Expressed sequence tag-based prediction of putative genes responsive to drought tolerance in rice (Oryza sativa) using in silico approach
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Published
Mar 7, 2023
Akula Dinesh
Borka Soundarya
B Muralidhara
K Jagadeesh
Abstract
In present genomic era, rapid genetic gains can be achieved by exploitation of novel genes associated with the trait of interest employing molecular breeding and genetic engineering. In the present study genes responsible for drought stress in rice 10746 expressed sequence tags (ESTs), expressed under drought stress condition were retrieved from the NCBI. The downloaded ESTs were clustered and assembled into 1120 contigs and 5559 singletones using CAP3 programme. The contigs were further subjected to identification of transcription factor, a total of 62 putative transcription factors were identified and sorted into 17 putative TF families. The contigs were subjected to BLASTX in NCBI to identify unique sequence which were further aligned to Oryza sativa Indica Group (ASM465v1) in gramene database using BLAT to retrieve the upstream and downstream sequences for putative gene identification. The retrieved sequences were analysed for transcription start site, PolyA tails and coding sequences which are essential features of gene using online tool fsgene. The present study found that, 46 contigs out of 1120 contigs has key gene structure and was considered as putative novel genes which may contribute to the drought tolerance in indica rice. These genes may be useful in development of drought tolerant varieties through smart breeding
How to Cite
Dinesh, A., Soundarya, B., Muralidhara, B., & Jagadeesh, K. (2023). Expressed sequence tag-based prediction of putative genes responsive to drought tolerance in rice (Oryza sativa) using in silico approach. Environment Conservation Journal, 24(2), 228–235. https://doi.org/10.36953/ECJ.12842364
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Keywords
BLAST EST Drought stress Gene prediction Rice
References
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Chukwu, S. C., Rafii, M. Y., Ramlee, S. I., Ismail, S. I., Hasan, M. M., Oladosu, Y. A., &Olalekan, K. K. (2019). Bacterial leaf blight resistance in rice: a review of conventional breeding to molecular approach. Molecular biology reports, 46(1), 1519-1532.
Czikkel, B. E., & Maxwell, D. P. (2007). NtGRAS1, a novel stress-induced member of the GRAS family in tobacco, localizes to the nucleus. Journal of plant physiology, 164(9), 1220-1230.
Goff, S. A., Ricke, D., Lan, T. H., Presting, G., Wang, R., Dunn, M., & Briggs, S. (2002). A draft sequence of the rice genome (Oryzasativa L. ssp. japonica). Science, 296(5565), 92-100.
Guo, J. W., Li, Q., Chen, W. Q., Li, X., Li, L. Q., Liu, T. G., &Luo, P. G. (2015). In silico cloning and chromosomal localization of EST sequences that are related to leaf senescence using nulli-tetrasomes in wheat. Cereal research communications, 43(3), 364-373.
Gupta, A., Rico-Medina, A., &Caño-Delgado, A. I. (2020).The physiology of plant responses to drought. Science, 368(6488), 266-269.
Huang, J., Wang, J. F., Wang, Q. H., & Zhang, H. S. (2005). Identification of a rice zinc finger protein whose expression is transiently induced by drought, cold but not by salinity and abscisic acid. DNA Sequence, 16(2), 130-136.
Huang, X., & Madan, A. (1999). CAP3: A DNA sequence assembly program. Genome research, 9(9), 868-877.
Kent, W. J. (2002). BLAT—the BLAST-like alignment tool. Genome research, 12(4), 656-664.
Kim, J. C., Lee, S. H., Cheong, Y. H., Yoo, C. M., Lee, S. I., Chun, H. J., & Cho, M. J. (2001). A novel cold‐inducible zinc finger protein from soybean, SCOF‐1, enhances cold tolerance in transgenic plants. The Plant Journal, 25(3), 247-259.
Kim, S. H., Ahn, Y. O., Ahn, M. J., Jeong, J. C., Lee, H. S., &Kwak, S. S. (2013). Cloning and characterization of an Orange gene that increases carotenoid accumulation and salt stress tolerance in transgenic sweetpotato cultures. Plant Physiology and Biochemistry, 70, 445-454.
Luo, J., Zhou, J. J., & Zhang, J. Z. (2018). Aux/IAA gene family in plants: molecular structure, regulation, and function. International Journal of Molecular Sciences, 19(1), 259.
Masoudi-Nejad, A., Tonomura, K., Kawashima, S., Moriya, Y., Suzuki, M., Itoh, M., & Goto, S. (2006). EGassembler: online bioinformatics service for large-scale processing, clustering and assembling ESTs and genomic DNA fragments. Nucleic acids research, 34(suppl_2), W459-W462.
Miura, K., Ashikari, M., & Matsuoka, M. (2011).The role of QTLs in the breeding of high-yielding rice. Trends in plant science, 16(6), 319-326.
Muthamilarasan, M., Bonthala, V. S., Mishra, A. K., Khandelwal, R., Khan, Y., Roy, R., & Prasad, M. (2014). C2H2 type of zinc finger transcription factors in foxtail millet define response to abiotic stresses. Functional & Integrative Genomics, 14(3), 531-543.
Nahas, L. D., Al-Husein,N., Lababidi, G., & Hamwieh,. (2019). A. In-silico prediction of novel genes responsive to drought and salinity stress tolerance in bread wheat (Triticum aestivum). PLoS One. 214(10):e022396
Nakashima, K., Ito, Y., & Yamaguchi-Shinozaki, K. (2009).Transcriptional regulatory networks in response to abiotic stresses in Arabidopsis and grasses. Plant physiology, 149(1), 88-95.
Nelson, D. E., Repetti, P. P., Adams, T. R., Creelman, R. A., Wu, J., Warner, D. C., & Heard, J. E. (2007). Plant nuclear factor Y (NF-Y) B subunits confer drought tolerance and lead to improved corn yields on water-limited acres. Proceedings of the National Academy of Sciences, 104(42), 16450-16455.
Ni, Z., Hu, Z., Jiang, Q., & Zhang, H. (2013). GmNFYA3, a target gene of miR169, is a positive regulator of plant tolerance to drought stress. Plant molecular biology, 82(1), 113-129.
Nuruzzaman, M., Sharoni, A. M., & Kikuchi, S. (2013). Roles of NAC transcription factors in the regulation of biotic and abiotic stress responses in plants. Frontiers in microbiology, 4, 248.
Oladosu, Y., Rafii, M. Y., Samuel, C., Fatai, A., Magaji, U., Kareem, I., & Kolapo, K. (2019). Drought resistance in rice from conventional to molecular breeding: a review. International journal of molecular sciences, 20(14), 3519.
Pandey, V., & Shukla, A. (2015). Acclimation and tolerance strategies of rice under drought stress. Rice Sci, 22(4), 147-161
Rollins, J. A., Habte, E., Templer, S. E., Colby, T., Schmidt, J., & Von Korff, M. (2013). Leaf proteome alterations in the context of physiological and morphological responses to drought and heat stress in barley (Hordeumvulgare L.). Journal of experimental botany, 64(11), 3201-3212.
Sahebi, M., Hanafi, M. M., Rafii, M. Y., Mahmud, T. M. M., Azizi, P., Osman, M., Abiri, R., Taheri, S., Kalhori, N., Shabanimofrad, M., Miah, G., & Atabaki, N. (2018). Improvement of Drought Tolerance in Rice (Oryza sativa): Genetics, Genomic Tools, and the WRKY Gene Family. Biomed Res Int, 3158474.
Salamov, A. A., &Solovyev, V. V. (2000).Ab initio gene finding in Drosophila genomic DNA. Genome research, 10(4), 516-522.
Sanchez, D. H., Pieckenstain, F. L., Szymanski, J., Erban, A., Bromke, M., Hannah, M. A., ...&Udvardi, M. K. (2011). Comparative functional genomics of salt stress in related model and cultivated plants identifies and overcomes limitations to translational genomics. PloS one, 6(2), e17094.
Shani, E., Salehin, M., Zhang, Y., Sanchez, S. E., Doherty, C., Wang, R., ...& Estelle, M. (2017). Plant stress tolerance requires auxin-sensitive Aux/IAA transcriptional repressors. Current Biology, 27(3), 437-444.
Singhal, P., Jan, A. T., Azam, M., &Haq, Q. M. R. (2016). Plant abiotic stress: a prospective strategy of exploiting promoters as alternative to overcome the escalating burden. Frontiers in Life Science, 9(1), 52-63.
Statista.(2021). https://www.statista.com/study/48366/India.
Su, H., Cao, Y., Ku, L., Yao, W., Cao, Y., Ren, Z., ...& Chen, Y. (2018). Dual functions of ZmNF-YA3 in photoperiod-dependent flowering and abiotic stress responses in maize. Journal of experimental botany, 69(21), 5177-5189.
Swamy, B. M., & Kumar, A. (2013). Genomics-based precision breeding approaches to improve drought tolerance in rice. Biotechnology advances, 31(8), 1308-1318.
Upadhyaya, H., & Panda, S. K. (2019).Drought stress responses and its management in rice.In Advances in rice research for abiotic stress tolerance (pp. 177-200).Woodhead Publishing.
Wang, H., Wang, H., Shao, H., & Tang, X. (2016). Recent advances in utilizing transcription factors to improve plant abiotic stress tolerance by transgenic technology. Frontiers in plant science, 7, 67.
Xu, K., Chen, S., Li, T., Ma, X., Liang, X., Ding, X., ...&Luo, L. (2015). OsGRAS23, a rice GRAS transcription factor gene, is involved in drought stress response through regulating expression of stress-responsive genes. BMC plant biology, 15(1), 1-13.
Yamaguchi, T. & Blumwald, E. (2005) Developing salt-tolerant crop plants: challenges and opportunities. Trends Plant Sci., 10 (12): 615-620
Yamaguchi-Shinozaki, K., & Shinozaki, K. (2006). Transcriptional regulatory networks in cellular responses and tolerance to dehydration and cold stresses. Annual review of plant biology, 57(1), 781-803.
Yang, X., Wang, B., Chen, L., Li, P., & Cao, C. (2019). The different influences of drought stress at the flowering stage on rice physiological traits, grain yield, and quality. Sci Rep, 9(1):1–2.
Yu, J., Hu, S., Wang, J., Wong, G. K. S., Li, S., Liu, B., & Yang, H. (2002). A draft sequence of the rice genome (Oryzasativa L. ssp. indica). Science, 296(5565), 79-92.
Yuan, Y., Fang, L., Karungo, S. K., Zhang, L., Gao, Y., Li, S., & Xin, H. (2016). Overexpression of VaPAT1, a GRAS transcription factor from Vitis amurensis, confers abiotic stress tolerance in Arabidopsis. Plant Cell Reports, 35(3), 655-666.
Zhang, A., Yang, X., Lu, J., Song, F., Sun, J., Wang, C., ..& Zhao, B. (2021). OsIAA20, an Aux/IAA protein, mediates abiotic stress tolerance in rice through an ABA pathway. Plant Science, 308, 110903.
Chow, C. N., Zheng, H. Q., Wu, N. Y., Chien, C. H., Huang, H. D., Lee, T. Y., & Chang, W. C. (2016). PlantPAN 2.0: an update of plant promoter analysis navigator for reconstructing transcriptional regulatory networks in plants. Nucleic acids research, 44(D1), D1154-D1160.
Chukwu, S. C., Rafii, M. Y., Ramlee, S. I., Ismail, S. I., Hasan, M. M., Oladosu, Y. A., &Olalekan, K. K. (2019). Bacterial leaf blight resistance in rice: a review of conventional breeding to molecular approach. Molecular biology reports, 46(1), 1519-1532.
Czikkel, B. E., & Maxwell, D. P. (2007). NtGRAS1, a novel stress-induced member of the GRAS family in tobacco, localizes to the nucleus. Journal of plant physiology, 164(9), 1220-1230.
Goff, S. A., Ricke, D., Lan, T. H., Presting, G., Wang, R., Dunn, M., & Briggs, S. (2002). A draft sequence of the rice genome (Oryzasativa L. ssp. japonica). Science, 296(5565), 92-100.
Guo, J. W., Li, Q., Chen, W. Q., Li, X., Li, L. Q., Liu, T. G., &Luo, P. G. (2015). In silico cloning and chromosomal localization of EST sequences that are related to leaf senescence using nulli-tetrasomes in wheat. Cereal research communications, 43(3), 364-373.
Gupta, A., Rico-Medina, A., &Caño-Delgado, A. I. (2020).The physiology of plant responses to drought. Science, 368(6488), 266-269.
Huang, J., Wang, J. F., Wang, Q. H., & Zhang, H. S. (2005). Identification of a rice zinc finger protein whose expression is transiently induced by drought, cold but not by salinity and abscisic acid. DNA Sequence, 16(2), 130-136.
Huang, X., & Madan, A. (1999). CAP3: A DNA sequence assembly program. Genome research, 9(9), 868-877.
Kent, W. J. (2002). BLAT—the BLAST-like alignment tool. Genome research, 12(4), 656-664.
Kim, J. C., Lee, S. H., Cheong, Y. H., Yoo, C. M., Lee, S. I., Chun, H. J., & Cho, M. J. (2001). A novel cold‐inducible zinc finger protein from soybean, SCOF‐1, enhances cold tolerance in transgenic plants. The Plant Journal, 25(3), 247-259.
Kim, S. H., Ahn, Y. O., Ahn, M. J., Jeong, J. C., Lee, H. S., &Kwak, S. S. (2013). Cloning and characterization of an Orange gene that increases carotenoid accumulation and salt stress tolerance in transgenic sweetpotato cultures. Plant Physiology and Biochemistry, 70, 445-454.
Luo, J., Zhou, J. J., & Zhang, J. Z. (2018). Aux/IAA gene family in plants: molecular structure, regulation, and function. International Journal of Molecular Sciences, 19(1), 259.
Masoudi-Nejad, A., Tonomura, K., Kawashima, S., Moriya, Y., Suzuki, M., Itoh, M., & Goto, S. (2006). EGassembler: online bioinformatics service for large-scale processing, clustering and assembling ESTs and genomic DNA fragments. Nucleic acids research, 34(suppl_2), W459-W462.
Miura, K., Ashikari, M., & Matsuoka, M. (2011).The role of QTLs in the breeding of high-yielding rice. Trends in plant science, 16(6), 319-326.
Muthamilarasan, M., Bonthala, V. S., Mishra, A. K., Khandelwal, R., Khan, Y., Roy, R., & Prasad, M. (2014). C2H2 type of zinc finger transcription factors in foxtail millet define response to abiotic stresses. Functional & Integrative Genomics, 14(3), 531-543.
Nahas, L. D., Al-Husein,N., Lababidi, G., & Hamwieh,. (2019). A. In-silico prediction of novel genes responsive to drought and salinity stress tolerance in bread wheat (Triticum aestivum). PLoS One. 214(10):e022396
Nakashima, K., Ito, Y., & Yamaguchi-Shinozaki, K. (2009).Transcriptional regulatory networks in response to abiotic stresses in Arabidopsis and grasses. Plant physiology, 149(1), 88-95.
Nelson, D. E., Repetti, P. P., Adams, T. R., Creelman, R. A., Wu, J., Warner, D. C., & Heard, J. E. (2007). Plant nuclear factor Y (NF-Y) B subunits confer drought tolerance and lead to improved corn yields on water-limited acres. Proceedings of the National Academy of Sciences, 104(42), 16450-16455.
Ni, Z., Hu, Z., Jiang, Q., & Zhang, H. (2013). GmNFYA3, a target gene of miR169, is a positive regulator of plant tolerance to drought stress. Plant molecular biology, 82(1), 113-129.
Nuruzzaman, M., Sharoni, A. M., & Kikuchi, S. (2013). Roles of NAC transcription factors in the regulation of biotic and abiotic stress responses in plants. Frontiers in microbiology, 4, 248.
Oladosu, Y., Rafii, M. Y., Samuel, C., Fatai, A., Magaji, U., Kareem, I., & Kolapo, K. (2019). Drought resistance in rice from conventional to molecular breeding: a review. International journal of molecular sciences, 20(14), 3519.
Pandey, V., & Shukla, A. (2015). Acclimation and tolerance strategies of rice under drought stress. Rice Sci, 22(4), 147-161
Rollins, J. A., Habte, E., Templer, S. E., Colby, T., Schmidt, J., & Von Korff, M. (2013). Leaf proteome alterations in the context of physiological and morphological responses to drought and heat stress in barley (Hordeumvulgare L.). Journal of experimental botany, 64(11), 3201-3212.
Sahebi, M., Hanafi, M. M., Rafii, M. Y., Mahmud, T. M. M., Azizi, P., Osman, M., Abiri, R., Taheri, S., Kalhori, N., Shabanimofrad, M., Miah, G., & Atabaki, N. (2018). Improvement of Drought Tolerance in Rice (Oryza sativa): Genetics, Genomic Tools, and the WRKY Gene Family. Biomed Res Int, 3158474.
Salamov, A. A., &Solovyev, V. V. (2000).Ab initio gene finding in Drosophila genomic DNA. Genome research, 10(4), 516-522.
Sanchez, D. H., Pieckenstain, F. L., Szymanski, J., Erban, A., Bromke, M., Hannah, M. A., ...&Udvardi, M. K. (2011). Comparative functional genomics of salt stress in related model and cultivated plants identifies and overcomes limitations to translational genomics. PloS one, 6(2), e17094.
Shani, E., Salehin, M., Zhang, Y., Sanchez, S. E., Doherty, C., Wang, R., ...& Estelle, M. (2017). Plant stress tolerance requires auxin-sensitive Aux/IAA transcriptional repressors. Current Biology, 27(3), 437-444.
Singhal, P., Jan, A. T., Azam, M., &Haq, Q. M. R. (2016). Plant abiotic stress: a prospective strategy of exploiting promoters as alternative to overcome the escalating burden. Frontiers in Life Science, 9(1), 52-63.
Statista.(2021). https://www.statista.com/study/48366/India.
Su, H., Cao, Y., Ku, L., Yao, W., Cao, Y., Ren, Z., ...& Chen, Y. (2018). Dual functions of ZmNF-YA3 in photoperiod-dependent flowering and abiotic stress responses in maize. Journal of experimental botany, 69(21), 5177-5189.
Swamy, B. M., & Kumar, A. (2013). Genomics-based precision breeding approaches to improve drought tolerance in rice. Biotechnology advances, 31(8), 1308-1318.
Upadhyaya, H., & Panda, S. K. (2019).Drought stress responses and its management in rice.In Advances in rice research for abiotic stress tolerance (pp. 177-200).Woodhead Publishing.
Wang, H., Wang, H., Shao, H., & Tang, X. (2016). Recent advances in utilizing transcription factors to improve plant abiotic stress tolerance by transgenic technology. Frontiers in plant science, 7, 67.
Xu, K., Chen, S., Li, T., Ma, X., Liang, X., Ding, X., ...&Luo, L. (2015). OsGRAS23, a rice GRAS transcription factor gene, is involved in drought stress response through regulating expression of stress-responsive genes. BMC plant biology, 15(1), 1-13.
Yamaguchi, T. & Blumwald, E. (2005) Developing salt-tolerant crop plants: challenges and opportunities. Trends Plant Sci., 10 (12): 615-620
Yamaguchi-Shinozaki, K., & Shinozaki, K. (2006). Transcriptional regulatory networks in cellular responses and tolerance to dehydration and cold stresses. Annual review of plant biology, 57(1), 781-803.
Yang, X., Wang, B., Chen, L., Li, P., & Cao, C. (2019). The different influences of drought stress at the flowering stage on rice physiological traits, grain yield, and quality. Sci Rep, 9(1):1–2.
Yu, J., Hu, S., Wang, J., Wong, G. K. S., Li, S., Liu, B., & Yang, H. (2002). A draft sequence of the rice genome (Oryzasativa L. ssp. indica). Science, 296(5565), 79-92.
Yuan, Y., Fang, L., Karungo, S. K., Zhang, L., Gao, Y., Li, S., & Xin, H. (2016). Overexpression of VaPAT1, a GRAS transcription factor from Vitis amurensis, confers abiotic stress tolerance in Arabidopsis. Plant Cell Reports, 35(3), 655-666.
Zhang, A., Yang, X., Lu, J., Song, F., Sun, J., Wang, C., ..& Zhao, B. (2021). OsIAA20, an Aux/IAA protein, mediates abiotic stress tolerance in rice through an ABA pathway. Plant Science, 308, 110903.
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