Expression Profiling and MicroRNA Regulatory Networks of Homeobox Family Genes in Sugarcane Saccharum spontaneum L

Genomic investigation of duplication, functional conservation, and divergence in the LRR-RLK Family of Saccharum

BACKGROUND

Sugarcane (Saccharum spp.) holds exceptional global significance as a vital crop, serving as a primary source of sucrose, bioenergy, and various by-products. The optimization of sugarcane breeding by fine-tuning essential traits has become crucial for enhancing crop productivity and stress resilience. Leucine-rich repeat receptor-like kinases (LRR-RLK) genes present promising targets for this purpose, as they are involved in various aspects of plant development and defense processes.

RESULTS

Here, we present a detailed overview of phylogeny and expression of 288 (495 alleles) and 312 (1365 alleles) LRR-RLK genes from two founding Saccharum species, respectively. Phylogenetic analysis categorized these genes into 15 subfamilies, revealing considerable expansion or reduction in certain LRR-type subfamilies. Compared to other plant species, both Saccharum species had more significant LRR-RLK genes. Examination of cis-acting elements demonstrated that SsLRR-RLK and SoLRR-RLK genes exhibited no significant difference in the types of elements included, primarily involved in four physiological processes. This suggests a broad conservation of LRR-RLK gene function during Saccharum evolution. Synteny analysis indicated that all LRR-RLK genes in both Saccharum species underwent gene duplication, primarily through whole-genome duplication (WGD) or segmental duplication. We identified 28 LRR-RLK genes exhibiting novel expression patterns in response to different tissues, gradient development leaves, and circadian rhythm in the two Saccharum species. Additionally, SoLRR-RLK104, SoLRR-RLK7, SoLRR-RLK113, and SsLRR-RLK134 were identified as candidate genes for sugarcane disease defense response regulators through transcriptome data analysis of two disease stresses. This suggests LRR-RLK genes of sugarcane involvement in regulating various biological processes, including leaf development, plant morphology, photosynthesis, maintenance of circadian rhythm stability, and defense against sugarcane diseases.

CONCLUSIONS

This investigation into gene duplication, functional conservation, and divergence of LRR-RLK genes in two founding Saccharum species lays the groundwork for a comprehensive genomic analysis of the entire LRR-RLK gene family in Saccharum. The results reveal LRR-RLK gene played a critical role in Saccharum adaptation to diverse conditions, offering valuable insights for targeted breeding and precise phenotypic adjustments.

Enhancement of healthful novel sugar contents in genetically engineered sugarcane juice integrated with molecularly characterized ThSyGII (CEMB-SIG2)

Enhancement of sugar contents and yielding healthful sugar products from sugarcane demand high profile scientific strategies. Previous efforts to foster manipulation in metabolic pathways or triggering sugar production through combating abiotic stresses fail to yield high sugar recovery in Saccharum officinarum L. Novel sucrose isomers trehalulose (TH) and isomaltulose (IM) are naturally manufactured in microbial sources. In pursuance of novel scientific methodology, codon optimized sucrose isomerase gene, Trehalulose synthase gene II(CEMB-SIG2) cloned under dual combined stem specific constitutive promoters in pCAMBIA1301 expression vector integrated with Vacuole targeted signal peptide (VTS) to concentrate gene product into the vacuole. The resultant mRNA expression obtained by Real Time PCR validated extremely increased transgene expression in sugarcane culms than leaf tissues. Overall sugar estimation from transgenic sugarcane lines was executed through refractometer. HPLC based quantifications of Trehalulose (TH) alongside different internodes of transgenic sugarcane confirmed the enhancement of boosted sugar concentrations in mature sugarcane culms. Trehalulose synthase gene II receptive sugarcane lines indicated the unprecedented impressions of duly combined constitutive stem regulated promoters. Transgenic sugarcane lines produce highest sugar recovery percentages, 14.9% as compared to control lines (8.5%). The increased sugar recovery percentage in transgenic sugarcane validated the utmost performance and expression of ThSyGII gene .High Profile Liquid chromatography based sugar contents estimation of Trehalulose (TH) and Isomaltulose (IM) yielded unprecedented improvement in the whole sugar recovery percentage as compared to control lines.⁠.