Research Article
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ASSOCIATION MAPPING OF GERMINATION AND SOME EARLY SEEDLING STAGE TRAITS OF A TURKISH ORIGIN OAT COLLECTION

Year 2022, Volume: 27 Issue: 1, 41 - 50, 20.06.2022
https://doi.org/10.17557/tjfc.1022408

Abstract

In recent years, oat plant especially for hay yield is on demand in Turkey. In this study, 167 oat landraces originated from Turkey were evaluated for germination and some early seedling stage traits and genotyped by 6K SNP Chip assay to detect candidate markers using association mapping analysis. Principal component analysis (PCA) were also performed to determine relationships among investigated traits.
The variation in local oat genotypes for germination and other investigated traits was found significant at the 5% significance level, except for germination rate (GR). The values for germination rate was found between 52-76% and 52-100% for germination ratio, while 12.33 to 45 mm for coleoptile length and 8 to 21 mm for radicle length. On the other hand, plumula length varied between 2 to 28.45 mm and 1301.33 to 5494.40 for seed vigor index.
In the research, PC1 and PC2 value was found 41.5% and 21.5%, respectively, explaining the 63% of the total variation. Germination rate and germination ratio (GP) were positively and significantly correlated with the other investigated traits.
According to the results of the association mapping analysis a total number of 43 candidate markers were observed, 10 candidate markers for germination rate, five candidate markers for germination ratio (GP), five markers for radicle length (RL), eight markers for coleoptile length (CL), seven markers for plumula length (PL) and eight markers for seed vigor index (SVI).
These candidate markers identified in this study for germination and early seedling stage traits could be used in future studies.

Thanks

This phenotypic data of this study is obtained from the MSc Thesis of Berk Abdullah KOÇER. Authors thanks to General Mills Inc. Minnesota, USA for the 6K SNP Chipset genotyping.

References

  • Abdurakhmonov, I. and Abdukarimov, A. 2008. Application of association mapping to understanding the genetic diversity of plant germplasm resources. International Journal of Plant Genomics. 2008:1-18.
  • Akyol, Z. 2014. The effect of different pH level and soaking time on germination of oats types. MSc Thesis. Kahramanmaraş. pp. 50.
  • Bekele, W.A., Wight, C.P., Chao, S., Howarth, C.J. and Tinker, N.A. 2018. Haplotype-based genotyping-by-sequencing in oat genome research. Plant Biotechnology Journal 16: 1452-1463.
  • Brooke, J. 2017. Genetic analysis of loose smut (Ustilago avenae Pers. (Rostr. )) resistance in oat. Master Thesis. University of Saskatchewan Plant Science. Saskatchewan. pp 123.
  • Chaffin, A.S., Huang, Y.-F., Smith, S., Bekele, W.A., Babiker, E., Gnanesh, B.N., Foresman, B.J. et al. 2016. A consensus map in cultivated hexaploid oat reveals conserved grass synteny with substantial sub-genome rearrangement. Plant Genome, 9(2).
  • Cömertpay, G., Habyarimana, E., Baloch, F. S., Güngör, H., Dokuyucu, T., Akkaya, A. and Dumlupinar, Z. 2018. Geographical description and molecular characterization of genetic structure and diversity using a 6K SNP array in Turkish oat germplasm. Canadian Journal of Plant Science, 99(1): 12-21.
  • Dumlupınar, Z., Maral, H., Kara, R., Dokuyucu, T. andAkkaya, A. 2011a. Evaluation of Turkish oat landraces based on grain yield, yield components and some quality traits. Turkish Journal of Field Crops, 16: 190-196.
  • Dumlupınar, Z., Dokuyucu T. and Akkaya, A. 2011b. Determination cold tolerance of Turkish and USA origin oat genotypes under Kahramanmaraş-Afşin condition. KSU J. Nat. Sci. 14(2): 35-42.
  • FAO, (2019). http://www.fao.org/faostat/en. (Accessed: 18.03.2021).
  • Flint-Garcia, S.A., Thornsberry, J.M., and Buckler, E. 2003. Structure of linkage disequilibrium in plants. Annual Review of Plant Biology, 54(1): 357-374.
  • Gungor, H., Çıkılı, Y. and Dumlupinar, Z. 2017. The effects of salt stress on germination and seedling development of some commercial and landraces of oat genotypes. KSU J. Nat. Sci. 20 (Special Issue): 263-267.
  • Gungor, H., Çıkılı, Y. and Dumlupinar, Z. 2021. Screening of oat varieties and landraces at early vegetative stage under salt stress conditions: Morpho-physiological and PCA biplot analysis. Cereal Research Communications, 49(4): 587-597.
  • Huang, C. T., Klos, K.E. and Huang, Y. F. 2020. Genome-wide association study reveals the genetic architecture of seed vigor in oats. G3, Genes, Genomes, Genetics, 10: 4489-4503.
  • JMP®, 2020. Version 15.1. SAS Institute Inc., Cary, NC, 1989–2020.
  • Kılınç, M. F. 2020. Association mapping analysis and determination of some agronomical traits for Turkey origin oat genotypes. PhD Thesis Kahramanmaraş. pp. 225.
  • Lin, Y., Gnanesh, B.N., Chong, J. et al. 2014. A major quantitative trait locus conferring adult plant partial resistance to crown rust in oat. BMC Plant Biol 14, 250. https://doi.org/10.1186/s12870-014-0250-2.
  • Mackay, T. 2001. The genetic architecture of quantitative traits. Annu. Rev. Genet. 35: 303-339.
  • McCartney, C.A., Kebede, A.Z., Menzies, J.G., Admassu-Yimer, B., Bekele, W.A., Wight, C.P., Tinker, N.A., Gordon, T., Bonman, J.M., Kols, K.E., Babiker, E., Gale, S., Beattie, A.D., Fetch, J.M. and Fetch, T.G. 2019. Mapping of the stem rust resistance gene Pg13 in cultivated oat. Theoretical and Applied Genetics, 133: 259-270.
  • Mohler, V. 2021. Allocation of the oat powdery mildew resistance gene Pm3 to oat chromosome 1A. Cereal Research Communications, 1-8. https:doi.org/10.1007/s42976-021-00152-2.
  • Nadeem, M.A., Nawaz, M.A., Shadid, M.Q., Doğan, Y., Comertpay, G., Chung, G. and Baloch, F.S. 2018. DNA molecular markers in plant breeding: current status and recent advancements in genomic selection and genome editing. Biotechnology & Biotechnological Equipment, 32(2): 261-285.
  • Oliver R.E., Lazo G.R., Lutz J.D., Rubenfield M.J., Tinker N.A., Anderson J.M., Wisniewski Morehead N.H., Adhikary D., Jellen E.N., et al. 2011. Model SNP development for complex genomes based on hexaploid oat using high-throughput 454 sequencing technology. BMC Genomics, 12: 77.
  • Oliver R.E., Tinker N.A., Lazo G.R., Chao S., Jellen E.N., Carson M.L., Rines H.W., Obert D.E., Lutz J.D., Shackelford I., Korol A.B., Wight C.P., Gardner K.M., Hattori J., Beattie A.D., et al. 2013. SNP discovery and chromosome anchoring provide the first physically-anchored hexaploid oat map and reveal synteny with model species. PLoS ONE, 8(3): e58068.
  • Oner, F., Özkorkmaz, F. and Yılmaz, N. 2018. The Effect of Gibberellic Acid Applications on Some Germination Parameters in Oats under Salt Stress. International Journal of Agricultural and Natural Sciences, 1(1): 33-35.
  • Rajjou, L., Duval, M., Gallardo, K., Catusse, J., Bally, J., Job, C., and Job, D. 2012. Seed germination and vigor. Annu. Rev. Plant. Biol. 63: 507-533.
  • Şakiroğlu, M. 2020. Bioinformatic methods for Genomic analysis. ISBN: 978-605-282-541-9, Turkey, pp 245.
  • Tang, Y., Liu, X., Wang, J., Li, M., Wang, Q., Tian, F. et al. 2016. GAPIT Version 2: an enhanced integrated tool for genomic association and prediction. Plant Genome, 9:0120. http://dx.doi.org/10.3835/plantgenome2015.11.0120.
  • Tulum, I., Morgil, H., Gerçek, Y. C. 2020. Single nucleotid polymorphisms (SNPS) in plant genetics and breeding. (Editor: Çalışkan, M.). IntechOpen Limited, London, pp. 137-145.
  • TUIK, 2019. Turkish Statistical Foundation. Crops Production Database. http://www.tuik.gov.tr/PreTablo (Accessed on 25.06.2020).
  • VanRaden, M.P. 2008. Efficient methods to compute genomic predictions. J. Dairy. Sci: 4414-4423. http://dx.doi.org/10.368/jds.2007-0980.
  • Yan, W. and Tinker, N.A. 2006. Biplot analysis of multi-environment trial data: Principles and applications. Can. J. Plant. Sci. 86: 623-645. http://dx.doi.org/10.4141/P05-169.
  • Yu, J. and Buckler, E.S. 2006. Genetic association mapping and genome organization of maize. Curr. Opin. Biotechnol. 17: 155-160.
  • Wang, S. X., Zhu, Y.L., Zhang, D.X., Shao, H., Liu, P., Hu, J. B. et al. 2017. Genome-wide association study for grain yield and related traits in elite wheat varieties and advanced lines using SNP markers. PLoS One, 12(11): e0188662. https://doi.org/10.1371/journal.pone.0188662.
  • Zimmer, C. M., McNish, I. G., Klos, K. E., Oro, T., Arruda, K. M. A. Gutkoski, L. C. and Federizzi, L.C. 2020. Genome-wide association for 𝛽-glucan content, population structure and linkage disequilibrium in elite oat germplasm adapted to subtropical environments. Molecular Breeding, 40:103. doi:10.1007/s11032-020-01182-0.
  • Zimmer, C. M., Oliveira, G., Arruda, K. M. A. Pacheco, M. T. and Federizzi, L.C. 2021. Genome-wide association mapping for heading date in oats under subtropical environments. Genetics and Plant Breeding, 1-8. http://doi.org/10.1590/1678-992X-2020-0355.
Year 2022, Volume: 27 Issue: 1, 41 - 50, 20.06.2022
https://doi.org/10.17557/tjfc.1022408

Abstract

References

  • Abdurakhmonov, I. and Abdukarimov, A. 2008. Application of association mapping to understanding the genetic diversity of plant germplasm resources. International Journal of Plant Genomics. 2008:1-18.
  • Akyol, Z. 2014. The effect of different pH level and soaking time on germination of oats types. MSc Thesis. Kahramanmaraş. pp. 50.
  • Bekele, W.A., Wight, C.P., Chao, S., Howarth, C.J. and Tinker, N.A. 2018. Haplotype-based genotyping-by-sequencing in oat genome research. Plant Biotechnology Journal 16: 1452-1463.
  • Brooke, J. 2017. Genetic analysis of loose smut (Ustilago avenae Pers. (Rostr. )) resistance in oat. Master Thesis. University of Saskatchewan Plant Science. Saskatchewan. pp 123.
  • Chaffin, A.S., Huang, Y.-F., Smith, S., Bekele, W.A., Babiker, E., Gnanesh, B.N., Foresman, B.J. et al. 2016. A consensus map in cultivated hexaploid oat reveals conserved grass synteny with substantial sub-genome rearrangement. Plant Genome, 9(2).
  • Cömertpay, G., Habyarimana, E., Baloch, F. S., Güngör, H., Dokuyucu, T., Akkaya, A. and Dumlupinar, Z. 2018. Geographical description and molecular characterization of genetic structure and diversity using a 6K SNP array in Turkish oat germplasm. Canadian Journal of Plant Science, 99(1): 12-21.
  • Dumlupınar, Z., Maral, H., Kara, R., Dokuyucu, T. andAkkaya, A. 2011a. Evaluation of Turkish oat landraces based on grain yield, yield components and some quality traits. Turkish Journal of Field Crops, 16: 190-196.
  • Dumlupınar, Z., Dokuyucu T. and Akkaya, A. 2011b. Determination cold tolerance of Turkish and USA origin oat genotypes under Kahramanmaraş-Afşin condition. KSU J. Nat. Sci. 14(2): 35-42.
  • FAO, (2019). http://www.fao.org/faostat/en. (Accessed: 18.03.2021).
  • Flint-Garcia, S.A., Thornsberry, J.M., and Buckler, E. 2003. Structure of linkage disequilibrium in plants. Annual Review of Plant Biology, 54(1): 357-374.
  • Gungor, H., Çıkılı, Y. and Dumlupinar, Z. 2017. The effects of salt stress on germination and seedling development of some commercial and landraces of oat genotypes. KSU J. Nat. Sci. 20 (Special Issue): 263-267.
  • Gungor, H., Çıkılı, Y. and Dumlupinar, Z. 2021. Screening of oat varieties and landraces at early vegetative stage under salt stress conditions: Morpho-physiological and PCA biplot analysis. Cereal Research Communications, 49(4): 587-597.
  • Huang, C. T., Klos, K.E. and Huang, Y. F. 2020. Genome-wide association study reveals the genetic architecture of seed vigor in oats. G3, Genes, Genomes, Genetics, 10: 4489-4503.
  • JMP®, 2020. Version 15.1. SAS Institute Inc., Cary, NC, 1989–2020.
  • Kılınç, M. F. 2020. Association mapping analysis and determination of some agronomical traits for Turkey origin oat genotypes. PhD Thesis Kahramanmaraş. pp. 225.
  • Lin, Y., Gnanesh, B.N., Chong, J. et al. 2014. A major quantitative trait locus conferring adult plant partial resistance to crown rust in oat. BMC Plant Biol 14, 250. https://doi.org/10.1186/s12870-014-0250-2.
  • Mackay, T. 2001. The genetic architecture of quantitative traits. Annu. Rev. Genet. 35: 303-339.
  • McCartney, C.A., Kebede, A.Z., Menzies, J.G., Admassu-Yimer, B., Bekele, W.A., Wight, C.P., Tinker, N.A., Gordon, T., Bonman, J.M., Kols, K.E., Babiker, E., Gale, S., Beattie, A.D., Fetch, J.M. and Fetch, T.G. 2019. Mapping of the stem rust resistance gene Pg13 in cultivated oat. Theoretical and Applied Genetics, 133: 259-270.
  • Mohler, V. 2021. Allocation of the oat powdery mildew resistance gene Pm3 to oat chromosome 1A. Cereal Research Communications, 1-8. https:doi.org/10.1007/s42976-021-00152-2.
  • Nadeem, M.A., Nawaz, M.A., Shadid, M.Q., Doğan, Y., Comertpay, G., Chung, G. and Baloch, F.S. 2018. DNA molecular markers in plant breeding: current status and recent advancements in genomic selection and genome editing. Biotechnology & Biotechnological Equipment, 32(2): 261-285.
  • Oliver R.E., Lazo G.R., Lutz J.D., Rubenfield M.J., Tinker N.A., Anderson J.M., Wisniewski Morehead N.H., Adhikary D., Jellen E.N., et al. 2011. Model SNP development for complex genomes based on hexaploid oat using high-throughput 454 sequencing technology. BMC Genomics, 12: 77.
  • Oliver R.E., Tinker N.A., Lazo G.R., Chao S., Jellen E.N., Carson M.L., Rines H.W., Obert D.E., Lutz J.D., Shackelford I., Korol A.B., Wight C.P., Gardner K.M., Hattori J., Beattie A.D., et al. 2013. SNP discovery and chromosome anchoring provide the first physically-anchored hexaploid oat map and reveal synteny with model species. PLoS ONE, 8(3): e58068.
  • Oner, F., Özkorkmaz, F. and Yılmaz, N. 2018. The Effect of Gibberellic Acid Applications on Some Germination Parameters in Oats under Salt Stress. International Journal of Agricultural and Natural Sciences, 1(1): 33-35.
  • Rajjou, L., Duval, M., Gallardo, K., Catusse, J., Bally, J., Job, C., and Job, D. 2012. Seed germination and vigor. Annu. Rev. Plant. Biol. 63: 507-533.
  • Şakiroğlu, M. 2020. Bioinformatic methods for Genomic analysis. ISBN: 978-605-282-541-9, Turkey, pp 245.
  • Tang, Y., Liu, X., Wang, J., Li, M., Wang, Q., Tian, F. et al. 2016. GAPIT Version 2: an enhanced integrated tool for genomic association and prediction. Plant Genome, 9:0120. http://dx.doi.org/10.3835/plantgenome2015.11.0120.
  • Tulum, I., Morgil, H., Gerçek, Y. C. 2020. Single nucleotid polymorphisms (SNPS) in plant genetics and breeding. (Editor: Çalışkan, M.). IntechOpen Limited, London, pp. 137-145.
  • TUIK, 2019. Turkish Statistical Foundation. Crops Production Database. http://www.tuik.gov.tr/PreTablo (Accessed on 25.06.2020).
  • VanRaden, M.P. 2008. Efficient methods to compute genomic predictions. J. Dairy. Sci: 4414-4423. http://dx.doi.org/10.368/jds.2007-0980.
  • Yan, W. and Tinker, N.A. 2006. Biplot analysis of multi-environment trial data: Principles and applications. Can. J. Plant. Sci. 86: 623-645. http://dx.doi.org/10.4141/P05-169.
  • Yu, J. and Buckler, E.S. 2006. Genetic association mapping and genome organization of maize. Curr. Opin. Biotechnol. 17: 155-160.
  • Wang, S. X., Zhu, Y.L., Zhang, D.X., Shao, H., Liu, P., Hu, J. B. et al. 2017. Genome-wide association study for grain yield and related traits in elite wheat varieties and advanced lines using SNP markers. PLoS One, 12(11): e0188662. https://doi.org/10.1371/journal.pone.0188662.
  • Zimmer, C. M., McNish, I. G., Klos, K. E., Oro, T., Arruda, K. M. A. Gutkoski, L. C. and Federizzi, L.C. 2020. Genome-wide association for 𝛽-glucan content, population structure and linkage disequilibrium in elite oat germplasm adapted to subtropical environments. Molecular Breeding, 40:103. doi:10.1007/s11032-020-01182-0.
  • Zimmer, C. M., Oliveira, G., Arruda, K. M. A. Pacheco, M. T. and Federizzi, L.C. 2021. Genome-wide association mapping for heading date in oats under subtropical environments. Genetics and Plant Breeding, 1-8. http://doi.org/10.1590/1678-992X-2020-0355.
There are 34 citations in total.

Details

Primary Language English
Subjects Botany
Journal Section Articles
Authors

Berk Abdullah Koçak 0000-0002-6854-1781

Fatih Kılınc 0000-0001-6780-030X

Adem Bardak 0000-0002-5715-302X

Hüseyin Güngör 0000-0001-6708-6337

Tevrican Dokuyucu 0000-0002-7704-6790

Aydın Akkaya 0000-0001-9560-1922

Ziya Dumlupınar 0000-0003-3119-6926

Publication Date June 20, 2022
Published in Issue Year 2022 Volume: 27 Issue: 1

Cite

APA Koçak, B. A., Kılınc, F., Bardak, A., Güngör, H., et al. (2022). ASSOCIATION MAPPING OF GERMINATION AND SOME EARLY SEEDLING STAGE TRAITS OF A TURKISH ORIGIN OAT COLLECTION. Turkish Journal Of Field Crops, 27(1), 41-50. https://doi.org/10.17557/tjfc.1022408
AMA Koçak BA, Kılınc F, Bardak A, Güngör H, Dokuyucu T, Akkaya A, Dumlupınar Z. ASSOCIATION MAPPING OF GERMINATION AND SOME EARLY SEEDLING STAGE TRAITS OF A TURKISH ORIGIN OAT COLLECTION. TJFC. June 2022;27(1):41-50. doi:10.17557/tjfc.1022408
Chicago Koçak, Berk Abdullah, Fatih Kılınc, Adem Bardak, Hüseyin Güngör, Tevrican Dokuyucu, Aydın Akkaya, and Ziya Dumlupınar. “ASSOCIATION MAPPING OF GERMINATION AND SOME EARLY SEEDLING STAGE TRAITS OF A TURKISH ORIGIN OAT COLLECTION”. Turkish Journal Of Field Crops 27, no. 1 (June 2022): 41-50. https://doi.org/10.17557/tjfc.1022408.
EndNote Koçak BA, Kılınc F, Bardak A, Güngör H, Dokuyucu T, Akkaya A, Dumlupınar Z (June 1, 2022) ASSOCIATION MAPPING OF GERMINATION AND SOME EARLY SEEDLING STAGE TRAITS OF A TURKISH ORIGIN OAT COLLECTION. Turkish Journal Of Field Crops 27 1 41–50.
IEEE B. A. Koçak, “ASSOCIATION MAPPING OF GERMINATION AND SOME EARLY SEEDLING STAGE TRAITS OF A TURKISH ORIGIN OAT COLLECTION”, TJFC, vol. 27, no. 1, pp. 41–50, 2022, doi: 10.17557/tjfc.1022408.
ISNAD Koçak, Berk Abdullah et al. “ASSOCIATION MAPPING OF GERMINATION AND SOME EARLY SEEDLING STAGE TRAITS OF A TURKISH ORIGIN OAT COLLECTION”. Turkish Journal Of Field Crops 27/1 (June 2022), 41-50. https://doi.org/10.17557/tjfc.1022408.
JAMA Koçak BA, Kılınc F, Bardak A, Güngör H, Dokuyucu T, Akkaya A, Dumlupınar Z. ASSOCIATION MAPPING OF GERMINATION AND SOME EARLY SEEDLING STAGE TRAITS OF A TURKISH ORIGIN OAT COLLECTION. TJFC. 2022;27:41–50.
MLA Koçak, Berk Abdullah et al. “ASSOCIATION MAPPING OF GERMINATION AND SOME EARLY SEEDLING STAGE TRAITS OF A TURKISH ORIGIN OAT COLLECTION”. Turkish Journal Of Field Crops, vol. 27, no. 1, 2022, pp. 41-50, doi:10.17557/tjfc.1022408.
Vancouver Koçak BA, Kılınc F, Bardak A, Güngör H, Dokuyucu T, Akkaya A, Dumlupınar Z. ASSOCIATION MAPPING OF GERMINATION AND SOME EARLY SEEDLING STAGE TRAITS OF A TURKISH ORIGIN OAT COLLECTION. TJFC. 2022;27(1):41-50.

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