Transcriptome Analysis from leaf during non-flowering vegetative growth phase of mango (Mangifera indica L. var Fazli) from Murshidabad district of West Bengal, India.
Abstract
Mango (Mangifera indica L.) is a major fruit crop in numerous tropical and subtropical countries, facing various problems such as susceptibility to diseases, bi-annual production, low yield and a brief shelf life of the fruit, in cultivation. Traditional breeding methods have limited success in improving the quality of this fruit crop due to prolonged time of maturity, self-incompatibility and high degree of heterozygosity in breeding lines. However, recent studies utilizing genomic analysis have identified key genes responsible for economically important characters, suggesting the possibility of Marker Assisted Selection (MAS) in breeding lines through transgenic or specific genotype selection from seedlings. With the rapid advancements in genome sequencing and bioinformatics, it is now feasible to identify, label, clone, and manipulate numerous genes related to economically important characters. While research on the flowering and fruiting of mango has been extensive, research studies to preliminarily identify the functions of mango genes during the vegetative growth phase is very few. The major findings include few highly active genes viz. WRKY, NAM, MYB, GoGID1 which is channelizing the energy towards vegetative growth and inhibit flowering genes.
Keywords:
Fazli, Mango, MYB, Transcriptomics, West Bengal, WRKY
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References
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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. https://doi.org/10.1093/nar/gkv1035
De, M., Das, J., Saha, M., Pal, A., & Dey, S. R. (2014). Documentation and Characterization of the Indigenous Mango (Mangifera indica L.) varieties of Malda and Murshidabad districts of West Bengal. J. Environ. & Sociobiol, 11(2), 187-198.
De, M., Dutta, S., Pahari, G. K., Ganguli, S., Ray, S., & Dey, S. R. (2019). Variation in flowering and fruit set among indigenous mango varieties from Malda and Murshidabad conserved as Field Gene Bank in Gurudas College, Kolkata, India. International Journal of Advancement in Life Sciences Research, 2(4)48-61. https://doi.org/10.31632/ijalsr.2019v02i04.006
De, M., Dutta, S., Ray, S., & Dey, S. R. (2021b). Visual Clustering Analysis of some traditional Mango (Mangifera indica L.) varieties of Murshidabad District, West Bengal using Clust Vis web tool. International Journal of Advancement in Life Sciences Research, 4 (3), 42-43. https://doi.org/10.31632/ijalsr.2019v02i04.006
De, M., Pahari, G., Pal, A., Ganguli, S., Ray, S., Mandal, M., Dhar, S., Dutta, S., & Dey, S. (2019). Mango (Mangifera indica L.) field gene bank (FGB) in Gurudas College, Kolkata-54. Int. J. Exp. Res. Rev., 18, 6-14.
De, M., Ray, S., Dutta, S., & Dey, S. R. (2021). Eugenol Found by GC-MS Analysis of The Methanolic Extract of The Fruit Pulp of Indigenous Mango (Mangifera indica L.) Variety, Champa from Murshidabad District of West Bengal, India. International Journal of Advancement in Life Sciences Research, 4(1), 22-30. https://doi.org/10.31632/ijalsr.20.v04i01.004
De, Mitu and Dey, S. R., (2021c). Assessment of the pulp quality of some rare indigenous mango (Mangifera indica L.) varieties of West Bengal, India. International Journal of Experimental Research and Review, 26, 70-78. https://doi.org/10.52756/ijerr.2021.v26.005
Dey, S. R., Dutta, S., & De, M. (2020). Neuro-Steroid Compound Found by GC-MS Analysis of The Methanolic Extract of The Leaves of Aegle marmelos (L) Corr. International Journal of Advancement in Life Sciences Research, 3(4), 51-56. https://doi.org/10.31632/ijalsr.20.v03i04.006
Dutta, S., De, S. R., & De, M. (2020). Characterisation of the mango (Mangifera indica L.) fruit and fruit pulp of some indigenous mango varieties of Murshidabad district of West Bengal. International Journal of Advancement in Life Sciences Research, 3(2), 23-28. https://doi.org/10.31632/ijalsr.20.v03i02.003
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Haas, B., & Papanicolaou, A. J. G. S. (2016). TransDecoder (find coding regions within transcripts). https://transdecoder.github.io
Iyer, C. P. A., & Dinesh, M. R. (1997). Advances in classical breeding and genetics in mango. Acta Hortic, 455, 252-267. https://doi.org/10.17660/ActaHortic.1997.455.34
Iyer, C. P. A., & Subramanyam, M. D. (1991). Breeding mango for developing new varieties. Acta Hortica, 291, 151-153. https://doi.org/10.17660/ActaHortic.1991.291.17
Johnson, M., Zaretskaya, I., Raytselis, Y., Merezhuk, Y., McGinnis, S., & Madden, T. L. (2008). NCBI BLAST: a better web interface. Nucleic acids research, 36(2), W5-W9. https://doi.org/10.1093/nar/gkn201
Kaur, H., Sidhu, G. S., Mittal, A., Yadav, I. S., Mittal, M., Singla, D., ... & Chhuneja, P. (2023). Comparative transcriptomics in alternate bearing cultivar Dashehari reveals the genetic model of flowering in mango. Frontiers in Genetics, 13, 1-13. https://doi.org/10.3389/fgene.2022.1061168
Kuhn, D. N., Bally, I. S., Dillon, N. L., Innes, D., Groh, A. M., Rahaman, J., ... & Sherman, A. (2017). Genetic map of mango: a tool for mango breeding. Frontiers in plant science, 8, 1-11. https://doi.org/10.3389/fpls.2017.00577
Ledesma, N., & Campbell, R. J. (2019). The status of mango cultivars, market perspectives and mango cultivar improvement for the future. Acta horticulturae, (1244), 23-27. https://doi.org/10.17660/ActaHortic.2019.1244.3
Mahato, A. K., Sharma, N., Singh, A., Srivastav, M., Jaiprakash, Singh, S. K., ... & Singh, N. K. (2016). Leaf transcriptome sequencing for identifying genic-SSR markers and SNP heterozygosity in crossbred mango variety ‘Amrapali’(Mangifera indica L.). PloS one, 11(10), 1-16. https://doi.org/10.1371/journal.pone.0164325
Mukherjee, S. K. (1953). The mango—its botany, cultivation, uses and future improvement, especially as observed in India. Economic botany, 7(2), 130-162. https://doi.org/10.1007/BF02863059
Mukherjee, S. K., & Litz, R. E. (2009). Introduction: botany and importance. In The mango: Botany, production and uses, 2,.1-18.
Nashima, K., Terakami, S., Kunihisa, M., Nishitani, C., Shoda, M., Matsumura, M., ... & Yamamoto, T. (2017). Retrotransposon-based insertion polymorphism markers in mango. Tree genetics & genomes, 13, 1-10. https://doi.org/10.1007/s11295-017-1192-2
Peng, L., Gao, W., Song, M., Li, M., He, D., & Wang, Z. (2022). Integrated metabolome and transcriptome analysis of fruit flavor and carotenoids biosynthesis differences between mature-green and tree-ripe of cv.“Golden Phoenix” mangoes (Mangifera indica L.). Frontiers in plant science, 13, 1-15. https://doi.org/10.3389/fpls.2022.816492
Sagar, V. R., Khurdiya, D. S., & Balakrishnan, K. A. (1999). Quality of dehydrated ripe mango slices as affected by packaging material and mode of packaging. Journal of food science and technology (Mysore), 36(1), 67-70.
Shudo, A., Tarora, K., Makishi, Y., Ichi, R., Takahashi, K., Matsumura, M., ... & Urasaki, N. (2013). Development of CAPS markers and their application in breeding for mango, Mangifera indica L. Euphytica, 190(3), 345-355. https://doi.org/10.1007/s10681-012-0774-1
Sivankalyani, V., Sela, N., Feygenberg, O., Zemach, H., Maurer, D., & Alkan, N. (2016). Transcriptome dynamics in mango fruit peel reveals mechanisms of chilling stress. Frontiers in plant science, 7, 1-17. https://doi.org/10.3389/fpls.2016.01579
Song, M., Wang, H., Fan, Z., Huang, H., & Ma, H. (2023). Advances in sequencing and key character analysis of mango (Mangifera indica L.). Horticulture Research, 10(2), 1-16. https://doi.org/10.1093/hr/uhac259
Subramanyam, H., Krishnamurthy, S., & Parpia, H. A. B. (1975). Physiology and biochemistry of mango fruit. Advances in Food Research, 21, 223-305. https://doi.org/10.1016/S0065-2628(08)60092-0
Tafolla-Arellano, J. C., Zheng, Y., Sun, H., Jiao, C., Ruiz-May, E., Hernández-Oñate, M. A., ... & Tiznado-Hernández, M. E. (2017). Transcriptome analysis of mango (Mangifera indica L.) fruit epidermal peel to identify putative cuticle-associated genes. Scientific reports, 7(1), 1-13. https://doi.org/10.1038/srep46163
Tharanathan, R. N., Yashoda, H. M., & Prabha, T. N. (2006). Mango (Mangifera indica L.),“The king of fruits”—An overview. Food Reviews International, 22(2), 95-123. https://doi.org/10.1080/87559120600574493
Thiel, T. (2003). MISA—Microsatellite identification tool. Website http://pgrc.ipk-gatersleben.de/misa/ [accessed 17 June 2016].
Tsai, C. C., Chen, Y. K. H., Chen, C. H., Weng, I. S., Tsai, C. M., Lee, S. R., ... & Chiang, Y. C. (2013). Cultivar identification and genetic relationship of mango (Mangifera indica) in Taiwan using 37 SSR markers. Scientia Horticulturae, 164, 196-201. https://doi.org/10.1016/j.scienta.2013.09.037
Viruel, M. A., Escribano, P., Barbieri, M., Ferri, M., & Hormaza, J. I. (2005). Fingerprinting, embryo type and geographic differentiation in mango (Mangifera indica L., Anacardiaceae) with microsatellites. Molecular breeding, 15, 383-393. https://doi.org/10.1007/s11032-004-7982-x
Wang, P., Luo, Y., Huang, J., Gao, S., Zhu, G., Dang, Z., ... & Chen, Y. (2020). The genome evolution and domestication of tropical fruit mango. Genome biology, 21, 1-17. https://doi.org/10.1186/s13059-020-01959-8
Yamanaka, S., Hosaka, F., Matsumura, M., Onoue-Makishi, Y., Nashima, K., Urasaki, N., ... & Yamamoto, T. (2019). Genetic diversity and relatedness of mango cultivars assessed by SSR markers. Breeding science, 69(2), 332-344. https://doi.org/10.1270/jsbbs.18204
Arumuganathan, K., & Earle, E. D. (1991). Nuclear DNA content of some important plant species. Plant molecular biology reporter, 9, 208-218. https://doi.org/10.1007/BF02672069
Azim, M. K., Khan, I. A., & Zhang, Y. (2014). Characterization of mango (Mangifera indica L.) transcriptome and chloroplast genome. Plant molecular biology, 85, 193-208. https://doi.org/10.1007/s11103-014-0179-8
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. https://doi.org/10.1093/nar/gkv1035
De, M., Das, J., Saha, M., Pal, A., & Dey, S. R. (2014). Documentation and Characterization of the Indigenous Mango (Mangifera indica L.) varieties of Malda and Murshidabad districts of West Bengal. J. Environ. & Sociobiol, 11(2), 187-198.
De, M., Dutta, S., Pahari, G. K., Ganguli, S., Ray, S., & Dey, S. R. (2019). Variation in flowering and fruit set among indigenous mango varieties from Malda and Murshidabad conserved as Field Gene Bank in Gurudas College, Kolkata, India. International Journal of Advancement in Life Sciences Research, 2(4)48-61. https://doi.org/10.31632/ijalsr.2019v02i04.006
De, M., Dutta, S., Ray, S., & Dey, S. R. (2021b). Visual Clustering Analysis of some traditional Mango (Mangifera indica L.) varieties of Murshidabad District, West Bengal using Clust Vis web tool. International Journal of Advancement in Life Sciences Research, 4 (3), 42-43. https://doi.org/10.31632/ijalsr.2019v02i04.006
De, M., Pahari, G., Pal, A., Ganguli, S., Ray, S., Mandal, M., Dhar, S., Dutta, S., & Dey, S. (2019). Mango (Mangifera indica L.) field gene bank (FGB) in Gurudas College, Kolkata-54. Int. J. Exp. Res. Rev., 18, 6-14.
De, M., Ray, S., Dutta, S., & Dey, S. R. (2021). Eugenol Found by GC-MS Analysis of The Methanolic Extract of The Fruit Pulp of Indigenous Mango (Mangifera indica L.) Variety, Champa from Murshidabad District of West Bengal, India. International Journal of Advancement in Life Sciences Research, 4(1), 22-30. https://doi.org/10.31632/ijalsr.20.v04i01.004
De, Mitu and Dey, S. R., (2021c). Assessment of the pulp quality of some rare indigenous mango (Mangifera indica L.) varieties of West Bengal, India. International Journal of Experimental Research and Review, 26, 70-78. https://doi.org/10.52756/ijerr.2021.v26.005
Dey, S. R., Dutta, S., & De, M. (2020). Neuro-Steroid Compound Found by GC-MS Analysis of The Methanolic Extract of The Leaves of Aegle marmelos (L) Corr. International Journal of Advancement in Life Sciences Research, 3(4), 51-56. https://doi.org/10.31632/ijalsr.20.v03i04.006
Dutta, S., De, S. R., & De, M. (2020). Characterisation of the mango (Mangifera indica L.) fruit and fruit pulp of some indigenous mango varieties of Murshidabad district of West Bengal. International Journal of Advancement in Life Sciences Research, 3(2), 23-28. https://doi.org/10.31632/ijalsr.20.v03i02.003
Gómez-Ollé, A., Bullones, A., Hormaza, J.I., Mueller, L.A. and Fernandez-Pozo, N. (2023). MangoBase: A Genomics Portal and Gene Expression Atlas for Mangifera indica. Plants, 12(6), 1-12. https://doi.org/10.3390/plants12061273
Grabherr, M. G., Haas, B. J., Yassour, M., Levin, J. Z., Thompson, D. A., Amit, I., ... & Regev, A. (2011). Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nature biotechnology, 29(7), 644-652. https://doi.org/10.1038/nbt.1883
Haas, B., & Papanicolaou, A. J. G. S. (2016). TransDecoder (find coding regions within transcripts). https://transdecoder.github.io
Iyer, C. P. A., & Dinesh, M. R. (1997). Advances in classical breeding and genetics in mango. Acta Hortic, 455, 252-267. https://doi.org/10.17660/ActaHortic.1997.455.34
Iyer, C. P. A., & Subramanyam, M. D. (1991). Breeding mango for developing new varieties. Acta Hortica, 291, 151-153. https://doi.org/10.17660/ActaHortic.1991.291.17
Johnson, M., Zaretskaya, I., Raytselis, Y., Merezhuk, Y., McGinnis, S., & Madden, T. L. (2008). NCBI BLAST: a better web interface. Nucleic acids research, 36(2), W5-W9. https://doi.org/10.1093/nar/gkn201
Kaur, H., Sidhu, G. S., Mittal, A., Yadav, I. S., Mittal, M., Singla, D., ... & Chhuneja, P. (2023). Comparative transcriptomics in alternate bearing cultivar Dashehari reveals the genetic model of flowering in mango. Frontiers in Genetics, 13, 1-13. https://doi.org/10.3389/fgene.2022.1061168
Kuhn, D. N., Bally, I. S., Dillon, N. L., Innes, D., Groh, A. M., Rahaman, J., ... & Sherman, A. (2017). Genetic map of mango: a tool for mango breeding. Frontiers in plant science, 8, 1-11. https://doi.org/10.3389/fpls.2017.00577
Ledesma, N., & Campbell, R. J. (2019). The status of mango cultivars, market perspectives and mango cultivar improvement for the future. Acta horticulturae, (1244), 23-27. https://doi.org/10.17660/ActaHortic.2019.1244.3
Mahato, A. K., Sharma, N., Singh, A., Srivastav, M., Jaiprakash, Singh, S. K., ... & Singh, N. K. (2016). Leaf transcriptome sequencing for identifying genic-SSR markers and SNP heterozygosity in crossbred mango variety ‘Amrapali’(Mangifera indica L.). PloS one, 11(10), 1-16. https://doi.org/10.1371/journal.pone.0164325
Mukherjee, S. K. (1953). The mango—its botany, cultivation, uses and future improvement, especially as observed in India. Economic botany, 7(2), 130-162. https://doi.org/10.1007/BF02863059
Mukherjee, S. K., & Litz, R. E. (2009). Introduction: botany and importance. In The mango: Botany, production and uses, 2,.1-18.
Nashima, K., Terakami, S., Kunihisa, M., Nishitani, C., Shoda, M., Matsumura, M., ... & Yamamoto, T. (2017). Retrotransposon-based insertion polymorphism markers in mango. Tree genetics & genomes, 13, 1-10. https://doi.org/10.1007/s11295-017-1192-2
Peng, L., Gao, W., Song, M., Li, M., He, D., & Wang, Z. (2022). Integrated metabolome and transcriptome analysis of fruit flavor and carotenoids biosynthesis differences between mature-green and tree-ripe of cv.“Golden Phoenix” mangoes (Mangifera indica L.). Frontiers in plant science, 13, 1-15. https://doi.org/10.3389/fpls.2022.816492
Sagar, V. R., Khurdiya, D. S., & Balakrishnan, K. A. (1999). Quality of dehydrated ripe mango slices as affected by packaging material and mode of packaging. Journal of food science and technology (Mysore), 36(1), 67-70.
Shudo, A., Tarora, K., Makishi, Y., Ichi, R., Takahashi, K., Matsumura, M., ... & Urasaki, N. (2013). Development of CAPS markers and their application in breeding for mango, Mangifera indica L. Euphytica, 190(3), 345-355. https://doi.org/10.1007/s10681-012-0774-1
Sivankalyani, V., Sela, N., Feygenberg, O., Zemach, H., Maurer, D., & Alkan, N. (2016). Transcriptome dynamics in mango fruit peel reveals mechanisms of chilling stress. Frontiers in plant science, 7, 1-17. https://doi.org/10.3389/fpls.2016.01579
Song, M., Wang, H., Fan, Z., Huang, H., & Ma, H. (2023). Advances in sequencing and key character analysis of mango (Mangifera indica L.). Horticulture Research, 10(2), 1-16. https://doi.org/10.1093/hr/uhac259
Subramanyam, H., Krishnamurthy, S., & Parpia, H. A. B. (1975). Physiology and biochemistry of mango fruit. Advances in Food Research, 21, 223-305. https://doi.org/10.1016/S0065-2628(08)60092-0
Tafolla-Arellano, J. C., Zheng, Y., Sun, H., Jiao, C., Ruiz-May, E., Hernández-Oñate, M. A., ... & Tiznado-Hernández, M. E. (2017). Transcriptome analysis of mango (Mangifera indica L.) fruit epidermal peel to identify putative cuticle-associated genes. Scientific reports, 7(1), 1-13. https://doi.org/10.1038/srep46163
Tharanathan, R. N., Yashoda, H. M., & Prabha, T. N. (2006). Mango (Mangifera indica L.),“The king of fruits”—An overview. Food Reviews International, 22(2), 95-123. https://doi.org/10.1080/87559120600574493
Thiel, T. (2003). MISA—Microsatellite identification tool. Website http://pgrc.ipk-gatersleben.de/misa/ [accessed 17 June 2016].
Tsai, C. C., Chen, Y. K. H., Chen, C. H., Weng, I. S., Tsai, C. M., Lee, S. R., ... & Chiang, Y. C. (2013). Cultivar identification and genetic relationship of mango (Mangifera indica) in Taiwan using 37 SSR markers. Scientia Horticulturae, 164, 196-201. https://doi.org/10.1016/j.scienta.2013.09.037
Viruel, M. A., Escribano, P., Barbieri, M., Ferri, M., & Hormaza, J. I. (2005). Fingerprinting, embryo type and geographic differentiation in mango (Mangifera indica L., Anacardiaceae) with microsatellites. Molecular breeding, 15, 383-393. https://doi.org/10.1007/s11032-004-7982-x
Wang, P., Luo, Y., Huang, J., Gao, S., Zhu, G., Dang, Z., ... & Chen, Y. (2020). The genome evolution and domestication of tropical fruit mango. Genome biology, 21, 1-17. https://doi.org/10.1186/s13059-020-01959-8
Yamanaka, S., Hosaka, F., Matsumura, M., Onoue-Makishi, Y., Nashima, K., Urasaki, N., ... & Yamamoto, T. (2019). Genetic diversity and relatedness of mango cultivars assessed by SSR markers. Breeding science, 69(2), 332-344. https://doi.org/10.1270/jsbbs.18204
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Dey, S., Ganguli, S. and De, M. (2024) “Transcriptome Analysis from leaf during non-flowering vegetative growth phase of mango (Mangifera indica L. var Fazli) from Murshidabad district of West Bengal, India.”, International Journal of Advancement in Life Sciences Research, 7(2), pp. 143-162. doi: https://doi.org/10.31632/ijalsr.2024.v07i02.012.
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