Molecular analysis of the gibberellin signaling pathway genes in cultivated rye (Secale cereale L.)
Abstract
Gibberellin signaling pathway genes encoding the DELLA protein and gibberellin receptor GID1 were sequenced in several varieties (Alpha, Valdai, Orlovskaya 9, Pracha) and one line of rye (EM-1) using next generation methods. The revealed multiple alleles of these genes differ mainly in single-nucleotide polymorphisms, and less frequently in insertions and deletions. Most of the detected mutations turned out to be synonymous or located in the non-coding regions of the genes. Changes in the amino acid sequences of proteins associated with other mutations are probably functionally neutral. Mutations similar to wheat reduced-height gibberellin-insensitive alleles were not detected.
About the Authors
M. S. Bazhenov
All-Russia Research Institute of Agricultural Biotechnology
Russian Federation
Russian Federation
Laboratory of Applied Genomics and Breeding of Agricultural Plants
Timiryazevskaya st. 42, Moscow, 127550
A. G. Chernook
All-Russia Research Institute of Agricultural Biotechnology
Russian Federation
Russian Federation
Laboratory of Applied Genomics and Breeding of Agricultural Plants
Timiryazevskaya st. 42, Moscow, 127550
M. G. Divashuk
All-Russia Research Institute of Agricultural Biotechnology; Russian State Agrarian University - Moscow Timiryazev Agricultural Academy
Russian Federation
Russian Federation
Laboratory of Applied Genomics and Breeding of Agricultural Plants, Center for Molecular Biotechnology
Timiryazevskaya st. 42, Moscow, 127550
Timiryazevskaya st. 49, Moscow, 127550
References
1. Schlegel R.H.J. Rye: genetics, breeding, and cultivation. CRC Press, 2013. 382 pp.
2. Davière J.-M., Achard P. Gibberellin signaling in plants // Development. 2013. Vol. 140. N 6. P. 1147–1151.
3. Peng J., Richards D.E., Hartley N.M., Murphy G.P., Devos K.M., Flintham J.E., Beales J., Fish L.J., Worland A.J., Pelica F., Sudhakar D., Christou P., Snape J.W., Gale M.D., Harberd N.P. ‘Green revolution’ genes encode mutant gibberellin response modulators // Nature. 1999. Vol. 400. N 6741. P. 256–261.
4. Pearce S., Saville R., Vaughan S.P., Chandler P.M., Wilhelm E.P., Sparks C.A., Al-Kaff N., Korolev A., Boulton M.I., Phillips A.L., Hedden P., Nicholson P., Thomas S.G. Molecular characterization of Rht-1 dwarfing genes in hexaploid wheat // Plant Physiol. 2011. Vol. 157. N 4. P. 1820–1831.
5. Yoshida H., Hirano K., Sato T., Mitsuda N., Nomoto M., Maeo K., Koketsu E., Mitani R., Kawamura M., Ishiguro S., Tada Y., Ohme-Takagi M., Matsuoka M., Ueguchi-Tanaka M. DELLA protein functions as a transcriptional activator through the DNA binding of the indeterminate domain family proteins // Proc. Natl. Acad. Sci. U.S.A. 2014. Vol. 111. N 21. P. 7861–7866.
6. Li S., Tian Y., Wu K., Ye Y., Yu J., Zhang J., Liu Q., Hu M., Li H., Tong Y., Harberd N.P., Fu X. Modulating plant growth–metabolism coordination for sustainable agriculture // Nature. 2018. Vol. 560. N 7720. P. 595–600.
7. Hirsch S., Oldroyd G.E. GRAS-domain transcription factors that regulate plant development //Plant Signal Behav. 2009. Vol. 4. N 8. P. 698–700.
8. Ueguchi-Tanaka M., Nakajima M., Katoh E., Ohmiya H., Asano K., Saji S., Hongyu X., Ashikari M., Kitano H., Yamaguchi I., Matsuoka M. Molecular interactions of a soluble gibberellin receptor, GID1, with a rice DELLA protein, SLR1, and gibberellin // Plant Cell. 2007. Vol. 19. N 7. P. 2140–2155.
9. Fu X., Richards D.E., Ait-Ali T., Hynes L.W., Ougham H., Peng J., Harberd N.P. Gibberellin-mediated proteasomedependent degradation of the barley DELLA protein SLN1 repressor // Plant Cell. 2002. Vol. 14. N 12. P. 3191–3200.
10. Börner A., Plaschke J., Korzun V., Worland A.J. The relationships between the dwarfing genes of wheat and rye // Euphytica. 1996. Vol. 89. N 1. P. 69–75.
11. Braun E.-M., Tsvetkova N., Rotter B., Siekmann D., Schwefel K., Krezdorn N., Plieske J., Winter P., Melz G., Voylokov Voylokov A.V., Hackauf B. Gene expression profiling and fine mapping identifies a gibberellin 2-oxidase gene co-segregating with the dominant dwarfing gene Ddw1 in rye (Secale cereale L.) // Front. Plant Sci. Frontiers. 2019. Vol. 10: 857.
12. Kantarek Z., Masojć P., Bienias A., Milczarski P. Identification of a novel, dominant dwarfing gene (Ddw4) and its effect on morphological traits of rye // PLoS ONE. 2018. Vol. 13. N 6: e0199335.
13. Grądzielewska A., Milczarski P., Molik K., Pawłowska E. Identification and mapping of a new recessive dwarfing gene dw9 on the 6RL rye chromosome and its phenotypic effects // PLOS ONE. 2020. Vol. 15. N 3: e0229564.
14. Doyle P.J. DNA protocols for plants // Molecular techniques in taxonomy / Eds. G.M.Hewitt, A.W.B. Johnston, and J.P.W. Young. Berlin–Heidelberg: Springer, 1991. P. 283–293.
15. Bauer E., Schmutzer T., Barilar I., et al. Towards a whole-genome sequence for rye (Secale cereale L.) // Plant J. 2017. Vol. 89. N 5. P. 853–869. 16. IPK Rye blast server [Electronic resource]. URL: https://webblast.ipk-gatersleben.de/ryeselect/ (accessed: 27.06.2020).
16. Razumova O.V., Bazhenov M.S., Nikitina E.A., Nazarova L.A., Romanov D.V., Chernook A.G., Sokolov P.A., Kuznetsova V.M., Semenov O.G., Karlov G.I., Kharchenko P.N., Divashuk M.G. Molecular analysis of gibberellin receptor gene GID1 in Dasypyrum villosum and development of DNA marker for its identification // RUDN J. Agron. Animal Ind. 2020. Vol. 15. N 1. P. 62–85.
17. Lischer H.E.L., Shimizu K.K. Reference-guided de novo assembly approach improves genome reconstruction for related species // BMC Bioinformatics. 2017. Vol. 18. N 1. P. 474.
18. Bankevich A., Nurk S., Antipov D., et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing // J. Comput. Biol. 2012. Vol. 19. N 5. P. 455–477.
19. Huang X., Madan A. CAP3: A DNA sequence assembly program // Genome Res. 1999. Vol. 9. N 9. P. 868–877.
20. Zaharia M., Bolosky W.J., Curtis K., Fox A., Patterson D., Shenker S., Stoica I., Karp R.M., Sittler T. Faster and more accurate sequence alignment with SNAP // arXiv:1111.5572 [cs, q-bio]. 2011.
21. Garrison E., Marth G. Haplotype-based variant detection from short-read sequencing // arXiv:1207.3907 [q-bio]. 2012.
22. Li H., Handsaker B., Wysoker A., Fennell T., Ruan J., Homer N., Marth G., Abecasis G., Durbin R., 1000 Genome Project Data Processing Subgroup. The sequence alignment/map format and SAMtools // Bioinformatics. 2009. Vol. 25. N 16. P. 2078–2079.
23. Nicholas K.B., Nikolas H.B., Jr. GeneDoc: a tool for editing and annotating multiple sequence alignments. Pittsburgh Supercomputing Center’s National Resource for Biomedical Supercomputing, 1997.
24. Choi Y., Chan A.P. PROVEAN web server: a tool to predict the functional effect of amino acid substitutions and indels // Bioinformatics. 2015. Vol. 31. N 16. P. 2745–2747.
25. NCBI Conserved Domain Search [Electronic resource]. URL: https://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi (accessed: 29.06.2020).
Review
For citations:
Bazhenov M.S., Chernook A.G., Divashuk M.G. Molecular analysis of the gibberellin signaling pathway genes in cultivated rye (Secale cereale L.). Vestnik Moskovskogo universiteta. Seriya 16. Biologiya. 2020;75(3):153-157. (In Russ.)
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