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Identification of novel antisense long non-coding RNA APMAP-AS that modulates porcine adipogenic differentiation and inflammatory responses

ZHANG Lin-zhen, HE Li, WANG Ning, AN Jia-hua, ZHANG Gen, CHAI Jin, WU Yu-jie, DAI Chang-jiu, LI Xiao-han, LIAN Ting, LI Ming-zhou, JIN Long

2023, 22 (8): 2483-2499. DOI: 10.1016/j.jia.2022.11.005

Abstract （208） PDF in ScienceDirect

Long non-coding RNAs (lncRNAs) are emerging as powerful regulators of adipocyte differentiation, fat metabolism and gene expression. However, the functional roles and mechanisms of lncRNAs in these processes remain unclear. Here, we identified a novel antisense transcript, named APMAP-AS, transcribed from adipocyte membrane-associated protein (APMAP) in the pig genome. APMAP-AS and APMAP were highly expressed in retroperitoneal adipose of obese pigs, compared with that in control pigs. Using a bone mesenchymal stem cells (BMSCs) adipogenic differentiation model, we found that APMAP-AS positively regulated adipogenic differentiation. APMAP-AS had the potential to form an RNA–RNA duplex with APMAP, and increased the stability of APMAP mRNA. Additionally, APMAP-AS promoted lipid metabolism and inhibited the expression of inflammatory factors. These findings of a natural antisense transcript for a regulatory gene associated with lipid synthesis might further our understanding of lncRNAs in driving adaptive adipose tissue remodeling and preserving metabolic health.

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Ensiling vine tea (Ampelopsis grossedentata) residue with Lactobacillus plantarum inoculant as an animal unconventional fodder

WANG Yuan, ZHOU Hong-zhang, GAO Yu, WANG Ning-wei, LIU Han, YANG Fu-yu, NI Kui-kui

2023, 22 (4): 1172-1183. DOI: 10.1016/j.jia.2022.10.001

Abstract （221） PDF in ScienceDirect

The study aimed to evaluate the application of silage fermentation in storing vine tea residue. Dynamic of fermentation-related product, chemical component and bacterial community of silage with or without Lactobacillus plantarum F1 inoculant were analyzed. The results showed that F1 treatment had a significant (P<0.05) impact on the lactic acid and ammoniacal nitrogen concentrations and pH value. Total phenols were well preserved in both treatments. After 30 days of ensiling, L. plantarum occupied the majority of Lactobacillus genus (more than 95%) in all silage samples. Spearman revealed a positive (P<0.01) correlation between lactic acid content and Lactobacillus. Overall, ensiling vine tea residue with L. plantarum can effectively preserve the nutritional attributes and total phenols, which offers a new insight into utilizing vine tea residue.

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PpMAPK6 regulates peach bud endodormancy release through interactions with PpDAM6

ZHANG Yu-zheng, XU Chen, LU Wen-li, WANG Xiao-zhe, WANG Ning, MENG Xiang-guang, FANG Yu-hui, TAN Qiu-ping, CHEN Xiu-de, FU Xi-ling, LI Ling

2023, 22 (1): 139-148. DOI: 10.1016/j.jia.2022.09.010

Abstract （205） PDF in ScienceDirect

The MADS-box (DAM) gene PpDAM6, which is related to dormancy, plays a key role in bud endodormancy release, and the expression of PpDAM6 decreases during endodormancy release. However, the interaction network that governs its regulation of the endodormancy release of flower buds in peach remains unclear. In this study, we used yeast two-hybrid (Y2H) assays to identify a mitogen-activated protein kinase, PpMAPK6, that interacts with PpDAM6 in a peach dormancy-associated SSHcDNA library. PpMAPK6 is primarily located in the nucleus, and Y2H and bimolecular fluorescence complementation (BiFC) assays verified that PpMAPK6 interacts with PpDAM6 by binding to the MADS-box domain of PpDAM6. Quantitative real-time PCR (qRT-PCR) analysis showed that the expression of PpMAPK6 was opposite that of PpDAM6 in the endodormancy release of three cultivars with different chilling requirements (Prunus persica ‘Chunjie’, Prunus persica var. nectarina ‘Zhongyou 5’, Prunus persica ‘Qingzhou peach’). In addition, abscisic acid (ABA) inhibited the expression of PpMAPK6 and promoted the expression of PpDAM6 in flower buds. The results indicated that PpMAPK6 might phosphorylate PpDAM6 to accelerate its degradation by interacting with PpDAM6. The expression of PpMAPK6 increased with decreasing ABA content during endodormancy release in peach flower buds, which in turn decreased the expression of PpDAM6 and promoted endodormancy release.

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PPAR gamma2: The main isoform of PPARγ that positively regulates the expression of the chicken Plin1 gene

SUN Yu-hang, ZHAI Gui-ying, PANG Yong-jia, LI Rui, LI Yu-mao, CAO Zhi-ping, WANG Ning, LI Hui, WANG Yu-xiang

2022, 21 (8): 2357-2371. DOI: 10.1016/S2095-3119(21)63896-0

Abstract （152） PDF in ScienceDirect

Perilipin1 (PLIN1) is a major phosphorylated protein that specifically coats the surface of neutral lipid droplets (LDs) in adipocytes and plays a crucial role in regulating the accumulation and hydrolysis of triacylglycerol (TG). Mammalian studies have shown that Plin1 gene transcription is mainly regulated by peroxisome proliferator-activated receptor-gamma (PPARγ), the master regulator of adipogenesis. However, the regulatory mechanism of the chicken Plin1 (cPlin1) gene is poorly understood. The present study aimed to investigate whether Plin1 is regulated by PPARγ in chickens and identify its exact molecular mechanism. Reporter gene and expression assays showed that PPARγ2, but not PPARγ1, activated (P<0.01) the cPlin1 gene promoter. An electrophoretic mobility shift assay and mutational analysis revealed that PPARγ2 bound to a special site in the cPlin1 gene promoter to enhance its expression. In summary, our results show that PPARγ promotes the expression of the cPlin1 gene and that PPARγ2 is the main regulatory isoform.

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Integration of genome-wide association study and selection signatures reveals genetic determinants for skeletal muscle production traits in an F₂ chicken population

LI Yu-dong, BAI Xue, LIU Xin , WANG Wei-jia, LI Zi-wei, WANG Ning, XIAO Fan, GAO Hai-he, GUO Huai-shun, LI Hui, WANG Shou-zhi

2022, 21 (7): 2065-2075. DOI: 10.1016/S2095-3119(21)63805-4

Abstract （318） PDF in ScienceDirect

Improving the production of broiler chicken meat has been a goal of broiler breeding programs worldwide for many years. However, the genetic architectures of skeletal muscle production traits in chickens have not yet been fully elucidated. In the present study, a total of 519 F₂ birds, derived from a cross of Arbor Acres broiler and Baier layer, were re-sequenced (26 F₀ individuals were re-sequenced at a 10-fold depth; 519 F₂ individuals were re-sequenced at a 3-fold depth) and the coupling of genome-wide association study (GWAS) and selection signatures (F_ST (fixation index) and θ_π (nucleotide diversity)) was carried out to pinpoint the associated loci and genes that contribute to pectoral muscle weight (PMW) and thigh muscle weight (TMW). A total of 7 890 258 single nucleotide polymorphisms (SNPs) remained to be analyzed after quality control and imputation. The integration of GWAS and selection signature analyses revealed that genetic determinants responsible for skeletal muscle production traits were mainly localized on chromosomes 1 (168.95–172.43 Mb) and 4 (74.37–75.23 Mb). A total of 17 positional candidate genes (PCGs) (LRCH1, CDADC1, CAB39L, LOC112531568, LOC112531569, FAM124A, FOXO1, NBEA, GPALPP1, RUBCNL, ARL11, KPNA3, LHFP, GBA3, LOC112532426, KCNIP4, and SLIT2) were identified in these regions. In particular, KPNA3 and FOXO1 were the most promising candidates for meat production in chickens. These findings will help enhance our understanding of the genetic architecture of chicken muscle production traits, and the significant SNPs identified could be promising candidates for integration into practical breeding programs such as genome-wide selection (GS) to improve the meat yield of chickens.

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Integration of association and computational methods reveals functional variants of LEPR gene for abdominal fat content in chickens

LI Yu-dong, WANG Wei-jia, LI Zi-wei, WANG Ning, XIAO Fan, GAO Hai-he, GUO Huai-shun, LI Hui, WANG Shou-zhi

2021, 20 (10): 2734-2748. DOI: 10.1016/S2095-3119(20)63575-4

Abstract （149） PDF in ScienceDirect

Leptin receptor (LEPR) plays a vital role in obesity in humans and animals. The objective of this study is to assess LEPR functional variants for chicken adipose deposition by integration of association and in-silico analysis using a unique chicken population, the Northeast Agricultural University broiler lines divergently selected for abdominal fat content (NEAUHLF). Five online bioinformatics tools were used to predict the functionality of the single nucleotide polymorphisms (SNPs) in coding region. Further, the possible structure–function relationship of high confidence SNPs was determined by bioinformatics analyses, including the conservation and stability analysis based on amino acid residues, prediction of protein ligand-binding sites, and the superposition of protein tertiary structure. Meanwhile, we analyzed the association between abdominal fat traits and 20 polymorphisms of chicken LEPR gene. The integrated results showed that rs731962924 (N867I) and rs13684622 (C1002R) could lead to striking changes in the structure and function of proteins, of which rs13684622 (C1002R) was significantly associated with abdominal fat weight (AFW, P=0.0413) and abdominal fat percentage (AFP, P=0.0260) in chickens. Therefore, we are of the opinion that rs13684622 (C1002R) may be an essential functional SNP affecting chicken abdominal fat deposition, and potentially applied to improvement of broiler abdominal fat in molecular marker-assisted selection (MAS) program. Additionally, the coupling of association with computer electronic predictive analysis provides a new avenue to identify important molecular markers for breeders.

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Molecular characterization and functional analysis of two new lysozyme genes from soybean cyst nematode (Heterodera glycines)

WANG Ning, PENG Huan, LIU Shi-ming, HUANG Wen-kun, Ricardo Holgado, Jihong Liu-Clarke, PENG De-liang

2019, 18 (12): 2806-2813. DOI: 10.1016/S2095-3119(19)62766-8

Abstract （111） PDF in ScienceDirect

Soybean cyst nematode (SCN, Heterodera glycines (I.)) is one of the most important soil-borne pathogens for soybeans. In plant parasitic nematodes, including SCN, lysozyme plays important roles in the innate defense system. In this study, two new lysozyme genes (Hg-lys1 and Hg-lys2) from SCN were cloned and characterized. The in situ hybridization analyses indicated that the transcripts of both Hg-lys1 and Hg-lys2 accumulated in the intestine of SCN. The qRT-PCR analyses showed that both Hg-lys1 and Hg-lys2 were upregulated after SCN second stage juveniles (J2s) were exposed to the Gram-positive bacteria Bacillus thuringiensis, Bacillus subtilis or Staphylococcus aureus. Knockdown of the identified lysozyme genes by in vitro RNA interference caused a significant decrease in the survival rate of SCN. All of the obtained results indicate that lysozyme is very important in the defense system and survival of SCN.

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Transcriptomic responses to aluminum (Al) stress in maize

XU Li-ming, LIU Chan, CUI Bao-ming, WANG Ning, ZHAO Zhuo, ZHOU Li-na, HUANG Kai-feng, DING Jian-zhou, DU Han-mei, JIANG Wei, ZHANG Su-zhi

2018, 17 (09): 1946-1958. DOI: 10.1016/S2095-3119(17)61832-X

Abstract （485） PDF in ScienceDirect

Aluminum (Al) toxicity is a major factor limiting crop production and plant growth in acid soils. The complex inheritance of Al toxicity and tolerance mechanisms in maize has uncharacterized yet. In this study, the maize inbred line 178 seedlings were treated with 200 μmol L^–1 CaCl₂+0 μmol L^–1 AlCl₃ (control) and 200 μmol L^–1 CaCl₂+60 μmol L^–1 AlCl₃ (Al treatment) for 1 and 6 h, respectively. The experiment was repeated three times. Then a detailed temporal analysis of root gene expression was performed using an Agilent GeneChip with 34 715 genes, only the genes showing more than 2.0-fold difference (P<0.01) between the control and the Al treatment maize seedlings were analyzed further. Thus, a total of 832 different expression genes, 689 significantly up-regulated and 143 down-regulated, were identified after the seedlings were treated with Al for 6 h. And 60 genes, 59 up-regulated and one down-regulated, were also detected after the seedlings were treated for 1 h. Replicated transcriptome analyses further showed that about 61% of total significantly genes could be annotated based on plant genome resources. Quantitative real-time PCR (qRT-PCT) of some selected candidate genes was used to demonstrate the microarray data, indicating significant differences between the control and Al-treated seedlings. Exposure to Al for 6 h triggered changes in the transcript levels for several genes, which were primarily related to cell wall structure and metabolism, oxidative stress response, membrane transporters, organic acid metabolism, signaling and hormones, and transcription factors, etc. After Al-treated for 1 h, differential abundance of transcripts for several transporters, kinase, and transcription factors were specifically induced. In this study, the diversity of the putative functions of these genes indicates that Al stress for a short stage induced a complex transcriptome changes in maize. These results would further help us to understand rapid and early mechanisms of Al toxicity and tolerance in maize regulated at the transcriptional level.

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Seed priming improves early seedling vigor, growth and productivity of spring maize

Hafeez ur Rehman, Hassan Iqbal, Shahzad M A Basra, Irfan Afzal, Muhammad Farooq, Abdul Wakeel, WANG Ning

2015, 14 (9): 1745-1754. DOI: 10.1016/S2095-3119(14)61000-5

Abstract （2665） PDF in ScienceDirect

Potential of seed priming treatments in improving the performance of early planted maize was evaluated against timely planting. Seeds of maize hybrid FH-810 were soaked in water (hydropriming), CaCl2 (2.2%, osmopriming), moringa leaf extracts (MLE 3.3%, osmopriming) and salicylic acid (SA, 50 mg L–1, hormonal priming) each for 18 h. Untreated and hydroprimed seeds were taken as control. Seeds primed with SA took less time in emergence and had high vigor in early planted maize. Amongst treatments, hormonal priming, reduced the electrical conductivity, increased the leaf relative and chlorophyll contents followed by osmopriming with CaCl2 at seedling stage. Likewise, plant height, grain rows and 1 000-grain weight, grain and biological yield and harvest index were also improved by seed priming; however hormonal priming and osmopriming with MLE were more effective in this regard. Improved yield performance by hormonal priming or osmopriming with MLE in early planting primarily owed to increased leaf area index, crop growth and net assimilation rates, and maintenance of green leaf area at maturity. In conclusion, osmopriming with MLE and hormonal priming with SA were the most economical treatments in improving productivity of early planted spring maize through stimulation of early seedling growth at low temperature.

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