (1996) Studies on the diagnosis of hop stunt viroid in fruit trees: Identification of new hosts and application of nucleic acid extraction procedure based on non-organic solvents. European Journal of Plant Pathology 102(9): 837-846.
  • Bailiss KW, Offei SK (1990) Alfalfa mosaic virus in lucerne seed during seed maturation and storage, and in seedlings. Plant Pathology 39: 539-47.
  • Bergua M, Luis-Arteaga M, Escriu F (2014) Genetic diversity, reassortment and recombination in Alfalfa mosaic virus population in Spain. Phytopathology 104: 1241-1250.
  • Bol JF (2003) Alfalfa mosaic virus: Coat protein dependent initiation of infection. Molecular Plant Pathology 4(1): 1-8.
  • Bol JF (2008) Alfalfa mosaic virus. Encyclopaedia of Virology (3rd ed.), pp. 81-87.
  • Brunt A, Crabtree K, Gibbs A (1990) Viruses of Tropical Plants. CAB International, London.
  • Buzkan N, Demir M, Öztekin V, Mart C, Çağlar BK, Yilmaz MA (2006) Evaluation of the status of capsicum viruses in the main growing regions of Turkey. Bulletin European and Mediterranean Plant Protection Organization 36(1): 15-19.
  • Çarpar H, Sertkaya G (2016) Hatay İli Patates Üretiminde Önemli Bazı Viral Sorunların Belirlenmesi. Nevşehir Bilim ve Teknoloji Dergisi 5: 135-143.
  • Çetinkıran AD, Baloğlu S (2011) Detection of the Alfalfa mosaic virus in pepper fields in Adana and Mersin. Çukurova Üniversitesi Fen ve Mühendislik Bilimleri Dergisi 26(2): 89-98.
  • Çulal Kılıç H, Yardımcı N (2015) Occurrence of Alfalfa mosaic virus (AMV) infecting bean crop in Burdur Province, Turkey. Asian Journal of Agriculture and Food Sciences 3(2): 173-177.
  • Demir M (2005) Kahramanmaraş’ta Yetiştirilen Kırmızı Biberlerde Yaprakbiti İle Taşınan Virüslerin Saptanması. Kahramanmaraş Sütçü İmam Üniversitesi. Fen Bilimleri Enstitüsü. Bitki Koruma Anabilimdalı. Yüksek Lisans Tezi, Kahramanmaraş.
  • Güller A, Usta M, Korkmaz G (2022) Phylogenetic Relationship of Alfalfa Mosaic Virus (AMV) Isolate Identified in Bingöl Province of Turkey. Turkish Journal of Agricultural and Natural Sciences 9(1): 166-172.
  • Hameed A, Iqbal Z, Asad S, Mansoor S (2014) Detection of Multiple Potato Viruses in the Field Suggests Synergistic Interactions among Potato Viruses in Pakistan. Plant Pathology Journal 30(4): 407-415.
  • Hemmati K, Mclean D (1977) Gamete-seed Transmission of Alfalfa mosaic virus and its effect of Seed Germination and Yield in Alfalfa Plants. Phytopathology 67: 576-579.
  • Jung HW, Hye HJ, Yun WS, Kim HJ, Hahm YI, Kim KH, Choi1 JK (2000) Characterization and partial nucleotide sequence analysis of Alfalfa mosaic alfamoviruses isolated from potato and azuki bean in Korea. Plant Pathology Journal 16: 269-279.
  • Kolychikhina M S, Beloshapkina O O, Phiri C (2021) Change in potato productivity under the impact of viral diseases. IOP Conference Series Earth and Environmental Science 663(1): 012035.
  • Kumar S, Stecher, Tamura K (2016) MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets. Molecular Biology and Evolution 33: 1870-1874.
  • Martínez-Priego L, Córdoba M C, Jordá C (2004) First report of Alfalfa mosaic virus in Lavandula officinalis. Plant Disease 88(8): 908.
  • Milošević D (2013) Diversity and characterization of pepper viruses in Serbia. Doctoral dissertation, Faculty of Agriculture, University in Belgrade, Belgrade.
  • Muhire BM, Varsani A, Martin DP (2014) SDT: A virus classification tool based on pairwise sequence alignment and identity calculation. PLoS One 9: 0108277.
  • Nie X, De Koyner D, Liang Z, Dickison V, Singh M, Hawkins G (2015) Identification and first report of a potato tuber necrosis-inducing isolate of Alfalfa mosaic virus in Canada. Plant Disease 99: 1658.
  • Nie X, Dickison V, Singh M, De Koeyer D, Xu H, Bai Y, Hawkins G (2020) Potato Tuber Necrosis Induced by Alfalfa Mosaic Virus Depends on Potato Cultivar Rather Than on Virus Strain. Plant Disease 104(2): 340-347.
  • Özdemir S, Erilmez S (2007) Denizli ilinde yetiştirilen biber, patlıcan ve marul üretim alanlarında bazı viral etmenlerin saptanması. Türkiye II. Bitki Koruma Kongresi Bildirileri, Isparta.
  • Özdemir S, Erilmez S, Paylan Cİ (2011) Serological and Molecular Identification of Alfalfa mosaic alfamovirus in Potato Production Areas in Aegean Region. Türkiye IV. Bitki Koruma Kongresi Bildirileri.
  • Parrella G, Lanave C, Marchoux G, Finetti Sialer MM, Di Franco A, Gallitelli D (2000) Evidence for two distinct subgroups of Alfalfa mosaic virus (AAMV) from France and Italy and their relationships with other AAMV strains. Archive of Virology 145: 2659-2667.
  • Parrella G, Acanfora N, Bellardi MG (2010) First record and complete nucleotide sequence of Alfalfa mosaic virus from Lavandula stoechas in Italy. Plant Disease 94: 924-924.
  • Parrella G, Acanfora N, Orílio A, Navas-Castillo J (2011) Complete nucleotide sequence of a Spanish isolate of Alfalfa mosaic virus: Evidence for additional genetic variability. Archives of Virology, 156: 1049-1052.
  • Ragsdale DW, Radcliffe EB, DiFonzo CD (2001) Epidemiology and field control of PVY and PLRV. In: Virus and Virus-like Diseases of Potatoes and Production of Seed-potatoes. Eds. Loebenstein G., PH Berger, AA Brunt and RH Lawson. Huwer Academic Publishers, Dordrecht.
  • Rusevski R, Bandzo K, Kuzmanovska B, Stanoevska M (2011) Virus status of pepper plants cultivated on open fields. XVI International meeting on Biotechnology – Book of Proceedings, Čačak, Serbia 16(18): 429-434.
  • Rusevski R, Bandzo K, Kuzmanovska B, Sotırovskı K, Rısteskı M (2013) Occurrence, distribution and Dynamics of virus antigen accumulation in pepper cultivation on open fields in Republic of Macedonia during 2008-2009. African Journal of Agricultural Research 8(28): 3836-3841.
  • Sertkaya G, Çarpar H, Sertkaya E (2017) Detection of Alfalfa mosaic virus (AMV) in Potato Production Areas in Hatay Province of Turkey. Journal of the Institute of Science and Technology (JIST) 7(1): 23-29.
  • Stanković I, Vrandečıć K, Ćosıć J, Mılojevıć K, Bulajıć A, Krstıć B (2014) The spreading of Alfalfa mosaic virus in lavandin in Croatia. Pesticidi i fitomedicina 29: 115-122.
  • Tenllado F, Bol JF (2000) Genetic detection of the multiple functions of Alfalfa mosaic virus coat protein in viral RNA replication, encapsidation, and movement. Virology 268: 29-40.
  • Topkaya S (2020) Determination of some viruses by serological and molecular techniques in potato production areas in Tokat Province. Journal of Agricultural Faculty of Gaziosmanpasa University 37(1): 53-59.
  • TUIK (2020) Türkiye İstatistik Kurumu, Bitkisel üretim istatistikleri.. https://biruni.tuik.gov.tr /bitkiselapp/bitkisel.zul. Accessed 15 January 2022.
  • Usta M, Güller A (2020) Molecular Analysis of Coat Protein Genom of two Alfalfa mosaic virus (AMV) isolates in alfalfa by RT-PCR from Van province, Turkey. Journal of the Institute of Science and Technology 10(4): 2366-2377.
  • Wang P, Guo Y, Cheng J, Dong Q, Ding X, Guo J, Jiang Y (2012) Application of multiplex reverse transcription-ligase detection reaction-polymerase chain reaction (MRLP) mediated universal DNA microarray for detecting potato viruses in field samples. European Journal of Plant Pathology 132(2): 217-227.
  • Xu H, Nie J (2006) Identification, characterization and molecular detection of Alfalfa mosaic virus in potato. Phytopathology 96: 1237-1242.
  • Yardımcı N, Culal Kılıç H, Demir Y (2015) Detection of PVY, PVX, PVS, PVA, and PLRV on Different Potato Varieties in Turkey Using DAS-ELISA. Journal of Agricultural Science and Technology 17: 757-764.

Molecular characterisation of Alfalfa mosaic virus isolates in potato from the Tokat province, Türkiye

Year 2022, Volume: 35 Issue: 2, 75 - 81, 02.08.2022
https://doi.org/10.29136/mediterranean.1045447

Abstract

The Alfalfa mosaic virus (AMV) was detected in potato fields in the Tokat province. The coat protein (CP) sequences of AMV isolates from the Tokat province were determined and compared with sequences of reference AMV isolates from GenBank. Total nucleic acid (TNA) was extracted from plants with positive results according to serological test results. Then, reverse-transcription polymerase chain reaction (RT-PCR) was performed using primer pair specific to partial the coat protein region, and positive PCR products were sent for sequence analysis in both directions. Two Turkish AMV isolates (AMV-PN3-5 and AMV-PN3-6) had a 96-99% nt homology amongst themselves, according to nucleotides (nt) sequence analysis. Based on the phylogenetic tree obtained from 24 AMV isolates from GenBank for both sequences, the two Turkish AMV isolates were clustered in subgroup I containing Iranian, Canadian, Turkish, Korean, and Serbian isolates, at the nucleotide level. Sequence comparison showed that these two isolates of AMV shared 96% to 99.7% sequence similarity with the twenty-six reported isolates of AMV obtained from GenBank. This is the first report on the genetic variability of AMV isolates infecting potato crops in the Tokat province.

References

  • Abdel Aleem EE, Taha RM, Fattouh FA (2018) Biodiversity and full genome sequence of potato viruses Alfalfa mosaic virus and potato leaf roll virus in Egypt. Zeitschrift für Naturforschung C Journal of biosciences 73(11-12): 423-438.
  • Al-Saleh, MA, Amer MA, AL-Shahwan IM, Abdalla OA, Shakeel MT (2014) Molecular characterization of two alfalfa mosaic virus isolates infecting potato crop in central region of Saudi Arabia. International Journal of Agriculture and Biology 16: 976-980.
  • Arlı-Sökmen M, Mennan H, Sevik MA, Ecevit O (2005) Occurrence of viruses in field-grown pepper crops and some of their reservoir weeds hosts in Samsun, Turkey. Phytoparasitica 33(4): 347-358.
  • Astruc N, Marcos JF, Macquaire G, Candresse T, Pallas V (1996) Studies on the diagnosis of hop stunt viroid in fruit trees: Identification of new hosts and application of nucleic acid extraction procedure based on non-organic solvents. European Journal of Plant Pathology 102(9): 837-846.
  • Bailiss KW, Offei SK (1990) Alfalfa mosaic virus in lucerne seed during seed maturation and storage, and in seedlings. Plant Pathology 39: 539-47.
  • Bergua M, Luis-Arteaga M, Escriu F (2014) Genetic diversity, reassortment and recombination in Alfalfa mosaic virus population in Spain. Phytopathology 104: 1241-1250.
  • Bol JF (2003) Alfalfa mosaic virus: Coat protein dependent initiation of infection. Molecular Plant Pathology 4(1): 1-8.
  • Bol JF (2008) Alfalfa mosaic virus. Encyclopaedia of Virology (3rd ed.), pp. 81-87.
  • Brunt A, Crabtree K, Gibbs A (1990) Viruses of Tropical Plants. CAB International, London.
  • Buzkan N, Demir M, Öztekin V, Mart C, Çağlar BK, Yilmaz MA (2006) Evaluation of the status of capsicum viruses in the main growing regions of Turkey. Bulletin European and Mediterranean Plant Protection Organization 36(1): 15-19.
  • Çarpar H, Sertkaya G (2016) Hatay İli Patates Üretiminde Önemli Bazı Viral Sorunların Belirlenmesi. Nevşehir Bilim ve Teknoloji Dergisi 5: 135-143.
  • Çetinkıran AD, Baloğlu S (2011) Detection of the Alfalfa mosaic virus in pepper fields in Adana and Mersin. Çukurova Üniversitesi Fen ve Mühendislik Bilimleri Dergisi 26(2): 89-98.
  • Çulal Kılıç H, Yardımcı N (2015) Occurrence of Alfalfa mosaic virus (AMV) infecting bean crop in Burdur Province, Turkey. Asian Journal of Agriculture and Food Sciences 3(2): 173-177.
  • Demir M (2005) Kahramanmaraş’ta Yetiştirilen Kırmızı Biberlerde Yaprakbiti İle Taşınan Virüslerin Saptanması. Kahramanmaraş Sütçü İmam Üniversitesi. Fen Bilimleri Enstitüsü. Bitki Koruma Anabilimdalı. Yüksek Lisans Tezi, Kahramanmaraş.
  • Güller A, Usta M, Korkmaz G (2022) Phylogenetic Relationship of Alfalfa Mosaic Virus (AMV) Isolate Identified in Bingöl Province of Turkey. Turkish Journal of Agricultural and Natural Sciences 9(1): 166-172.
  • Hameed A, Iqbal Z, Asad S, Mansoor S (2014) Detection of Multiple Potato Viruses in the Field Suggests Synergistic Interactions among Potato Viruses in Pakistan. Plant Pathology Journal 30(4): 407-415.
  • Hemmati K, Mclean D (1977) Gamete-seed Transmission of Alfalfa mosaic virus and its effect of Seed Germination and Yield in Alfalfa Plants. Phytopathology 67: 576-579.
  • Jung HW, Hye HJ, Yun WS, Kim HJ, Hahm YI, Kim KH, Choi1 JK (2000) Characterization and partial nucleotide sequence analysis of Alfalfa mosaic alfamoviruses isolated from potato and azuki bean in Korea. Plant Pathology Journal 16: 269-279.
  • Kolychikhina M S, Beloshapkina O O, Phiri C (2021) Change in potato productivity under the impact of viral diseases. IOP Conference Series Earth and Environmental Science 663(1): 012035.
  • Kumar S, Stecher, Tamura K (2016) MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets. Molecular Biology and Evolution 33: 1870-1874.
  • Martínez-Priego L, Córdoba M C, Jordá C (2004) First report of Alfalfa mosaic virus in Lavandula officinalis. Plant Disease 88(8): 908.
  • Milošević D (2013) Diversity and characterization of pepper viruses in Serbia. Doctoral dissertation, Faculty of Agriculture, University in Belgrade, Belgrade.
  • Muhire BM, Varsani A, Martin DP (2014) SDT: A virus classification tool based on pairwise sequence alignment and identity calculation. PLoS One 9: 0108277.
  • Nie X, De Koyner D, Liang Z, Dickison V, Singh M, Hawkins G (2015) Identification and first report of a potato tuber necrosis-inducing isolate of Alfalfa mosaic virus in Canada. Plant Disease 99: 1658.
  • Nie X, Dickison V, Singh M, De Koeyer D, Xu H, Bai Y, Hawkins G (2020) Potato Tuber Necrosis Induced by Alfalfa Mosaic Virus Depends on Potato Cultivar Rather Than on Virus Strain. Plant Disease 104(2): 340-347.
  • Özdemir S, Erilmez S (2007) Denizli ilinde yetiştirilen biber, patlıcan ve marul üretim alanlarında bazı viral etmenlerin saptanması. Türkiye II. Bitki Koruma Kongresi Bildirileri, Isparta.
  • Özdemir S, Erilmez S, Paylan Cİ (2011) Serological and Molecular Identification of Alfalfa mosaic alfamovirus in Potato Production Areas in Aegean Region. Türkiye IV. Bitki Koruma Kongresi Bildirileri.
  • Parrella G, Lanave C, Marchoux G, Finetti Sialer MM, Di Franco A, Gallitelli D (2000) Evidence for two distinct subgroups of Alfalfa mosaic virus (AAMV) from France and Italy and their relationships with other AAMV strains. Archive of Virology 145: 2659-2667.
  • Parrella G, Acanfora N, Bellardi MG (2010) First record and complete nucleotide sequence of Alfalfa mosaic virus from Lavandula stoechas in Italy. Plant Disease 94: 924-924.
  • Parrella G, Acanfora N, Orílio A, Navas-Castillo J (2011) Complete nucleotide sequence of a Spanish isolate of Alfalfa mosaic virus: Evidence for additional genetic variability. Archives of Virology, 156: 1049-1052.
  • Ragsdale DW, Radcliffe EB, DiFonzo CD (2001) Epidemiology and field control of PVY and PLRV. In: Virus and Virus-like Diseases of Potatoes and Production of Seed-potatoes. Eds. Loebenstein G., PH Berger, AA Brunt and RH Lawson. Huwer Academic Publishers, Dordrecht.
  • Rusevski R, Bandzo K, Kuzmanovska B, Stanoevska M (2011) Virus status of pepper plants cultivated on open fields. XVI International meeting on Biotechnology – Book of Proceedings, Čačak, Serbia 16(18): 429-434.
  • Rusevski R, Bandzo K, Kuzmanovska B, Sotırovskı K, Rısteskı M (2013) Occurrence, distribution and Dynamics of virus antigen accumulation in pepper cultivation on open fields in Republic of Macedonia during 2008-2009. African Journal of Agricultural Research 8(28): 3836-3841.
  • Sertkaya G, Çarpar H, Sertkaya E (2017) Detection of Alfalfa mosaic virus (AMV) in Potato Production Areas in Hatay Province of Turkey. Journal of the Institute of Science and Technology (JIST) 7(1): 23-29.
  • Stanković I, Vrandečıć K, Ćosıć J, Mılojevıć K, Bulajıć A, Krstıć B (2014) The spreading of Alfalfa mosaic virus in lavandin in Croatia. Pesticidi i fitomedicina 29: 115-122.
  • Tenllado F, Bol JF (2000) Genetic detection of the multiple functions of Alfalfa mosaic virus coat protein in viral RNA replication, encapsidation, and movement. Virology 268: 29-40.
  • Topkaya S (2020) Determination of some viruses by serological and molecular techniques in potato production areas in Tokat Province. Journal of Agricultural Faculty of Gaziosmanpasa University 37(1): 53-59.
  • TUIK (2020) Türkiye İstatistik Kurumu, Bitkisel üretim istatistikleri.. https://biruni.tuik.gov.tr /bitkiselapp/bitkisel.zul. Accessed 15 January 2022.
  • Usta M, Güller A (2020) Molecular Analysis of Coat Protein Genom of two Alfalfa mosaic virus (AMV) isolates in alfalfa by RT-PCR from Van province, Turkey. Journal of the Institute of Science and Technology 10(4): 2366-2377.
  • Wang P, Guo Y, Cheng J, Dong Q, Ding X, Guo J, Jiang Y (2012) Application of multiplex reverse transcription-ligase detection reaction-polymerase chain reaction (MRLP) mediated universal DNA microarray for detecting potato viruses in field samples. European Journal of Plant Pathology 132(2): 217-227.
  • Xu H, Nie J (2006) Identification, characterization and molecular detection of Alfalfa mosaic virus in potato. Phytopathology 96: 1237-1242.
  • Yardımcı N, Culal Kılıç H, Demir Y (2015) Detection of PVY, PVX, PVS, PVA, and PLRV on Different Potato Varieties in Turkey Using DAS-ELISA. Journal of Agricultural Science and Technology 17: 757-764.
There are 42 citations in total.

Details

Primary Language English
Subjects Agricultural Engineering
Journal Section Makaleler
Authors

Şerife Topkaya 0000-0002-0095-474X

Publication Date August 2, 2022
Submission Date December 25, 2021
Published in Issue Year 2022 Volume: 35 Issue: 2

Cite

APA Topkaya, Ş. (2022). Molecular characterisation of Alfalfa mosaic virus isolates in potato from the Tokat province, Türkiye. Mediterranean Agricultural Sciences, 35(2), 75-81. https://doi.org/10.29136/mediterranean.1045447
AMA Topkaya Ş. Molecular characterisation of Alfalfa mosaic virus isolates in potato from the Tokat province, Türkiye. Mediterranean Agricultural Sciences. August 2022;35(2):75-81. doi:10.29136/mediterranean.1045447
Chicago Topkaya, Şerife. “Molecular Characterisation of Alfalfa Mosaic Virus Isolates in Potato from the Tokat Province, Türkiye”. Mediterranean Agricultural Sciences 35, no. 2 (August 2022): 75-81. https://doi.org/10.29136/mediterranean.1045447.
EndNote Topkaya Ş (August 1, 2022) Molecular characterisation of Alfalfa mosaic virus isolates in potato from the Tokat province, Türkiye. Mediterranean Agricultural Sciences 35 2 75–81.
IEEE Ş. Topkaya, “Molecular characterisation of Alfalfa mosaic virus isolates in potato from the Tokat province, Türkiye”, Mediterranean Agricultural Sciences, vol. 35, no. 2, pp. 75–81, 2022, doi: 10.29136/mediterranean.1045447.
ISNAD Topkaya, Şerife. “Molecular Characterisation of Alfalfa Mosaic Virus Isolates in Potato from the Tokat Province, Türkiye”. Mediterranean Agricultural Sciences 35/2 (August 2022), 75-81. https://doi.org/10.29136/mediterranean.1045447.
JAMA Topkaya Ş. Molecular characterisation of Alfalfa mosaic virus isolates in potato from the Tokat province, Türkiye. Mediterranean Agricultural Sciences. 2022;35:75–81.
MLA Topkaya, Şerife. “Molecular Characterisation of Alfalfa Mosaic Virus Isolates in Potato from the Tokat Province, Türkiye”. Mediterranean Agricultural Sciences, vol. 35, no. 2, 2022, pp. 75-81, doi:10.29136/mediterranean.1045447.
Vancouver Topkaya Ş. Molecular characterisation of Alfalfa mosaic virus isolates in potato from the Tokat province, Türkiye. Mediterranean Agricultural Sciences. 2022;35(2):75-81.

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