تنوع ژنتیکی و ساختار جمعیتی جدایه های باکتریایی عامل پوسیدگی نرم سیب زمینی در ایران
الموضوعات :
جواد رزمی
1
(دانش آموخته دکتری، گروه گیاه پزشکی، واحد علوم و تحقیقات، دانشگاه آزاد اسلامی، تهران، ایران)
حشمت اله رحیمیان
2
(استاد، گروه گیاه پزشکی، دانشگاه علوم کشاورزی و منابع طبیعی ساری، ساری، مازندران، ایران)
محسن مردی
3
(دانشیار، بخش ژنومیکس، موسسه تحقیقات بیوتکنولوژی کشاورزی ایران، سازمان تحقیقات آموزش و ترویج کشاورزی، کرج، ایران)
حمیدرضا زمانی زاده
4
(استاد، گروه گیاه پزشکی، واحد علوم و تحقیقات، دانشگاه آزاد اسلامی، تهران، ایران)
الکلمات المفتاحية: انگشت نگاری ژنتیکی, پکتوباکتریوم, ساق سیاه, پوسیدگی نرم سیب,
ملخص المقالة :
سابقه و هدف: پوسیدگی نرم از مهمترین بیماری های باکتریایی سیب زمینی در ایران و جهان است. هدف از این مطالعه بررسی تنوع فنوتیپی و ژنوتیپی جدایه های موثر در ایجاد بیماری پوسیدگی نرم در مناطق مهم سیب زمینی کاری ایران بود.مواد و روش ها: غدد مشکوک به پوسیدگی نرم، در طی عملیات برداشت جمع آوری و مطالعه فنوتیپی جدایه ها بر اساس روش های متداول انجام شد. گوناگونی ژنتیکی نیز توسط روش انگشت نگاری ژنتیکی صورت گرفت. آنالیز کلاستر و بررسی ساختار جمعیت جدایه ها با نرم افزارهای SplitsTree 4.11.3 ،STRUCTURE 2.3.4 وArlequin 3.11 انجام شد.یافته ها: مطالعه انجام شده بیانگر تنوع قابل توجه در میان جدایه ها بود. به طوری که برخی از آنها ویژگی های فنوتیپی متفاوتی نسبت به جدایه های معرفی شده در مطالعات قبلی داشتند. جدایه ها در دو گروه فنوتیپی مرتبط با پکتوباکتریوم واسابیئی و پکتوباکتریوم کاروتووروم زیرگونه کاروتووروم قرار گرفتند. انگشت نگاری ژنومی نشان داد که جدایه ها از نظر ژنتیکی ناهمگن هستند و به سه جمعیت ژنتیکی قابل تقسیم بندی می باشند. پنجاه درصد جدایه های گروه فنوتیپی 1 و 77/3 درصد جدایه های گروه فنوتیپی 2 به ترتیب به جمعیت ژنتیکی 1 و 3 تعلق داشتند. همبستگی بین پروفایل انگشت نگاری ژنومی، مناطق جغرافیایی و ارقام سیب زمینی مشاهده نشد. اما فاصله ژنتیکی و کمینه و بیشینه جریان ژنی با فاصله جغرافیایی همبستگی نشان داد.نتیجه گیری: یافته های این مطالعه نشان داد که تجارت غدد بذری یکی از دلایل توسعه بیماری پوسیدگی نرم سیب زمینی به مناطق جغرافیایی هم جوار محسوب می شود.
April 10, 2018).
2. FAO. Potato world: Asia and Oceania. Available at: http://www.fao.org/potato-2008/en/world/
asia.html (Accessed March 13, 2018).
3. Motyka A, Zoledowska S, Sledz W, Lojkowska E. Molecular methods as tools to control plant
diseases caused by Dickeya and Pectobacterium spp: A minireview. N Biotechnol. 2017; 39:
181-189.
4. Adeolu M, Alnajar S, Naushad S, Gupta RS. Genome-based phylogeny and taxonomy of the
‘Enterobacteriales’: proposal for Enterobacterales ord. nov. divided into the families
Enterobacteriaceae, Erwiniaceae fam. nov., Pectobacteriaceae fam. nov., Yersiniaceae fam.
nov., Hafniaceae fam. nov., Morganellaceae fam. nov., and Budviciaceae fam. nov. Int J Syst
Evol Microbiol. 2016; 66(12): 5575-5599.
5. Mansfield J, Genin S, Magori S, Citovsky V, Sriariyanum M, Ronald P, Dow MA, Verdier V,
emphasized the need for re-evaluation and
pathology. Mol Plant Pathol. 2012; 13(6): 614-629.
6. Czajkowski R, Pérombelon MC, Jafra S, Lojkowska E, Potrykus M, Van Der Wolf JM, Sledz
W. Detection, identification and differentiation of Pectobacterium and Dickeya species causing
potato blackleg and tuber soft rot: a review. Ann Appl Biol. 2015; 166(1): 18-38.
7. Bahar M, Danesh D, 1986. Occurrence of potato black leg in lsfahan. Proceedings of the 8th
Plant Protection Congress. Esfehan, Iran. 105.
8. Akramipour N, Abdollahi M, Taghavi SM, Rezaei R. Genetic diversity of some isolates of soft
rot Pectobacterium, from different host plants in Fars province, Iran, using RAPD marker. J
Pure Appl Microbiol. 2016; 10(3): 1825-1834.
9. Baghaee-Ravari S, Rahimian H, Shams-Bakhsh M, Lopez-Solanilla E, Antúnez-Lamas M,
Rodríguez-Palenzuela P. Characterization of Pectobacterium species from Iran using
biochemical and molecular methods. Eur J Plant Pathol. 2011; 129(3): 413-425.
10. Baghaee-Ravari S, Gerayeli N. Detection of Pectobacterium carotovorum subsp.
carotovorum associated with bacterial soft rot of two succulent plants in Iran using recA and
pmrA genes. J Plant Pathol. 2015; 97(1): 143-148.
11. Tavasoli E, Marefat AR, Hassanzadeh N. Identity and genetic diversity of Pectobacterium
spp., causal agents of potato soft rot in Zanjan, Iran. Afr J Plant Sci. 2011; 5(6): 329-336.
12. Rahmanifar B, Hasanzadeh N, Razmi J, Ghasemi A. Genetic diversity of Iranian potato soft
rot bacteria based on polymerase chain reaction-restriction fragment length polymorphism
(PCR-RFLP) analysis. Afr J Biotechnol. 2012; 11(6): 1314-1320.
13. Dahaghin L, Shams-Bakhsh M. Identification and genetic diversity of pectolytic
phytopathogenic bacteria of mono-and dicotyledonous ornamental plants in Iran. J Plant
Pathol. 2014; 96(2): 271-279.
14. Terta M, Azelmat S, M’hand RA, Achbani EH, Barakate M, Bouteau F, Ennaji MM.
Molecular typing of Pectobacterium carotovorum isolated from potato tuber soft rot in
Morocco. Ann Microbiol. 2012; 62(4): 1411-1417.
15. Degefu Y, Potrykus M, Golanowska M, Virtanen E, Lojkowska E. A new clade of Dickeya
spp. plays a major role in potato blackleg outbreaks in North Finland. Ann Appl Biol. 2013;
162(2): 231-241.
16. van der Merwe JJ, Coutinho TA, Korsten L, van der Waals JE. Pectobacterium carotovorum
subsp. brasiliensis causing blackleg on potatoes in South Africa. Eur J Plant Pathol. 2010; 126
(2): 175-185.
17. Nabhan S, Wydra K, Linde M, Debener T. The use of two complementary DNA assays,
AFLP and MLSA, for epidemic and phylogenetic studies of pectolytic enterobacterial strains
with focus on the heterogeneous species Pectobacterium carotovorum. Plant Pathol. 2012; 61
(3): 498-508.
18. Versalovic J, Schneider M, De Bruijn FJ, Lupski JR. Genomic fingerprinting of bacteria using
repetitive sequence-based polymerase chain reaction. Methods Mol Cell Biol. 1994; 5(1):
25-40.
19. Golanowska M, Lojkowska E. A review on Dickeya solani, a new pathogenic bacterium
causing loss in potato yield in Europe. Bio Technologia. 2016; 97(2): 109-127.
20. Suárez MB, Feria FJ, Martín-Robles MJ, del Rey FJ, Palomo JL. Pectobacterium parmentieri
causing soft rot on potato tubers in southern Europe. Plant Dis. 2017; 101(6): 1029.
21. Gallois A, Samson R, Ageron E, Grimont PA. Erwinia carotovora subsp. odorifera subsp.
nov., associated with odorous soft rot of chicory (Cichorium intybus L.). Int J Syst Evol
Microbiol. 1992; 42(4): 582-588.
22. Gardan L, Gouy C, Christen R, Samson R. Elevation of three subspecies of Pectobacterium
carotovorum to species level: Pectobacterium atrosepticum sp. nov., Pectobacterium
betavasculorum sp. nov. and Pectobacterium wasabiae sp. nov. Int J Syst Evol Microbiol.
2003; 53(2): 381-391.
23. Schaad NW, Jones JB, Chun W. Laboratory guide for the identification of plant pathogenic
bacteria. APS Press; 2001.
24. De Bruijn FJ, Rademaker J, Schneider M, Rossbach U, Louws FJ. Rep-PCR genomic
fingerprinting of plant-associated bacteria and computer-assisted phylogenetic analyses. In:
Stacey G, Mullin B, Gresshoff P, editors. Proceedings of the 8th International Congress of
Molecular Plant-Microbe Interactions. St. Paul, APS Press; 1996: 497-502.
25. Sambrook J, Russell DW. Gel electrophoresis of DNA and pulsed-field agarose gel
electrophoresis. In: Molecular cloning: a laboratory manual. 3rd ed. New York. Cold Spring
harbor Laboratory Press; 2001: 5.4-5.17.
26. Huson DH, Bryant D. Application of phylogenetic networks in evolutionary studies. Mol Biol
Evol. 2006; 23(2): 254-267.
27. Falush D, Stephens M, Pritchard JK. Inference of population structure using multilocus
genotype data: dominant markers and null alleles. Mol Ecol Resour. 2007; 7(4): 574-578.
28. Bryant D, Moulton V. Neighbor-net: an agglomerative method for the construction of
phylogenetic networks. Mol Biol Evol. 2004; 21(2): 255-265.
29. Excoffier L, Laval G, Schneider S. Arlequin (version 3.0): an integrated software package for
population genetics data analysis. Evol Bioinform Online. 2005; 1: 47-50
30. Excoffier L, Smouse PE, Quattro JM. Analysis of molecular variance inferred from metric
distances among DNA haplotypes: application to human mitochondrial DNA restriction data.
Genetics. 1992; 131(2): 479-491.
31. Nei M. Estimation of average heterozygosity and genetic distance from a small number of
individuals. Genetics. 1978; 89(3): 583-590.
32. Holt JG, Krieg NR, Sneath Pa, Staley JT, Williams ST. Bergey's Manual of determinate
bacteriology. Williams and Wilkins Publishers; 1994.
33. Khayi S, Cigna J, Chong TM, Quêtu-Laurent A, Chan KG, Hélias V, Faure D. Transfer of the
potato plant isolates of Pectobacterium wasabiae to Pectobacterium parmentieri sp. nov. Int J
Syst Evol Microbiol. 2016; 66(12): 5379-5383.
34. Zohour Paralak E, Rahimian H, Banihashemi Z. A comparative study on pectolytic Erwinias
isolated from potato in the Fars province. Iran. J Plant Pathol. 2007; 43: 121-144.
35. Ahmadvand R, Rahimian H. 2002. Study on diversity of the pectolytic Erwinias infecting
potato in Hamedan province. Proceedings of the 15th Iranian Plant Protection Congress, 7–11
Sep, Kermanshah, Iran, 115.
36. Houle D, Govindaraju DR, Omholt S. Phenomics: the next challenge. Nat Rev Genet. 2010;
11(12): 855-866.
37. Duarte V, De Boer SH, Ward LJ, Oliveira AM. Characterization of atypical Erwinia
carotovora strains causing blackleg of potato in Brazil. J Appl Microbiol. 2004; 96(3):
535-545.
38. Costa AB, Eloy M, Cruz L, Janse JD, Oliveira H. Studies on pectolytic Erwinia spp. in
Portugal reveal unusual strains of E. carotovora subsp. atroseptica. J Plant Patho. 2006; 88(2):
161-169.
39. Vimal BM, Anuradha SN. Characterization and differentiation of soft rot causing
Pectobacterium carotovorum of Indian origin. Eur J Plant Pathol. 2013; 136(1): 87-102.
40. Yap MN, Barak JD, Charkowski AO. Genomic diversity of Erwinia carotovora subsp.
carotovora and its correlation with virulence. Appl Environ Microbiol. 2004; 70(5):
3013-3023.
41. Faquihi H, Terta M, Amdan M, Achbani EH, Ennaji MM, Mhand RA. Phenotypic and
genotypic diversity of Pectobacterium carotovorum subsp. carotovorum causing soft rot
disease of potatoes in Morocco. Eur J Plant Pathol. 2015; 143(4): 801-811.
42. Baghaee-Ravari S, Moslemkhani K, Khodaygan P. Assessment of genetic variability of
prevalent pectinolytic bacteria causing potato tuber soft rot in eastern Iran. J Plant Pathol.
2013; 95(1): 107-113.
43. Dees MW, Lysøe E, Rossmann S, Perminow J, Brurberg MB. Pectobacterium polaris sp.
nov., isolated from potato (Solanum tuberosum). Int J Syst Evol Microbiol. 2017; 67(12):
5222-5229.
_||_
April 10, 2018).
2. FAO. Potato world: Asia and Oceania. Available at: http://www.fao.org/potato-2008/en/world/
asia.html (Accessed March 13, 2018).
3. Motyka A, Zoledowska S, Sledz W, Lojkowska E. Molecular methods as tools to control plant
diseases caused by Dickeya and Pectobacterium spp: A minireview. N Biotechnol. 2017; 39:
181-189.
4. Adeolu M, Alnajar S, Naushad S, Gupta RS. Genome-based phylogeny and taxonomy of the
‘Enterobacteriales’: proposal for Enterobacterales ord. nov. divided into the families
Enterobacteriaceae, Erwiniaceae fam. nov., Pectobacteriaceae fam. nov., Yersiniaceae fam.
nov., Hafniaceae fam. nov., Morganellaceae fam. nov., and Budviciaceae fam. nov. Int J Syst
Evol Microbiol. 2016; 66(12): 5575-5599.
5. Mansfield J, Genin S, Magori S, Citovsky V, Sriariyanum M, Ronald P, Dow MA, Verdier V,
emphasized the need for re-evaluation and
pathology. Mol Plant Pathol. 2012; 13(6): 614-629.
6. Czajkowski R, Pérombelon MC, Jafra S, Lojkowska E, Potrykus M, Van Der Wolf JM, Sledz
W. Detection, identification and differentiation of Pectobacterium and Dickeya species causing
potato blackleg and tuber soft rot: a review. Ann Appl Biol. 2015; 166(1): 18-38.
7. Bahar M, Danesh D, 1986. Occurrence of potato black leg in lsfahan. Proceedings of the 8th
Plant Protection Congress. Esfehan, Iran. 105.
8. Akramipour N, Abdollahi M, Taghavi SM, Rezaei R. Genetic diversity of some isolates of soft
rot Pectobacterium, from different host plants in Fars province, Iran, using RAPD marker. J
Pure Appl Microbiol. 2016; 10(3): 1825-1834.
9. Baghaee-Ravari S, Rahimian H, Shams-Bakhsh M, Lopez-Solanilla E, Antúnez-Lamas M,
Rodríguez-Palenzuela P. Characterization of Pectobacterium species from Iran using
biochemical and molecular methods. Eur J Plant Pathol. 2011; 129(3): 413-425.
10. Baghaee-Ravari S, Gerayeli N. Detection of Pectobacterium carotovorum subsp.
carotovorum associated with bacterial soft rot of two succulent plants in Iran using recA and
pmrA genes. J Plant Pathol. 2015; 97(1): 143-148.
11. Tavasoli E, Marefat AR, Hassanzadeh N. Identity and genetic diversity of Pectobacterium
spp., causal agents of potato soft rot in Zanjan, Iran. Afr J Plant Sci. 2011; 5(6): 329-336.
12. Rahmanifar B, Hasanzadeh N, Razmi J, Ghasemi A. Genetic diversity of Iranian potato soft
rot bacteria based on polymerase chain reaction-restriction fragment length polymorphism
(PCR-RFLP) analysis. Afr J Biotechnol. 2012; 11(6): 1314-1320.
13. Dahaghin L, Shams-Bakhsh M. Identification and genetic diversity of pectolytic
phytopathogenic bacteria of mono-and dicotyledonous ornamental plants in Iran. J Plant
Pathol. 2014; 96(2): 271-279.
14. Terta M, Azelmat S, M’hand RA, Achbani EH, Barakate M, Bouteau F, Ennaji MM.
Molecular typing of Pectobacterium carotovorum isolated from potato tuber soft rot in
Morocco. Ann Microbiol. 2012; 62(4): 1411-1417.
15. Degefu Y, Potrykus M, Golanowska M, Virtanen E, Lojkowska E. A new clade of Dickeya
spp. plays a major role in potato blackleg outbreaks in North Finland. Ann Appl Biol. 2013;
162(2): 231-241.
16. van der Merwe JJ, Coutinho TA, Korsten L, van der Waals JE. Pectobacterium carotovorum
subsp. brasiliensis causing blackleg on potatoes in South Africa. Eur J Plant Pathol. 2010; 126
(2): 175-185.
17. Nabhan S, Wydra K, Linde M, Debener T. The use of two complementary DNA assays,
AFLP and MLSA, for epidemic and phylogenetic studies of pectolytic enterobacterial strains
with focus on the heterogeneous species Pectobacterium carotovorum. Plant Pathol. 2012; 61
(3): 498-508.
18. Versalovic J, Schneider M, De Bruijn FJ, Lupski JR. Genomic fingerprinting of bacteria using
repetitive sequence-based polymerase chain reaction. Methods Mol Cell Biol. 1994; 5(1):
25-40.
19. Golanowska M, Lojkowska E. A review on Dickeya solani, a new pathogenic bacterium
causing loss in potato yield in Europe. Bio Technologia. 2016; 97(2): 109-127.
20. Suárez MB, Feria FJ, Martín-Robles MJ, del Rey FJ, Palomo JL. Pectobacterium parmentieri
causing soft rot on potato tubers in southern Europe. Plant Dis. 2017; 101(6): 1029.
21. Gallois A, Samson R, Ageron E, Grimont PA. Erwinia carotovora subsp. odorifera subsp.
nov., associated with odorous soft rot of chicory (Cichorium intybus L.). Int J Syst Evol
Microbiol. 1992; 42(4): 582-588.
22. Gardan L, Gouy C, Christen R, Samson R. Elevation of three subspecies of Pectobacterium
carotovorum to species level: Pectobacterium atrosepticum sp. nov., Pectobacterium
betavasculorum sp. nov. and Pectobacterium wasabiae sp. nov. Int J Syst Evol Microbiol.
2003; 53(2): 381-391.
23. Schaad NW, Jones JB, Chun W. Laboratory guide for the identification of plant pathogenic
bacteria. APS Press; 2001.
24. De Bruijn FJ, Rademaker J, Schneider M, Rossbach U, Louws FJ. Rep-PCR genomic
fingerprinting of plant-associated bacteria and computer-assisted phylogenetic analyses. In:
Stacey G, Mullin B, Gresshoff P, editors. Proceedings of the 8th International Congress of
Molecular Plant-Microbe Interactions. St. Paul, APS Press; 1996: 497-502.
25. Sambrook J, Russell DW. Gel electrophoresis of DNA and pulsed-field agarose gel
electrophoresis. In: Molecular cloning: a laboratory manual. 3rd ed. New York. Cold Spring
harbor Laboratory Press; 2001: 5.4-5.17.
26. Huson DH, Bryant D. Application of phylogenetic networks in evolutionary studies. Mol Biol
Evol. 2006; 23(2): 254-267.
27. Falush D, Stephens M, Pritchard JK. Inference of population structure using multilocus
genotype data: dominant markers and null alleles. Mol Ecol Resour. 2007; 7(4): 574-578.
28. Bryant D, Moulton V. Neighbor-net: an agglomerative method for the construction of
phylogenetic networks. Mol Biol Evol. 2004; 21(2): 255-265.
29. Excoffier L, Laval G, Schneider S. Arlequin (version 3.0): an integrated software package for
population genetics data analysis. Evol Bioinform Online. 2005; 1: 47-50
30. Excoffier L, Smouse PE, Quattro JM. Analysis of molecular variance inferred from metric
distances among DNA haplotypes: application to human mitochondrial DNA restriction data.
Genetics. 1992; 131(2): 479-491.
31. Nei M. Estimation of average heterozygosity and genetic distance from a small number of
individuals. Genetics. 1978; 89(3): 583-590.
32. Holt JG, Krieg NR, Sneath Pa, Staley JT, Williams ST. Bergey's Manual of determinate
bacteriology. Williams and Wilkins Publishers; 1994.
33. Khayi S, Cigna J, Chong TM, Quêtu-Laurent A, Chan KG, Hélias V, Faure D. Transfer of the
potato plant isolates of Pectobacterium wasabiae to Pectobacterium parmentieri sp. nov. Int J
Syst Evol Microbiol. 2016; 66(12): 5379-5383.
34. Zohour Paralak E, Rahimian H, Banihashemi Z. A comparative study on pectolytic Erwinias
isolated from potato in the Fars province. Iran. J Plant Pathol. 2007; 43: 121-144.
35. Ahmadvand R, Rahimian H. 2002. Study on diversity of the pectolytic Erwinias infecting
potato in Hamedan province. Proceedings of the 15th Iranian Plant Protection Congress, 7–11
Sep, Kermanshah, Iran, 115.
36. Houle D, Govindaraju DR, Omholt S. Phenomics: the next challenge. Nat Rev Genet. 2010;
11(12): 855-866.
37. Duarte V, De Boer SH, Ward LJ, Oliveira AM. Characterization of atypical Erwinia
carotovora strains causing blackleg of potato in Brazil. J Appl Microbiol. 2004; 96(3):
535-545.
38. Costa AB, Eloy M, Cruz L, Janse JD, Oliveira H. Studies on pectolytic Erwinia spp. in
Portugal reveal unusual strains of E. carotovora subsp. atroseptica. J Plant Patho. 2006; 88(2):
161-169.
39. Vimal BM, Anuradha SN. Characterization and differentiation of soft rot causing
Pectobacterium carotovorum of Indian origin. Eur J Plant Pathol. 2013; 136(1): 87-102.
40. Yap MN, Barak JD, Charkowski AO. Genomic diversity of Erwinia carotovora subsp.
carotovora and its correlation with virulence. Appl Environ Microbiol. 2004; 70(5):
3013-3023.
41. Faquihi H, Terta M, Amdan M, Achbani EH, Ennaji MM, Mhand RA. Phenotypic and
genotypic diversity of Pectobacterium carotovorum subsp. carotovorum causing soft rot
disease of potatoes in Morocco. Eur J Plant Pathol. 2015; 143(4): 801-811.
42. Baghaee-Ravari S, Moslemkhani K, Khodaygan P. Assessment of genetic variability of
prevalent pectinolytic bacteria causing potato tuber soft rot in eastern Iran. J Plant Pathol.
2013; 95(1): 107-113.
43. Dees MW, Lysøe E, Rossmann S, Perminow J, Brurberg MB. Pectobacterium polaris sp.
nov., isolated from potato (Solanum tuberosum). Int J Syst Evol Microbiol. 2017; 67(12):
5222-5229.
