A chromosomal-scale genome assembly of modern cultivated hybrid sugarcane provides insights into origination and evolution.

Sugarcane is a vital crop with significant economic and industrial value. However, the cultivated sugarcane's ultra-complex genome still needs to be resolved due to its high ploidy and extensive recombination between the two subgenomes. Here, we generate a chromosomal-scale, haplotype-resolved genome assembly for a hybrid sugarcane cultivar ZZ1. This assembly contains 10.4 Gb genomic sequences and 68,509 annotated genes with defined alleles in two sub-genomes distributed in 99 original and 15 recombined chromosomes. RNA-seq data analysis shows that sugar accumulation-associated gene families have been primarily expanded from the ZZSO subgenome. However, genes responding to pokkah boeng disease susceptibility have been derived dominantly from the ZZSS subgenome. The region harboring the possible smut resistance genes has expanded significantly. Among them, the expansion of WAK and FLS2 families is proposed to have occurred during the breeding of ZZ1. Our findings provide insights into the complex genome of hybrid sugarcane cultivars and pave the way for future genomics and molecular breeding studies in sugarcane.

Application of improved YOLOv7-based sugarcane stem node recognition algorithm in complex environments.

Introduction: Sugarcane stem node detection is one of the key functions of a small intelligent sugarcane harvesting robot, but the accuracy of sugarcane stem node detection is severely degraded in complex field environments when the sugarcane is in the shadow of confusing backgrounds and other objects. Methods: To address the problem of low accuracy of sugarcane arise node detection in complex environments, this paper proposes an improved sugarcane stem node detection model based on YOLOv7. First, the SimAM (A Simple Parameter-Free Attention Module for Convolutional Neural Networks) attention mechanism is added to solve the problem of feature loss due to the loss of image global context information in the convolution process, which improves the detection accuracy of the model in the case of image blurring; Second, the Deformable convolution Network is used to replace some of the traditional convolution layers in the original YOLOv7. Finally, a new bounding box regression loss function WIoU Loss is introduced to solve the problem of unbalanced sample quality, improve the model robustness and generalization ability, and accelerate the convergence speed of the network. Results: The experimental results show that the mAP of the improved algorithm model is 94.53% and the F1 value is 92.41, which are 3.43% and 2.21 respectively compared with the YOLOv7 model, and compared with the mAP of the SOTA method which is 94.1%, an improvement of 0.43% is achieved, which effectively improves the detection performance of the target detection model. Discussion: This study provides a theoretical basis and technical support for the development of a small intelligent sugarcane harvesting robot, and may also provide a reference for the detection of other types of crops in similar environments.

Height detection of crop divider toes of sugarcane harvester based on Kalman adaptive adjustment.

Crop divider toes are an essential device of sugarcane harvester. Moving forward against the ground is a critical way to improve the harvesting rate of lodged sugarcane. Height detection is the basis for precise control of crop divider toes moving forward against the ground. Due to the current problem of operating difficulties in manually adjusting the height of crop divider, a height detection system based on a millimeter wave radar sensor was designed to detect the height of crop divider toes from the ground. This paper proposed a height detection method of crop divider toes for sugarcane harvester based on Kalman adaptive adjustment. The data measured by the sensor was pretreated to determine whether the height had changed. Reset the Kalman filter and adjust the parameters when changes occur to improve the filter response speed and ranging accuracy. To adapt to the scenario of quickly adjusting the height of crop divider during the traveling process of sugarcane harvester. A one-way ANOVA test and a two-way ANOVA test were conducted on a simulated test platform. The results of the one-way ANOVA test showed that both forward speed and vegetation cover thickness had a significant effect on height detection accuracy. The results of the two-way ANOVA test showed that the interaction of forward speed and vegetation cover thickness did not have a significant effect on ranging accuracy. It was verified through experiments that both the ranging accuracy and the response speed of height change were significantly improved after the processing of the method in this paper. The mean square error after processing was lower than 2.5 cm. The feasibility of the height detection system was verified by field trials. The results of this study will provide a reference for the design of automatic elevation of crop divider.

Quantitative evaluation of variation in defoliation traits among sugarcane genotypes.

Development of easily defoliating sugarcane varieties is urgently needed to facilitate efficient mechanical harvesting, reduce production costs, and increase sugar yield in China. In order to quantify the defoliation characteristics of sugarcane, we investigated eight traits in two field experiments with a range of sugarcane varieties at maturity. The length (LSR) and angle (ASR) of the sheath ruptured from the stalk, defoliation force (DF), and self-defoliation (SD) were the traits with the greatest contribution to the quantitative assessment of sugarcane defoliation based on a principal component analysis, which accounted for more than 75% of the cumulative variability. A small set of traits, namely SD, ASR, and DF measured at the 10th leaf were selected as predictors. Using these predictors, 37 out of 38 sugarcane cultivars were correctly classified into three groups (easy, difficult and intermediate in terms of ease of defoliation) that had been clustered based on six traits. These simplified measurements will be applied to screen new lines in the sugarcane breeding program in China.

Field Evaluation of Integrated Management for Mitigating Citrus Huanglongbing in Florida.

Citrus huanglongbing (HLB) is extremely difficult to control because the psyllid-transmitted bacterial pathogen resides inside the citrus phloem and the disease is systemic. In Florida, the nine billion dollar citrus industry has been significantly impacted by severe HLB epidemics. To combat citrus HLB, in this study we implemented an integrated strategy that includes chemotherapy, thermotherapy, and additional nutrition treatment in three different field trials over three consecutive years. In these trials, only trees already showing HLB symptoms with Ct values ranging from 25.1 to 27.7 were selected for treatments. To assess the complex interactions, we used several methods for evaluating the effectiveness of integrated management, including the slopes (b) of the Ct increase (dy/dt), the pathogenic index (PI) and the decline index (DI) from Ct value and tree scores, and the therapeutic efficacies from PI and DI. This comprehensive analysis showed that most of the tested chemicals were effective to some degree in killing or suppressing the Las bacterium, with higher therapeutic efficacies seen for Grove B, where citrus trees were severely affected by HLB, and it had a higher number of psyllids, relative to Grove E and P in the first 2 years. Trunk-injected penicillin G potassium was the most effective chemical treatment in all groves, followed by Oxytetracycline Calcium Complex, and Silver Nitrate delivered as foliar sprays. Although the steam heat treatment and additional nutrition did not eliminate or suppress Las over the long term, these treatments did positively affect tree growth and recovery in the short term. Overall, our results provide new insights into HLB control method and strategy for integrated management for HLB epidemic plantations.

Antimicrobial Compounds Effective against Candidatus Liberibacter asiaticus Discovered via Graft-based Assay in Citrus.

Huanglongbing (HLB), the most destructive citrus disease, is caused by three species of phloem-limited Candidatus Liberibacter. Chemical control is a critical short-term strategy against Candidatus Liberibacter asiaticus (Las). Currently, application of antibiotics in agricultural practices is limited due to public concerns regarding emergence of antibiotic-resistant bacteria and potential side effects in humans. The present study screened 39 antimicrobials (non-antibiotics) for effectiveness against Las using an optimized graft-based screening system. Results of principal component, hierarchical clustering and membership function analyses demonstrated that 39 antimicrobials were clustered into three groups: "effective" (Group I), "partly effective" (Group II), and "ineffective" (Group III). Despite different modes of action, 8 antimicrobials (aluminum hydroxide, D,L-buthionine sulfoximine, nicotine, surfactin from Bacillus subtilis, SilverDYNE, colloidal silver, EBI-601, and EBI-602), were all as highly effective at eliminating or suppressing Las, showing both the lowest Las infection rates and titers in treated scions and inoculated rootstock. The ineffective group, which included 21 antimicrobials, did not eliminate or suppress Las, resulting in plants with increased titers of Candidatus Liberibacter. The other 10 antimicrobials partly eliminated/suppressed Las in treated and graft-inoculated plants. These effective antimicrobials are potential candidates for HLB control either via rescuing infected citrus germplasms or restricted field application.

Transcriptomic characterization and potential marker development of contrasting sugarcane cultivars.

Sugarcane (Saccharum officinarum L.) is an important crop for sugar production and bioenergy worldwide. In this study, we performed transcriptome sequencing for six contrasting sugarcane genotypes involved in leaf abscission, tolerance to pokkah boeng disease and drought stress. More than 465 million high-quality reads were generated, which were de novo assembled into 93,115 unigenes. Based on a similarity search, 43,526 (46.74%) unigenes were annotated against at least one of the public databases. Functional classification analyses showed that these unigenes are involved in a wide range of metabolic pathways. Comparative transcriptome analysis revealed that many unigenes involved in response to abscisic acid and ethylene were up-regulated in the easy leaf abscission genotype, and unigenes associated with response to jasmonic acid and salicylic acid were up-regulated in response to the pokkah boeng disease in the tolerance genotype. Moreover, unigenes related to peroxidase, antioxidant activity and signal transduction were up-regulated in response to drought stress in the tolerant genotype. Finally, we identified a number of putative markers, including 8,630 simple sequence repeats (SSRs) and 442,152 single-nucleotide polymorphisms (SNPs). Our data will be important resources for future gene discovery, molecular marker development, and genome studies in sugarcane.

Interaction of salinity and cadmium stresses on mineral nutrients, sodium, and cadmium accumulation in four barley genotypes.

Interaction of salinity (NaCl) and cadmium (Cd) on growth, mineral nutrients, Na and Cd accumulation in four barley genotypes differing in salt tolerance was studied in a hydroponic experiment. Cd, NaCl and their combined stresses reduced Ca and Mg concentrations in roots and shoots, K concentration in shoots, increased K and Cu concentrations in roots relative to control, but had non-significant effect on micronutrients Cu, Fe and Mn concentrations in shoot. The three stresses reduced accumulation of most tested nutrients in both roots and shoots, except NaCl and NaCl+Cd stresses for root K and shoot Cu accumulation in salt tolerant genotypes. The salt tolerant genotypes did not have higher nutrient concentration and accumulation than the sensitive ones when exposed to Cd and NaCl stresses. In conclusion, the affecting mechanism of Cd stress on nutrients was to some extent different from salinity stress, and the NaCl+Cd stress was not equal to additional Cd and NaCl stresses, probably due to the different valence and competitive site of Na(+) and Cd(2+). NaCl addition in the Cd-containing medium caused remarkable reductions in both Cd concentration and accumulation, with the extent of reduction being also dependent on genotypes. The salt-tolerant genotypes had lower Na concentration than sensitive ones.

Genetic mapping of quantitative trait loci associated with beta-amylase and limit dextrinase activities and beta-glucan and protein fraction contents in barley.

High malting quality of barley (Hordeum vulgare L.) relies on many traits, such as beta-amylase and limit dextrinase activities and beta-glucan and protein fraction contents. In this study, interval mapping was utilized to detect quantitative trait loci (QTLs) affecting these malting quality parameters using a doubled haploid (DH) population from a cross of CM72 (six-rowed) by Gairdner (two-rowed) barley cultivars. A total of nine QTLs for eight traits were mapped to chromosomes 3H, 4H, 5H, and 7H. Five of the nine QTLs mapped to chromosome 3H, indicating a possible role of loci on chromosome 3H on malting quality. The phenotypic variation accounted by individual QTL ranged from 8.08% to 30.25%. The loci of QTLs for beta-glucan and limit dextrinase were identified on chromosomes 4H and 5H, respectively. QTL for hordeins was coincident with the region of silica eluate (SE) protein on 3HS, while QTLs for albumins, globulins, and total protein exhibited overlapping. One locus on chromosome 3H was found to be related to beta-amylase, and two loci on chromosomes 5H and 7H were found to be associated with glutelins. The identification of these novel QTLs controlling malting quality may be useful for marker-assisted selection in improving barley malting quality.