Jiayong Liu

Selecting superior families at the seedling stage is crucial for accelerating genetic gain in sugarcane, yet systematic comparisons of selection methods remain limited. This study evaluated seven selection strategies: phenotypic check-based selection (Pheno), a three-trait combined index (CI3), Best Linear Unbiased Prediction (BLUP), Best Linear Unbiased Estimation (BLUE), tiered family selection (Tiered), logistic regression (LASSO), and the Multi-Trait Family Ideotype Distance Index (MFIDI). The experiment followed an augmented block design with four blocks, two check varieties, and included 125 test families comprising 10,955 seedlings. Using a combined index of standardized cane and sugar yields, families were classified as elite (top 20%), moderate (60%), and weak (bottom 20%). BLUP and BLUE rankings were consistent (Spearman’s ρ > 0.95, TCI = 88%, Jaccard = 0.79). Elite families showed median index values of 0.90 (BLUP) and 0.88 (BLUE) with wide interquartile ranges, whereas weak families had medians of −0.70 with narrow ranges. LASSO achieved excellent predictive performance: AUC = 0.95, accuracy = 0.92, sensitivity = 0.90, specificity = 0.94, identifying cane yield, sugar yield, and millable cane as key drivers. Agreement for inferior families was lower across methods (BCI ≤ 68%). BLUP with a multi-trait index proved most effective for discriminating elite families. Families F31 and F71 consistently ranked top. Combining selection approaches with agreement indices improves early-stage decisions for family selection in sugarcane breeding.

The improvement of sucrose yield in sugarcane is impeded by the crop’s complex polyploid genome and slow progress in breeding. To clarify how arginine (Arg) regulates sugar metabolism and identify key genes associated with sucrose transport and accumulation in sugarcane, a screening experiment was performed by spraying L-arginine hydrochloride on the leaves and leaf sheaths of three sugarcane varieties (YZ05-51, YZ08-1609, and YT93-159), which differ in growth vigor, leaf morphology and other phenotypic traits. YZ05-51 exhibited the most prominent sugar-increasing effect, and subsequent optimization experiments on its leaf sheaths revealed that 20 g/mu L-arginine hydrochloride at pH 7.0 was optimal, significantly enhancing stem sucrose content. Transcriptomic analysis revealed the upregulation of genes related to sucrose synthesis and transport, with candidate genes enriched in pathways such as starch-sucrose metabolism, glycolysis/gluconeogenesis, and ATP-binding cassette (ABC) transporters. Metabolomic analysis detected 32 sugar metabolites across three categories, of which 24 were differentially abundant (e.g., glucose, galactose, fructose, and mannose). Integrated multi-omics analysis identified key regulatory genes, including SBEs and TPS1 (sucrose synthesis and carbon flux regulation), RBSK, α-amylases, GH28 (starch breakdown, glycolysis, and sugar mobilization), ABC transporters, GTs, and TIM10/TIM12 (sucrose transporter). Collectively, these analyses demonstrate enhanced activity of genes and metabolites involved in sucrose synthesis/transport in leaf sheaths, accompanied by reduced synthesis of other monosaccharides and oligosaccharides. Vigorously metabolizing leaf sheaths is more conducive to sucrose transport. This study provides valuable insights into the molecular mechanisms underlying Arg-mediated sucrose accumulation specifically in the sugarcane YZ05-51 sugarcane, highlighting its critical regulatory roles.

Axillary bud germination in sugarcane is a critical agronomic trait that directly determines seedling emergence and tillering capacity; however, its molecular regulatory mechanisms remain poorly understood. In this study, we systematically investigated the hormonal dynamics and transcriptomic profiles of the sugarcane cultivar XTT22 across five developmental stages (from dormancy to the first new leaf stage). Our results revealed that abscisic acid (ABA) content fluctuated during germination, whereas indole-3-acetic acid (IAA) and gibberellin (GA) levels decreased significantly, suggesting their negative regulatory roles. In contrast, cytokinin (CTK) and ethylene (ETH) contents increased at the initiation stage, indicating positive promoting functions. Transcriptome analysis identified 31,513 differentially expressed genes (DEGs), which were significantly enriched in pathways related to hormone signal transduction, starch/sucrose metabolism, and photosynthesis. Weighted gene co-expression network analysis (WGCNA) constructed 12 co-expression modules, among which the antiquewhite4 module (negatively correlated with IAA, GA, and ABA contents) and the darkorange2 module (positively correlated with cytokinin content) were identified as key regulatory modules. From these modules, seven core hub transcription factors (e.g., ScTCP5, ScSCR, and ScSHR1) were screened, and their expression patterns were validated by RT-qPCR. Furthermore, the expression trends of six hormone-related DEGs were highly consistent with the RNA-seq data. Collectively, this study elucidates the hormonal dynamics and gene regulatory networks underlying axillary bud germination in sugarcane, providing candidate gene resources for breeding high-yield varieties with enhanced emergence and tillering capacity.

Saccharum spontaneum L. (wild sugarcane) possesses advantages such as strong perenniality, high stress resistance, and broad adaptability, making it the most successfully utilized wild species in sugarcane hybrid breeding. However, previous exploitation of S. spontaneum has been limited. To further explore its breeding potential, this study employed recurrent selection to improve the population of S. spontaneum (S0) before its application in germplasm innovation. Subsequently, S1 (containing two S. spontaneum bloodlines) were developed and optimized. Using S1 as dual parents, S2 (containing three or more S. spontaneum bloodlines) were further created and selected. Genetic diversity among 199 materials from seven populations (S0, S1 and S2) was evaluated using simple sequence repeat (SSR) markers. The results showed that an unweighted pair-group method with arithmetic means (UPGMA) cluster analysis based on genetic distance classified the 199 S. spontaneum materials into seven groups, largely consistent with their original population divisions. Compared to their parents, the S1 population generated an average of 18.79 novel loci (mutation rate: 25.00%), while the S2 population produced an average of 15.40 novel loci (mutation rate: 19.00%). The polymer of S. spontaneum exhibited rich genetic diversity, with Nei’s gene diversity index of 0.3390 and Shannon information index of 0.5082. Due to the increased number of original parents and trait pyramiding, the polymer of S. spontaneum demonstrated expanded genetic backgrounds and enhanced heterogeneity. Furthermore, hybridization and recombination generated novel elite loci compared to their parents, further enriching the overall genetic background and diversity of the polymer of S. spontaneum.

Potassium (K) is a critical macronutrient for sugarcane (Saccharum spp.), playing a vital role in metabolic processes, sucrose accumulation, and yield formation. Herein, this study systematically evaluated the effects of potassium oxide (K₂O) application on sugarcane (cultivar YZ1696) growth at the seedling and tillering stages. Hydroponic experiments demonstrated that 6 mmol/L K₂O optimally promoted seedling growth, whereas field trials revealed that 150 kg/ha K₂O maximized growth rate, yield, and sucrose content. Sugarcane growth exhibited a biphasic response—stimulation followed by inhibition—with increasing K₂O dosage at both developmental stages. Transcriptomic profiling of sugarcane roots under low-potassium (K-deficient), optimal potassium, and high-potassium conditions identified 10,266 differentially expressed genes (DEGs), with the most pronounced transcriptional shifts occurring under K deficiency. Functional enrichment analysis identified DEGs associated with potassium transport, calcium signaling, and carbohydrate metabolism. Notably, potassium uptake was mediated by distinct mechanisms: Shaker family channels (AKT1, AKT2, SPIKE) and the TPK family member KCO1 were induced under optimal K supply, whereas HAK/KUP/KT transporters (HAK1/5/10/21/25) exhibited broad activation across K concentrations, underscoring their key role in K homeostasis. Furthermore, calcium signaling genes (e.g., CIPK23) displayed K-dependent expression patterns. Weighted gene co-expression network analysis identified key gene modules that correlated strongly with agronomic traits, including plant height, yield, and sucrose content. Optimal K conditions favored the expression of yield- and sucrose-associated genes, suggesting a molecular basis for K-mediated productivity enhancement. Our findings revealed the genetic and physiological mechanisms underlying K-dependent sugarcane improvement, providing actionable insights for precise potassium fertilization to maximize the yield and sugar content.

Sugarcane is a complex polyploid aneuploid cash crop, and transgenic varieties are important for molecular genetic and traditional breeding approaches. Herein, the sugarcane variety ROC22 served as the receptor, the Bar gene served as a screening marker, and positive and negative fragments of the ScD27.2 gene, upstream of strigolactones (SLs) biosynthesis genes driven by the 35S promoter, were introduced by Agrobacterium tumefaciens-mediated transformation. Regenerated plants were obtained by co-culture, screening culture, and differentiation induction, and 27 sense and antisense ScD27.2 transgenic seedlings were obtained by herbicide screening. PCR detection and 1% Basta (Glufosinate) application on leaves revealed Bar in all lines, with all testing positive for herbicide application and 23 containing the target gene (positive resistance screening rate = 87.5%). q-PCR and phenotypic analyses showed that ScD27.2 expression, plant height, tiller number, root length, stem diameter, and fresh weight were decreased in transgenic (ScD27.2R-9) compared with non-transgenic (NT and ScD27.2F-2) lines. ScD27.2 expression was downregulated, and growth potential was inhibited. Under 20% PEG treatment, malondialdehyde (MDA) content in ScD27.2R-9 was higher than in NT, while proline content was lower. Under drought stress, ScD27.2 expression, MDA levels, and proline content in ScD27.2F-2 and NT were higher than in non-treated controls, ScD27.2 expression increased with time, and MDA and proline levels also increased. ScD27.2 expression in ScD27.2R-9 decreased under 20% PEG treatment, MDA and proline increased (but not to NT levels), and growth was lower than NT. The 20% PEG treatment also increased the levels of (±)-2′-epi-5-deoxystrigol and (+)-abscisic acid in the rooting culture media of ScD27.2F-2, ScD27.2R-9, and NT lines, but the levels of (+)-abscisic acid content in ScD27.2R-9 was lower than in NT. Thus, interfering with ScD27.2 expression decreased resistance to 20% PEG treatment. ScD27.2 encodes a β-carotene isomerase involved in SLs biosynthesis that might function in sugarcane resistance to drought stress. It explains the role of SLs in sugarcane growth and development and responses to drought stress.

In China, sugarcane (Saccharum spp.) hybrid cross-breeding began in 1953; approximately 70 years since then, >100 commercial sugarcane varieties have been created. In this study, 88 commercial varieties bred in China between 1953 and 2010 and 12 original foundational varieties were planted to investigate the effect of improving sugarcane varieties in China. Considering 20 years as a time node, the commercial varieties were classified into four improved generations. Retrospective analysis showed significant improvements in sucrose and other technological characteristics of commercial sugarcane varieties. The adoption of improved varieties over generations has continuously increased sugarcane’s sucrose, juice sugar, and gravity purity, and the difference was significant between Gen1 and Gen3, and between Gen2 and Gen4. Gen4 showed 2.06%, 2.35%, and 3.69% higher sugarcane sucrose (p < 0.01), juice sugar (p < 0.01), and purity (p < 0.05), respectively, and 1.13% lower sugarcane fiber (p < 0.01) than Gen1, the original foundational hybrid varieties. The development of new varieties has improved the technological characteristics of Chinese sugarcane. Sugarcane sucrose, juice sugar, and purity showed an increasing trend. Sugarcane fiber content did not significantly change with the development of new varieties but declined in comparison with the original foundational hybrid varieties.

In the breeding of new sugarcane varieties, the survey data do not always conform with a normal or linear distribution. To apply non-normal or non-linear data to evaluate new material requires a suitable evaluation model or method. The projection pursuit clustering (PPC) model is a statistical method that does not require making normal assumptions or other model assumptions on sample data, and is suitable to analyze high-dimensional, non-linear, and non-normal data. However, this model has been applied infrequently to crop variety evaluation. In this study, 103 varieties that have been bred over the last 70 years in China were planted, and their main industrial and agronomic traits were collected. Through the exploratory analysis of the data structure characteristics, the PPC model was used to evaluate these sugarcane varieties. The model provided good projection directions of agronomic and industrial traits, with accurate projection values. PPC models could evaluate sugarcane resources well, and the results were objective and reliable. Thus, the PPC model could be used as a new method for crop variety evaluation. At the same time, 51 excellent industrial and agronomic variety resources were screened for application in breeding.

Sugarcane (Saccharum spp.) breeding in China has a history of nearly 70 years. Yunnan province represents the second largest sugarcane planting area in China; therefore, by studying the evolution of sugarcane varieties in this region, it is possible to gain an understanding of the process of improvement since the foundation of sugarcane hybrid breeding. In this study, we compared the main industrial and agronomical characteristics of 107 sugarcane varieties, developed between 1952 and 2020, and discussed the reasons for replacement and exchange. Overall, significant differences were observed (p < 0.01), highlighting notable improvements, especially in terms of yield; however, disease incidence remains a serious issue and the fundamental reason for variety replacement. Meanwhile, analysis of parent traceability revealed that the main varieties cultivated at present have a similar parental relationship based around CP, F, and YC series germplasms. Taken together, these findings suggest that disease-resistant breeding should be strengthened, and susceptible varieties eliminated, while making full use of existing varieties as core parents.

Sugarcane (Saccharum spp.) is an important economic crop, supplying up to 80% of the table sugar and ~60% of bio-ethanol worldwide. Due to population growth and dwindling fossil-fuel reserves, the demand for sugar and bio-ethanol requires significant improvement in sugarcane production. Breeding sugarcane cultivars with high-performance agronomic traits is undoubtedly the most efficient way to achieve this goal. Therefore, evaluating agronomic traits and dissecting underlying loci are critically important for this aim steps in providing genetic resources and molecular markers for selection. In this study, we assembled a diversity panel of 236 elite sugarcane germplasms originally collected from 12 countries. We evaluated 28 agronomic traits in the diversity panel with three replicates. The diversity panel was genotyped using amplified fragment length polymorphism markers, and a total of 1,359 markers were generated. Through the genome-wide association study, we identified three markers significantly associated with three traits evaluated at a stringent threshold (P < 0.05 after Bonferroni correction). The genotypes of the three associated markers grouped respective trait values into two distinct groups, supporting the reliability of these markers for breeding selection. Our study provides putative molecular markers linked to agronomic traits for breeding robust sugarcane cultivars. Additionally, this study emphasized the importance of sugarcane germplasm introduced from other countries and suggested that the use of these germplasms in breeding programs depends on local industrial needs.