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The roles of microRNAs in regulating root formation and growth in plants
YAN Xiao-xiao, LIU Xiang-yang, CUI Hong, ZHAO Ming-qin
2022, 21 (4): 901-916.   DOI: 10.1016/S2095-3119(21)63818-2
Abstract174)      PDF in ScienceDirect      
MicroRNAs (miRNAs) are small (ca. 20–24 nucleotides) non-coding RNAs that have recently been recognized as key post-transcriptional modulators of gene expression; and they are involved in many biological processes in plants, such as root growth and development.  The miRNAs regulate root elongation, lateral root (LR) formation and adventitious root (AR) development in response to hormone signaling, nutrient uptake and biotic/abiotic stress.  This review provides multiple perspectives on the involvement of miRNAs in regulating root growth and development in plants.  We also discuss several crucial mechanisms of miRNAs, their relationships with transcription factors and the target gene-mediated hormone signaling interactions in the regulation of root growth and development.
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Genome-wide association study and metabolic pathway prediction of barrenness in maize as a response to high planting density
ZHANG Xu-huan, LIU Hao, MA Xu-hui, ZHOU Gu-yi, RUAN Hong-qiang, CUI Hong-wei, PANG Jun-ling, SIFFAT Ullah Khan, ZONG Na, WANG Ren-zhong, LENG Peng-fei, ZHAO Jun
2022, 21 (12): 3514-3523.   DOI: 10.1016/j.jia.2022.08.089
Abstract247)      PDF in ScienceDirect      

Increasing the planting density is one way to enhance grain production in maize.  However, high planting density brings about growth and developmental defects such as barrenness, which is the major factor limiting grain yield.  In this study, the barrenness was characterized in an association panel comprising 280 inbred lines under normal (67 500 plants ha–1, ND) and high (120 000 plants ha–1, HD) planting densities in 2017 and 2018.  The population was genotyped using 776 254 single nucleotide polymorphism (SNP) markers with criteria of minor allele frequency >5% and <20% missing data.  A genome-wide association study (GWAS) was conducted for barrenness under ND and HD, as well as the barrenness ratio (HD/ND), by applying a Mixed Linear Model that controls both population structure and relative kinship (Q+K).  In total, 20 SNPs located in nine genes were significantly (P<6.44×10–8) associated with barrenness under the different planting densities.  Among them, seven SNPs for barrenness at ND and HD were located in two genes, four of which were common under both ND and HD.  In addition, 13 SNPs for the barrenness ratio were located in seven genes.  A complementary pathway analysis indicated that the metabolic pathways of amino acids, such as glutamate and arginine, and the mitogen-activated protein kinase (MAPK) signaling pathway might play important roles in tolerance to high planting density.  These results provide insights into the genetic basis of high planting density tolerance and will facilitate high yield maize breeding.

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An improved scheme for infectious bursal disease virus genotype classification based on both genome-segments A and B
WANG Yu-long, FAN Lin-jin, JIANG Nan, GAO Li, LI Kai, GAO Yu-long, LIU Chang-jun, CUI Hong-yu, PAN Qing, ZHANG Yan-ping, WANG Xiao-mei, QI Xiao-le
2021, 20 (5): 1372-1381.   DOI: 10.1016/S2095-3119(20)63424-4
Abstract141)      PDF in ScienceDirect      
Infectious bursal disease (IBD) is caused by infectious bursal disease virus (IBDV), which has a genome consisting of two segments of double-stranded linear RNA.  IBDVs have been traditionally divided into four phenotypes based on their pathogenicity and antigenicity, including classic, variant, very virulent, and attenuated IBDV.  With the emergences of divergent molecular characteristics of novel strains produced by continuous mutations and recombination, it is increasingly difficult to define new IBDV strains using the traditional descriptive classification method.  The most common classification scheme for IBDV with segmented genome is based solely on segment A, while the significance of segment B has been largely neglected.  In this study, an improved scheme for IBDV genotype classification based on the molecular characteristics of both VP2 (a viral capsid protein encoded by segment A) and VP1 (an RNA-dependent RNA polymerase protein encoded by segment B) was proposed for the first time.  In this scheme, IBDV was classified into nine genogroups of A and five genogroups of B, respectively; the genogroup A2 was further divided into four lineages.  The commonly used phenotypic classifications of classic, variant, very virulent, and attenuated IBDVs correspond to the A1B1, A2B1, A3B2, and A8B1 genotypes of the proposed classification scheme.  The novel variant IBDVs including the strains identified in this study were classified as belonging to genotype A2dB1.  The flexibility and versatility of this improved classification scheme will allow the unambiguous identification of existing and emerging IBDV strains, which will greatly facilitate molecular epidemiology studies of IBDV.
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The circulation of unique reassortment strains of infectious bursal disease virus in Pakistan
Altaf HUSSAIN, WU Tian-tian, FAN Lin-jin, WANG Yu-long, Farooq Khalid MUHAMMAD, JIANG Nan, GAO Li, LI Kai, GAO Yu-long, LIU Chang-jun, CUI Hong-yu, PAN Qing, ZHANG Yan-ping, Asim ASLAM, Khan MUTI-UR-REHMAN, Muhammad Imran ARSHAD, Hafiz Muhammad ABDULLAH, WANG Xiao-mei, QI Xiao-le
2020, 19 (7): 1867-1875.   DOI: 10.1016/S2095-3119(20)63183-5
Abstract177)      PDF in ScienceDirect      
Infectious bursal disease (IBD), caused by IBD virus (IBDV), is one of the most devastating and immunosuppressive diseases of the poultry and has been a constraint on the sustainable poultry production around the globe including Pakistan.  While the disease is threatening the poultry industry, the nature of predominant strains of IBDV in Pakistan remained ill-defined.  In this study, an epidemiology survey was conducted in the main chicken-farming regions of Pakistan.  The batch of Pakistan IBDVs genes simultaneously covering both VP1 and VP2 were amplified, sequenced, and analyzed.  The unique segment-reassortant IBDVs (vv-A/Uniq-B), carrying segment A from vvIBDV and segment B from one unique ancestor, were identified as one important type of circulating strains in Pakistan.  The data also discovered the characteristic molecular features of Pakistan IBDVs, which will contribute to scientific vaccine selection and effective prevention of the disease.
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Feeding effects of dsNPF interference in Ostrinia furnacalis
CUI Hong-ying, WANG Yuan, PENG Xin, WANG Yi-tong, ZHAO Zhang-wu
2020, 19 (6): 1475-1481.   DOI: 10.1016/S2095-3119(19)62788-7
Abstract96)      PDF in ScienceDirect      
The corn borer is a world-wide agricultural pest.  In this study, a high-efficiency RNAi method was explored to knock down the neuropeptide F (NPF) to determine if NPF regulates larval feeding in the Asian corn borer, Ostrinia furnacalis.  Results showed that the expression peaks of npf mRNA in both midgut and fat body are at 28 h of early 5th instar larvae.  When NPF was knocked down either by feeding dsNPF-containing artificial diet or direct dsNPF injection into the 5th instar larvae, npf expression was effectively inhibited in the midgut.  Larval feeding, body weight and development time were significantly impacted.  In contrast, the expression of the npf receptors npfr1 and npfr2 in fat body of 5th instar larvae was significantly increased by dsNPF injection.  These results indicate that NPF can be effectively knocked down in O. furnacalis, and dsNPF by injection is an effective and fast way to silence npf expression.  This study provides a critical basis for further exploration in mechanism of feeding regulation in O. furnacalis.
 
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Structure and function of neuropeptide F in insects
CUI Hong-ying, ZHAO Zhang-wu
2020, 19 (6): 1429-1438.   DOI: 10.1016/S2095-3119(19)62804-2
Abstract114)      PDF in ScienceDirect      
Insect neuropeptides are a group of brain neuro-regulatory factors, which plays very important roles in growth and development, molting and metamorphosis, as well as mating and reproduction.  The neuropeptide F (NPF), a multi-functional neuropeptide, is one of neuropeptides identified in numerous insect species, which plays important roles in feeding, metabolism, courtship, reproduction, aggression, ethanol sensitivity, locomotor circadian rhythms, learning and stress responses.  These roles of NPF are implemented through NPF receptors (NPFR).  The NPFR1, a G protein-coupled receptor with 7 transmembrane domains, is one of these receptors and is found to be important for NPF regulation.  The NPF usually is consisted of around 36–40 amino acid residues, but the short neuropeptide F (sNPF) consisted of 7–16 amino acid residues have also been found in some insects.  In this review, the structure and function of both NPF and sNPF in insects are discussed. 
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