Research Article
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Year 2022, Volume: 5 Issue: 3, 504 - 518, 15.12.2022
https://doi.org/10.38001/ijlsb.1122987

Abstract

Project Number

KSU, BAP Grant #: 2009/2-3

References

  • 1. Hueze, V., G. Tran, and R. Baumont, Common vetch (Vicia sativa). Feedipedia., 2011. 12: p. 53–56.
  • 2. Sullivan, P., Overview of cover crops and green manures. , in Fundementals of sustainable agriculture., P. Williams, Editor. 2013, ATTRA, National center for appropriate technology Fayetteville. p. 1–16.
  • 3. Sherasia, P.L., M.R. Garg, and B.M. Bhanderi, Pulses and their by-products as animal feed, edited by T. Calles & H. P. S. Makkar. 2017, Rome: FAO.
  • 4. Firincioglu, H.K., et al., A selection strategy for low toxin vetches (Vicia sativa spp.). Turkish Journal of Agriculture and Forestry., 2007. 31(5): p. 303-311.
  • 5. Georgieva, N., I. Nikolova, and Y. Naydenova, Nutritive value of forage vetch cultivars (Vicia sativa L., Vicia villosa ROTH.). Banats Journal of Biotechnology., 2016. 7(14): p. 5-12.
  • 6. Huang, Y.F., et al., Potential value of the common vetch (Vicia sativa L.) as an animal feedstuff: a review. Journal of Animal Physiology and Animal Nutrition., 2017. 101(5): p. 807-823.
  • 7. Huang, Y.F., et al., Comparative Grain Chemical Composition, Ruminal Degradation In Vivo, and Intestinal Digestibility In Vitro of Vicia Sativa L. Varieties Grown on the Tibetan Plateau. Animals., 2019. 9(5).
  • 8. Lenka, S.K., et al., Genome-wide targeted prediction of ABA responsive genes in rice based on over-represented cis-motif in co-expressed genes. Plant Molecular Biology, 2009. 69(3): p. 261-71.
  • 9. Zhang, Y.J., et al., DNA isolation and optimization of sequence-related amplified polymorphism-polymerase chain reaction (SRAP-PCR) condition for endangered Polyporus umbellatus. Journal of Medicinal Plants Research., 2011. 5(31): p. 6890-6894.
  • 10. Poczai, P., et al., Phylogenetic Analyses of Teleki Grapevine Rootstocks Using Three Chloroplast DNA Markers. Plant Molecular Biology Reporter., 2013. 31(2): p. 371-386.
  • 11. Li, M., et al., A simple method for normalization of DNA extraction to improve the quantitative detection of soil-borne plant pathogenic oomycetes by real-time PCR. Letters in Applied Microbiology., 2015. 61(2): p. 179-85.
  • 12. Tinker, N., M. Fortin, and D. Mather, Random amplified polymorphic DNA and pedigree relationships in spring barley. . Theoretical and Applied Genetics., 1993. 85: p. 976-984.
  • 13. Babic, V., et al., UPOV morphological versus molecular markers for maize inbred lines variability determination. Chilean Journal of Agricultural Research., 2016. 76(4): p. 417-426.
  • 14. Wan, Q.H., et al., Which genetic marker for which conservation genetics issue? Electrophoresis., 2004. 25(14): p. 2165-76.
  • 15. Potokina, E., et al., Population diversity of the Vicia sativa agg. (Fabaceae) in the flora of the former USSR deduced from RAPD and seed protein analyses. Genetic Resources and Crop Evolution., 2000. 47: p. 171-183.
  • 16. Kartal, G.K., et al., Hybridization studies in Vicia sativa complex. Euphytica., 2020. 216(2).
  • 17. Cil, A. and I. Tiryaki, Sequence-related amplified polymorphism and inter-simple sequence repeat marker-based genetic diversity and nuclear DNA content variation in common vetch (Vicia sativa L.). Plant Genetic Resources-Characterization and Utilization., 2016. 14(3): p. 183-191.
  • 18. Potokina, E., et al., AFLP diversity in the common vetch (Vicia sativa L.) on the world scale. . Theoritical and Applied Genetics., 2002. 105: p. 58-67.
  • 19. Raveendar, S., et al., Cross-Amplification of Vicia sativa subsp sativa Microsatellites across 22 Other Vicia Species. Molecules., 2015. 20(1): p. 1543-1550.
  • 20. Liu, Z.P., et al., Exploiting Illumina Sequencing for the Development of 95 Novel Polymorphic EST-SSR Markers in Common Vetch (Vicia sativa subsp sativa). Molecules., 2014. 19(5): p. 5777-5789.
  • 21. Chung, J.W., et al., Development of 65 Novel Polymorphic cDNA-SSR Markers in Common Vetch (Vicia sativa subsp sativa) Using Next Generation Sequencing. Molecules., 2013. 18(7): p. 8376-8392.
  • 22. Chung, J.W., et al., New cDNA-SSR markers in the narrow-leaved vetch (Vicia sativa subsp nigra) using 454 pyrosequencing. Molecular Breeding., 2014. 33(3): p. 749-754.
  • 23. Chai, X.T., et al., Optimizing Sample Size to Assess the Genetic Diversity in Common Vetch (Vicia sativa L.) Populations Using Start Codon Targeted (SCoT) Markers. Molecules., 2017. 22(4).
  • 24. Kim, T.S., et al., Transcriptome Analysis of Two Vicia sativa Subspecies: Mining Molecular Markers to Enhance Genomic Resources for Vetch Improvement. Genes., 2015. 6(4): p. 1164-1182.
  • 25. De la Rosa, L., E. Zambrana, and E. Ramirez-Parra, Molecular bases for drought tolerance in common vetch: designing new molecular breeding tools. BMC Plant Biology, 2020. 20(1): p. 71.
  • 26. Abbasi, A.R., et al., Expression Analysis of Candidate Genes in Common Vetch (Vicia sativa L.) Under Drought Stress. Journal of Agricultural Science and Technology., 2015. 17(5): p. 1291-1302.
  • 27. Silva, C.C., et al., Leaf-panel- and latex-expressed sequenced tags from the rubber tree (Hevea brasiliensis) under cold-stressed and suboptimal growing conditions: the development of gene-targeted functional markers for stress response. Molecular Breeding, 2014. 34(3): p. 1035-1053.
  • 28. Poczai, P., et al., Advances in plant gene-targeted and functional markers: a review. Plant Methods., 2013. 9(1): p. 6. 29. Wang, T.Z., et al., Identification and characterization of long non-coding RNAs involved in osmotic and salt stress in Medicago truncatula using genome-wide high-throughput sequencing. BMC Plant Biology., 2015. 15: p. 131.
  • 30. Aggarwal, R., et al., URP based DNA fingerprinting of Bipolaris sorokiniana isolates causing spot blotch of wheat. . Journal of Phytopathology, 2010. 158: p. 210-216.
  • 31. Kang, H.W., PCR Fingerprinting of diverse genomes from bacterial strains using universal rice primer (URP). International Journal of Bioscience and Biotechnology, 2018. 6: p. 51-64.
  • 32. Kang, H.W., et al., Fingerprinting of diverse genomes using PCR with universal rice primers generated from repetitive sequence of Korean weedy rice. Molecules and Cells, 2002. 13(2): p. 281-7.
  • 33. Sharma, A., et al., Analysis of genetic diversity in earthworms using DNA markers. Zoolog Sci, 2011. 28(1): p. 25-31. 34. Dawson, I.K., et al., Detection and pattern of interspecific hybridization between Gliricida sepium and G. maculata in Meso-America revealed by PCR-based assays. Mol Ecol, 1996. 5(1): p. 89-98.
  • 35. Powell, W., et al., Genepool variation in genus Glycine subgenus Soja revealed by polymorphic nuclear and chloroplast microsatellites. Genetics, 1996. 144(2): p. 793-803.
  • 36. Dice, L.R., Measures of the Amount of Ecologic Association Between Species. Ecology, 1945. 26: p. 297–302. 37. Nei, M., Genetic distance between populations. American Naturalist 1972. 106: p. 283-292.
  • 38. Devi, S.P., et al., Single primer amplification reaction (SPAR) methods reveal subsequent increase in genetic variations in micropropagated plants of Nepenthes khasiana Hook. f. maintained for three consecutive regenerations. Gene., 2014. 538(1): p. 23-29.
  • 39. Sharma, S.K., et al., Single primer amplification reaction (SPAR) reveals inter- and intra-specific natural genetic variation in five species of Cymbidium (Orchidaceae). Gene., 2011. 483(1-2): p. 54-62.
  • 40. Heath, D.D., G.K. Iwama, and R.H. Devlin, PCR primed with VNTR core sequences yields species specific patterns and hypervariable probes. Nucleic Acids Research., 1993. 21(24): p. 5782-5.
  • 41. Zhang, Y., et al., Assessment of cyto- and genotoxic effects of Cesium-133 in Vicia faba using single-cell gel electrophoresis and random amplified polymorphic DNA assays. Ecotoxicology and Environmental Safety., 2020. 197: p. 110620.
  • 42. Yildirim, N. and G. Agar, Determination of genotoxic effects of fipronil in Vicia faba using random amplified polymorphic DNA analysis. Toxicology & Industrial Health., 2016. 32(8): p. 1450-1455.
  • 43. Xiong, F., et al., Molecular profiling of genetic variability in domesticated groundnut (Arachis hypogaea L.) based on ISJ, URP, and DAMD markers. Biochem Genet, 2013. 51(11-12): p. 889-900.
  • 44. Lee, H.H., et al., Characterization of Newly Bred Cordyceps militaris Strains for Higher Production of Cordycepin through HPLC and URP-PCR Analysis. Journal of Microbiology and Biotechnology., 2017. 27(7): p. 1223-1232.
  • 45. Saleh, B., Molecular Characterization using Directed Amplification of Minisatellite-region DNA (DAMD) Marker in Ficus sycomorus L. (Moraceae). The Open Agriculture Journal., 2019. 13: p. 74-81.
  • 46. Sharmaa, R., S. Sharmaa, and S. Kumar, Pair-wise combinations of RAPD primers for diversity analysis with reference to protein and single primer RAPD in soybean. Annals of Agrarian Science., 2018. 16: p. 243-249.

Diversity Analysis of Common Vetch (Vicia Sativa L.) Lines and Cultivars Using Pairwise Combinations of Universal Rice Primers

Year 2022, Volume: 5 Issue: 3, 504 - 518, 15.12.2022
https://doi.org/10.38001/ijlsb.1122987

Abstract

This study has been conducted to determine genetic diversity of the common vetch lines and cultivars by using pairwise combinations of universal rice primers (URPs). A total number of 37 URP marker pairs were tested and twenty of those provided amplicons in the common vetch genome. The pairs of amplified URP markers provided a total of 83 bands and 62 of them were determined as polymorphic and were scattered to the whole genome. The average polymorphism rate of the primers was calculated as 73.5% while the polymorphism information content (PIC) values have ranged from 0.11 to 0.47 with an average of 0.24. The phylogenetic tree constructed based on UPGMA analysis provided three main clades. Two-dimensional plot of PCA and the UPGMA analysis showed that the URP markers successfully distinguished the genetic material based on their genetic origin. In conclusion, this study revealed that the use of pairwise combinations of URP markers could have a better power to reveal the level of polymorphism in plant genome.

Supporting Institution

Kahramanmaras Sutcu Imam University

Project Number

KSU, BAP Grant #: 2009/2-3

References

  • 1. Hueze, V., G. Tran, and R. Baumont, Common vetch (Vicia sativa). Feedipedia., 2011. 12: p. 53–56.
  • 2. Sullivan, P., Overview of cover crops and green manures. , in Fundementals of sustainable agriculture., P. Williams, Editor. 2013, ATTRA, National center for appropriate technology Fayetteville. p. 1–16.
  • 3. Sherasia, P.L., M.R. Garg, and B.M. Bhanderi, Pulses and their by-products as animal feed, edited by T. Calles & H. P. S. Makkar. 2017, Rome: FAO.
  • 4. Firincioglu, H.K., et al., A selection strategy for low toxin vetches (Vicia sativa spp.). Turkish Journal of Agriculture and Forestry., 2007. 31(5): p. 303-311.
  • 5. Georgieva, N., I. Nikolova, and Y. Naydenova, Nutritive value of forage vetch cultivars (Vicia sativa L., Vicia villosa ROTH.). Banats Journal of Biotechnology., 2016. 7(14): p. 5-12.
  • 6. Huang, Y.F., et al., Potential value of the common vetch (Vicia sativa L.) as an animal feedstuff: a review. Journal of Animal Physiology and Animal Nutrition., 2017. 101(5): p. 807-823.
  • 7. Huang, Y.F., et al., Comparative Grain Chemical Composition, Ruminal Degradation In Vivo, and Intestinal Digestibility In Vitro of Vicia Sativa L. Varieties Grown on the Tibetan Plateau. Animals., 2019. 9(5).
  • 8. Lenka, S.K., et al., Genome-wide targeted prediction of ABA responsive genes in rice based on over-represented cis-motif in co-expressed genes. Plant Molecular Biology, 2009. 69(3): p. 261-71.
  • 9. Zhang, Y.J., et al., DNA isolation and optimization of sequence-related amplified polymorphism-polymerase chain reaction (SRAP-PCR) condition for endangered Polyporus umbellatus. Journal of Medicinal Plants Research., 2011. 5(31): p. 6890-6894.
  • 10. Poczai, P., et al., Phylogenetic Analyses of Teleki Grapevine Rootstocks Using Three Chloroplast DNA Markers. Plant Molecular Biology Reporter., 2013. 31(2): p. 371-386.
  • 11. Li, M., et al., A simple method for normalization of DNA extraction to improve the quantitative detection of soil-borne plant pathogenic oomycetes by real-time PCR. Letters in Applied Microbiology., 2015. 61(2): p. 179-85.
  • 12. Tinker, N., M. Fortin, and D. Mather, Random amplified polymorphic DNA and pedigree relationships in spring barley. . Theoretical and Applied Genetics., 1993. 85: p. 976-984.
  • 13. Babic, V., et al., UPOV morphological versus molecular markers for maize inbred lines variability determination. Chilean Journal of Agricultural Research., 2016. 76(4): p. 417-426.
  • 14. Wan, Q.H., et al., Which genetic marker for which conservation genetics issue? Electrophoresis., 2004. 25(14): p. 2165-76.
  • 15. Potokina, E., et al., Population diversity of the Vicia sativa agg. (Fabaceae) in the flora of the former USSR deduced from RAPD and seed protein analyses. Genetic Resources and Crop Evolution., 2000. 47: p. 171-183.
  • 16. Kartal, G.K., et al., Hybridization studies in Vicia sativa complex. Euphytica., 2020. 216(2).
  • 17. Cil, A. and I. Tiryaki, Sequence-related amplified polymorphism and inter-simple sequence repeat marker-based genetic diversity and nuclear DNA content variation in common vetch (Vicia sativa L.). Plant Genetic Resources-Characterization and Utilization., 2016. 14(3): p. 183-191.
  • 18. Potokina, E., et al., AFLP diversity in the common vetch (Vicia sativa L.) on the world scale. . Theoritical and Applied Genetics., 2002. 105: p. 58-67.
  • 19. Raveendar, S., et al., Cross-Amplification of Vicia sativa subsp sativa Microsatellites across 22 Other Vicia Species. Molecules., 2015. 20(1): p. 1543-1550.
  • 20. Liu, Z.P., et al., Exploiting Illumina Sequencing for the Development of 95 Novel Polymorphic EST-SSR Markers in Common Vetch (Vicia sativa subsp sativa). Molecules., 2014. 19(5): p. 5777-5789.
  • 21. Chung, J.W., et al., Development of 65 Novel Polymorphic cDNA-SSR Markers in Common Vetch (Vicia sativa subsp sativa) Using Next Generation Sequencing. Molecules., 2013. 18(7): p. 8376-8392.
  • 22. Chung, J.W., et al., New cDNA-SSR markers in the narrow-leaved vetch (Vicia sativa subsp nigra) using 454 pyrosequencing. Molecular Breeding., 2014. 33(3): p. 749-754.
  • 23. Chai, X.T., et al., Optimizing Sample Size to Assess the Genetic Diversity in Common Vetch (Vicia sativa L.) Populations Using Start Codon Targeted (SCoT) Markers. Molecules., 2017. 22(4).
  • 24. Kim, T.S., et al., Transcriptome Analysis of Two Vicia sativa Subspecies: Mining Molecular Markers to Enhance Genomic Resources for Vetch Improvement. Genes., 2015. 6(4): p. 1164-1182.
  • 25. De la Rosa, L., E. Zambrana, and E. Ramirez-Parra, Molecular bases for drought tolerance in common vetch: designing new molecular breeding tools. BMC Plant Biology, 2020. 20(1): p. 71.
  • 26. Abbasi, A.R., et al., Expression Analysis of Candidate Genes in Common Vetch (Vicia sativa L.) Under Drought Stress. Journal of Agricultural Science and Technology., 2015. 17(5): p. 1291-1302.
  • 27. Silva, C.C., et al., Leaf-panel- and latex-expressed sequenced tags from the rubber tree (Hevea brasiliensis) under cold-stressed and suboptimal growing conditions: the development of gene-targeted functional markers for stress response. Molecular Breeding, 2014. 34(3): p. 1035-1053.
  • 28. Poczai, P., et al., Advances in plant gene-targeted and functional markers: a review. Plant Methods., 2013. 9(1): p. 6. 29. Wang, T.Z., et al., Identification and characterization of long non-coding RNAs involved in osmotic and salt stress in Medicago truncatula using genome-wide high-throughput sequencing. BMC Plant Biology., 2015. 15: p. 131.
  • 30. Aggarwal, R., et al., URP based DNA fingerprinting of Bipolaris sorokiniana isolates causing spot blotch of wheat. . Journal of Phytopathology, 2010. 158: p. 210-216.
  • 31. Kang, H.W., PCR Fingerprinting of diverse genomes from bacterial strains using universal rice primer (URP). International Journal of Bioscience and Biotechnology, 2018. 6: p. 51-64.
  • 32. Kang, H.W., et al., Fingerprinting of diverse genomes using PCR with universal rice primers generated from repetitive sequence of Korean weedy rice. Molecules and Cells, 2002. 13(2): p. 281-7.
  • 33. Sharma, A., et al., Analysis of genetic diversity in earthworms using DNA markers. Zoolog Sci, 2011. 28(1): p. 25-31. 34. Dawson, I.K., et al., Detection and pattern of interspecific hybridization between Gliricida sepium and G. maculata in Meso-America revealed by PCR-based assays. Mol Ecol, 1996. 5(1): p. 89-98.
  • 35. Powell, W., et al., Genepool variation in genus Glycine subgenus Soja revealed by polymorphic nuclear and chloroplast microsatellites. Genetics, 1996. 144(2): p. 793-803.
  • 36. Dice, L.R., Measures of the Amount of Ecologic Association Between Species. Ecology, 1945. 26: p. 297–302. 37. Nei, M., Genetic distance between populations. American Naturalist 1972. 106: p. 283-292.
  • 38. Devi, S.P., et al., Single primer amplification reaction (SPAR) methods reveal subsequent increase in genetic variations in micropropagated plants of Nepenthes khasiana Hook. f. maintained for three consecutive regenerations. Gene., 2014. 538(1): p. 23-29.
  • 39. Sharma, S.K., et al., Single primer amplification reaction (SPAR) reveals inter- and intra-specific natural genetic variation in five species of Cymbidium (Orchidaceae). Gene., 2011. 483(1-2): p. 54-62.
  • 40. Heath, D.D., G.K. Iwama, and R.H. Devlin, PCR primed with VNTR core sequences yields species specific patterns and hypervariable probes. Nucleic Acids Research., 1993. 21(24): p. 5782-5.
  • 41. Zhang, Y., et al., Assessment of cyto- and genotoxic effects of Cesium-133 in Vicia faba using single-cell gel electrophoresis and random amplified polymorphic DNA assays. Ecotoxicology and Environmental Safety., 2020. 197: p. 110620.
  • 42. Yildirim, N. and G. Agar, Determination of genotoxic effects of fipronil in Vicia faba using random amplified polymorphic DNA analysis. Toxicology & Industrial Health., 2016. 32(8): p. 1450-1455.
  • 43. Xiong, F., et al., Molecular profiling of genetic variability in domesticated groundnut (Arachis hypogaea L.) based on ISJ, URP, and DAMD markers. Biochem Genet, 2013. 51(11-12): p. 889-900.
  • 44. Lee, H.H., et al., Characterization of Newly Bred Cordyceps militaris Strains for Higher Production of Cordycepin through HPLC and URP-PCR Analysis. Journal of Microbiology and Biotechnology., 2017. 27(7): p. 1223-1232.
  • 45. Saleh, B., Molecular Characterization using Directed Amplification of Minisatellite-region DNA (DAMD) Marker in Ficus sycomorus L. (Moraceae). The Open Agriculture Journal., 2019. 13: p. 74-81.
  • 46. Sharmaa, R., S. Sharmaa, and S. Kumar, Pair-wise combinations of RAPD primers for diversity analysis with reference to protein and single primer RAPD in soybean. Annals of Agrarian Science., 2018. 16: p. 243-249.
There are 43 citations in total.

Details

Primary Language English
Subjects Agricultural Engineering
Journal Section Research Articles
Authors

Mustafa Topu 0000-0001-9654-3891

İskender Tiryaki 0000-0002-7504-2892

Project Number KSU, BAP Grant #: 2009/2-3
Early Pub Date May 14, 2022
Publication Date December 15, 2022
Published in Issue Year 2022 Volume: 5 Issue: 3

Cite

EndNote Topu M, Tiryaki İ (December 1, 2022) Diversity Analysis of Common Vetch (Vicia Sativa L.) Lines and Cultivars Using Pairwise Combinations of Universal Rice Primers. International Journal of Life Sciences and Biotechnology 5 3 504–518.



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