Transcriptomic exploration of a high sucrose mutant in comparison with the low sucrose mother genotype in sugarcane during sugar accumulating stage

Abstract

Sugarcane (Saccharum spp. hybrid) is a noteworthy crop in the world for sugar and bioenergy production. In the present study, transcriptomic analysis was steered for a high sucrose mutant Guixuan B9 (GXB9) and the low sucrose mother genotype B9 of sugarcane during sugar accumulating stage. A total of 112,170 unigenes were obtained, and 106,026 (94.52%) were annotated by using the available public databases nonredundant, Gene ontology, COG, Kyoto Encyclopedia of Genes and Genomes, Swiss‐Prot, and Pfam. Functional assignment analysis of unigenes exhibited that they were active in a diversity of metabolic pathways. The vital unigenes for sucrose metabolism and accumulation were relatively characterized in the immature internodes (int. 5, 6) and maturing internodes (int. 13, 14) of GXB9 in comparison with B9. The differentially expressed unigenes (DEGs) encoding sucrose phosphate synthase (SPS, http://www.chem.qmul.ac.uk/iubmb/enzyme/EC2/4/1/14.html), sucrose synthase (SuSy, http://www.chem.qmul.ac.uk/iubmb/enzyme/EC2/4/1/13.html), and invertase (http://www.chem.qmul.ac.uk/iubmb/enzyme/EC3/2/1/26.html), which are the vital enzymes functioning in the biosynthesis and splitting of sucrose, in the internodal tissues were revealed by using Illumina Hiseq 2000 platform, and verified by quantitative reverse transcription‐polymerase chain reaction analysis. The DEGs encoding SPS proteins SPS1, SPS2, SPS4, and SPS5 were upregulated in the maturing internodes of GXB9 compared with B9. The DEGs encoding SuSy proteins were majorly upregulated in the immature internodes of GXB9, and those encoding the enzymes involved in trehalose synthesis were downregulated in GXB9 compared with B9. The results in this study have revealed the opportunities for future sugarcane improvement by concentrating on the DEGs linked to sucrose metabolic pathways by applying omics technologies.

Herbivory-Induced Emission of Volatile Terpenes in Chrysanthemum morifolium Functions as an Indirect Defense against Spodoptera litura Larvae by Attracting Natural Enemies

“…The raw paired-end reads were trimmed and quality-controlled by SeqPrep () and Sickle () with default parameters . Clean data from the C.…”

“…Further RNA purification, reverse transcription, library construction, and sequencing of the RNA extracted in 2.7 were performed at Shanghai Majorbio Bio-Pharm Biotechnology Co., Ltd. (Shanghai, China) as per the manufacturer's instructions (Illumina, San Diego, CA) as previously described. 25 2.9. De Novo Assembly and Annotation.…”

“…The raw paired-end reads were trimmed and quality-controlled by SeqPrep (https:// github.com/jstjohn/SeqPrep) and Sickle (https://github.com/ najoshi/sickle) with default parameters. 25 Clean data from the C. morifolium leaf samples were used for de novo assembly with Trinity (http://trinityrnaseq.sourceforge.net/). 26 All the assembled transcripts were searched against the NCBI protein nonredundant, String, and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases using BLASTX to identify the proteins that had the highest sequence similarity with the given transcripts to determine their functional annotations; the typical cutoff e-value less than 1.0 × 10 −5 was used.…”

Morphological, agronomical, physiological and molecular characterization of a high sugar mutant of sugarcane in comparison to mother variety

“…After that, for several years field trials were carried out to compare the performance of GXB9 in comparison to B9 mother clone. The performance data displayed that both clones have apparently similar morphological appearance, however consistently significant difference in sugar content in cane [ 34 ]. So, it was considered that GXB9 clone has mutated, and a systematic study was planned to observe the variation in morphological, physiological, and agronomic traits of GXB9 mutant in comparison to low sucrose B9 mother clone in field under normal environmental conditions.…”

Comprehensive analysis of the mechanism underlying plastic microbiome and plants interaction, with future perspectives

“…Currently many microbial investigating tools and techniques are available including microbial cultivation by plating methods, electron microscopy-SEM-TEM (Goldsmith and Miller, 2009;Wisse et al, 2010) , nucleic acid extraction, DNA sequencing, PCR/qPCR (Del Mar Lleò et al, 2000;Garibyan and Avashia, 2013;Khan et al, 2016;Overbergh et al, 2003;Pagano et al, 2011;v. Wintzingerode et al, 1997), clone genomic libraries, stable isotope probing, microarrays, next generation technique (NGS) metagenomics (Marchev et al, 2021), transcriptomic (Handelsman, 2004;Khan et al, 2021), proteomics , molecular finger printings techniques, denaturing gradient gel electrophoresis (DGGE) (Al-Mailem et al, 2017), terminalrestriction length polymorphism (T-RFLP) (Portillo et al, 2011), temperature gradient gel electrophoresis (TGGE) (Ritchie et al, 2000), single-strand conformational polymorphisms (SSCP) (Johnston -Monje and Lopez Mejia, 2020), ribosomal internal spacer analysis (RISA) (Osborn et al, 2000) , length heterogeneity-PCR (LH-PCR) (DeAngelis et al, 2011), random amplified polymorphic DNA (RAPD) (Bardakci, 2001;Broadway, 2012) and biosensors (Gavrilaș et al, 2022) etc. However, the methods, tools, and techniques are selected according to the need of the research goals and directions.…”