Transcriptomic Analysis of Changes in Gene Expression During Flowering Induction in Sugarcane Under Controlled Photoperiodic Conditions

Abstract

Flowering is of utmost relevance for the agricultural productivity of the sugarcane bioeconomy, but data and knowledge of the genetic mechanisms underlying its photoperiodic induction are still scarce. An understanding of the molecular mechanisms that regulate the transition from vegetative to reproductive growth in sugarcane could provide better control of flowering for breeding. This study aimed to investigate the transcriptome of +1 mature leaves of a sugarcane cultivar subjected to florally inductive and non-inductive photoperiodic treatments to identify gene expression patterns and molecular regulatory modules. We identified 7,083 differentially expressed (DE) genes, of which 5,623 showed significant identity to other plant genes. Functional group analysis showed differential regulation of important metabolic pathways involved in plant development, such as plant hormones (i.e., cytokinin, gibberellin, and abscisic acid), light reactions, and photorespiration. Gene ontology enrichment analysis revealed evidence of upregulated processes and functions related to the response to abiotic stress, photoprotection, photosynthesis, light harvesting, and pigment biosynthesis, whereas important categories related to growth and vegetative development of plants, such as plant organ morphogenesis, shoot system development, macromolecule metabolic process, and lignin biosynthesis, were downregulated. Also, out of 76 sugarcane transcripts considered putative orthologs to flowering genes from other plants (such as Arabidopsis thaliana, Oryza sativa, and Sorghum bicolor), 21 transcripts were DE. Nine DE genes related to flowering and response to photoperiod were analyzed either at mature or spindle leaves at two development stages corresponding to the early stage of induction and inflorescence primordia formation. Finally, we report a set of flowering-induced long non-coding RNAs and describe their level of conservation to other crops, many of which showed expression patterns correlated against those in the functionally grouped gene network.

ScRpb4, Encoding an RNA Polymerase Subunit from Sugarcane, Is Ubiquitously Expressed and Resilient to Changes in Response to Stress Conditions

“…Sugarcane transcriptomic studies [18][19][20] have allowed the identification of genes involved in stress tolerance [30,42] as well as in plant development [43]. However, to date, there are no studies characterizing sugarcane RNA polymerase II, a key enzyme that transcribes thousands of protein-coding genes and non-coding RNAs with diverse functions.…”

“…The lack of a sugarcane reference genome due to its complexity and extreme polyploidy level has limited the characterization of many gene families [17]. Many studies focused on picturing transcriptional landscapes under drought stress, phosphate starvation, methyl jasmonate, abscisic acid, and flowering induction have been conducted in sugarcane [18][19][20]. Together with others from different plant species, these studies have significantly improved our understanding of the transcriptional changes during plant development and in response to biotic and abiotic stresses [21][22][23].…”

A Selection of Reliable Reference Genes for Gene Expression Analysis in the Female and Male Flowers of Salix suchowensis

“…Therefore, we selected S. suchowensis to mine for stably expressed reference genes in male and female flowers at different developmental stages. Flower development is an important integrated development process in the life cycle of angiosperms [ 33 ]. In this study, the four important stages of male and female flower development of S. suchowensis were selected (T1–T4) to verify the stability of reference genes.…”

“…Previously, due to the cumbersome steps, heavy workload, and small application scope of discovering new reference genes, the development of new reference genes has been limited [ 33 ]. At present, many statistical algorithms have been developed to identify the most stable reference genes for the standardization of target gene expression [ 34 , 35 ].…”

Transcriptome Analysis Reveals a Gene Expression Pattern That Contributes to Sugarcane Bud Propagation Induced by Indole-3-Butyric Acid

“…A protein phosphatase 2A gene was upregulated during the IBA-induced adventitious root formation on Arabidopsis stem segments ( Fattorini et al, 2017 ). Transcriptome analysis has previously been performed on sugarcane internodes ( Kasirajan et al, 2018 ; Wang et al, 2019 ), root ( Zeng et al, 2015 ; Dharshini et al, 2019 ; Malviya et al, 2020 ), leaves ( Li et al, 2016a ; Liu et al, 2018 ), mature and furled immature leaves ( Manechini et al, 2021 ), and stalk ( Zhu et al, 2021 ). To the best of our knowledge, this is the first-of-its-kind attempt to study the transcriptome analysis of the single bud of sugarcane in response to IBA.…”