Whole-genome sequencing of a worldwide collection of sugarcane cultivars (Saccharum spp.) reveals the genetic basis of cultivar improvement.

Sugarcane is the main source of sugar worldwide, and 80% of the sucrose production comes from sugarcane. However, the genetic differentiation and basis of agronomic traits remain obscure. Here, we sequenced the whole-genome of 219 elite worldwide sugarcane cultivar accessions. A total of approximately 6 million high-quality genome-wide single nucleotide polymorphisms (SNPs) were detected. A genome-wide association study identified a total of 2198 SNPs that were significantly associated with sucrose content, stalk number, plant height, stalk diameter, cane yield, and sugar yield. We observed homozygous tendency of favor alleles of these loci, and over 80% of cultivar accessions carried the favor alleles of the SNPs or haplotypes associated with sucrose content. Gene introgression analysis showed that the number of chromosome segments from Saccharum spontaneum decreased with the breeding time of cultivars, while those from S. officinarum increased in recent cultivars. A series of selection signatures were identified in sugarcane improvement procession, of which 104 were simultaneously associated with agronomic traits and 45 of them were mainly associated with sucrose content. We further proposed that as per sugarcane transgenic experiments, ShN/AINV3.1 plays a positive role in increasing stalk number, plant height, and stalk diameter. These findings provide comprehensive resources for understanding the genetic basis of agronomic traits and will be beneficial to germplasm innovation, screening molecular markers, and future sugarcane cultivar improvement.

Genome-wide association study of kernel colour traits and mining of elite alleles from the major loci in maize.

BACKGROUND: Maize kernel colour is an important index for evaluating maize quality and value and mainly entails two natural pigments, carotenoids and anthocyanins. To analyse the genetic mechanism of maize kernel colour and mine single nucleotide polymorphisms (SNPs) related to kernel colour traits, an association panel including 244 superior maize inbred lines was used to measure and analyse the six traits related to kernel colour in two environments and was then combined with the about 3 million SNPs covering the whole maize genome in this study. Two models (Q + K, PCA + K) were used for genome-wide association analysis (GWAS) of kernel colour traits. RESULTS: We identified 1029QTLs, and two SNPs contained in those QTLs were located in coding regions of Y1 and R1 respectively, two known genes that regulate kernel colour. Fourteen QTLs which contain 19 SNPs were within 200 kb interval of the genes involved in the regulation of kernel colour. 13 high-confidence SNPs repeatedly detected for specific traits, and AA genotypes of rs1_40605594 and rs5_2392770 were the most popular alleles appeared in inbred lines with higher levels. By searching the confident interval of the 13 high-confidence SNPs, a total of 95 candidate genes were identified. CONCLUSIONS: The genetic loci and candidate genes of maize kernel colour provided in this study will be useful for uncovering the genetic mechanism of maize kernel colour, gene cloning in the future. Furthermore, the identified elite alleles can be used to molecular marker-assisted selection of kernel colour traits.

Genetic dissection of maize (Zea maysL.) trace element traits using genome-wide association studies.

Maize (Zea mays L.) is an important food and feed crop worldwide and serves as a a vital source of biological trace elements, which are important breeding targets. In this study, 170 maize materials were used to detect QTNs related to the content of Mn, Fe and Mo in maize grains through two GWAS models, namely MLM_Q + K and MLM_PCA + K. The results identified 87 (Mn), 205 (Fe), and 310 (Mo) QTNs using both methods in the three environments. Considering comprehensive factors such as co-location across multiple environments, strict significance threshold, and phenotypic value in multiple environments, 8 QTNs related to Mn, 10 QTNs related to Fe, and 26 QTNs related to Mo were used to identify 44 superior alleles. Consequently, three cross combinations with higher Mn element, two combinations with higher Fe element, six combinations with higher Mo element, and two combinations with multiple element (Mn/Fe/Mo) were predicted to yield offspring with higher numbers of superior alleles, thereby increasing the likelihood of enriching the corresponding elements. Additionally, the candidate genes identified 100 kb downstream and upstream the QTNs featured function and pathways related to maize elemental transport and accumulation. These results are expected to facilitate the screening and development of high-quality maize varieties enriched with trace elements, establish an important theoretical foundation for molecular marker assisted breeding and contribute to a better understanding of the regulatory network governing trace elements in maize.

Genome-wide identification and expression analysis of the cyclic nucleotide-gated ion channel (CNGC) gene family in Saccharum spontaneum.

BACKGROUND: Cyclic nucleotide-gated ion channels (CNGCs) are nonselective cation channels that are ubiquitous in eukaryotic organisms. As Ca2+ channels, some CNGCs have also proven to be K+-permeable and involved in plant development and responses to environmental stimuli. Sugarcane is an important sugar and energy crop worldwide. However, reports on CNGC genes in sugarcane are limited. RESULTS: In this study, 16 CNGC genes and their alleles were identified from Saccharum spontaneum and classified into 5 groups based on phylogenetic analysis. Investigation of gene duplication and syntenic relationships between S. spontaneum and both rice and Arabidopsis demonstrated that the CNGC gene family in S. spontaneum expanded primarily by segmental duplication events. Many SsCNGCs showed variable expression during growth and development as well as in tissues, suggesting functional divergence. Light-responsive cis-acting elements were discovered in the promoters of all the identified SsCNGCs, and the expression of most of the SsCNGCs showed a diurnal rhythm. In sugarcane, the expression of some SsCNGCs was regulated by low-K+ treatment. Notably, SsCNGC13 may be involved in both sugarcane development and its response to environmental stimuli, including response to low-K+ stress. CONCLUSION: This study identified the CNGC genes in S. spontaneum and provided insights into the transcriptional regulation of these SsCNGCs during development, circadian rhythm and under low-K+ stress. These findings lay a theoretical foundation for future investigations of the CNGC gene family in sugarcane.

Integrated Analysis of miRNAs Associated With Sugarcane Responses to Low-Potassium Stress.

Sugarcane is among the most important global crops and a key bioenergy source. Sugarcane production is restricted by limited levels of available soil potassium (K+). The ability of plants to respond to stressors can be regulated by a range of microRNAs (miRNAs). However, there have been few studies regarding the roles of miRNAs in the regulation of sugarcane responses to K+-deficiency. To understand how these non-coding RNAs may influence sugarcane responses to low-K+ stress, we conducted expression profiling of miRNAs in sugarcane roots under low-K+ conditions via high-throughput sequencing. This approach led to the identification of 324 and 42 known and novel miRNAs, respectively, of which 36 were found to be differentially expressed miRNAs (DEMs) under low-K+ conditions. These results also suggested that miR156-x/z and miR171-x are involved in these responses as potential regulators of lateral root formation and the ethylene signaling pathway, respectively. A total of 705 putative targets of these DEMs were further identified through bioinformatics predictions and degradome analyses, and GO and KEGG enrichment analyses revealed these target mRNAs to be enriched for catalytic activity, binding functions, metabolic processes, plant hormone signal transduction, and mitogen-activated protein kinase (MAPK) signaling. In summary, these data provide an overview of the roles of miRNAs in the regulation of sugarcane response to low-K+ conditions.

Use of Hematocrit for Short-Term Prognosis of Patients with Traumatic Brain Injury After Decompressive Craniectomy.

OBJECTIVE: To discuss the effects of the hematocrit (Hct) in patients with traumatic brain injury after decompressive craniectomy (DC). METHODS: Demographic data, inspection and treatment procedures, and 30-day prognosis were obtained for 158 patients with head injury who underwent unilateral DC in our hospital between January 2013 and June 2018. Uni- and multivariate logistic regression was applied to analyze independent risk factors for 30-day outcome. The quantitative analysis of postoperative Hct, ΔHct (postoperative Hct minus initial Hct), and their combination for the prognosis of patients with TBI was displayed graphically using receiver operating characteristic (ROC) curves. Multiple linear regression was used to explore factors influencing postoperative Hct and ΔHct. RESULTS: Short-term mortality was 29.7%. Uni- and multivariate logistic regression analysis showed that age (odds ratio [OR], 1.064; P = 0.024), Glasgow Coma Scale score (OR, 0.711; P = 0.027), Injury Severity Score (ISS) (OR, 1.156; P = 0.047), midline shift in millimeters (OR, 1.809; P <0.001), postoperative Hct (OR, 0.743; P = 0.001), and ΔHct (OR, 1.242; P =0.048) were independent risk factors for short-term death. In ROC curves, a combination of postoperative Hct and ΔHct showed the highest sensitivity (77.5%) and highest specificity (89.4%). When using this combination to predict prognosis, we could achieve an accuracy of 94.5%. ISS (ß = -0.172, P = 0.022), initial Hct (ß = 0.243, P = 0.001), principal hematoma location (ß = -2.628, P < 0.001), hours of operation (ß = -0.884, P = 0.048), and colloid quantity (ß = -0.002, P = 0.001) were independent contributing factors for ΔHct, which was similar to postoperative Hct. CONCLUSIONS: A combination of postoperative Hct and ΔHct could better predict short-term survival of patients with TBI. Developing an appropriate treatment strategy to increase postoperative Hct and reduce the ΔHct may be good for the short-term prognosis of patients with TBI after DC.

Benzothiadiazole-Mediated Induced Resistance to Colletotrichum musae and Delayed Ripening of Harvested Banana Fruit.

Benzothiadiazole (BTH) works as a plant activator. The effects of different BTH treatments and fungicides SPORGON on fruit ripening and disease incidence were investigated. The results showed that BTH treatment significantly delayed fruit ripening, maintained fruit firmness, color, and good fruit quality, and dramatically reduced the incidence of disease. BTH effectively inhibited the invasion and development of pathogenic bacteria and controlled the occurrence of disease. BTH treatment enhanced the activities of defense-related enzymes, including chitinase, phenylalanine ammonia-lyase, peroxidase, and polyphenol oxidase, increased the content of hydrogen peroxide and total antioxidant capacity, and reduced malondialdehyde content. Cellular structure analysis after inoculation confirmed that BTH treatment effectively maintained the cell structural integrity. SPORGON did not provide benefits for delaying fruit ripening or for the resistance system, while it can control the disease only during the earlier stage and not at later stages.