茉莉酸介导的番茄韧皮部表达谱对根结线虫侵染的响应

为了研究茉莉酸介导的基因对根结线虫侵染的响应,以番茄野生型和茉莉酸缺失突变体为试材,采用数字表达谱技术检测分析根结线虫侵染后主茎韧皮部中的差异表达基因。结果表明,茉莉酸缺失突变体中有2 427个基因差异表达,其中1 390个差异基因可富集到112个KEGG(Kyoto Encyclopedia of Genes and Genomes)通路。18个差异基因涉及茉莉酸合成前体α-亚麻酸代谢,100个差异基因参与植物和病原体的相互作用。     

Genome Array on Differentially Expressed Genes of Skin Tissue in Cashmere Goat at Early Anagen of Cashmere Growth Cycle Using DNA Microarray

In order to study the molecular mechanism involved in cashmere regeneration, this study investigated the gene expression profile of skin tissue at various stages of the cashmere growth cycle and screen differentially expressed genes at proangen in 10 cashmere goats at 2 years of age using agilent sheep oligo microarray. Significance analysis of microarray （SAM） methods was used to identify the differentially expressed genes, Hierarchical clustering was performed to clarify these genes in association with different cashmere growth stages, and GO （Gene ontology） and the pathway analyses were con-ducted by a free web-based Molecular Annotation System3.0 （MAS 3.0）. Approximately 10200 probe sets were detected in skin tissue of 2-yr-old cashmere goat. After SAM analysis of the microarray data, totally 417 genes were shown to be differentially expressed at different cashmere growth stages, and 24 genes are significantly up-regulated （21） or down-regulated （3） at proangen concurrently compared to angen and telogen. Hierarchical clustering analysis clearly distinguished the differentially expressed genes of each stage. GO analysis indicated that these altered genes at proangen were predominantly involved in collagen fibril organization, integrin-mediated signaling pathway, cell-matrix adhesion, cell adhesion, transforming growth factor-β （TGF-β） receptor signaling pathway, regulation of cell growth. Kyoto encyclopedia of genes and genomes （KEGG） analysis showed that the significant pathways involved mainly included focal adhesion and extracellular matrixc （ECM）-receptor interaction. Some important genes involved in these biological processes, such as COL1A1, COL1A2, COL3A1, SPARC, CYR61 and CTGF, were related to tissue remolding and repairing and detected by more than one probe with similar expression trends at different stages of cashmere growth cycle. The different expression of these genes may contribute to understanding the molecular mechanism of cashmere regeneration.     

Differential Expression and Regulation of Switchgrass Root MicroRNA in Response to Alkali-salt Stress Using High-throughput Deep Sequencing

Switchgrass (Panicum virgatum L.) as a high-quality bioenergy crop that can effectively improve saline-alkali soil has strong resistance to stress and grows well in marginal soil and some abiotic stress environments.This study used alkali-sensitive genotype AM (AM-314/MS-155) and alkali-tolerant genotype ALA (Alamo) as experimental materials to investigate molecular mechanisms of switchgrass tolerance to alkali-salt stress.When the plants were grown to E5 stage,the alkali-salt stress treatment was carried out by soaking method (Na_2CO_3:NaHCO_3=1:9,C_((Na+))=150 mmol·L~(-1) and pH=9.0) and fresh root samples were taken after treatments for 0 (CK),6 and 24 h,respectively,the differentially expressed microRNAs and their regulatory network were analyzed.A total of 1 049 known miRNAs and 68 novel miRNAs were identified.Seventy-two differentially expressed miRNAs in ALA were more than three times higher than those in AM and 36.1% differentially expressed miRNAs was significantly down-regulated (p0.05).Through analyses of differentially expressed miRNAs and their target genes,it was found that under alkali-salt stress,differentially expressed miRNAs in AM were mainly involved in the regulation of cellular ROS clearance,ethylene signal transduction,and root,leaf and flower development.MiRNAs in ALA were also involved in water transport,DNA methylation,response to high osmotic pressure,activation of stress-related genes and more complex responses to alkali-salt stress processes,but those in AM were not.ALA was significantly higher than AM in the number of microRNAs responding to alkali-salt stress and in the functional diversity of their regulatory target genes.     

Identification of novel and differentially expressed micro RNAs in ovine ovary and testis tissues using Solexa sequencing and bioinformatics

Micro RNAs(mi RNAs) are small, single stranded, non-coding RNA molecules, about 19–25 nucleotides in length, which regulate the development and functions of reproductive system of mammal.To discover novel mi RNAs and identify the differential expression of them in ovine ovary and testis tissues, the study constructed two libraries by using next-generation sequencing technologies(Solexa high-throughput sequencing technique).As a result, 9 321 775 and 9 511 538 clean reads were obtained from the ovary and testis separately, which included 130 562(90 genes of ovary) and 56 272(85 genes of testis) of known mi RNAs and 486 potential novel mi RNAs reads.In this study, a total of 65 conserved mi RNAs were significantly differentially expressed(P0.01) between the two samples.Among them, 28 mi RNAs were up-regulated and 3 mi RNAs were down-regulated on ovary compared with testis.In addition, the known mi RNAs with the highest expression level(5 mi RNAs) and 30 novel mi RNAs with the functions related to reproduction were validated using the real-time quantitative RT-PCR.Moreover, the gene ontology(GO) annotation and Kyoto encyclopedia of genes and genomes(KEGG) pathway analysis showed that differentially expressed mi RNAs were involved in ovary and testis physiology, including signal transduction, gonad development, sex differentiation, gematogenesis, fertilization and embryo development.The results will be helpful to facilitate studies on the regulation of mi RNAs during ruminant reproduction.     

Differential Gene Expression in Response to Drought Stress in Maize Seedling

To provide the useful information for the choice of molecular marker used in marker-assisted selection of drought tolerance, it is necessary to find out more candidate genes and fulfill the information gaps in gene expression regulation under drought stress. In this study, we isolated four differentially expressed cDNA fragments from leaves of a droughttolerant inbred line by suppression subtractive hybridization and reverse Northern hybridization, and validated their differential expression patterns among six inbred lines with different drought tolerance in response to drought stress by quantitative real-time PCR. Sequence similarity analysis indicated that two of four differentially expressed cDNA showed homology to gene DegP encoding trypsin-like serine protease, and gene PGAM-i encoding cofactor-independent phosphoglyceromutase, respectively. Expressions of the genes corresponding to four cDNA fragments was decreased at 6 h after drought stress treatment in most of the six inbred lines, and then returned to the control level with further stress in three of the tolerant inbred lines. The expression of the gene PGAM-i and the genes corresponding to fragments E4 and F4 were increased to a high level in tolerant inbred line 81565. In the two drought-sensitive inbred lines （Dan340 and ES40）, the expression of these genes was still down-regulated. The probable mechanisms of these genes in response to drought stress were discussed. These results indicated that the drought-tolerant inbred lines upregulated the expression of the drought-tolerant candidate genes, in contrast, drought-sensitive inbred lines downregulated the expression of the genes.     

Identification of novel genes associated with duck OASL in response to influenza A virus

2′-5′-Oligoadenylate synthetase like protein(OASL) plays a key role in response to viral infections through selectively activating the OAS/RNase L or OASL/RIG-I signaling pathway. Although classic pathway of OASL is well-known, its regulated genes or co-actors are largely unknown. To study the possible molecular mechanism of duck OASL(dOASL), we performed RNA-sequencing(RNA-seq) and immunoprecipitation and mass spectrometry(IP-MS) at the level of mRNA and protein, respectively. For RNA-seq, we used DF1 cell lines(DF1 dO ASL+/+, DF1 cO ASL–/–, and DF1) with or without the CK/0513 H5 N1 virus(A/chicken/huabei/0513/2007) infection. 1 737 differentially expressed genes(DEGs) were identified as candidate target genes regulated by dOASL. Gene Ontology(GO), Kyoto Encyclopedia of Genes and Genomes(KEGG) analysis and Weighted Correlation Network Analysis(WGCNA) were performed. We identified one important yellow co-expression module correlated with antiviral immune response. In this module, Ankyrin repeat and FYVE domain containing 1(ANKFY1), harboring a BTB domain similar to the methyl CpG-binding protein 1(MBD1) which bound to OASL in human, was regulated by dOASL. At protein level, 133 host proteins were detected. Interestingly, ANKFY1 was one of them binding to dOASL protein. Further phylogenomic and chromosomal syntenic analysis demonstrated MBD1 was absent in birds, while mammals retained. It is suggested that OASL-ANKFY1 interaction might act as a compensatory mechanism to regulate gene expression in birds. Our findings will provide a useful resource for the molecular mechanism research of dOASL.     

Cluster Analysis of Differentially Expressed Heat Stress Genes in Rat Jejunal Mucosal

[Objective] The aim was to study the heat stress mechanism of differen tially expressed genes in rat jejunal mucosal.[Method] Variable cluster analysis and cluster analysis of samples on the differentially expressed heat stress genes in rat jejunal mucosal were carried out with SAS software,and statistics of distribution of the differentially expressed genes on chromosomes were conducted.[Result] The differentially expressed genes were divided into seven categories,of which,the upregulated genes included three categories （i.e.：Category A：Hspa1a,Hspa1b,Hspb1,Hsph1,Dnaja4,Ahsa2 and P4ha1; Category B：Cyp1a2,Zbtb16,Gucy2g,Fgb,Cyp4a3 and Etv2; and Category C：Cyp1a2,Chac1 and Cyp4b1） and the down-regulated genes included four categories （i.e.：Category D：Tlr2,Noxo1,LOC286989 and Aspg; Category E：RGD1560395,Alb and BQ194726; Category F：Ccl4,Gzmk,Al228153,Anxa10,S100a9 and Ascl5; and Category G：Reg1a and Slc13a1）.The classification,function and reasons of differential expression for each gene category were analyzed.[Conclusion] Most of the three categories of up-regulated genes were related to the heat shock proteins; and most of the four categories of down-regulated genes were related to the immunity,providing reference for discussion of the heat stress mechanism.     

Sources for Heat-Stable Resistance to Southern Root-Knot Nematode （Meloidogyne incognita） in Solanum lycopersicum

Southern root-knot nematode （Meloidogyne incognita） is a major problem in vegetable production in China due to the expansion of plastic tunnel and solar greenhouse. Using resistant cultivars is an effective approach to control the disease. Nine genes, Mi-1 to Mi-9, have been reported and only Mi-1 has been successfully used in tomato breeding. However, Mi-1 is inactive at a temperature above 28~C. In order to identify sources for heat-stable resistance to southern root-knot nematode, 53 genotypes of tomato （Solarium spp.） were inoculated with an isolate of M. incognita in the growth chamber at 28 or 32℃ for initial screening. 28 lines had less than 25 galls and were considered as resistant candidates. The top 60% （16 in total） of resistant candidates obtained from each temperature were subject to re-evaluation at 32~C using the same nematode isolate. Three lines ZN17, ZN 48, and LA0385 showed heat-stable resistance with an average of 10 galls or less per plant. LA0385 is a wild species, while ZNI7 and ZN48 are elite breeding lines. These lines were grown in a greenhouse for two seasons, and also showed high resistance with less than 10 galls per plant. Thus they were considered as good sources for breeding resistance to southern root-knot nematode in tomato.     

Cloning and Molecular Identification of A Fatty Acid Desaturase 2 Gene in a and C Genome of Brassica Species

The fatty acid desaturase 2 (fad2) gene was proven to be a major locus for high oleic acid (C18:1). Brassica napus is an amphidiploid species originating from a spontaneous hybridization of Brassica rapa and Brassica oleracea. B. napus contains multiple copies in genome for most of the genes, including fad2 genes. The research cloned nine fad2 genes from 3 varieties of B. rapa and 3 varieties of B. oleracea, respectively. Alignment of the nine fad2 sequences from B. rapa and B. oleracea detect-ed 6 single nucleotide polymorphic sites, which resulted in 6 amino-acid substitutions. The nucleotide substitutions at position 743 bp in the fad2-A gene and position 947 bp in the fad2-C gene were used as 3’ end of al ele-specific primers. In use of the al-lele-specific primers to amplify fad2 gene, we could identify if the fad2 gene originated from A genome or C genome. Besides, the research found that fad2 genes in C genome are more conserved in evolutionary process than those in A genome. The fad2 expression data reported in this study revealed that fad2-A from B. rapa was not only expressed in siliques same as fad2-C from B. oleracea, but also expressed in a high level in stems. Not even the less, fad2 gene from B. napus was expressed higher in roots and flowers. Al these results provided evidences that fad2, though it was expressed differently in B. rapa and B. oleracea, but it was regulated by the same approach in B. napus.     

Genome-wide identification and expression analysis of StPP2C gene family in response to multiple stresses in potato(Solanum tuberosum L.)

The plant protein phosphatase 2Cs(PP2Cs) play an essential role in response to stress and abscisic acid(ABA) signaling pathway. However, to date, no systemic characterization of the PP2Cs has yet been conducted in potato(Solanum tuberosum L.). In the study, a comprehensive research was performed on genome-wide identification and expression analysis of StPP2C genes in potato. A total of 78 potato StPP2C genes were identified based on specific structure of PP2C domain, which were distributed across 11 out of 12 potato chromosomes and divided into 12(A–L) phylogenetic branches. The result from gene duplication analysis showed that 14 StPP2Cs were involved in gene tandem duplication and 8 genes formed fragment duplication events, which indicated that both tandem and fragment duplication contributed to the expansion of the gene family in evolution. Exon–intron structural analysis showed that they had a wide range of exon numbers. Analysis of protein conservative motif demonstrated that StPP2Cs contained more similar motif structures in the same phylogenetic branches. The cis-elements in StPP2C gene promoter regions were mainly responded to light, phytohormone and abiotic stress. Most of them exhibited tissue-specific expression patterns, and some members could differentially express under abiotic stress. The evidence suggested that StPP2C genes may contribute to different functions in several physiological stress and environmental stress conditions. This study could provide new insights to further investigate StPP2C functional characteristics responding to various stresses in potato.     

高原雨点鸽与詹森鸽胸肌转录组差异表达基因筛选与功能分析

筛选高原雨点鸽与詹森鸽胸肌飞行能力差异的关键基因,为赛鸽选育奠定基础.选择性别相同、体况与日龄相近的高原雨点鸽、詹森鸽各3只,屠宰后取胸肌,进行转录组测序,筛选差异表达基因,对差异基因进行Gene Ontology(GO)分析、Kyoto Encyclopedia of Genes and Genomes(KEGG)分...