Theory to practice: a success in breeding sugarcane variety YZ08-1609 known as the King of Sugar.

Sugarcane, a significant cash crop in tropical and subtropical regions, contributes to 80% of sugar production and 40% of bioethanol production in the world. It is a key sugar crop, accounting for 85% of sugar production in China. Developing new varieties with high yield, high sugar, and better stress resistance is crucial for the sustainable growth of sugar industry. Hybrid breeding is the most widely used and effective method, with over 98% of Chinese sugarcane varieties resulting from this approach. Over the past two decades, Chinese breeders have developed the theory of high-heterogeneous composite high-sugar breeding, leading to the successful breeding of the fifth-generation sugarcane varieties. Among them, YZ08-1609, a complex hybrid of Saccharum spp., was developed by Sugarcane Research Institute (YSRI) of Yunnan Academy of Agricultural Sciences. The average cane yield of YZ08-1609 was 14.4% higher than ROC22. It is highly resistant to mosaic disease, and highly tolerant to drought stress, but moderately susceptible to smut disease. Notably, YZ08-1609 stands out with a sucrose content of 20.3%, setting an international record, earning the reputation as "King of Sugar". To summarize experience and inspire breeding, we provided here the detailed insights into the selection of parents, breeding process, and characteristics of YZ08-1609. Besides, the biological mechanisms underlying its high yield and high sugar was excavated at both transcriptional and metabolic levels. The challenges and prospects in breeding sugarcane varieties especially with high sugar were also discussed, offering a foundation for the future development of high-sugar varieties.

CRISPR/Cas12a-based approaches for efficient and accurate detection of Phytophthora ramorum.

Introduction: Phytophthora ramorum is a quarantine pathogen that causes leaf blight and shoot dieback of the crown, bark cankers and death on a number of both ornamental and forest trees, especially in North America and northern Europe, where it has produced severe outbreaks. Symptoms caused by P. ramorum can be confused with those by other Phytophthora and fungal species. Early and accurate detection of the causal pathogen P. ramorum is crucial for effective prevention and control of Sudden Oak Death. Methods: In this study, we developed a P. ramorum detection technique based on a combination of recombinase polymerase amplification (RPA) with CRISPR/Cas12a technology (termed RPACRISPR/ Cas12a). Results: This novel method can be utilized for the molecular identification of P. ramorum under UV light and readout coming from fluorophores, and can specifically detect P. ramorum at DNA concentrations as low as 100 pg within 25 min at 37°C. Discussion: We have developed a simple, rapid, sensitive, unaided-eye visualization, RPA CRISPR/Cas12a-based detection system for the molecular identification of P. ramorum that does not require technical expertise or expensive ancillary equipment. And this system is sensitive for both standard laboratory samples and samples from the field.

RPA-CRISPR/Cas12a mediated isothermal amplification for visual detection of Phytophthora sojae.

Introduction: Phytophthora sojae is among the most devastating pathogens of soybean (Glycine max) and severely impacts soybean production in several countries. The resulting disease can be difficult to diagnose and other Phytophthora species can also infect soybean. Accurate diagnosis is important for management of the disease caused by P. sojae. Methods: In this study, recombinase polymerase amplification (RPA) in combination with the CRISPR/Cas12a system were used for detection of P. sojae. The assay was highly specific to P. sojae. Results: The test results were positive for 29 isolates of P. sojae, but negative for 64 isolates of 29 Phytophthora species, 7 Phytopythium and Pythium species, 32 fungal species, and 2 Bursaphelenchus species. The method was highly sensitive, detecting as little as 10 pg.µL-1 of P. sojae genomic DNA at 37°C in 20 min. The test results were visible under UV light and readout coming from fluorophores. In addition, P. sojae was detected from natural inoculated hypocotyls of soybean seedlings using this novel assay. The rapidity and accuracy of the method were verified using 30 soybean rhizosphere samples. Discussion: In conclusion, the RPA-CRISPR/Cas12a detection assay developed here is sensitive, efficient, and convenient, and has potential for further development as a kit for monitoring root rot of soybean in the field.

A Frontline, Rapid, Nucleic Acid-Based Fusarium circinatum Detection System Using CRISPR/Cas12a Combined with Recombinase Polymerase Amplification.

Pitch canker caused by the fungus Fusarium circinatum is a damaging disease that affects pines in Europe, South Africa, and North America in both the southeast and west coast of the United States. Several countries, including China, have listed F. circinatum as a quarantine pathogen. Timely detection, an important pillar of the quarantine effort, can efficiently prevent the introduction of F. circinatum into new areas or facilitate management and eradication strategies in already infested sites. In this study, we developed an F. circinatum detection technique based on a combination of recombinase polymerase amplification (RPA) with CRISPR/Cas12a technology (termed RPA-CRISPR/Cas12a). After obtaining DNA, this novel method can be utilized for the molecular identification of F. circinatum using the naked eye and can specifically detect F. circinatum at DNA concentrations as low as 200 fg within 30 min at 37°C. The system is sensitive for both standard laboratory samples and samples from the field. In summary, we have developed a simple, rapid, sensitive, unaided-eye visualization, RPA-CRISPR/Cas12a-based detection system for the molecular identification of F. circinatum that does not require technical expertise or expensive ancillary equipment.

First Report of Fusarium acuminatum Causing Dianthus chinensis root rot and foliage blight in China.

Dianthus chinensis is a popular ornamental plant that is widely cultivated in China. In May 2020, a disease was found at several landscape sites in Xuanwu District, Nanjing, China, causing symptoms of foliage blight and root discoloration on approximately 52% of one-year old D. chinensis plants. To recover the causal pathogen, samples of infected roots and leaves were cut into 5×5 mm2 pieces, surface-disinfected in 75% ethanol for 30 sec, followed by 1% NaClO for 90 sec, rinsed with sterile water three times and placed on potato dextrose agar (PDA) with 0.1 mg/mL of ampicillin at 25 °C. Hyphae growing on PDA were visible from both root and leaf tissues after three days. Individual hyphal tips were transferred to new PDA plates to obtain pure isolates. Three representative isolates were deposited in the China Forestry Culture Collection Center (CFCC 57545,57546, 57547). The hyphae grew radially, densely, and the aerial hyphae were velvety, white, yellow-white, or pink-white. Representative isolate Facu-DCY5 produced three types of conidia (microconidia, macroconidia, and chlamydospores). Macroconidia were sickle-shaped, measuring 25.7-55.4 µm × 3.2-4.6 µm (n=50). Microconidia were numerous, oval or kidney-shaped, measuring 6.8-11.9 µm × 3.5-4.8 µm (n=50). Conidia produced in the aerial mycelium were 16-34 × 2.2-5.3 µm (n=50). The ITS region, TEF1, calmodulin (CMDA), and RNA polymerase II second largest subunit (RPB2) were amplified with primers ITS1/ITS4, EF1/EF2, CL1/CL2A and 5F2/7CR , respectively and sequenced at Sangon Biotech (Nanjing, China). The ITS sequence of isolate Facu-DCY5 (GenBank No. ON307073.1) was identical to HQ165938.1, ON306850.1, OM964482.1. TEF1 (ON331997.1) was identical to LC546967.1, HQ165866.1, MZ158155.1. CMDA (ON331996.1) was identical to HQ412345.1, MZ921595.1 and MZ921597.1. RPB2 (ON331995.1) was identical to MZ997370.1. Maximum parsimony and maximum likelihood phylogenies of the Facu-DCY5 multilocus sequence data and those of several species within the F. tricinctum species complex identified the isolate from D. chinensis as F. acuminatum . Pathogenicity tests were performed using a conidial suspension (104 conidia/mL). Each plant (approx. 0.3 m in -height) was inoculated with 1 mL of the conidial suspension by mixing it into the potting soil (500 g). Control plants were treated with sterile distilled water. All inoculated plants (n=9) in three repeats of the assay exhibited foliage blight and root rot after 15 days, whereas all control plants (n=9) remained asymptomatic. Fusarium isolates with identical morphological features and molecular marker sequences to those of Facu-DCY5 were recovered from foliage blight and root tissues of all the inoculated plants. In China, F. acuminatum has been reported as a pathogen of Cucurbita maxima, Actinidia arguta, Polygonatum odoratumand Schisandra chinensis. This is the first report of F. acuminatum on D. chinensis in China. Considering the importance of D. chinensis to both ornamental nurseries and landscaping industries, we recommend that diseased plants be removed to prevent the spread of F. acuminatum, and that identification of the infecting isolates from D. chinensis at other sites and landscape locations be performed.

First Report of Crown and Root Rot Caused by Fusarium solani on Photinia × fraseri Dress in China.

Photinia × fraseri Dress was introduced to China at the end of the 20th century. It is a kind of colorful ornamental tree species with great ornamental value. From 2020 to 2021, a disease was found in Railway Gymnasium, Xuanwu district of Nanjing which approximately 40% P. × fraseri showed symptoms of blight with discoloration and dieback of crown and root . Symptomatic root tissues collected from three 2-year-old plants were rinsed with water, cut into 2-mm pieces which were surface-sterilized in 70 % ethanol for 60 s, and plated onto Potato Dextrose Agar (PDA), and incubated in the dark at 26 °C for 3 days. Mycelium emerged from 75 % of the samples. Two representative isolates (SG31, SG32) were obtained and deposited in China's Forestry Culture Collection Center. The colony growed in a circular shape, and the early aerial hyphae were white. Later a floccose, white, colony which was dull yellow on the underside was observed . The two isolates had identical morphological features. The macroconidia were sickle-shaped with two to three septa, 22.8 - 43.7 µm × 4.1 - 5.8 µm in size (n=50). The microconidia were numerous, oval, fusiform, renal, or oblong, with zero or one septum, 10.96 - 14.63 µm × 3.89 - 5.76 µm in size (n=50). The hyphae begin to germinate from one or both ends of the spore . Thus, the two isolates were identified as Fusarium solani. For molecular identification, the DNA of the two isolates was extracted. The internal transcribed spacer (ITS) region, ß-tubulin (TUB2), and actin gene (ACT) region were amplified using the primer pairs ITS5 / ITS4, T1 / T2 , and ACT-512F / ACT-783R), respectively. The sequences were deposited in GenBank under accession numbers ON329814, ON366356, and ON366358 for SG31 and ON329813, ON366357, and ON366359 for SG32. The ITS, TUB2, and ACT sequences of isolate SG31 were 99.83% (574 / 575 nt), 99.81% (517 / 518 nt), and 100% (248 / 248 nt) identical to those of SF_450 (MT529726.1), CH64 (KU938961.1), and Co.Karbala-IQ1 (MW080737.1), respectively (The comparison results of SG32 were shown in Appendix.). Based on morphological and molecular analysis, the two isolates were identified as F. solani. The pathogenicity of SG31 and SG32 were tested on potted 1-yr-old (30-cm tall) P. × fraseri. Nine plants were dug up to expose root balls, which were wounded before inoculations with a sterile needle, and then inoculated with conidial suspension (106 conidia / mL). Controls were treated with ddH2O. Three seedlings/isolate were used for each treatment. All plants were repotted using the original sterilized potting mix and pots. After inoculation, the plants were covered with plastic bags, and sterilized H2O was sprayed into the bags twice per day to maintain humidity and kept in a greenhouse at the day/night temperatures at 25 ± 2 / 16 ± 2 ℃. Within 30 days, all the inoculated plants showed lesions similar to those observed in the field, whereas controls were asymptomatic. The isolates were reisolated from the lesions (whereas not from controls) and sequenced as F. solani. Globally, this is the first report of F. solani causing crown blight and root rot of P. × fraseri. Additional surveys are being conducted for mapping the distribution of F. solani in Jiangsu Province of China.

Correction: Genetic analysis of agronomic traits in elite sugarcane (Saccharum spp.) germplasm.

[This corrects the article DOI: 10.1371/journal.pone.0233752.].

Electrospinning Superassembled Mesoporous AIEgen-Organosilica Frameworks Featuring Diversified Forms and Superstability for Wearable and Washable Solid-State Fluorescence Smart Sensors.

Flexible optical sensors are widely studied and applied in many fields. However, developing highly stable and washable wearable sensors in optics is still facing significant challenges. Here, we demonstrate an AIEgen-organosilica framework (TPEPMO) hybrid nanostructure-based flexible optical sensor, which is prepared by a two-step co-condensation and electrospinning superassembly process. Organosilica precursors with aggregation-induced emission (AIE) features are covalently linked into periodic mesoporous organosilica (PMO) frameworks with high fluorescent efficiency due to the restriction of intramolecular motion. The three-dimensional space of ordered porous materials provides abundant reaction sites, allowing rapid and sensitive monitoring of analytes. TPEPMOs exhibit good properties as acidic pH fluorescent sensors with a pKa of 4.3. A flexible film is obtained by dispersing TPEPMO nanospheres in a poly(lactic-co-glycolic acid) (PLGA) and polyacrylonitrile (PAN) hybrid fibrous matrix (TPEPMO-CFs) using the electrospinning superassembly technique and is successfully served as an efficient fluorescent probe for the naked eye detection of ammonia gas and HCl vapor by emission changes. The fluorescence of TPEPMO-CFs can be reversed in the presence of volatile acidic/alkaline gas for more than five cycles, exhibiting excellent recyclability. In addition, TPEPMO-CF sensors show excellent washability and long-term photostability (fluorescence was maintained above 94% after washing 10 times). These stimuli-responsive AIEgen-organosilica frameworks featuring diversified forms and superstability for wearable and washable solid-state fluorescence exhibit great potential for smart gas sensors, wearable devices, and solid-state lighting applications.

Genetic analysis of agronomic traits in elite sugarcane (Saccharum spp.) germplasm.

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.