A chromosome-level genome assembly of an early matured aromatic Japonica rice variety Qigeng10 to accelerate rice breeding for high grain quality in Northeast China.

Early-matured aromatic japonica rice from the Northeast is the most popular rice commodity in the Chinese market. The Qigeng10 (QG10) was one of the varieties with the largest planting area in this region in recent years. It was an early-matured japonica rice variety with a lot of superior traits such as semi-dwarf, lodging resistance, long grain, aromatic and good quality. Therefore, a high-quality assembly of Qigeng10 genome is critical and useful for japonica research and breeding. In this study, we produced a high-precision QG10 chromosome-level genome by using a combination of Nanopore and Hi-C platforms. Finally, we assembled the QG10 genome into 77 contigs with an N50 length of 11.80 Mb in 27 scaffolds with an N50 length of 30.55 Mb. The assembled genome size was 378.31Mb with 65 contigs and constituted approximately 99.59% of the 12 chromosomes. We identified a total of 1,080,819 SNPs and 682,392 InDels between QG10 and Nipponbare. We also annotated 57,599 genes by the Ab initio method, homology-based technique, and RNA-seq. Based on the assembled genome sequence, we detected the sequence variation in a total of 63 cloned genes involved in grain yield, grain size, disease tolerance, lodging resistance, fragrance, and many other important traits. Finally, we identified five elite alleles (qTGW2Nipponbare , qTGW3Nanyangzhan , GW5IR24 , GW6Suyunuo , and qGW8Basmati385 ) controlling long grain size, four elite alleles (COLD1Nipponbare , bZIP73Nipponbare , CTB4aKunmingxiaobaigu , and CTB2Kunmingxiaobaigu ) controlling cold tolerance, three non-functional alleles (DTH7Kitaake , Ghd7Hejiang19 , and Hd1Longgeng31 ) for early heading, two resistant alleles (PiaAkihikari and Pid4Digu ) for rice blast, a resistant allele STV11Kasalath for rice stripe virus, an NRT1.1BIR24 allele for higher nitrate absorption activity, an elite allele SCM3Chugoku117 for stronger culms, and the typical aromatic gene badh2-E2 for fragrance in QG10. These results not only help us to better elucidate the genetic mechanisms underlying excellent agronomic traits in QG10 but also have wide-ranging implications for genomics-assisted breeding in early-matured fragrant japonica rice.

OncoPubMiner: a platform for mining oncology publications.

Updated and expert-quality knowledge bases are fundamental to biomedical research. A knowledge base established with human participation and subject to multiple inspections is needed to support clinical decision making, especially in the growing field of precision oncology. The number of original publications in this field has risen dramatically with the advances in technology and the evolution of in-depth research. Consequently, the issue of how to gather and mine these articles accurately and efficiently now requires close consideration. In this study, we present OncoPubMiner (https://oncopubminer.chosenmedinfo.com), a free and powerful system that combines text mining, data structure customisation, publication search with online reading and project-centred and team-based data collection to form a one-stop 'keyword in-knowledge out' oncology publication mining platform. The platform was constructed by integrating all open-access abstracts from PubMed and full-text articles from PubMed Central, and it is updated daily. OncoPubMiner makes obtaining precision oncology knowledge from scientific articles straightforward and will assist researchers in efficiently developing structured knowledge base systems and bring us closer to achieving precision oncology goals.

Intelligent Classification of Japonica Rice Growth Duration (GD) Based on CapsNets.

Rice cultivation in cold regions of China is mainly distributed in Heilongjiang Province, where the growing season of rice is susceptible to low temperature and cold damage. Choosing and planting rice varieties with suitable GD according to the accumulated temperate zone is an important measure to prevent low temperature and cold damage. However, the traditional identification method of rice GD requires lots of field investigations, which are time consuming and susceptible to environmental interference. Therefore, an efficient, accurate, and intelligent identification method is urgently needed. In response to this problem, we took seven rice varieties suitable for three accumulated temperature zones in Heilongjiang Province as the research objects, and we carried out research on the identification of japonica rice GD based on Raman spectroscopy and capsule neural networks (CapsNets). The data preprocessing stage used a variety of methods (signal.filtfilt, difference, segmentation, and superposition) to process Raman spectral data to complete the fusion of local features and global features and data dimension transformation. A CapsNets containing three neuron layers (one convolutional layer and two capsule layers) and a dynamic routing protocol was constructed and implemented in Python. After training 160 epochs on the CapsNets, the model achieved 89% and 93% accuracy on the training and test datasets, respectively. The results showed that Raman spectroscopy combined with CapsNets can provide an efficient and accurate intelligent identification method for the classification and identification of rice GD in Heilongjiang Province.

Intelligent Identification and Features Attribution of Saline-Alkali-Tolerant Rice Varieties Based on Raman Spectroscopy.

Planting rice in saline-alkali land can effectively improve saline-alkali soil and increase grain yield, but traditional identification methods for saline-alkali-tolerant rice varieties require tedious and time-consuming field investigations based on growth indicators by rice breeders. In this study, the Python machine deep learning method was used to analyze the Raman molecular spectroscopy of rice and assist in feature attribution, in order to study a fast and efficient identification method of saline-alkali-tolerant rice varieties. A total of 156 Raman spectra of four rice varieties (two saline-alkali-tolerant rice varieties and two saline-alkali-sensitive rice varieties) were analyzed, and the wave crests were extracted by an improved signal filtering difference method and the feature information of the wave crest was automatically extracted by scipy.signal.find_peaks. Select K Best (SKB), Recursive Feature Elimination (RFE) and Select F Model (SFM) were used to select useful molecular features. Based on these feature selection methods, a Logistic Regression Model (LRM) and Random Forests Model (RFM) were established for discriminant analysis. The experimental results showed that the RFM identification model based on the RFE method reached a higher recognition rate of 89.36%. According to the identification results of RFM and the identification of feature attribution materials, amylum was the most significant substance in the identification of saline-alkali-tolerant rice varieties. Therefore, an intelligent method for the identification of saline-alkali-tolerant rice varieties based on Raman molecular spectroscopy is proposed.

Preventive Effects of Fluoro-Substituted Benzothiadiazole Derivatives and Chitosan Oligosaccharide against the Rice Seedling Blight Induced by Fusarium oxysporum.

Rice seedling blight, caused by Fusarium oxysporum, significantly affects global rice production levels. Fluoro-substituted benzothiadiazole derivatives (FBT) and chitosan oligosaccharide (COS) are elicitors that can enhance plant resistance to pathogen infection. However, there is a lack of information regarding FBT and COS used as elicitors in rice seedlings blight. Therefore, the aim of this study was to evaluate the effect of FBT and COS treatments on rice seedling blight and elucidate the molecular mechanisms of the two elicitors for inducing resistance using proteomic technique. Results indicated that FBT and COS significantly reduced the disease incidence and index, and relived the root growth inhibition caused by F. oxysporum (p < 0.05). Biochemical analyses demonstrated that these two elicitors effectively enhanced activities of defense enzymes. Moreover, the proteomic results of rice root tissues disclosed more differentially expressed proteins in diterpenoid biosynthesis pathway that were particularly stimulated by two elicitors compared to the other pathways studied, resulting in the accumulation of antimicrobial substance, momilactone. Findings of this study could provide sound theoretical basis for further applications of FBT and COS used as rice elicitors against seedling blight.

[Nutrition effectiveness of infants and young children aged 6 to 23 months by Yingyangbao in Lixian County affected by Wenchuan earthquake in Sichuan Province].

OBJECTIVE: This project aimed to investigate the nutrition status of infants and young children aged 6-23 months before and after the Yingyangbao intervention in Lixian county in Sichuan province. METHODS: The infants and young children aged 6-23 months in Lixian county were fed one sachet Yingyangbao which contains protein, vitamins and micronutrients per day for 15 months. The length, body weight and hemoglobin were measured for 510 infants and young children featured representative characteristics in Lixian County before and after Yingyangbao intervention. The statistical analysis was conducted to analyze the WAZ, HAZ, the low weight rate, the stunting rate, the anemia rate and the hemoglobin concentration of the infants and young children aged 6-11 months, 12-17 months, 18-23 months and 24-29 months, respectively. RESULTS: The results of the statistical analysis showed that the HAZ scores of the infants and young children aged 6-11 and 18-23 months increased 0.51 and 0.44 compared to the baseline, respectively. They were significantly higher than those of the baseline (P < 0.05). The stunting rate of young children aged 18-23 months was significantly lower than the baseline (P < 0.05). The concentration of the hemoglobin in each group among the 4 groups increased 12.7, 11.4, 16.7 and 15.7 g/L compared to the baseline, respectively. The total anemia prevalence among infants and young childre in each age group was significantly lower than the baseline (chi2 = 15.863, 24.302, 37.365, 25.990, respectively, P < 0.001). CONCLUSION: It was concluded that Yingyangbao which contains quality protein, vitamins and micronutrients intervened 15 months could be effective for the growth and improvement of anemia of infants and young children aged 6-23 months.

[The nutrition status of children aged 6-23 months after three months of Wenchuan Earthquake in Beichuan and Lixian, Sichuan Province].

OBJECTIVE: This project aims to investigate the nutrition status of children aged from 6 to 23 months living in Beichuan and Lixian where were seriously affected by the earthquake in 2008. METHODS: The height, body weight and hemoglobin concentration were measured for 478 children from Leigu township, Qushan township in Beichuan county and Zagunao township, Xuecheng township and Putou township in Lixian county; the number of group 6 - 11, 12 - 17, 18 - 23 months were 190, 144, 144 respectively. The height for age (HAZ), the body weight for age (WAZ) and the weight for height (WHZ) were calculated respectively. The low weight, stunting, wasting prevalence, anemic rate were analyzed. RESULTS: The WAZ scores of 6 - 23 months males and females in Beichuan county and Lixian county ranged from -0.97 to -0.13 and from -0.67 to -0.23, HAZ scores ranged from -1.23 to -0.31 and from -1.25 to -0.38, respectively. The WAZ (-0.89 ± 1.16) and HAZ (-1.20 ± 1.60) of 18 - 23 months infants in Beichuan county were significantly different from the WAZ and HAZ of 6 - 11 months (WAZ: -0.32 ± 0.92; HAZ: -0.58 ± 0.98) and 12 - 17 months (WAZ: -0.47 ± 1.00; HAZ: -0.68 ± 1.34) infants (F values were 7.161 and 4.584, respectively; all P values < 0.05). The WAZ (-0.63 ± 1.03) and HAZ (-1.11 ± 1.15) of 18 - 23 months in Lixian county infants were significantly different from the WAZ and HAZ of 6 - 11 months (WAZ: -0.23 ± 0.93; HAZ: -0.51 ± 1.55) infants and 12 - 17 months (WAZ: -0.58 ± 0.52; HAZ: -0.80 ± 1.19) (F values were 3.156, 4.345, all P values < 0.05). The prevalence of low weight infants (18 - 23 months) these two counties were 15.6% (12/77) and 9.1% (6/66), respectively. The prevalence of stunting in Beichuan and Lixian have reached 26% (20/77) and 24.2% (16/66), respectively. The wasting rate of 18 - 23 months infants had reached 9.1% (7/77) in Beichuan. The total anemia prevalence among infants reached 49.6% (123/248) and 78.8% (178/226) in Beichuan and Lixian, respectively. The prevalence of moderate anemia have reached 7.7% (19/248) and 19.9% (45/226), respectively. CONCLUSION: After the earthquake in Beichuan, Lixian, the growth of infants aged 6 to 23 months old was below average. The prevalence of anemia was high. The malnutrition status of infant and young children aged from 18 to 23 months in Beichuan and Lixian was more serious, should be targeted of nutrition interventions.