Application of GBS profiling in ornamental plants

Samiei, leila; hadizadeh, hanieh

doi:10.52547/flowerjournal.6.2.95

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Volume 6, Issue 2 (Fall and Winter 2021)

FOP 2021, 6(2): 95-106

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Application of GBS profiling in ornamental plants

Leila Samiei ^*

, Hanieh Hadizadeh

ferdowsi University of Mashhad

Abstract: (1740 Views)

The lack of sufficient genomic information of ornamental plants besides their polyploidy and large genome size are the main challenges ahead of their molecular breeding. Next-generation sequencing (NGS) is a viable method capable of developing a large number of DNA markers in a short course of time. Currently, single-nucleotide polymorphisms (SNPs) are recognized as one of the most studied and popular DNA markers using for various purposes in plant breeding. GBS (genotyping-by-sequencing) approach is one of the leading techniques that has emerged to evaluate the molecular characteristics of plants possessing complex or non-sequenced genomes using SNP markers. This method has so far been used for breeding and germplasm evaluation of some ornamental plant species including Rosa, Petunia, Hydrangea, and Gloxinia. Among these studies, one study is done to perform GWAS on Hydrangea macrophylla L., ten studies to investigate the genetic diversity of various ornamental species including Gloxinia, Dendrobium orchid, as well as ornamental trees Franklinia alatamaha Marshall and Cornus florida L., four studies to construct and elaborate the genetic map of plants species including Rosa and Petunia, three studies to develop molecular markers in rose, lilac and Hydrangea species and one study to investigate the genetic diversity within and between Iranian Eremurus spp. This is a potential method for examination of genetic diversity of plants, assembling high density genetic linkage maps, discovering the required molecular markers in QTL and GWAS studies, and verifying candidate genes including genes controlling the flowering process. Owing to the high efficiency and accuracy as well as the low cost per marker of this method compared to other genotyping techniques, GBS can be widely used in genetic studies, sequencing and breeding of ornamental plants.

Keywords: Next generation sequencing, Genotyping-by-sequencing, Ornamental plants, Molecular markers

Full-Text [PDF 515 kb] (724 Downloads)

Type of Study: Review | Subject: Special
Received: 2021/04/26 | Accepted: 2021/09/13 | Published: 2022/02/25

References

1. Ahrens, C.W., Supple, M.A., Aitken, N.C., Cantrill, D.J., Borevitz, J.O., James, E.A. (2017). Genomic diversity guides conservation strategies among rare terrestrial orchid species when taxonomy remains uncertain. Annals of Botany, 119(8), 1267-1277. [DOI:10.1093/aob/mcx022]

2. Bagheri, H., Saki, S. (2017). Requirements and guidelines for the preservation of genetic resources of ornamental plants in Iran. Journal of Flower and Ornamental Plants, 1(2), 24-33 (In Persian).

3. Beissinger, T.M., Hirsch, C.N., Sekhon, R.S., Foerster, J.M., Johnson, J.M., Muttoni, G., de Leon, N. (2013). Marker density and read depth for genotyping populations using genotyping-by-sequencing. Genetics, 193(4), 1073-1081. [DOI:10.1534/genetics.112.147710]

4. Buti, M., Sargent, D.J., Mhelembe, K.G., Delfino, P., Tobutt, K.R., Velasco, R. (2016). Genotyping-by-sequencing in an orphan plant species Physocarpus opulifolius helps identify the evolutionary origins of the genus Prunus. BMC Research Notes, 9(1), 268-276. [DOI:10.1186/s13104-016-2069-4]

5. Chen, H., Lattier, J.D., Vining, K., Contreras, R.N. (2020). Two SNP markers identified using genotyping-by-sequencing are associated with remontancy in a segregating F1 population of Syringa meyeri 'Palibin'× S. pubescens 'Penda'Bloomerang®. Journal of the American Society for Horticultural Science, 145(2), 104-109. [DOI:10.21273/JASHS04847-20]

6. Chen, W., Hou, L., Zhang, Z., Pang, X., Li, Y. (2017). Genetic diversity, population structure, and linkage disequilibrium of a core collection of Ziziphus jujuba assessed with genome-wide SNPs developed by genotyping-by-sequencing and SSR markers. Frontiers in Plant Science, 8, 575. [DOI:10.3389/fpls.2017.00575]

7. Davey, J.W, Hohenlohe, P.A, Etter, P.D, Boone, J.Q, Catchen, J.M. (2011). Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nature Reviews Genetics, 12 (7): 499-510. [DOI:10.1038/nrg3012]

8. Deschamps, S., Llaca, V., May, G.D. Genotyping-by-sequencing in plants. (2012). Biology. 1(3), 460-483. [DOI:10.3390/biology1030460]

9. Elshire, R.J. Glaubits, J.C., Sun, Q., Poland, J.A., Kawamoto, K., Buckler, E.S., Mitchell, S.E. (2011). A robust, simple genotyping by sequencing approach for high diversity species. PLoSONE, 6(5), e19379. [DOI:10.1371/journal.pone.0019379]

10. Fu, Y.B., Cheng, B., Peterson, G.W. (2014). Genetic diversity analysis of yellow mustard (Sinapis alba L.) germplasm based on genotyping by sequencing. Genetic Resources and Crop Evolution, 61(3), 579-594 [DOI:10.1007/s10722-013-0058-1]

11. Gladfelter, H.J., Yadav, L.K., Merkle, S.A., Wilde, H.D. (2020). Genetic diversity and population structure analysis of Franklinia alatamaha, a tree species existing only in cultivation. Tree Genetics & Genomes, 16(4), 1-9. [DOI:10.1007/s11295-020-01455-x]

12. Guo, Y., Lin, W.K., Chen, Q., Vallejo, V.A., Warner, R.M. (2017). Genetic determinants of crop timing and quality traits in two interspecific Petunia recombinant inbred line populations. Scientific Reports, 7(1), 1-12 [DOI:10.1038/s41598-017-03528-9]

13. Hadizadeh, H., Bahri, B.A., Qi, P., Wilde, H.D., Devos, K.M. (2020). Intra-and interspecific diversity analyses in the genus Eremurus in Iran using genotyping-by-sequencing reveal geographic population structure. Horticulture Research, 7(1), 1-13. [DOI:10.1038/s41438-020-0265-9]

14. Hasing, T., Rinaldi, E., Manrique, S., Colombo, L., Haak, D., Zaitlin, D., Bobarely, A. (2019). Extensive phenotypic diversity in the cultivated Florist's Gloxinia, Sinningia speciosa (Lodd.) Hiern, is derived from the domestication of a single founder population. Plants, People, Planet Journal, 1 (4), 363-374. [DOI:10.1002/ppp3.10065]

15. He, J., Zhao, X., Laroche, A., Lu, Zh., Liu, H., Li., Z. (2014). Genotyping-by-sequencing (GBS), an ultimate marker-assisted selection (MAS) tool to accelerate plant breeding. Frontiers in Plant Science, 5, 484 [DOI:10.3389/fpls.2014.00484]

16. Heo, M.S., Han, K., Kwon, J.K., Kang, B.C. (2017). Development of SNP markers using genotyping-by sequencing for cultivar identification in rose (Rosa hybrida). Horticulture, Environment, and Biotechnology, 58(3), 292-302. [DOI:10.1007/s13580-017-0268-0]

17. Myles, S., Peiffer, J., Brown, P.J., Ersoz, E.S., Zhang, Z., Costich, D.E., Buckler, E.S. (2009). Association mapping: critical considerations shift from genotyping to experimental design. The Plant Cell, 21(8), 2194-2202. [DOI:10.1105/tpc.109.068437]

18. Novembre, J. (2014). Variations on a common STRUCTURE: new algorithms for a valuable model. Genetics, 197(3), 809-811. [DOI:10.1534/genetics.114.166264]

19. Pais, A.L., Whetten, R.W., Xiang, Q.J. (2016). Ecological genomics of local adaptation in Cornus florida L. by genotyping by sequencing. Ecology and Evolution, 7(1): 441-465. [DOI:10.1002/ece3.2623]

20. Peterson, G.W., Dong, Y., Horbach, C., Fu, Y.B. (2014). Genotyping-by-sequencing for plant genetic diversity analysis: a lab guide for SNP genotyping. Diversity, 6(4), 665-680. [DOI:10.3390/d6040665]

21. Poland, J.A., Rife, T.W. (2012). Genotyping-by-sequencing for plant breeding and genetics. Plant Genome. 5: 92-102. [DOI:10.3835/plantgenome2012.05.0005]

22. Qi, P., Gimode, D., Saha, D., Schröder, S., Chakraborty, D., Wang, X., Devos, K.M. (2018). UGbS-Flex, a novel bioinformatics pipeline for imputation-free SNP discovery in polyploids without a reference genome: finger millet as a case study. BMC Plant Biology, 18(1), 1-19. [DOI:10.1186/s12870-018-1316-3]

23. Rabinowicz, P.D., Citek, R., Budiman, M.A., Nunberg, A., Bedell, J.A., Lakey, N., O'Shaughnessy, A.L., Nascimento, L.U., McCombie, W.R., Martienssen, R.A. (2005). Differential methylation of genes and repeats in land plants. Genome Research, 15, 1431-1440. [DOI:10.1101/gr.4100405]

24. Rafalski, J.A. (2010). Association genetics in crop improvement. Current Opinion in Plant Biology, 13(2), 174-180. [DOI:10.1016/j.pbi.2009.12.004]

25. Ryu, J., Kim, W. J., Im, J., Kang, K.W., Kim, S.H., Jo, Y.D., Ha, B.K. (2019). Single nucleotide polymorphism (SNP) discovery through genotyping-by-sequencing (GBS) and genetic characterization of Dendrobium mutants and cultivars. Scientia Horticulturae, 244, 225-233. [DOI:10.1016/j.scienta.2018.09.053]

26. Smulders, M.J., Arens, P. (2018). New Developments in Molecular Techniques for Breeding in Ornamentals. In Ornamental Crops. Johan Van Huylenbroeck. (pp. 213-230). Springer, Cham. [DOI:10.1007/978-3-319-90698-0_9]

27. Tamaki, I., Yoichi, W., Matsuki, Y., Suyama, Y., Mizuno, M. (2017). Inconsistency between morphological traits and ancestry of individuals in the hybrid zone between two Rhododendron japonoheptamerum varieties revealed by a genotyping-by-sequencing approach. Tree Genetics & Genomes, 13(1), 1-10. [DOI:10.1007/s11295-016-1084-x]

28. Tränkner, C., Krüger, J., Wanke, S., Naumann, J., Wenke, T., Engel, F. (2019). Rapid identification of inflorescence type markers by genotyping-by-sequencing of diploid and triploid F 1 plants of Hydrangea macrophylla. BMC Genetics, 20(1), 1-12. [DOI:10.1186/s12863-019-0764-6]

29. Wu, X., Alexander, L. (2019). Genetic diversity and population structure analysis of Bigleaf Hydrangea using genotyping by sequencing. Journal of the American Society for Horticultural Science, 144 (4), 257-263 [DOI:10.21273/JASHS04683-19]

30. Wu, X., Alexander, L.W. (2020). Genome-wide association studies for inflorescence type and remontancy in Hydrangea macrophylla. Horticulture Research, 7(1), 1-9. [DOI:10.1038/s41438-020-0255-y]

31. Yadav, L.K., McAssey, E.V., Wilde, H.D. (2019). Genetic diversity and population structure of Rhododendron canescens, a native Azalea for urban landscaping. HortScience, 54(4), 647-651. [DOI:10.21273/HORTSCI13840-18]

32. Yagi, M. (2015). Recent progress in genomic analysis of ornamental plants, with a focus on carnation. The Horticulture Journal, 84(1), 3-13. [DOI:10.2503/hortj.MI-IR01]

33. Yan, M. Byrne, David, H. Klein, P., Yang, J., Dong, Q. (2018). Genotyping-by-sequencing application on diploid rose and a resulting high-density SNP-based consensus map. Horticulture Research, 5(17), 1-14. [DOI:10.1038/s41438-018-0021-6]

34. Yoichi, W., Kawamata, I., Matsuki, Y., Suyama, Y., Uehara, K., Ito, M. (2018). Phylogeographic analysis suggests two origins for the riparian azalea Rhododendron indicum (L.) Sweet. Heredity, 121(6), 594-604. [DOI:10.1038/s41437-018-0064-3]

35. Zhang, L., Guo, D., Guo, L., Guo, Q., Wang, H., Hou, X. (2019). Construction of a high-density genetic map and QTLs mapping with GBS from the interspecific F1 population of P. ostii 'Fengdan Bai'and P. suffruticosa 'Xin Riyuejin'. Scientia Horticulturae, 246, 190-200. [DOI:10.1016/j.scienta.2018.10.039]

36. • Ahrens, C. W., Supple, M. A., Aitken, N. C., Cantrill, D. J., Borevitz, J. O., & James, E. A. (2017). Genomic diversity guides conservation strategies among rare terrestrial orchid species when taxonomy remains uncertain. Annals of botany, 119(8), 1267-1277. [DOI:10.1093/aob/mcx022]

37. • Buti, M., Sargent, D. J., Mhelembe, K. G., Delfino, P., Tobutt, K. R., & Velasco, R. (2016). Genotyping-by-sequencing in an orphan plant species Physocarpus opulifolius helps identify the evolutionary origins of the genus Prunus. BMC research notes, 9(1), 268-276. [DOI:10.1186/s13104-016-2069-4]

38. • Chen, H., Lattier, J. D., Vining, K., & Contreras, R. N. (2020). Two SNP Markers Identified Using Genotyping-by-Sequencing Are Associated with Remontancy in a Segregating F1 Population of Syringa meyeri 'Palibin'× S. pubescens 'Penda'Bloomerang®. . Journal of the American Society for Horticultural Science, 145(2), 104-109. [DOI:10.21273/JASHS04847-20]

39. • Davey, J.W, Hohenlohe, P.A, Etter, P.D, Boone, J.Q, Catchen, J. M. (2011). Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nature Reviews Genetics. 12 (7): 499-510. [DOI:10.1038/nrg3012]

40. • Deschamps, S., Llaca, V. & May, G. D. Genotyping-by-Sequencing in Plants. (2012). Biology. 1(3), 460-483. [DOI:10.3390/biology1030460]

41. • Elshire, R. J. Glaubits, J. C., Sun, Q., Poland, J. A., Kawamoto, K., Buckler, E. S. and Mitchell, S. E. (2011). A robust, simple genotyping by sequencing approach for high diversity species. PLoSONE. 6 (5), e19379. [DOI:10.1371/journal.pone.0019379]

42. • Gladfelter, H. J., Yadav, L. K., Merkle, S. A., & Wilde, H. D. (2020). Genetic diversity and population structure analysis of Franklinia alatamaha, a tree species existing only in cultivation. Tree Genetics & Genomes, 16(4), 1-9. [DOI:10.1007/s11295-020-01455-x]

43. • Guo, Y., Lin, W. K., Chen, Q., Vallejo, V. A., & Warner, R. M. (2017). Genetic determinants of crop timing and quality traits in two interspecific Petunia recombinant inbred line populations. Scientific reports, 7(1), 1-12 [DOI:10.1038/s41598-017-03528-9]

44. • Hadizadeh, H., Bahri, B. A., Qi, P., Wilde, H. D., & Devos, K. M. (2020). Intra-and interspecific diversity analyses in the genus Eremurus in Iran using genotyping-by-sequencing reveal geographic population structure. Horticulture research, 7(1), 1-13. [DOI:10.1038/s41438-020-0265-9]

45. • Hasing, T., Rinaldi, E., Manrique, S., Colombo, L., Haak, D., Zaitlin, D. and Bobarely, A. (2019). Extensive phenotypic diversity in the cultivated Florist's Gloxinia, Sinningia speciosa (Lodd.) Hiern, is derived from the domestication of a single founder population. Plants, People, Planet journal.1 (4), 363-374. [DOI:10.1002/ppp3.10065]

46. • He, J., Zhao, X., Laroche, A., Lu, Zh., Liu, H., and Li., Z. (2014). Genotyping-by-sequencing (GBS), an ultimate marker-assisted selection (MAS) tool to accelerate plant breeding. Frontiers in plant science. 5: 484 [DOI:10.3389/fpls.2014.00484]

47. • Heo, M.S., Han, K., Kwon, J.K., & Kang, B.C. (2017). Development of SNP markers using genotyping-by sequencing for cultivar identification in rose (Rosa hybrida). Horticulture, Environment, and Biotechnology, 58(3), 292-302. [DOI:10.1007/s13580-017-0268-0]

48. • Pais, A. L., Whetten, R. W., & Xiang, Q. J. (2016). Ecological genomics of local adaptation in Cornus florida L. by genotyping by sequencing. Ecology and Evolution. 7(1): 441-465. [DOI:10.1002/ece3.2623]

49. • Poland, J. A. and Rife, T. W. (2012). Genotyping-by-sequencing for plant breeding and genetics. Plant genome. 5: 92-102. [DOI:10.3835/plantgenome2012.05.0005]

50. • Rabinowicz, P. D., Citek, R., Budiman, M. A., Nunberg, A., Bedell, J. A., Lakey, N., O'Shaughnessy, A. L., Nascimento, L. U., McCombie, W. R., Martienssen, R. A. (2005). Differential methylation of genes and repeats in land plants. Genome Research.15: 1431-1440. [DOI:10.1101/gr.4100405]

51. • Ryu, J., Kim, W. J., Im, J., Kang, K. W., Kim, S. H., Jo, Y. D., ... & Ha, B. K. (2019). Single nucleotide polymorphism (SNP) discovery through genotyping-by-sequencing (GBS) and genetic characterization of Dendrobium mutants and cultivars. Scientia Horticulturae, 244, 225-233. [DOI:10.1016/j.scienta.2018.09.053]

52. • Smulders, M. J., & Arens, P. (2018). New developments in molecular techniques for breeding in ornamentals. In Ornamental Crops (pp. 213-230). Springer, Cham. [DOI:10.1007/978-3-319-90698-0_9]

53. • Tamaki, I., Yoichi, W., Matsuki, Y., Suyama, Y., & Mizuno, M. (2017). Inconsistency between morphological traits and ancestry of individuals in the hybrid zone between two Rhododendron japonoheptamerum varieties revealed by a genotyping-by-sequencing approach. Tree Genetics & Genomes, 13(1), 1-10. [DOI:10.1007/s11295-016-1084-x]

54. • Tränkner, C., Krüger, J., Wanke, S., Naumann, J., Wenke, T., & Engel, F. (2019). Rapid identification of inflorescence type markers by genotyping-by-sequencing of diploid and triploid F 1 plants of Hydrangea macrophylla. BMC genetics, 20(1), 1-12. [DOI:10.1186/s12863-019-0764-6]

55. • Wu, X and Alexander, L. (2019). Genetic diversity and population structure analysis of Bigleaf Hydrangea using genotypinf by sequencing. Journal of the American society for horticultural science. 144 (4). 257-263 [DOI:10.21273/JASHS04683-19]

56. • Wu, X., & Alexander, L. W. (2020). Genome-wide association studies for inflorescence type and remontancy in Hydrangea macrophylla. Horticulture research, 7(1), 1-9. [DOI:10.1038/s41438-020-0255-y]

57. • Yadav, L. K., McAssey, E. V., & Wilde, H. D. (2019). Genetic Diversity and Population Structure of Rhododendron canescens, a Native Azalea for Urban Landscaping. HortScience, 54(4), 647-651. [DOI:10.21273/HORTSCI13840-18]

58. • Yagi, M. (2015). Recent progress in genomic analysis of ornamental plants, with a focus on carnation. The Horticulture Journal, 84(1), 3-13. [DOI:10.2503/hortj.MI-IR01]

59. • Yan, M. Byrne, David, H. Klein, P., Yang, J., Dong, Q. (2018). Genotyping-by-sequencing application on diploid rose and a resulting high-density SNP-based consensus map. Horticulture Research. 5(17), 1-14. [DOI:10.1038/s41438-018-0021-6]

60. • Yoichi, W., Kawamata, I., Matsuki, Y., Suyama, Y., Uehara, K., & Ito, M. (2018). Phylogeographic analysis suggests two origins for the riparian azalea Rhododendron indicum (L.) Sweet. Heredity, 121(6), 594-604. [DOI:10.1038/s41437-018-0064-3]

61. • Zhang, L., Guo, D., Guo, L., Guo, Q., Wang, H., & Hou, X. (2019). Construction of a high-density genetic map and QTLs mapping with GBS from the interspecific F1 population of P. ostii 'Fengdan Bai'and P. suffruticosa 'Xin Riyuejin'. Scientia Horticulturae, 246, 190-200. [DOI:10.1016/j.scienta.2018.10.039]

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