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The Xuefeng black bone chicken (XFBC) represents an important poultry genetic resource. However, the darkness in breast muscle is heterogeneous. The molecular genetic mechanisms underlying melanogenesis of breast muscle in XFBC remains unclear. This study used RNA-seq to compare the difference in transcriptome between hyperpigmentation and hypopigmentation of breast muscle. Six cDNA libraries were constructed for hyperpigmentation and hypopigmentation groups in XFBC. We identified 395 differently expressed genes (DEGs) between hyperpigmentation and hypopigmentation group (P < 0.05, |[log.sub.2]FC|[greater than or equal to]1). Gene ontology (GO) enrichment and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicated several differentially enriched biological functions and pathways involved in melanogenesis of the breast muscle. Gene set enrichment analysis (GSEA) GO analysis identified two significant gene sets, including the pathways of pigment metabolic process and transmembrane receptor protein tyrosine kinase activity. GSEA-KEGG analysis identified the process of tyrosine metabolism and several genes related with melanogenesis in breast muscle of the XFBC. The protein-protein interaction network was constructed and eight genes were clustered in the module. We identified nine hub genes, including TYR, TYRP1, DCT, GPR143, MLANA, SLC24A5, GPNMB, MLPH, and EDNRB2. Taken together, the DEGs and hub genes identified in the study provide a solid basis for the study of the genetic regulatory mechanisms involved the melanogenesis in the breast muscle of the XFBC. Key words: Xuefeng black bone chicken, breast muscle, RNA-Seq, melanogenesis, 1. Introduction The black bone chicken is one of the most important poultry genetic resources in China (Li et al. 2020). The productions of black bone chicken are very popular [...]

1-Deoxy-d-xylulose-5-phosphate synthase and 1-deoxy-d-xylulose-5-phosphate reductoismerase are considered two key enzymes in the 2-C-methyl-d-erythritol-4-phosphate pathway of terpenoid biosynthesis and are related to the synthesis and accumulation of sesquiterpenoids. We cloned two DXS and DXR genes from Atractylodes lancea and analysed their expression in different tissues and in response to methyl jasmonate (MeJA). Subcellular localisation analysis revealed that the AlDXS and AlDXR1 proteins are located in the chloroplasts and cytoplasm, whereas AlDXR2 is only located in the chloroplasts. pET-AlDXS-28a and pGEX-AlDXR-4T-1 were expressed in Escherichia coli BL21(DE3) and BL21, respectively. Based on the abiotic stress analysis, the growth rate of the recombinant pGEX-AlDXR-4T-1 was higher than that of the control in HCl and NaOH. AlDXS exhibited the highest expression level in rhizomes of A. lancea from Hubei but was highest in leaves from Henan. In contrast, AlDXR showed maximum expression in the leaves of A. lancea from Hubei and Henan. Moreover, DXS and DXR gene expression, enzyme activities, and antioxidant enzyme activities oscillated in response to MeJA, with expression peaks appearing at different time points. Our findings indicated that the characterisation and function of AlDXS and AlDXR could be useful for further elucidating the functions of DXR and DXR genes in A. lancea. Key words: Atractylodes lancea, 1-deoxy-d-xylulose-5-phosphate synthase, 1-deoxy-d-xylulose-5-phosphate reductoismerase, subcellular localisation, gene expression, Introduction Terpenoids have a wide variety of pharmacological activities, including antimicrobial, antiallergenic, anticancer, anti-inflammatory, and immunomodulatory properties (Kuang et al. 2021). For example, the sesquiterpene lactone, artemisinin, from Artemisia annua [...]

C2H2-zinc finger (C2H2-ZF) genes are involved in various biological processes in plants including stress response; however, they lack characterization in Brassica napus. We identified 267 C2H2-ZF genes in B. napus and deciphered their physiological properties, subcellular localization, structure, synteny, and phylogeny and investigated the expression of 20 genes in response to different stresses and phytohormone treatments. The 267 genes were distributed on 19 chromosomes; phylogenetic analysis categorized them into five clades. They varied from 0.41 to 9.2 kb in length, had stress-responsive cis-acting elements in promoter regions, and their protein length varied from 9 to 1366 amino acids. About 42% of the genes had one exon, and 88% genes had orthologs in Arabidopsis thaliana. About 97% of the genes were located in nucleus and 3% in cytoplasmic organelles. qRT-PCR analysis showed a different expression pattern of these genes in response to biotic stresses (Plasmodiophora brassicae and Sclerotinia sclerotiorum) and abiotic stresses (cold, drought, and salinity) and hormonal treatments. Differential expression of the same gene was observed under multiple stress conditions, and a few genes showed similar expression in response to more than one phytohormones. Our results suggest that the C2H2-ZF genes can be targeted for the improvement of stress tolerance in canola. Key words: C2H2-zinc finger genes, Brassica napus, transcription factors, stress response, gene expression, 1. Introduction The genus Brassica includes 39 economically important vegetable and oilseed crop species (for review, see Warwick et al. 2006). Among them, Brassica napus (2n = 38, AACC), commonly [...]

Melanocytes play a major role in the formation of mammalian fur color and are regulated by several genes. Despite playing the pivotal role in the study of melanoma, the mechanistic role of NRAS (neuroblastoma RAS viral oncogene homolog) in the formation of mammalian epidermal color is still elusive. First of all, the expression levels of NRAS mRNA and protein in the dorsal skin of different colored Rex rabbits were detected by qRT-PCR and Western blot. Then, the subcellular localization of NRAS was identified in melanocytes by indirect immunofluorescence. Next, the expression of NRAS was overexpressed and knocked down in melanocytes, and its efficiency was verified by qRT-PCR and Western blot. Subsequently, NaOH, CCK-8, and Annexin V-FITC were used to verify the changes in melanin content, proliferation, and apoptosis in melanocytes. Finally, we analyzed the regulation of NRAS on other genes (MITF, TYR, DCT, PMEL, and CREB) that affect melanin production. In silico studies showed NRAS as a stable and hydrophilic protein, and it is localized in the cytoplasm and nucleus of melanocytes. The mRNA and protein expression levels of NRAS were significantly different in skin of different colored Rex rabbits, and the highest level was found in black skin (P < 0.01). Moreover, the NRAS demonstrated impact on the proliferation, apoptosis, and melanin production of melanocytes (P < 0.05), and the strong correlation of NRAS with melanin-related genes was evidently observed (P < 0.05). Our results suggested that NRAS can be used as a gene that regulates melanin production and controls melanocyte proliferation and apoptosis, providing a new theoretical basis for studying the mechanism of mammalian fur color formation. Key words: NRAS, melanocytes, melanin, Rex rabbit, melanin-related genes, Introduction Melanin is a biological pigment synthesized by melanocytes, which is transported outside the cells and deposited in various tissues such as hair, skin, and eyes through a specific transport [...]

In rapeseed (Brassica napus L.), lipid transfer protein (LTP) and seed storage albumin (SSA) gene families are involved in lipid and protein metabolism. Understanding the mechanism of oil biosynthesis has great value to increase oil production. The LTPs and SSA gene families were identified of Brassicaceae. The LTPs were divided into six groups according to their sequences, and LTPs of all five species in Brassicaceae also had the same pattern. The genes at a higher expression level were evenly distributed across five groups except group ii. The gene groups in these two gene families showed different expression patterns, with most of the LTP genes expressed at a higher level at 25 days after flowering (DAF), but SSA genes were highly expressed at 40 DAF stage. Gene Ontology (GO) enrichment analysis of the regulatory genes for LTPs also was performed, including response to biotic stimulus (GO:0009607), generation of precursor metabolites and energy (GO:0006091), electron transport chain (GO:0022900), oxidative phosphorylation (GO:0006119), adenosine triphosphate metabolic process (GO:0046034), and phosphorylation (GO:0016310). These results may facilitate further research to understand the expression patterns and regulatory mechanism of LTPs and SSAs. Key words: rapeseed (Brassica napus L.), oil biosynthesis, lipid transfer protein, seed storage albumin, regulatory network Chez le colza, les familles de gènes LTP (protéine de transfert des lipides) et SSA (albumine de stockage des graines) sont impliquées dans le métabolisme des lipides et des protéines. La compréhension du mécanisme de biosynthèse de l'huile a une grande importance pour augmenter la production d'huile. Les familles de gènes LTP et SSA ont été identifiées chez les Brassicaceae. Les LTP ont été divisés en six groupes selon leurs séquences, les LTP des cinq espèces de Brassicaceae présentant également le même profil. Les gènes dont le niveau d'expression est plus élevé étaient distribués de manière égale dans les cinq groupes, à l'exception du groupe ii. Les groupes de gènes de ces deux familles présentaient des profils d'expression différents, la plupart des gènes LTP étant exprimés à un niveau plus élevé à 25 jours après la floraison (DAF), mais les gènes SSA étaient fortement exprimés au stade 40 DAF. Une analyse d'enrichissement d'ontologie génétique (GO) des gènes régulateurs des LTP a également été réalisée, notamment la réponse à un stimulus biotique (GO:0009607), la génération de métabolites précurseurs et d'énergie (GO:0006091), la chaîne de transport des électrons (GO:0022900), la phosphorylation oxydative (GO:0006119), le processus métabolique de l'adénosine triphosphate (GO:0046034) et la phosphorylation (GO:0016310). Ces résultats peuvent faciliter des recherches ultérieures pour comprendre les profils d'expression et le mécanisme de régulation des LTP et des SSA. [Traduit par la Rédaction] Mots-clés : colza (Brassica napus L.), biosynthèse de l'huile, protéine de transfert des lipides, albumine de stockage des graines, réseau de régulation, Introduction Rapeseed (Brassica napus L.) is an important oil crop with high commercial value all over the world. Rapeseed is widely grown in China and Europe, providing above 40% of [...]

Genomic reorganization, such as rearrangements and inversions, influences how genetic information is organized within the bacterial genomes. Inversions, in particular, facilitate genome evolution through gene gain and loss, and can alter gene expression. Previous studies have investigated the impact inversions have on gene expression induced inversions targeting specific genes or examine inversions between distantly related species. This fails to encompass a genome-wide perspective of naturally occurring inversions and their post-adaptation impact on gene expression. Here, we used bioinformatic techniques and multiple RNA-seq datasets to investigate the short- and long-range impact inversions have on genomic gene expression within Escherichia coli. We observed differences in gene expression between homologous inverted and non-inverted genes even after long-term exposure to adaptive selection. In 4% of inversions representing 33 genes, differential gene expression between inverted and non-inverted homologs was detected, with greater than two-thirds (71%) of differentially expressed inverted genes having 9.4-85.6-fold higher gene expression. The identified inversions had more overlap than expected with nucleoid-associated protein binding sites, which assist in the regulation of genomic gene expression. Some inversions can drastically impact gene expression, even between different strains of E. coli, and could provide a mechanism for the diversification of genetic content through controlled expression changes. Key words: inversions, gene expression, nucleoid binding proteins, Escherichia coli, genomics. La reorganisation du genome, au moyen de rearrangements ou d'inversions, influence comment l'information genetique est organisee au sein des genomes bacteriens. Les inversions, en particulier, facilitent l'evolution du genome via le gain et la perte de genes, ce qui peut alterer l'expression genique. Les etudes anterieures sur l'impact des inversions sur l'expression genique ont principalement porte sur des inversions induites chez des genes specifiques ou encore se sont interessees aux inversions entre especes peu apparentees. Celles-ci n'ont donc pas apporte une perspective pangenomique sur les inversions d'origine naturelle et leur impact post-adaptatif sur l'expression genique. Dans ce travail, les auteurs emploient des approches bioinformatiques et de nombreux jeu de donnees RNA-seq pour etudier l'impact proximal et distal qu'ont les inversions sur l'expression genique a l'echelle genomique chez l'Escherichia coli. Les auteurs ont observe des differences dans l'expression genique entre genes homologues inverses et non-inverses, meme apres une longue periode de selection adaptative. Chez 4 % des inversions impliquant 33 genes, une expression differentielle entre les homologues inverses et non-inverses a ete decelee; chez plus de deux tiers (71 %) des genes a expression differentielle, l'amplitude de l'expression differentielle variait entre 9,4 et 85,6 fois. Les inversions identifiees presentaient un plus grand chevauchement qu'attendu entre les sites de liaison des proteines associees au nucleoide, lesquelles participent a la regulation de l'expression genique. Certaines inversions peuvent avoir un impact considerable sur l'expression genique, meme entre differentes souches d'E. coli. Celles-ci pourraient fournir un mecanisme pour expliquer la diversification du contenu genetique via des changements d'expression genique controles. Mots-cles : inversions, expression genique, proteines de liaison du nucleoide, Escherichia coli, genomique., Introduction Genomic reorganization in bacteria, such as rearrangements and inversions, provides a way to create new genetic diversity (Hughes et al. 2000; Belda et al. 2005) that can assist in [...]

Several pathogens, including nematodes, have severe effects on plant development and growth, and immense populations of parasitic nematodes may cause plant death and crop loss. Obligate plant-parasitic nematodes and root-knot nematodes belonging to the genus Meloidogyne are significant parasites in crops. During nematode infection, damage-associated molecular patterns play a role in the activation of plant defence responses to pathogens. Several genes are involved in Meloidogyne parasitism. However, the expression of nematode-responsive genes CRF1, WRKY45, and PR7 during infection with different parasitic nematode species is not well understood. Therefore, this study aimed to reveal plant responses to differential gene expression of nematode-responsive genes in tomato plants, and their relationship to nematode reproduction and comparative phylogeny. Molecular methods for gene expression, greenhouse work for nematode reproduction, and phylogenetic analysis were used to determine nematode--plant interactions. The results revealed that differential gene expression of CRF1, WRKY45, and PR7 depended on the nematode species. The relative CRF1 gene expression reached its highest level at 3 dpi, following nematode infection. In conclusion, plant defense responses disturbed the expression of nematode-responsive genes, and the differential expression of nematode-responsive genes was affected by nematode species and nematode parasitism. Key words: Meloidogyne, nematode, gene, CRF1, WRKY45, PR7. Plusieurs ravageurs dont les nematodes ont des impacts importants sur le developpement et la croissance des plantes. Les immenses populations de nematodes parasitaires peuvent entrainer la mort des plantes et des pertes de rendement. Les nematodes qui sont des parasites obligatoires des plantes comme les nematodes a galles du genre Meloidogyne sont des parasites importants des plantes cultivees. Au cours de l'infection par les nematodes, les signaux moleculaires associes aux blessures activent les reactions de defense aux pathogenes. Plusieurs genes chez les especes du genre Meloidogyne sont impliques dans le parasitisme des plantes. Cependant, l'expression des genes qui s'expriment en reponse au parasitisme resultant de l'attaque par plusieurs especes de nematodes (CRF1, WRKY45, PR7) n'ont pas fait l'objet de beaucoup d'etudes. Le but de ce travail etait de reveler les reactions des plantes qui entrainent une expression differentielle des genes qui sont connus pour s'exprimer en reponse a l'attaque des nematodes chez la tomate, d'etudier la phylogenie comparee de ces genes et leur impact sur la reproduction des nematodes. Des analyses moleculaires de l'expression genique, des travaux en serre pour mesurer la reproduction et des analyses phylogenetiques ont ete realisees pour caracteriser les interactions entre les nematodes et leur hote. Les resultats ont montre que l'expression differentielle des genes CRF1, WRKY45 et PR7 survenaient en reponse a l'attaque par certaines especes de nematodes. L'expression relative du gene CRF1 a atteint son maximum a 3 dpi lors d'attaque par les nematodes. En conclusion, les reactions de defense des plantes ont modifie l'expression des genes exprimes en reponse a l'attaque par les nematodes et l'expression differentielle de ces genes variait selon l'espece de nematode et le degre de parasitisme. [Traduit par la Redaction] Mots-cles : Meloidogyne, nematode, gene, CRF1, WRKY45, PR7., Introduction Plant-parasitic nematodes are important crop pests responsible for $173 billion crop losses worldwide (Elling 2013). Among plant-parasitic nematodes, root-knot nematode (RKN) species belonging to the genus Meloidogyne are among [...]

Despite several studies on genetic markers and differentially expressed genes related to ribeye area (REA) and tenderness traits in beef cattle, there is divergence in the results regarding the genes associated with these traits. Thirteen genes associated with or exhibiting biological functions that might influence such phenotypes were included in this study. A total of five genes for REA (IGF-1, IGF-2, MSTN, NEDD4,and UBE4A) and eight genes for meat tenderness (CAPN1, CAPN2, CAST, HSPB1, DNAJA1, FABP4, SCD,and PRKAG3)were selected from previous studies on beef cattle. Genes and their respective proteins expression were validated in a commercial population of Nellore cattle using quantitative real-time PCR (RT-qPCR) and advanced mass spectrometry (LC/MS-MS) techniques, respectively. The MSTN gene was upregulated in animals with low REA. The CAAPN1, CAPN2, CAST, HSPB1,and DNAJA1 genes were upregulated in animals with tough meat. The proteins translated by these genes were not differentially expressed. Our results confirm the potential of some of the studied genes as biomarkers for carcass and meat quality traits in Nellore cattle. Key words: beef cattle, biological processes, gene expression, meat quality, zebu. Malgre plusieurs etudes pour identifier des marqueurs genetiques et des genes exprimes de maniere differentielle qui seraient associes avec la dimension du faux-filet (REA pour 'ribeye area') et la tendrete chez les bovins de boucherie, il existe des divergences en ce qui a trait aux genes associes a ces caracteres. A partir d'etudes anterieures, treize genes associes ou qui presentaient des fonctions biologiques pouvant affecter ces phenotypes sont etudies dans ce travail. Cinq genes pour le REA (IGF-1, IGF-2, MSTN, NEDD4 et UBE4A)ethuit genes pour la tendrete de la viande (CAPN1, CAPN2, CAST, HSPB1, DNAJA1, FABP4, SCD et PRKAG3) ont ete choisis apartird'etudes realisees auparavant chez les bovins de boucherie. L'expression des genes et l'abondance des proteines respectives a ete mesuree chez une population de bovins de race Nelore au moyen de la PCR quantitative en temps reel (RT-qPCR) et de techniques avancees de spectrometrie de masse (LC/MS-MS). Le gene MSTN etait plus fortement exprime chez les individus dont la viande etait moins tendre. Les proteines traduites a partir de ces genes n'etaient pas exprimees de maniere differentielle. Les resultats de ce travail pourraient confirmer le potentiel de certains de ces genes en tant que biomarqueurs pour des caracteres de la carcasse et de la qualite de la viande chez les bovins Nelore. Mots-cles : bovins de boucherie, processus biologiques, expression genique, qualite de la viande, zebu., Introduction Brazilian beef cattle expansion is directly associated with competitiveness in the production sector. Although production and reproduction traits are crucial for beef cattle operations, carcass and meat quality traits [...]

Camellia oleifera Abel ('Huashuo') is an important woody oil species with high economic value. Low yield is the main factor restricting the rapid development of the tea-oil industry. The dynamics of sugars, oil, endogenous hormones, and the genes involved in these pathways, as well as the correlation with oil synthesis-related factors in Huashuo, were investigated. The results showed that oil content was positively correlated with sucrose and starch content but was negatively correlated with reducing sugar content. Pyruvate kinase (PK) and fructose-1,6-bisphosphate aldolase (FBA) of the glycolysis pathway could be beneficial for oil biosynthesis. Higher levels of acetyl CoA carboxylase (ACC), stearoyl-ACP desaturase (SAD), and WRINKLED1 (WRI1), as well as lower levels of omega-6 fatty acid desaturase 2 (FAD2) and lipoxygenase 5 (LOX5) could be responsible for the oil production. The higher expression of gibberellin 20 oxidase (GA20ox), lower expression of gibberellic acid insensitive (GAI), and the increase in 9-cis-epoxycarotenoid dioxygenase (NCED) at the mRNA level could contribute to oil accumulation. The results of this study could provide a reference for increasing the yield of plants related to Huashuo. Key words: Camellia oleifera Abel, Huashuo, sugar, fatty acids, endogenous hormones, gene expression profiles. Camellia oleifera Abel ('Huashuo') est une importante espece ligneuse productrice d'huile comestible a haute valeur economique. Le faible rendement constitue le principal facteur limitant le developpement rapide de l'industrie de l'huile de the. La dynamique des sucres, des lipides, des hormones endogenes et des genes impliques dans ces voies, ainsi que la correlation avec les facteurs lies a la synthese de l'huile chez Huashuo ont ete etudiees. Les resultats ont montre que la teneur en huile etait positivement correlee a la teneur en sucrose et en amidon, mais negativement correlee a la teneur en sucres reducteurs. La pyruvate kinase (PK) et la fructose-1, 6-bisphosphate aldolase (FBA) de la voie de la glycolyse pourraient etre benefiques a la biosynthese de l'huile. Des niveaux plus eleves d'acetyl CoA carboxylase (ACC), de stearoyl-ACP desaturase (SAD) et de WRINKLED1 (WRI1), mais des niveaux plus faibles de l'acide gras omega-6 desaturase 2 (FAD2) et de lipoxygenase 5 (LOX5) pourraient etre responsables de la production d'huile. L'expression plus elevee de la gibberelline 20 oxydase (GA20ox), mais l'expression plus faible de l'insensible a l'acide gibberellique (GAI) ainsi que l'augmentation de la 9-cis-epoxycarotenoide dioxygenase (NCED) au niveau de l'ARNm pourraient contribuer a l'accumulation d'huile. Les resultats de cette etude pourraient servir de reference pour accroître le rendement des plantes apparentees a Huashuo. [Traduit par la Redaction] Mots-cles : Camellia oleifera Abel, Huashuo, sucre, acides gras, hormones endogenes, profils d'expression genique., Introduction Camellia oleifera Abel, one of the main woody oil plants in the world, originated in China and is still widely cultivated throughout the country. The oil from C. oleifera [...]