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Transcriptomic and metabolomic analysis provides insights into lignin biosynthesis and accumulation and differences in lodging resistance in hybrid wheat

YANG Wei-bing, ZHANG Sheng-quan, HOU Qi-ling, GAO Jian-gang, WANG Han-Xia, CHEN Xian-Chao, LIAO Xiang-zheng, ZHANG Feng-ting, ZHAO Chang-ping, QIN Zhi-lie
2024, 23 (4): 1105-1117.   DOI: 10.1016/j.jia.2023.06.027
Abstract230)      PDF in ScienceDirect      

The use of hybrid wheat is one way to improve the yield in the future.  However, greater plant heights increase lodging risk to some extent.  In this study, two hybrid combinations with differences in lodging resistance were used to analyze the stem-related traits during the filling stage, and to investigate the mechanism of the difference in lodging resistance by analyzing lignin synthesis of the basal second internode (BSI).  The stem-related traits such as the breaking strength, stem pole substantial degree (SPSD), and rind penetration strength (RPS), as well as the lignin content of the lodging-resistant combination (LRC), were significantly higher than those of the lodging-sensitive combination (LSC).  The phenylpropanoid biosynthesis pathway was significantly and simultaneously enriched according to the transcriptomics and metabolomics analysis at the later filling stage.  A total of 35 critical regulatory genes involved in the phenylpropanoid pathway were identified.  Moreover, 42% of the identified genes were significantly and differentially expressed at the later grain-filling stage between the two combinations, among which more than 80% were strongly up-regulated at that stage in the LRC compared with LSC.  On the contrary, the LRC displayed lower contents of lignin intermediate metabolites than the LSC.  These results suggested that the key to the lodging resistance formation of LRC is largely the higher lignin synthesis at the later grain-filling stage.  Finally, breeding strategies for synergistically improving plant height and lodging resistance of hybrid wheat were put forward by comparing the LRC with the conventional wheat applied in large areas.

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Phenolic extract of Morchella angusticeps peck inhibited the proliferation of HepG2 cells in vitro by inducing the signal transduction pathway of p38/MAPK
LI Fu-hua, ZHENG Shao-jie, ZHAO Ji-chun, LIAO Xia, WU Su-rui, MING Jian
2020, 19 (11): 2829-2838.   DOI: 10.1016/S2095-3119(20)63322-6
Abstract126)      PDF in ScienceDirect      
Morchella angusticeps Peck, one of the most popular edible mushrooms, has attracted great attention due to its delicious taste and healthy properties.  However, both its biological effects and the possible mechanism of action have not yet been known.  We investigated the anti-proliferative activity of the phenolic extract derived from Morchella angusticeps Peck (MPE) against HepG2 human hepatocellular carcinoma cells.  Results showed that MPE at non-cytotoxicity doses significantly inhibited the proliferation of HepG2 cells in a dose-dependent manner with inhibitory rates ranging from 18 to 90% (P<0.01).  The possible mechanism might be that MPE induced apoptosis through initiating the mitochondrial death pathway by regulating Bax, Bcl-2 and cleaved caspase-3.  On the other hand, MPE might trigger cell cycle arrest at G0/G1/S phases by managing p21, Cyclin D1, cyclin-dependent kinases-4 (CDK4) and proliferating cell nuclear antigen (PCNA).  Additionally, MPE downregulated TRAF-2 and p-p53, while upregulated p-ASK1 and p-p38.  Therefore, it could be inferred that MPE might induce the anti-proliferative function to HepG2 cells through the p38/MAPK signal transduction pathway.
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Yield-related agronomic traits evaluation for hybrid wheat and relations of ethylene and polyamines biosynthesis to filling at the mid-grain filling stage
YANG Wei-bing, QIN Zhi-lie, SUN Hui, LIAO Xiang-zheng, GAO Jian-gang, WANG Yong-bo, HOU Qi-ling, CHEN Xian-chao, TIAN Li-ping, ZHANG li-ping, MA Jin-xiu, CHEN Zhao-bo, ZHANG Feng-ting, ZHAO Chang-ping
2020, 19 (10): 2407-2418.   DOI: 10.1016/S2095-3119(19)62873-X
Abstract106)      PDF in ScienceDirect      
Because of the yield increase of 3.5–15% compared to conventional wheat, hybrid wheat is considered to be one of the main ways to greatly improve the wheat yield in the future.  In this study, we performed a principal component analysis (PCA) on two-line hybrids wheat and their parents using the grain weight (GW), the length of spike (LS), the kernel number of spike (KSN), and spike number (SPN) as variables.  The results showed that the variables could be classified into three main factors, the weight factor (factor 1), the quantity factor 1 (factor 2) and the quantity factor 2 (factor 3), which accounted for 37.1, 22.6 and 18.5%, respectively of the total variance in different agronomic variables, suggesting that the GW is an important indicator for evaluating hybrid combinations, and the grain weight of restorer line (RGW) could be used as a reference for parents selection.  The hybrid combination with a higher score in factor 1 direction and larger mid-parent heterosis (MPH) of the GW and its parents were used to carry out the analysis of grain filling, 1-aminocylopropane-1-carboxylicacid (ACC) and polyamine synthesis related genes.  The results suggested that the GW of superior grain was significantly higher than that of inferior grains in BS1453×JS1 (H) and its parents.  Both grain types showed a weight of H between BS1453 (M) and JS1(R), and a larger MPH, which may be caused by their differences in the active filling stage and the grain filling rate.  The ADP-glucose pyrophosphorylase (AGPase), granule bound starch synthase I (GBSSI), starch synthase III (SSS), and starch branching enzyme-I (SBE-I) expression levels of H were intermediated between M and R, which might be closely related to MPH formation of the GW.  Compared with R and H, the GW of M at maturity was the lowest.  The expression levels of spermidine synthase 2 (Spd2), ornithine decarboxylase (ODC) and S-adenosylmethionine decarboxylase (SAMDC) had significantly positive correlations with the grain filling rate (r=0.77*, 0.51*, 0.59*), suggesting their major roles in the grain filling and heterosis formation.  These provide a theoretical basis for improving the GW of photo-thermo-sensitive male sterile lines (PTSMSL) by changing the endogenous polyamine synthesis in commercial applications.
  
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Complete genome sequence of Bacillus amyloliquefaciens YP6, a plant growth rhizobacterium efficiently degrading a wide range of organophosphorus pesticides
MENG Di, ZHAI Li-xin, TIAN Qiao-peng, GUAN Zheng-bing, CAI Yu-jie, LIAO Xiang-ru
2019, 18 (11): 2668-2672.   DOI: 10.1016/S2095-3119(19)62658-4
Abstract113)      PDF in ScienceDirect      
Bacillus amyloliquefaciens YP6, a plant growth promoting rhizobacteria, is capable of efficiently degrading a wide range of organophosphorus pesticides (OPs).  Here, we report the complete genome sequence of this bacterium with a genome size of 4 009 619 bp, 4 210 protein-coding genes and an average GC content of 45.9%.  Based on the genome sequence, several genes previously described as being involved in solubilizing-phosphorus, OPs-degradation, indole-3-acetic acid (IAA) and siderophores synthesis.  Interestingly, compared with the genomes of B. amyloliquefaciens species, strain YP6 had larger genome size and the most protein-coding genes.  Moreover, the four categories of “cell envelope biogenesis, outer membrane (M),” “translation, ribosomal structure and biogenesis (J),” “transcription (K),” and “signal transduction mechanisms (T)” were fewer.  These differences may be related to extensive environmental adaptability of the genus B. amyloliquefaciens.  These results expand the application potential of strain YP6 for environmental bioremediation, provide gene resources involved in OPs degradation for biotechnology and gene engineering, and contribute to provide insights into the relationship between microorganism and living environment.
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Identification of suitable reference genes in leaves and roots of rapeseed (Brassica napus L.) under different nutrient deficiencies
HAN Pei-pei, QIN Lu, LI Yin-shui, LIAO Xiang-sheng, XU Zi-xian, HU Xiao-jia, XIE Li-hua, YU Chang-bing, WU Yan-feng, LIAO Xing
2017, 16 (04): 809-819.   DOI: 10.1016/S2095-3119(16)61436-3
Abstract760)      PDF in ScienceDirect      
Nutrient deficiency stresses often occur simultaneously in soil.  Thus, it’s necessary to investigate the mechanisms underlying plant responses to multiple stresses through identification of some key stress-responsive genes.  Quantitative real-time PCR (qRT-PCR) is essential for detecting the expression of the interested genes, of which the selection of suitable reference genes is a crucial step before qRT-PCR.  To date, reliable reference genes to normalize qRT-PCR data under different nutrient deficiencies have not been reported in plants.  In this study, expression of ten candidate reference genes was detected in leaves and roots of rapeseed (Brassica napus L.) after implementing different nutrient deficiencies for 14 days.  These candidate genes, included two traditionally used reference genes and eight genes selected from an RNA-Seq dataset.  Two software packages (GeNorm, NormFinder) were employed to evaluate candidate gene stability.  Results showed that VHA-E1 was the highest-ranked gene in leaves of nutrient-deficient rapeseed, while VHA-G1 and UBC21 were most stable in nutrient-deficient roots.  When rapeseed leaves and roots were combined, UBC21, HTB1, VHA-G1 and ACT7 were most stable among all samples.  To evaluate the stabilities of the highest-ranked genes, the relative expression of two target genes, BnTrx1;1 and BnPht1;3 were further determined.  The results showed that the relative expression of BnTrx1;1 depended on reference gene selection, suggesting that it’s necessary to evaluate the stability of reference gene prior to qRT-PCR.  This study provides suitable reference genes for gene expression analysis of rapeseed responses to different nutrient deficiencies, which is essential for elucidation of mechanisms underlying rapeseed responses to multiple nutrient deficiency stresses.
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Influencing Factors on Rice Sheath Blight Epidemics in Integrated Rice-Duck System
SU Pin, LIAO Xiao-lan, ZHANG Ya, HUANG Huang
2012, 12 (9): 1462-1473.   DOI: 10.1016/S1671-2927(00)8678
Abstract1533)      PDF in ScienceDirect      
Sheath blight, a disease caused by the fungus Rhizoctonia solani Kuhn (anamorph), has been the most economically significant disease of rice. It was frequently reported that the disease was well-controlled in integrated rice-duck system without the employment of fungicides. However, the effecting factors behind this phenomenon were rarely reported. In this research, experiment was carried out between two treatments, rice combined with ducks (RD) and conventional rice field without ducks rearing (CK) in early season rice paddy, to investigate the variations of sclerotia in floodwater and on rice plant, microclimate 10 cm above the waterline in rice paddy and activity of protective enzymes in rice plants. The results showed that the floating sclerotia in floodwater in RD was 86-91% lower than that in CK, and adhering sclerotia in rice plant in RD was 67-78% lower than that in CK. The relative humidity tested significantly lower and light intensity tested significantly higher in RD. The temperature in the early rice growth stages in RD was slightly lower than that in CK, but it was significantly higher (32.3-36.5°C) in the middle stage rice growth stages. The polyphenoloxidase (PPO) activity in RD were lower than that in CK, but the enhanced activity of phenylalanine ammonia-lyase (PAL), peroxidase (POD) and Chitinase was observed in different stages of rice growth in RD, especially the Chitinase which showed higher activity in all investigating days.
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