Genome-Wide Association Study Unravels Quantitative Trait Loci and Genes Associated with Yield-Related Traits in Sugarcane.

Sugarcane, a major sugar and energy crop worldwide faces an increasing demand for higher yields. Identifying yield-related markers and candidate genes is valuable for breeding high-yield varieties using molecular techniques. In this work, seven yield-related traits were evaluated in a diversity panel of 159 genotypes, derived from Tripidium arundinaceum, Saccharum spontaneum, and modern sugarcane genotypes. All traits exhibited significant genetic variance with high heritability and high correlations. Genetic diversity analysis reveals a genomic decay of 23 kb and an average single nucleotide polymorphism (SNP) number of 25,429 per genotype. These 159 genotypes were divided into 4 subgroups. Genome-wide association analysis identified 47 SNPs associated with brix, spanning 36 quantitative trait loci (QTLs), and 138 SNPs for other traits across 104 QTLs, covering all 32 chromosomes. Interestingly, 12 stable QTLs associated with yield-related traits were identified, which contained 35 candidate genes. This work provides markers and candidate genes for marker-assisted breeding to improve sugarcane yields.

Cold-Induced Physiological and Biochemical Alternations and Proteomic Insight into the Response of Saccharum spontaneum to Low Temperature.

Sugarcane, a cash crop, is easily affected by low temperature, which results in a decrease in yield and sugar production. Breeding a new variety with cold tolerance is an essential strategy to reduce loss from cold stress. The identification of germplasms and genes/proteins with cold tolerance is a vital step in breeding sugarcane varieties with cold tolerance via a conventional program and molecular technology. In this study, the physiological and biochemical indices of 22 genotypes of S. spontaneum were measured, and the membership function analysis method was used to comprehensively evaluate the cold tolerance ability of these genotypes. The physiological and biochemical indices of these S. spontaneum genotypes showed a sophisticated response to low temperature. On the basis of the physiological and chemical indices, the genotypes were classified into different cold tolerance groups. Then, the high-tolerance genotype 1027 and the low-tolerance genotype 3217 were selected for DIA-based proteomic analysis by subjecting them to low temperature. From the four comparison groups, 1123, 1341, 751, and 1693 differentially abundant proteins (DAPs) were identified, respectively. The DAPs based on genotypes or treatments participated in distinct metabolic pathways. Through detailed analysis of the DAPs, some proteins related to protein homeostasis, carbohydrate and energy metabolism, amino acid transport and metabolism, signal transduction, and the cytoskeleton may be involved in sugarcane tolerance to cold stress. Furthermore, five important proteins related to cold tolerance were discovered for the first time in this study. This work not only provides the germplasms and candidate target proteins for breeding sugarcane varieties with cold tolerance via a conventional program and molecular breeding, but also helps to accelerate the determination of the molecular mechanism underlying cold tolerance in sugarcane.

Quantitative Trait Loci Mapping and Development of KASP Marker Smut Screening Assay Using High-Density Genetic Map and Bulked Segregant RNA Sequencing in Sugarcane (Saccharum spp.).

Sugarcane is one of the most important industrial crops globally. It is the second largest source of bioethanol, and a major crop for biomass-derived electricity and sugar worldwide. Smut, caused by Sporisorium scitamineum, is a major sugarcane disease in many countries, and is managed by smut-resistant varieties. In China, smut remains the single largest constraint for sugarcane production, and consequently it impacts the value of sugarcane as an energy feedstock. Quantitative trait loci (QTLs) associated with smut resistance and linked diagnostic markers are valuable tools for smut resistance breeding. Here, we developed an F1 population (192 progeny) by crossing two sugarcane varieties with contrasting smut resistance and used for genome-wide single nucleotide polymorphism (SNP) discovery and mapping, using a high-throughput genotyping method called "specific locus amplified fragment sequencing (SLAF-seq) and bulked-segregant RNA sequencing (BSR-seq). SLAF-seq generated 148,500 polymorphic SNP markers. Using SNP and previously identified SSR markers, an integrated genetic map with an average 1.96 cM marker interval was produced. With this genetic map and smut resistance scores of the F1 individuals from four crop years, 21 major QTLs were mapped, with a phenotypic variance explanation (PVE) > 8.0%. Among them, 10 QTLs were stable (repeatable) with PVEs ranging from 8.0 to 81.7%. Further, four QTLs were detected based on BSR-seq analysis. aligning major QTLs with the genome of a sugarcane progenitor Saccharum spontaneum, six markers were found co-localized. Markers located in QTLs and functional annotation of BSR-seq-derived unigenes helped identify four disease resistance candidate genes located in major QTLs. 77 SNPs from major QTLs were then converted to Kompetitive Allele-Specific PCR (KASP) markers, of which five were highly significantly linked to smut resistance. The co-localized QTLs, candidate resistance genes, and KASP markers identified in this study provide practically useful tools for marker-assisted sugarcane smut resistance breeding.

Metabolic and proteomic analysis of nitrogen metabolism mechanisms involved in the sugarcane - Fusarium verticillioides interaction.

Pokkah boeng disease (PBD) is a foliar disease causing severe losses in sugarcane crop production. Research into resistance mechanisms against the causal agent, Fusarium verticillioides, is particularly important for farmers and researchers. This work based on the comprehensive analysis of metabolic, proteomic, and bioinformatics data on nitrogen (N) metabolism, which revealed that this biosynthetic reactions was closely related to resistance mechanisms in the sugarcane- F. verticillioides interaction. Our results suggested that pathogen infection reduced the suppression of nitrate reductase (NR) activity, reducing ammonium nitrogen (NH4+-N) and nitrate nitrogen (NO3--N) assimilation, which reduces glutamine synthetase (GS), glutamate synthetase (GOGAT) activity and polynucleotide synthesis and promotes RNA degradation, resulting in a decrease in ribosome levels and protein synthesis. Cysteine was found to be associated with the symptoms of PBD, while alanine, lysine, proline, and glutamic acid were found to be involved in protective and regulatory mechanisms as well. Additionally, glutamate played an important role in sugarcane defense against pathogens through the biosynthesis of proline and polyamines. Cyanamide, glutamate, proline, tyrosine, and arachidonic acid metabolism actively participate in resistance and response to stress. C5XPZ6 and C5XCA6 were considered to be critical proteins and key effectors according to this study. In conclusion, we have identified potential proteins and pathways involved in sugarcane resistance to F. verticillioides, revealing new findings that may be useful in the design of future diagnostics or sugarcane protection strategies and providing new insights into the molecular mechanisms of sugarcane-pathogen interactions.

Analysis of clinical characteristics and laboratory findings of 95 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a retrospective analysis.

BACKGROUND: Since December 2019, 2019 novel coronavirus pneumonia emerged in Wuhan city and rapidly spread throughout China and even the world. We sought to analyse the clinical characteristics and laboratory findings of some cases with 2019 novel coronavirus pneumonia . METHODS: In this retrospective study, we extracted the data on 95 patients with laboratory-confirmed 2019 novel coronavirus pneumonia in Wuhan Xinzhou District People's Hospital from January 16th to February 25th, 2020. Cases were confirmed by real-time RT-PCR and abnormal radiologic findings. Outcomes were followed up until March 2th, 2020. RESULTS: Higher temperature, blood leukocyte count, neutrophil count, neutrophil percentage, C-reactive protein level, D-dimer level, alanine aminotransferase activity, aspartate aminotransferase activity, α - hydroxybutyrate dehydrogenase activity, lactate dehydrogenase activity and creatine kinase activity were related to severe 2019 novel coronavirus pneumonia and composite endpoint, and so were lower lymphocyte count, lymphocyte percentage and total protein level. Age below 40 or above 60 years old, male, higher Creatinine level, and lower platelet count also seemed related to severe 2019 novel coronavirus pneumonia and composite endpoint, however the P values were greater than 0.05, which mean under the same condition studies of larger samples are needed in the future. CONCLUSION: Multiple factors were related to severe 2019 novel coronavirus pneumonia and composite endpoint, and more related studies are needed in the future.

Raoultella sp. strain L03 fixes N2 in association with micropropagated sugarcane plants.

N2 -fixing bacteria belonging to the genus Raoultella of the family Enterobacteriaceae are widely associated with plants. Raoultella sp. strain L03 was isolated from surface-sterilized sugarcane roots. In this study, we inoculated the strain L03 to microbe-free micropropagated plantlets of the main sugarcane cultivar ROC22 grown in Guangxi, China and determined N2 -fixation and association between strain L03 and sugarcane plants. Inoculation of strain L03 increased plant biomass, total N, N concentration and chlorophyll, and relieved N-deficiency symptoms of plants under an N-limiting condition. An (15) N isotope dilution assay revealed (15) N isotope dilution in the inoculated sugarcane plants and incorporation of the fixed (14) N from air into chlorophyll. Moreover, a gfp-tagged and antibiotic-resistant L03 strain was reisolated from surface-sterilized sugarcane plants and was detected in plant tissues by fluorescent microscopy. This study for the first time demonstrates that a Raoultella bacterium is able to fix N2 in association with the plant host.