Molecular Characterization Of E1 And E3 Maturity Loci  Of Soybean [Glycine Max (L.) Merrill] Genotypes With  Contrasting Maturity

Manjushri Dongare; V P  Chimote; M P Deshmukh; A K Kale

doi:10.48165/

Authors

Manjushri Dongare State Level Biotechnology Centre, Mahatma Phule Krishi Vidyapeeth (M.P.K.V.), Rahuri, Ahmednagar – 413 732, Maharashtra (India)
V P Chimote State Level Biotechnology Centre, Mahatma Phule Krishi Vidyapeeth (M.P.K.V.), Rahuri, Ahmednagar – 413 732, Maharashtra (India)
M P Deshmukh Agricultural Research Station, M.P.K.V., Kasbe Digraj, Sangli – 416 305, Maharashtra (India)
A K Kale State Level Biotechnology Centre, Mahatma Phule Krishi Vidyapeeth (M.P.K.V.), Rahuri, Ahmednagar – 413 732, Maharashtra (India)

DOI:

https://doi.org/10.48165/

Keywords:

B3 conserved domain, maturity locus E1, phytochrome, soybean, SNPs

Abstract

Soybean has ten maturity loci governing its flowering time, maturity and photoperiodism. The E1 and E3 maturity loci delay maturity and induce photoperiod sensitivity, while their mutants are vice versa. In a field trial of 17 genotypes during kharif 2016, two early (JS 95-60 and JS 20-34) and two late maturing genotypes (MAUS 61 and MACS 1188) were identified for further molecular analysis. Full-length 525 bp E1 gene and partial 1688 bp E3 gene coding sequence were amplified, and sequence analysed along with reference sequence of early maturing Harosoy. In the partial E3 gene coding sequence studied, 26 substitution SNPs were observed, none of which was maturity specific. In E1 coding sequences, 87 substitution SNPs were observed, of which 17 SNPs were earliness specific conserved among JS 20-34, JS 95-60 and early Harosoy. Similarly, six amino acid frame polymorphisms were found to be earliness specific shared amongst them. Typical B3-like conserved domains with 11 trimeric DNA binding sites were found in the E1 gene within 172-504 and 178-504 bases interval intervals in early and late varieties, respectively. Thus, the molecular characterization of E1 maturity locus in local genotypes of soybean can contribute for more efficient plant breeding.

Downloads

Download data is not yet available.

References

Abe, J., Xu, D.H., Miyano, A., Komatsu, K., Kanazawa, A. and Shimamoto, Y. 2003. Photoperiod insensitive Japanese soybean landraces differ at two maturity loci. Crop Science, 43: 1300-1304. Artimo, P., Jonnalagedda, M., Arnold, K., Baratin, D., Csardi, G., De Castro, E., Duvaud, S., Flegel, V., Fortier, A., Gasteiger, E. and Grosdidier, A. 2012. ExPASy: SIB bioinformatics resource portal. Nucleic Acids Research, 40(W1): W597-W603.

Doyle, J.J. and Doyle, J.V. 1987. A rapid DNA isolation procedure for small quantity of fresh leaf tissue. Phytochemical Bulletin, 19: 11-15.

Gupta, S., Bhatia, V.S., Kumawat, G., Thakur, D., Singh, G., Tripathi, R., Satpute, G., Devadas, R., Husain, S.M. and Chand, S. 2017. Genetic analyses for deciphering the status and role of photoperiodic and maturity genes in major Indian soybean cultivars. Journal of Genetics, 96(1): 147-154.

Hou, Z., Liu, B. and Kong, F. 2022. Regulation of flowering and maturation in soybean. Advances in Botanical Research, 102: 43-75.

Johnson, M., Zaretskaya, I., Raytselis, Y., Merezhuk, Y., McGinnis, S. and Madden, T.L. 2008. NCBI BLAST: A better web interface. Nucleic Acids Research, 36(suppl.2): W5-W9. [https://doi.org/10.1093/nar/gkn201].

Kim, M., Shin, H., Kang, Y., Shim, S. and Lee, S. 2012. Divergence of flowering genes in soybean. Journal of Bioscience, 37(5): 857-870.

Kong, F.J., Liu, B.H., Xia, Z.J., Sato, S. and Kim, B.M. 2010. Two co-ordinately regulated homologs of flowering locus T are involved in control of photoperiodic flowering in soybean. Plant Physiology, 154: 1220-1231.

Langewisch, T., Lenis, J., Jiang, G.L., Wang, D., Pantalone, V. and Bilyeu, K. 2017. The development and use of a molecular model for soybean maturity groups. BMC Plant Biology, 17(1): 91. [https://doi.org/10.1186/s12870-017-1040-4].

Lin, X., Dong, L., Tang, Y., Li, H., Cheng, Q., Li, H., Zhang, T., Ma, L., Xiang, H., Chen, L. and Nan, H. 2022. Novel and multifaceted regulations of photoperiodic flowering by phytochrome

Manjushri Dongare et al.

A in soybean. Proceedings of the National Academy of Sciences, 119(41): p.e2208708119. [doi:10.1073/pnas.2208708119. Epub 2022 Oct 3. PMID: 36191205; PMCID: PMC9565047]. Lin, X., Liu, B., Weller, J.L., Abe, J. and Kong, F. 2021. Molecular mechanisms for the photoperiodic regulation of flowering in soybean. Journal of Integrative Plant Biology, 63(6): 981-994. Marchler-Bauer, A., Derbyshire, M.K., Gonzales, N.R., Lu, S., Chitsaz, F., Geer, L.Y., Geer, R.C., He, J., Gwadz, M., Hurwitz, D.I. and Lanczycki, C.J. 2015. CDD: NCBI's conserved domain database. Nucleic Acids Research, 43(D1): D222-D226.

No, D.H., Baek, D., Lee, S.H., Cheong, M.S., Chun, H.J., Park, M.S., Cho, H.M., Jin, B.J., Lim, L.H., Lee, Y.B. and Shim, S.I. 2021. High-temperature conditions promote soybean flowering through the transcriptional reprograming of flowering genes in photoperiod pathway. International Journal of Molecular Sciences, 2B2(3): 1314 [https://doi.org/10.3390/ijms22031314].

Roux, E., Touzet, P., Cuguen, J. and Corre, V.L. 2006. How to be early flowering: An evolutionary perspective. Trends in Plant Science, 11: 375-381.

Sievers, F. and Higgins, D.G. 2014. Clustal Omega, accurate alignment of very large numbers of sequences. pp. 105-116. In: Multiple Sequence Alignment Methods. Springer, [doi:10.1002/0471250953.bi0313s48].

Swaminathan, K., Peterson, K. and Jack, T. 2008. The plant B3 superfamily. Trends in Plant Science, 13: 647-655.

Tang, Y., Lu, S., Fang, C., Liu, H., Dong, L., Li, H., Su, T., Li, S., Wang, L., Cheng, Q. and Liu, B. 2022. Diverse flowering responses subjecting to ambient high temperature in soybean under short‐day conditions. Plant Biotechnology Journal, 21(4): 782-791.

Thakare, D., Kumudini, S. and Dinkins, R.D. 2011. The alleles at the E1 locus impact the expression pattern of two soybean FT like genes shown to induce flowering in Arabidopsis. Planta, 234: 933-943.

Tsubokura, Y., Watanabe, S., Xia, Z., Kanamori, H., Yamagata, H., Kaga, A., Katayose, Y., Abe, J., Ishimote, M. and Harada, K. 2014. Natural variation in the genes responsible for maturity loci E1, E2, E3 and E4 in soybean. Annals of Botany, 113: 429-411.

Watanabe, S., Harada, K. and Abe, J. 2012. Genetic and molecular bases of photoperiod responses of flowering in soybean. Breeding Science, 61: 531-543.

Watanabe, S., Hideshima, R., Xia, Z., Tsubokura, Y., Sato, S., Nakamoto, Y., Yamanaka, N., Takahashi, R., Ishimoto, M., Anai, T., Tabata, S. and Harada, K. 2009. Map-based cloning of the gene associated with the soybean maturity locus E3. Genetics, 182: 1251-1262.

Xia, Z., Watanabe, S., Yamadac, T., Tsubokurab, Y., Nakashimad, H., Zhaia, H., Anaid, T., Sato, S., Yamazakif, T., Lua, S., Wua, H., Tabatae, S. and Haradab, K. 2012. Positional cloning and characterization reveal the molecular basis for soybean maturity locus E1 that regulates photoperiodic flowering.Proceeding of the National Academy of Science (USA). 109: 2155-2164.

Xu, M., Xu, Z., Liu, B., Kong, F., Tasubokaru, Y., Watanabe, S., Xiu Z., Harada, K., Kanazawa, A., Yamada, T. and Abe, J. 2013. Genetic variation in four maturity genes affects photoperiod insensitivity and PHYA regulated post flowering responses in soybean. BMC Plant Biology, 13: 1-14.

Zhai, H., Lu, S., Wu, H., Zhang, Y., Zhang, X., Wang, Y., Yang, G., Cui, T. and Xia, Z. 2015. Diurnal expression pattern, allelic variation, and association analysis reveal functional feature of E1 gene in control of photoperiodic flowering in soybean. PLoS One, 10: 1-16.