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1. JIA-2021-0706 危害我国新疆甜菜的孢囊线虫种类首次鉴定
PENG Huan, LIU Hui, GAO Li, JIANG Ru, LI Guang-kuo, GAO Hai-feng, Wu Wei, WANG Jun, Zhang Yu, HUANG Wen-kun, KONG Ling-an, PENG De-liang
Journal of Integrative Agriculture    2022, 21 (6): 1694-1702.   DOI: 10.1016/S2095-3119(21)63797-8
摘要258)      PDF    收藏

为明确我国主要甜菜产区线虫的种类和危害程度,2015-2018年我们对我国甜菜主要产区进行了系统的调查和检测。在新疆伊犁州新源县的甜菜地调查发现,部分区域甜菜长势弱,植株黄化、矮化明显,受害植株根系有明显的须根团,根上有大量的白色雌虫。采用形态学和形态测量学的方法对孢囊线虫的雌虫、孢囊和二龄幼虫进行显微观察和测量,结果表明,在我国新疆新源县甜菜上发现的孢囊群体的2龄幼虫、孢囊及阴门锥的特征和关键形态测量值与国外已报道的甜菜孢囊线虫基本一致。采用分子生物学的方法对孢囊线虫新疆新源群体的核糖体DNA-ITS、28S-D2/D3和线粒体DNA COI基因进行克隆、测序和分析发现,新源群体的核糖体DNA-ITS, 28S-D2/D3 和线粒体DNA COI基因序列和国外已报道的甜菜孢囊线虫的一致性为99.81-100%,进化分析显示新疆新源群体与国外甜菜孢囊线虫群体聚类为一个进化分支,同时采用甜菜孢囊线虫特异性引物SHF6和rDNA2,从新疆新源群体中扩增出长度为255 bp的特异性条带,分子生物学检测结果表明:我国新疆甜菜上发现的孢囊线虫为甜菜孢囊线虫。采用柯赫氏法则,将500头二龄幼虫分别接种到甜菜(SD21816)和油菜(德油6号)根系中,15天后在甜菜和油菜根系上分别发现了137和157个孢囊和雌虫,表明新疆新源群体能够在甜菜和油菜上完成生活史,且形态学和分子生物学鉴定结果和田间样品完全一致。综上所述,经形态学鉴定和分子特征分析确认,在我国新疆新源县甜菜上发现的孢囊线虫为我国检疫性有害生物——甜菜孢囊线虫,这也是甜菜孢囊线虫在我国的首次明确报道。


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2. Genome-wide analysis of the SCPL gene family in grape (Vitis vinifera L.)
WANG Xi-cheng, WU Wei-min, ZHOU Bei-bei, WANG Zhuang-wei, QIAN Ya-ming, WANG Bo, YAN Li-chun
Journal of Integrative Agriculture    2021, 20 (10): 2666-2679.   DOI: 10.1016/S2095-3119(20)63587-0
摘要260)      PDF    收藏

本研究从葡萄基因组中共鉴定出59个SCPL蛋白,并对该基因家族进行了染色体定位、序列比对、基因结构、系统进化,及保守结构域等生物信息学分析,该基因家族的鉴定严格按照SCPL结构域进行。系统进化分析结果表明,VvSCPL基因家族可被划分成3个亚家族,每个亚家族内的基因均具有高度保守的结构域。VvSCPL基因家族外显子数量介于1-19之间,表明葡萄SCPL基因存在较大的变异。转录组测序与qRT-PCR分析结果表明,VvSCPL基因的表达受干旱和淹水胁迫的诱导或抑制,表明该家族基因可能在应答非生物胁迫过程中发挥着一定的作用。本研究为深入了解葡萄VvSCPL基因的生理与生物学功能提供了有力参考


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3. Identification and functional prediction of long intergenic noncoding RNAs in fetal porcine longissimus dorsi muscle
LI Cen-cen, YU Shu-long, REN Hai-feng, WU Wei, WANG Ya-ling, HAN Qiu, XU Hai-xia, XU Yong-jie, ZHANG Peng-peng
Journal of Integrative Agriculture    2021, 20 (1): 201-211.   DOI: 10.1016/S2095-3119(20)63261-0
摘要174)      PDF    收藏

猪是全球重要的家养动物,以骨骼肌的形式为人类重提供蛋白质。为了研究长链基因间非编码RNA(LincRNA)在猪骨骼肌发育中的功能,我们收集猪胚胎发育期间背最长肌(LDM)的RNA-seq数据,并坚定了739条lincRNA转录本,这些转录本分布在除Y染色体外的所有染色体上。然后我们对鉴定的lincRNA的分子特征进行分析,相比于蛋白编码基因,lincRNA具有较短的转录本长度、较长的外显子长度、较少的外显子数目及较高的组织特异性。除此之外,我们还对lincRNA在5个胚胎发育时期的表达丰度进行分析,鉴定了45个差异表达的lincRNA,其中有3个差异表达的lincRNA在不同的胚胎发育期均差异表达。最后我们对lincRNa的潜在靶基因进行预测,共鉴定了1537个顺式作用的靶基因及8571个反式作用的靶基因。结合上述结果我们鉴定了两个参与骨骼肌发育的关键候选lincRNA:XLOC_024652XLOC_001832。本研究在全基因组水平鉴定猪胚胎期骨骼肌发育过程中可能涉及的lincRNA,为进一步研究lincRNa的功能及猪的遗传育种提供有价值的素材。


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4. Detection and enumeration of wheat grains based on a deep learning method under various scenarios and scales
WU Wei, YANG Tian-le, LI Rui, CHEN Chen, LIU Tao, ZHOU Kai, SUN Cheng-ming, LI Chun-yan, ZHU Xin-kai, GUO Wen-shan
Journal of Integrative Agriculture    2020, 19 (8): 1998-2008.   DOI: 10.1016/S2095-3119(19)62803-0
摘要145)      PDF    收藏
Grain number is crucial for analysis of yield components and assessment of effects of cultivation measures.  The grain number per spike and thousand-grain weight can be measured by counting grains manually, but it is time-consuming, tedious and error-prone.  Previous image processing algorithms cannot work well with different backgrounds and different sizes.  This study used deep learning methods to resolve the limitations of traditional image processing algorithms.  Wheat grain image datasets were collected in the scenarios of three varieties, six background and two image acquisition devices with different heights, angles and grain numbers, 1 748 images in total.  All images were processed through color space conversion, image flipping and rotation.  The grain was manually annotated, and the datasets were divided into training set, validation set and test set.  We used the TensorFlow framework to construct the Faster Region-based Convolutional Neural Network Model.  Using the transfer learning method, we optimized the wheat grain detection and enumeration model.  The total loss of the model was less than 0.5 and the mean average precision was 0.91.  Compared with previous grain counting algorithms, the grain counting error rate of this model was less than 3% and the running time was less than 2 s.  The model can be effectively applied under a variety of backgrounds, image sizes, grain sizes, shooting angles, and shooting heights, as well as different levels of grain crowding.  It constitutes an effective detection and enumeration tool for wheat grain.  This study provides a reference for further grain testing and enumeration applications.
 
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5. Identification of SNPs and expression patterns of FZD3 gene and its effect on wool traits in Chinese Merino sheep (Xinjiang Type)
ZHAO Bing-ru, FU Xue-feng, TIAN Ke-chuan, HUANG Xi-xia, DI Jiang, BAI Yan, XU Xin-ming, TIAN Yue-zhen, WU Wei-wei, ABLAT Sulayman, ZENG Wei-dan, HANIKEZI Tulafu
Journal of Integrative Agriculture    2019, 18 (10): 2351-2360.   DOI: 10.1016/S2095-3119(19)62735-8
摘要153)      PDF    收藏
As a member of the Frizzled family, Frizzled3 (FZD3) is a receptor of the canonical Wnt signaling pathway and plays a vital role in mammalian hair follicle developmental processes.  However, its effects on wool traits are not clear.  The objectives of this study were to identify the single nucleotide polymorphisms (SNPs) and the expression patterns of FZD3 gene, and then to determine whether it affected wool traits of Chinese Merino sheep (Xinjiang Type) or not.  PCR-single stranded conformational polymorphism (PCR-SSCP) and sequencing were used to identify mutation loci, and general linear model (GLM) with SAS 9.1 was used for the association analysis between wool traits and SNPs.  Quantitative real-time PCR (qRT-PCR) was used to investigate FZD3 gene expression levels.  The results showed that six exons of FZD3 gene were amplified and two mutation loci were identified in exon 1 (NC_019459.2: g.101771685 T>C (SNP1)) and exon 3 (NC_019459.2: g.101810848, A>C (SNP2)), respectively.  Association analysis showed that SNP1 was significantly associated with mean fiber diameter (MFD) (P=0.04) and live weight (LW) (P=0.0004), SNP2 was significantly associated with greasy fleece weight (GFW) (P=0.04).  The expression level of FZD3 gene in skin tissues of the superfine wool (SF) group was significantly lower (P<0.05) than that of the fine wool (F) group.  Moreover, it had a higher expression level (P<0.01) in skin tissues than in other tissues of Chinese Merino ewes.  While, its expression level had a fluctuant expression in skin tissues at different developmental stages of embryos and born lambs, with the highest expression levels (P<0.01) at the 65th day of embryos.  Our study revealed the genetic relationship between FZD3 variants and wool traits and two identified SNPs might serve as potential and valuable genetic markers for sheep breeding and lay a molecular genetic foundation for sheep marker-assisted selection (MAS).
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6. Genetic mapping of quantitative trait loci for the stigma exsertion rate in rice (Oryza sativa L.)
Md Habibur Rahman, ZHANG Ying-xin, SUN Lian-ping, ZHANG Ke-qin, Md Sazzadur Rahman, WU Wei-xun, ZHAN Xiao-deng, CAO Li-yong, CHENG Shi-hua
Journal of Integrative Agriculture    2017, 16 (07): 1423-1431.   DOI: 10.1016/S2095-3119(16)61540-X
摘要1026)      PDF    收藏
    The efficiency of hybrid rice seed production can be improved by increasing the percentage of exserted stigmas. To identify quantitative trait loci (QTLs) for this trait, we conducted QTL mapping using 75 chromosome segment substitution lines (CSSLs) developed from a cross between the donor parent, Xieqingzao B (XQZB), a maintainer line which has high stigma exsertion and the recurrent parent, Zhonghui 9308 (ZH9308), a restorer line which has low stigma exsertion. A total of nine QTLs (qSSE5, qSSE10, qSSE11, qDSE10, qDSE11, qTSE5, qTSE6, qTSE10, and qTSE11) for single stigma exsertion (SSE), dual stigma exsertion (DSE) and total stigma exsertion (TSE) were assessed in two environments (Hainan and Zhejiang). Six of these QTLs (qSSE10, qSSE11, qDSE10, qDSE11, qTSE10, and qTSE11) were found in both environments, while one QTL (qTSE6) was found in only Hainan, and two QTLs (qSSE5 and qTSE5) were found in only Zhejiang. The qSSE10, qSSE11, qDSE10, qDSE11, qTSE6, qTSE10, and qTSE11 alleles, which are derived from the parent XQZB, exhibited a positive additive effect. In contrast, the qSSE5 and qTSE5 alleles, which are derived from the parent ZH9308, exhibited a negative additive effect. The SSE, DSE and TSE traits were significantly correlated with each other in an environmentally dependent manner. These results indicated that the lines showing higher values for SSE were more likely to exhibit increased values for DSE, which would ultimately increase TSE. To evaluate the advantage of exserted stigmas for cross-pollination, single, dual and total stigma exsertion should be considered separately in future attempts at genetic improvement to achieve increased production of rice hybrid seeds. This study also provides information for fine mapping, gene cloning and particularly marker-assisted selection (MAS), on the latter and with an emphasis the phenotypic effects and implications of the QTLs for practical use in hybrid rice breeding.
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7. Influence of gallic acid on porcine neutrophils phosphodiesterase 4, IL-6, TNF-α and rat arthritis model
JIANG Dai-xun, ZHANG Mei-hua, ZHANG Qian, CHEN Yi-shan, MA Wen-jing, WU Wei-peng, MU Xiang
Journal of Integrative Agriculture    2015, 14 (4): 758-764.   DOI: 10.1016/S2095-3119(14)60824-8
摘要1910)      PDF    收藏
Our previous studies showed that the anti-inflammatory effects of Paeonia lactiflora roots extract may be mediated, at least in part, through its gallic acid content, and this effect may be regulated in part by an inhibition on cAMP-phosphodiesterase (PDE). To explore the anti-inflammatory effect and mechanism, the influence of gallic acid on neutrophils PDE4 activity and expression, TNF-α and IL-6 content and rat arthritis model were further studied. PDE4 activity and gene express were calculated respectively by substrate cAMP change examined with HPLC and real-time RT-PCR. The concentration of IL-6 and TNF-α in supernatant were assayed by ELISA method. Model of rat arthritis was caused by complete Freund’s adjuvant. Results showed that gallic acid had a dose-dependent restraint on PDE4 activity of neutrophils in vitro, promoted significantly PDE4A expression (P<0.01), and had no influence on the expressions of PDE4B and 4D. However, PDE4C expression was not detected. Gallic acid could promote IL-6 release (P<0.05), and inhibit TNF-α release of neutrophils (P<0.05). The experiment in vivo showed that gallic acid had obvious restraint on local inflammation of animal model (P<0.05). Therefore, the anti-inflammatory effect of gallic acid may be mediated in part through an inhibition on PDE4 activity and further an increase of IL-6 and a decrease of TNF-α of neutrophils, and this effect seemed to have no relationship with PDE4 expression.
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8. Genome Array on Differentially Expressed Genes of Skin Tissue in Cashmere Goat at Early Anagen of Cashmere Growth Cycle Using DNA Microarray
DI Jiang, XU Xin-ming, Lazate Ainiwaer, ZHANG Yan-hua, TIAN Ke-chuan, YU Li-juan, WU Weiwei, Hanikezi Tulafu, FU Xue-feng , Marzeya Yasen
Journal of Integrative Agriculture    2014, 13 (10): 2243-2252.   DOI: 10.1016/S2095-3119(13)60606-1
摘要1192)      PDF    收藏
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.
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9. The Effect of Plastic-Covered Ridge and Furrow Planting on the Grain Filling and Hormonal Changes of Winter Wheat
LIU Yang, HAN Juan, WEN Xiao-xia, WU Wei, GUO Qiang, ZENG Ai , LIAO Yun-cheng
Journal of Integrative Agriculture    2013, 12 (10): 1771-1782.   DOI: 10.1016/S2095-3119(13)60337-8
摘要1915)      PDF    收藏
Although plastic-covered ridge and furrow planting (RF) has been reported to produce substantial increases in the grain weight of winter wheat, the underlying mechanism is not yet understood. The present study used two cultivars, Xinong 538 and Zhoumai 18, and RF and traditional flatten planting (TF, control) with the objective of investigating the effect of RF on wheat grain filling and the possible relationship of hormonal changes in the wheat grains under RF to grain filling. The results indicated that RF significantly increased the grain weight, although the effects on grain filling were different: RF significantly increased the grain-filling rate and grain weight of inferior grains, whereas RF had no significant effect on grainfilling rate and grain weight of superior grains. The ?nal grain weight of inferior grains under RF was 39.1 and 50.7 mg for Xinong 538 and Zhoumai 18, respectively, 3.6 and 3.4 mg higher than the values under TF. However, the final grain weight of superior grains under RF was only 0.6 and 0.8 mg higher than under TF for Xinong 538 and Zhoumai 18, respectively. RF significantly decreased the ethylene and gibberellic acid content in the inferior grains and increased the indole-3-acetic acid, abscisic acid and zeatin + zeatin riboside content in the inferior grains; however, no significant difference between RF and TF was observed for the hormonal content in the superior grains. Based on these results, we concluded that RF significantly modulated hormonal changes in the inferior grains and, thus, affected the grain filling and grain weight of the inferior grains; in contrast, RF had no significant effect on grain filling, grain weight and hormonal changes in the superior wheat grains.
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10. Genetic Analysis and Mapping of an Enclosed Panicle Mutant Locus esp1 in Rice (Oryza sativa L.)
DUAN Yuan-lin, GUAN Hua-zhong, ZHUO Ming, CHEN Zhi-wei, LI Wen-tao, PAN Run-sen, MAO Da-mei, ZHOU Yuan-chang, WU Wei-ren
Journal of Integrative Agriculture    2012, 12 (12): 1933-1939.   DOI: 10.1016/S1671-2927(00)8729
摘要1879)      PDF    收藏
A mutant was isolated from the M2 of 60Co-g ray mutagenized male-fertility restorer line Zao-R974 in rice. The mutant showed pleiotropic phenotypes including dwarfism, delayed heading time, short and partially enclosed panicles, short uppermost internode, decreased grain and secondary branch numbers per panicle, and partially degenerated spikelets. The mutant was named as esp1 (enclosed shorter panicle 1). Genetic analysis indicated that the mutant phenotype was controlled by a recessive locus. Spraying exogenous GA3 did not rescue the panicle enclosure. Using an F2 and a BC1 population of the cross between esp1 and a japonica cultivar Nipponbare, we mapped the ESP1 locus to a region of ~260 kb on chromosome 11. This result provides a basis for further map-based cloning of the ESP1 locus.
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11. Functional Characterization of a NEM1-Like Gene in Magnaporthe oryzae
WANG Ying, JIAO Tian-lei, LIU Xiao-hong, LIN Fu-cheng , WU Wei-ren
Journal of Integrative Agriculture    2011, 10 (9): 1385-1390.   DOI: 10.1016/S1671-2927(11)60131-4
摘要2095)      PDF    收藏
Magnaporthe oryzae, a filamentous ascomycete fungus, is well known as the causal agent of rice blast. With thetechnology of suppression subtractive hybridization (SSH), it was previously found that MGG_06001 (or named MoNEM1),a gene of M. oryzae homologous to the NEM1 (nuclear envelope morphology protein 1) gene of baker’s yeast(Saccharomyces cerevisiae), is differentially expressed between the mature appressium and the conidium and mycelium.This study aimed to characterize the function of MoNEM1 gene by knocking it out using the method of target genereplacement. The ΔMonem1 mutants exhibited reduced mycelial growth and conidiation. However, disruption of MoNEM1gene does not affect the pathogenicity of M. oryzae on barley and rice.
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12. Mapping of Mutant Gene prbs Controlling Poly-Row-and-Branched Spike in Barley (Hordeum vulgare L.) 
HUANG Bi-guang , WU Wei-ren
Journal of Integrative Agriculture    2011, 10 (10): 1501-1505.   DOI: 10.1016/S1671-2927(11)60144-2
摘要1563)      PDF    收藏
A row-type mutant of barley named poly-row-and-branched spike (prbs) was previously obtained from a two-rowed cultivar Pudamai-2 after treated by inflorescence soaking in maize total DNA solution. The mutant produces branched spikes with irregular multiple rows. Genetic analysis indicated that the mutant phenotype was caused by a recessive gene prbs, and the PRBS locus had a recessive epistatic effect on an independent locus (denoted as Vrsx) conferring the variation of two-rowed spike vs. six-rowed spike. This study aimed to map PRBS as well as Vrsx using simple sequence repeats (SSR) markers. We developed an F2 population from a cross between the prbs mutant and a six-rowed cultivar Putianwudu for the gene mapping. As the two target loci interacted to result in a segregation ratio of two-rowed type:sixrowed type:prbs=9:3:4 in the population, we adopted a special strategy to map the two loci. PRBS was mapped between SSR markers HvLTPPB and Bmag0508A on the short arm of chromosome 3H, with distances of 24.7 and 14.3 cM to the two markers, respectively. Vrsx was mapped between SSR markers Bmag0125 and Bmag0378 on chromosome 2H, with distances of 6.9 and 15.3 cM to the two markers, respectively. This suggests that Vrsx should be the known locus Vrs1, which predominantly controls row-type variation in barley cultivars, and PRBS is a new locus related to the row type of spikes in barley.
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