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In Silico Dissection and Expression Analysis of Sucrose Synthase Gene Family in Sugarcane

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Abstract

Sugarcane, the world’s largest source of sugar and biofuel, still carries an unassembled ~ 10 GB polyaneuploid genome, which is a major bottleneck in studying this crop at molecular level. Sugar is mainly derived from sugarcane; hence, the sucrose metabolism pathway is one of the most intriguing hotspot for sugar crop researchers. Four main gene families have been reported to be involved in sucrose metabolism including the SuSy (sucrose synthase) gene family. Sucrose synthase in plants degrades sucrose to UDP-glucose and fructose to ensure their availability for growth and developmental purposes. Here, we attempted to get deep insights into sugarcane SuSy gene family and carried out bioinformatics and expression analyses to get a high-resolution holistic snapshot. Multiple stress-responsive cis motifs, abscisic acid-responsive element (ABRE), anaerobic induction-responsive element (ARE), auxin-responsive element (AuxRE), low-temperature-responsive (LTR), wounding response element (WUN), WRKY transcription factors binding site (W-motif), predicted in the regulatory region showed their involvement in the stress signaling pathways, in addition to sucrose metabolism. Similarly, the protein interaction network analysis predicted an array of proteins of diverse range of functions. Moreover, the expression pattern of SuSy gene family in two varieties CPF251 (higher sugar level) and CPF252 (lower sugar level) was compared in leaf and internodes (top and bottom). qRT-PCR indicated the differential expression pattern of the SuSy genes in these two varieties. The expression of SoSuSy2 was high in leaf and top internodes, while low in bottom internodes indicating its activity in this tissue. In CPF251, both SoSuSy2 and SoSuSy4 displayed higher expression level; however, only SuSy2 had higher expression in CPF252. In contrast, SoSuSy6 and SoSuSy7 were the least expressed genes followed by SoSuSy1. This study highlights the candidate genes for gene manipulation and consequent metabolic engineering of sugarcane for enhanced sucrose contents.

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Funding

This research was funded by Pakistan Agricultural Research Council (PARC), grant number PSDP No. 719. The APC was funded by PARC.

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  1. Muhammad Noman and Iqra Siddique contributed equally to this work.

Authors and Affiliations

  1. National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Center, Islamabad, 44000, Pakistan

    Muhammad Noman, Iqra Siddique, Bilal Saleem, Shaukat Ali & Muhammad Ramzan Khan

  2. Biotechnology Department, Lahore College for Women University, Lahore, 23432, Pakistan

    Iqra Siddique & Saiqa Ilyas

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  1. Muhammad Noman
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  2. Iqra Siddique
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Contributions

Conceptualization was done by MN and MRK; methodology was done by MN; software was done by MN; validation was done by BS, IS and SI; formal analysis was carried out by SA; investigation was done by MN; resources were done by MRK; data curation was done by IS; writing—original draft preparation were done by MN; writing—review and editing were done by MRK and SA; visualization was done by IS; supervision was done by MN; project administration was done by MRK; funding acquisition was done by MRK.

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Correspondence to Muhammad Noman or Muhammad Ramzan Khan.

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Noman, M., Siddique, I., Saleem, B. et al. In Silico Dissection and Expression Analysis of Sucrose Synthase Gene Family in Sugarcane. Sugar Tech 24, 1766–1777 (2022). https://doi.org/10.1007/s12355-022-01151-1

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