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Comparative RNA sequencing based transcriptome profiling of regular bearing and alternate bearing mango (Mangifera indica L.) varieties reveals novel insights into the regulatory mechanisms underlying alternate bearing

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Abstract

Objective

This study is to understand a comprehensive perspective on the molecular mechanisms underlying alternate bearing in mango (Mangifera indica L.) via transcriptome wide gene expression profiling of both regular and irregular mango varieties.

Results

Transcriptome data of regular (Neelam) and irregular (Dashehari) mango varieties revealed a total of 42,397 genes. Out of that 12,557 significantly differentially expressed genes were identified, of which 6453 were found to be up-regulated and 6104 were found to be down-regulated genes. Further, many of the common unigenes which were involved in hormonal regulation, metabolic processes, oxidative stress, ion homeostasis, alternate bearing etc. showed significant differences between these two different bearing habit varieties. Pathway analysis showed the highest numbers of differentially expressed genes were related with the metabolic processes (523). A total of 26 alternate bearing genes were identified and principally three genes viz; SPL-like gene (GBVX01015803.1), Rumani GA-20-oxidase-like gene (GBVX01019650.1) and LOC103420644 (GBVX01016070.1) were significantly differentially expressed (at log2FC and pval less than 0.05) while, only single gene (gbGBVW01004309.1) related with flowering was found to be differentially expressed. A total of 15 differentially expressed genes from three important pathways viz; alternate bearing, carbohydrate metabolism and hormone synthesis were validated using Real time PCR and results were at par with in silico analysis.

Conclusions

Deciphering the differentially expressed genes (DEGs) and potential candidate genes associated with alternate bearing, hormone and carbohydrate metabolism pathways will help for illustrating the molecular mechanisms underlying the bearing tendencies in mango.

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Acknowledgements

This work was supported and funded by Department of Science and Technology- SERB, New Delhi, India (YSS/2015/001302). Authors are thankful to Director, ICAR-IARI, New Delhi for research facilities. We are also thankful to Dr H. Ravishankar, Ex-Director, CISH, Lucknow for helping us in language improvement.

Supporting information

Supplementary Fig. 1—Genes mapped to flowering genes of Arabidopsis thaliana and Citrus sinensis.

Supplementary Fig. 2—Details of amplification plots for selected genes used in RT-qPCR.

Supplementary Fig. 3—Details of melting curve for selected genes used in RT-qPCR.

Supplementary Fig. 4—Details of melting curve with no template control for selected genes used in RT-qPCR.

Supplementary Table 1—Detail information of differentially expressed genes.

Supplementary Table 2—Details of down-regulated and up-regulated genes in Neelam and Dashehari varieties of mango.

Supplementary Table 3—Details of gene information in different pathways like alternate bearing, hormone, metabolism, meristem, flowering, starvation, oxido-reductase.

Supplementary Table 4—Details of fold change and ct values statistics of real-time- qPCR.

Author information

Authors and Affiliations

Authors

Contributions

NS is the main coordinator of the project and participated in the conception of the study together with NKS, AKS and SKS. NS performed the research. AKS, NS, AKM and MS prepared the material for sequencing and analyzed the data. NS,SKS and NKS were responsible for drafting and revising the manuscript.

Corresponding author

Correspondence to Nimisha Sharma.

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The authors declare that they have no conflicts of interest.

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Informed consent was obtained from all individual participants included in the study.

Research involving human and animal participants

This article does not contain any studies with human participants or animals performed by any of the authors.

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Sharma, N., Singh, A.K., Singh, S.K. et al. Comparative RNA sequencing based transcriptome profiling of regular bearing and alternate bearing mango (Mangifera indica L.) varieties reveals novel insights into the regulatory mechanisms underlying alternate bearing. Biotechnol Lett 42, 1035–1050 (2020). https://doi.org/10.1007/s10529-020-02863-8

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  • DOI: https://doi.org/10.1007/s10529-020-02863-8

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