Sugarcane, derived from the hybridization of Saccharum officinarum×Saccharum spontaneum, is a vegetative crop in which the final yield is highly driven by culm biomass production. Cane yield under irrigated or rain-fed conditions could be improved by developing genotypes with leaves that have high intrinsic transpiration efficiency, TE_i (CO₂ assimilation/stomatal conductance), provided this is not offset by negative impacts from reduced conductance and growth rates. This study was conducted to partition genotypic variation in TE_i among a sample of diverse clones from the Chinese collection of sugarcane-related germplasm into that due to variation in stomatal conductance versus that due to variation in photosynthetic capacity. A secondary goal was to define protocols for optimized larger-scale screening of germplasm collections. Genotypic variation in TE_i was attributed to significant variation in both stomatal and photosynthetic components. A number of genotypes were found to possess high TE_i as a result of high photosynthetic capacity. This trait combination is expected to be of significant breeding value. It was determined that a small number of observations (16) is sufficient for efficiently screening TE_i in larger populations of sugarcane genotypes The research methodology and results reported are encouraging in supporting a larger-scale screening and introgression of high transpiration efficiency in sugarcane breeding. However, further research is required to quantify narrow sense heritability as well as the leaf-to-field translational potential of genotypic variation in transpiration efficiency-related traits observed in this study.

The sugarcane genus Saccharum is characterized by complex genomes with diverse ploidy levels. We developed a multiscale graph–based pangenome representation, which integrates nine genome assemblies into a unified reference, representing modern cultivars and founding species. Each homo(eo)logous (encompasses both homologous and homeologous relationships) chromosome set retains 47 to 57 haplotypes and ~74,000 to 271,000 gene alleles. This framework enables multiomics exploration, encompassing homo(eo)log systems and epigenomic signatures. The pangenome facilitates population genomics analyses of 417 mixed-ploidy Saccharum accessions, revealing convergent selection and identifying the Andropogoneae TB1 homolog linked to tillering as a promising gene-editing target to boost cane yield. Additionally, the pangenome supports dosage-informed genome-wide association study, improving heritability estimates and identification of sugar or leaf-angle–associated loci, including SaIRX10 and SaBAK5 . Our analytical framework establishes a foundation for graph-based genetic studies in sugarcane and other polyploid genomes.

Saccharum spontaneum L. is a crucial wild parent of modern sugarcane cultivars whose ploidy clones have been utilized successfully in improving the stress resistance and yield related traits of sugarcane cultivars. To establish knowledge regarding the genetic variances and evolutional relationships of ploidy clones of Saccharum spontaneum collected in China, the rDNA-ITS sequences of 62 ploidy clones including octaploid clones (2n = 64), nonaploid clones (2n = 72), decaploid clones (2n = 80), and dodecaploid clones (2n = 96), were obtained and analyzed. The rDNA-ITS sequences of four species from Saccharum and Sorghum bicolor selected as controls. The results showed that decaploid clones (2n = 80) possess the most abundant variances with 58 variable sites and 20 parsim-informative sites in ITS sequences, which were then followed by octaploid clones with 43 variable sites and 17 parsim-informative sites. In haplotype diversity, all four population exhibited high diversity, especially nonaploid and decaploid populations. By comparing the genetic distances among four ploidy populations, the dodecaploid population exhibited the closest relationship with the nonaploid population, and then the relationship strength decreased successively for the decaploid population and then for the octaploid population. Population differentiation analysis showed that the phenomena of population differentiation were not found among different ploidy populations, and low coefficient of gene differentiation(Gst) and high gene flow(Nm) occur among these populations possessing close genetic relationship. These results mentioned above will contribute to the understanding of the evolution of different ploidy populations of Saccharum spontaneum and provide vital knowledge for their utilization in sugarcane breeding and innovation.

Embryogenic callus induction and regeneration are useful in many aspects of plant biotechnology, especially in the functional characterization of economically important genes. However, in sugarcane, callus induction and regeneration vary across genotypes.Saccharum spontaneumis an important wild germplasm that confers disease resistance and stress tolerance to modern sugarcane cultivars, and its genome has been completely sequenced. The aim of this study was to investigate the effect of genetic variations on embryogenic callus induction and regeneration inS. spontaneumand to screen genotypes having high tissue culture susceptibility. The study was performed using nine genotypes ofS. spontaneumand the following five parameters were assessed to determine the response of genotypes to embryogenic callus induction and regeneration: callus induction, embryogenic callus ratio, embryogenic callus induction, embryonic callus regeneration and regeneration capacity. All the genotypes varied significantly (P< 0.01) in all the parameters, except for embryonic callus regeneration, which was high (>80%) for all the genotypes. High broad-sense heritability (86.1–96.8%) indicated that genetic differences are the major source of genotypic variations. Callus induction was found to be strongly positively correlated with embryogenic callus induction (r= 0.890,P< 0.01) and regeneration capacity (r= 0.881,P< 0.01). Among the nine tested genotypes, VN2 was found to be the most responsive to tissue culture and could therefore be used to characterize functional genes inS. spontaneum. We also suggested an approach with potential applications in facilitating the rapid identification of sugarcane genotypes susceptible to tissue culture.

The spontaneous adventitious bud (SAB) mutant of sugarcane, which forms clustered buds on the stem, provides a unique system for elucidating the mechanisms underlying in vivo regeneration and plant meristem differentiation anomalies. The present study investigated the mechanism underlying SAB formation in the sugarcane mutant 'YZ2018-81' through an integrated approach combining histological analysis, endogenous hormone profiling, and RNA-sequencing. Histological analysis revealed that the adventitious buds originated from the dedifferentiating cortical parenchyma cells, following a developmental sequence of dedifferentiation, proliferation, callus-like protrusion formation, and bud differentiation. Further profiling of the endogenous hormones revealed significantly elevated levels of trans-zeatin (tZ) in the second internode below the shoot apical meristem (SAM) (the 2nd IN) and upper stem nodes (the sixth internode below the SAM, the 6th IN), respectively, abscisic acid (ABA), and auxin (IAA) but lower levels of isopentenyladenine (IP) and jasmonic acid (JA) in SAB than in CK, suggesting synergistic roles for tZ, IAA, and ABA in bud initiation, and the inhibitory role of JA in cell division. Meanwhile, elevated gibberellin (GA₃) in the 6th IN indicated its participate in promoting bud elongation in the SAB mutant. Transcriptome analysis identified 20,858 differentially expressed genes (DEGs) in the samples, including upregulated genes such as meristem development regulators (RS1, REL2, and DCL), hormone signaling components (ARFs and RRs), and regeneration factors (GRF10, PLT2, and CYCD2-2). These DEGs were enriched in "plant hormone signal transduction" and "MAPK signaling pathway". The heterologous overexpression of ScGRF10 in rice induced ectopic roots at stem nodes, confirming its involvement in ectopic organogenesis. Our work elucidates the cellular, hormonal, and transcriptional framework of in vivo bud regeneration in sugarcane. The mutant also serves as a novel model for monocot regeneration and valuable genetic resources for enhancing sugarcane biotechnology.