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1.

GbLMI1过表达促进棉花地上部营养生长

Zhili Chong, Yunxiao Wei, Kaili Li, Muhammad Aneeq Ur Rahman, Chengzhen Liang, Zhigang Meng, Yuan Wang, Sandui Guo, Liangrong He, Rui Zhang
Journal of Integrative Agriculture    2024, 23 (10): 3457-3467.   DOI: 10.1016/j.jia.2023.05.037
摘要131)      PDF    收藏
棉花叶片是光合作用和有机物质合成的主要场所。叶形对光合效率和冠层形成具有重要影响,进而影响棉花产量。研究表明LMI1是调控叶形的关键基因。本研究利用35S启动子构建LMI1基因过表达载体,转化至棉花并获得了LMI1过表达植株。对过表达T1T2代植株田间性状统计分析,发现过表达植株叶片显著增大、茎变粗和干重显著增加。叶脉和叶柄的徒手切片观察发现过表达植株细胞数量显著增加。此外,转录组分析发现赤霉素合成通路NAC基因家族相关的基因差异表达,推测LMI1参与了细胞壁形成和细胞增殖,进而促进了茎变粗GO富集分析在钙离子结合条目KEGG富集分析在脂肪酸降解、磷脂酰肌醇信号转导系统和cAMP信号途径通路。结果表明,LMI1过表达植株响应赤霉素信号,通过第二信使信号(cAMPCA2+),进而增强功能,促进植物营养生长。本研究为探究LMI1促进棉花营养生长,进而提高产量提供理论基础。
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2. JIA-2021-0065 表观基因组甲基化分析揭示成华猪和青裕猪骨骼肌之间的差异甲基化模式
WANG Kai, WU Ping-xian, WANG Shu-jie, JI Xiang, CHEN Dong, JIANG An-an, XIAO Wei-hang, JIANG Yan-zhi, ZHU Li, ZENG Yang-shuang, XU Xu, QIU Xiao-tian, LI Ming-zhou, LI Xue-wei, TANG Guo-qing
Journal of Integrative Agriculture    2022, 21 (6): 1731-1739.   DOI: 10.1016/S2095-3119(21)63814-5
摘要271)      PDF    收藏

本研究基于20头成华猪和30头青裕猪的简化代表性甲基化测序数据使用全基因组分析的方法识别成华猪和青裕猪差异甲基化位点。当甲基化位点的甲基化差异大于0.25以及q值小于0.01时,把该位点识别为差异甲基化位点,然后基于差异甲基化位点搜索对应的差异甲基化基因。结果发现成华猪的几个肉质性状,包括45分钟的pH值 (pH45min),45分钟的肉色亮度值(L45min)以及24小时的肉色亮度值(L24h),均显著高于青裕猪。然后我们检测到10699个差异甲基化位点,并基于这些位点搜索到2760个差异甲基化基因。通过基因功能分析我们发现这些差异甲基化基因主要涉及AMPK信号通路,II型糖尿病,胰岛素信号通路,mTOR信号通路以及胰岛素抵抗等。此外,通过相关文献和研究资料,发现一些差异甲基化基因与脂质代谢,肌肉发育以及肉质性状相关。本研究结果表明成华猪和青裕猪有着不同的甲基化模式,这些甲基化模式的差异反映了二者表型性状的差异。本研究基于简化甲基化测序数据对成华猪和青裕猪进行全基因组甲基化差异分析,研究结果系统解析了成华猪和青裕猪的DNA甲基化模式和表观遗传调控机制


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3. Identifying SNPs associated with birth weight and days to 100 kg traits in Yorkshire pigs based on genotyping-by-sequencing
WU Ping-xian, ZHOU Jie, WANG Kai, CHEN De-juan, YANG Xi-di, LIU Yi-hui, JIANG An-an, SHEN Lin-yuan, JIN Long, XIAO Wei-hang, JIANG Yan-zhi, LI Ming-zhou, ZHU Li, ZENG Yang-shuang, XU Xu, QIU Xiao-tian, LI Xue-wei, TANG Guo-qing
Journal of Integrative Agriculture    2021, 20 (9): 2483-2490.   DOI: 10.1016/S2095-3119(20)63474-8
摘要130)      PDF    收藏

旨在基于简化基因组测序(Genotyping-by-sequencing,GBS)技术进一步挖掘与大白猪初生重(Birth weight,BW)和达百公斤日龄(Days to 100 kg,D100)性状相关的分子遗传标记,并挖掘同时影响两个性状的多效基因。简化基因组测序数据相较于SNP芯片分型数据能够获得更多的SNP位点信息,能够有效的提高全基因组关联分析的检测力。本研究采集600头大白猪的耳组织样品,提取基因组DNA,并利用GBS测序技术进行测序,测序共获得487.34Gb Clean data,测序结果经质量控制和基因型填充后,利用全基因组关联分析(Genome-wide association study,GWAS)鉴定影响大白猪BW和D100的SNP位点和候选基因,采用GEMMA软件对大白猪BW和D100性状进行全基因组关联分析。结果显示,通过GATK软件初步检测共获得10 445 924个SNPs,经过严格的质量控制后共获得279 787个高质量的SNPs位点,并利用Beagle 5.1软件对该基因型数据进行基因型填充。基于填充后的GBS数据采用全基因组关联分析,在基因组显著水平上鉴定到30个SNPs(P<1.79E-07)与D100相关;在建议显著水平上鉴定到22和2个SNPs(P<3.57E-06)分别与D100和BW相关。通过全基因组关联分析筛选到一个显著的SNPs(SSC12: 46,226,512 bp)同时影响BW和D100,暗示了基因在不同性状间具有的一因多效性。本文依据候选基因的相关分子生物学功能,最终确定了2个基因(NSRP1DOCK7)作为影响猪生长性状的最有希望的候选基因。本研究结果为猪BW和D100性状提供了重要的遗传变异位点和候选基因,可以为猪生长性状基因组选择提供重要遗传信息。



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4. Genome-wide scan for selection signatures based on whole-genome re-sequencing in Landrace and Yorkshire pigs
WANG Kai, WU Ping-xian, CHEN De-juan, ZHOU Jie, YANG Xi-di, JIANG An-an, MA Ji-deng, TANG Qian-zi, XIAO Wei-hang, JIANG Yan-zhi, ZHU Li, QIU Xiao-tian, LI Ming-zhou, LI Xue-wei, TANG Guo-qing
Journal of Integrative Agriculture    2021, 20 (7): 1898-1906.   DOI: 10.1016/S2095-3119(20)63488-8
摘要161)      PDF    收藏

长白猪和大白猪是重要的商品猪品种。在长期的育种过程中,由于两种猪的育种目标不同,经过强烈的人工选择,长白猪和大白猪在猪基因组上有不同的选择信号,这些选择信号反映了它们特定的表型特征。因此本研究旨在通过全基因组选择信号扫描检测长白猪和大白猪之间的选择痕迹差异,从而为长白猪和大白猪的育种历史提供基础数据支持。在本研究中我们使用了Z转换的FST(Z(FST))和Z转换的杂合度(ZHp)两种方法对长白猪和大白猪进行全基因组扫描。在扫描过程中我们使用滑动窗口(40-kb窗口和20-kb步长)来检验FST值和杂合度,然后对FST值和杂合度进行Z转换,当滑动窗口的Z(FST)>5或ZHp<-2.8时,我们将该窗口确定为显著窗口,然后基于该窗口的基因组范围搜索候选基因。我们使用Z(FST)的方法找到了17个显著窗口,基于这些窗口找到15个注释元件,其中包括13个基因,比如UGP2基因, RAB3C基因和TLL1基因;我们使用ZHp的方法鉴别了363个显著窗口,基于这些窗口找到208个注释元件,其中包括140个基因,比如PPP3CA基因,PTPN13基因和MAPK10基因。功能分析和相关研究结果表明,大部分候选基因与基础代谢、抗病、细胞过程和生化信号有关,有几个与机体形态和器官有关。研究结果表明由于长期的人工选择,长白猪和大白猪在猪基因组上有明显不同的选择足迹。本研究基于全基因组重测序数据对长白猪和大白猪进行全基因组选择信号扫描,与其他研究相比,我们鉴别出了两个品种特定的差异基因组区域和候选基因,这些结果可以帮助研究者更好的了解人工选择对长白猪和大白猪的选择作用以及为这两个品种的现代育种提供新的方向。


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5. Effects of molybdenum on nutrition, quality, and flavour compounds of strawberry (Fragaria×ananassa Duch. cv. Akihime) fruit
LIU Li, XIAO Wei, JI Mei-ling, YANG Chao, LI Ling, GAO Dong-sheng, FU Xi-ling
Journal of Integrative Agriculture    2017, 16 (07): 1502-1512.   DOI: 10.1016/S2095-3119(16)61518-6
摘要887)      PDF    收藏
    Molybdenum (Mo) is an essential trace element in plant nutrition and physiology. It affects photosynthesis and photosynthate accumulation, therefore also affecting fruit quality and nutritional content. This study assessed the effects of different sodium molybdate (Na2MoO4) concentrations on strawberry. Five different Mo concentrations were applied in this experiment, including 0, 67.5, 135, 168.75, 202.5 g ha–1, respectively. The mineral concentration, including nitrogen (N), Mo, iron (Fe), copper (Cu), and selenium (Se) was assessed in strawberry fruit, as well as chlorophyll content, nutrition quality, taste and aroma. Results showed that net photosynthetic rate (Pn) and chlorophyll content for the strawberry plants increased with an increase in Mo concentration; and the contents of N, Mo, Fe, Cu, total soluble solids (TSS), titratable acidity (TA), sweetness, some sugars, organic acids, and some volatile compounds in the fruit all increased, as well. However, the Mo concentration did not significantly affect the concentrations of Se, sucrose, lactic acid, acetic acid, and some aroma compounds. Fruit sprayed with 135 g ha–1 Mo exhibited the highest TSS and sweetness values, as well as the highest N and Fe concentrations among all the treatments. Pn value and chlorophyll content, fructose, glucose, sorbitol and total sugar contents in fruit supplied with 135 g ha–1 Mo were also higher than that in other treatments. Fruit sprayed with a Mo concentration of 67.5 g ha–1 exhibited significantly higher ascorbic acid (AsA) values than that of control. Ninety-seven volatile compounds were identified in fruit extracted by head-space solid-phase microextraction (HS-SPME) coupled with gas chromatography-mass spectrometry (GC-MS). Fruits sprayed with 135 g ha–1 Mo had the highest concentrations of six characteristic aroma compounds, including methyl butanoate, γ-decalactone, ethyl butanoate, methyl hexanoate, γ-dodecalactone, and ethyl caproate.
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6. Identification of the key chitinase genes in Tetranychus cinnabarinus (Boisduval) based on the expression and sequence characteristic analysis
XU Hao-ran, HE Lin, XIAO Wei, SHEN Guang-mao
Journal of Integrative Agriculture    2017, 16 (04): 892-899.   DOI: 10.1016/S2095-3119(16)61480-6
摘要745)      PDF    收藏
Chitin is an important content in the exoskeletons of arthropods, and its hydrolyzation is catalyzed by chitinases during the process of molting, thus, the chitinases are considered as ideal target to interfere the growth of arthropods.  This study intends to clarify the characteristic of the chitinases during the development of Tetranychus cinnabarinus, and screen out important genes as potential control targets.  The results showed that the total enzyme concentration of chitinases was significantly higher in larva, the first and second nymph than that in egg and adult.  Base on the transcriptome data, six unigenes encoding chitinases were identified and their expression patterns in different developmental stages were detected. The expressions of TcCHIT1 and TcCHIT10 showed high abundance during the molting process and their expression change during the developmental stages was consistent with the enzyme concentration.  The full-length of these two genes were further cloned, and the structural characteristics of their proteins were analyzed by constructing the three-dimensional structure model.  The results provide basic information to understand the characteristic of chitinases in T. cinnabarinus and might be considered as target for control.
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7. Antagonizing Aspergillus parasiticus and Promoting Peanut Growth of Bacillus Isolated from Peanut Geocarposphere Soil
XIAO Wei, YAN Pei-sheng, WU Han-qi and LIN Feng
Journal of Integrative Agriculture    2014, 13 (11): 2445-2451.   DOI: 10.1016/S2095-3119(13)60609-7
摘要1147)      PDF    收藏
A set of 38 Bacillus strains isolated from peanut geocarposphere soil were screened as potential biological control agent anti- Aspergillus parasiticus. Tip-culture method with rapid and quantitative characteristics was used to determine anti-A. parasiticus activity and the process of isolation could be accelerated with this method. 12 out of 38 Bacillus strains showed high anti-aflatoxin production activity. These 12 Bacillus strains were selected to identify the characteristics of promoting peanuts germination rate. Pot experiment in greenhouse was carried out by using these strains which can promote peanuts germination. Phytohormones in the fermentation broth were also detected as another important reference factor to select the isolates as biological control agent with PGPR features. These Bacillus strains isolated from peanut geocarposphere soil not only had high ability anti-Aspergillus parasiticus, but also promoted peanut growth. Therefore, these Bacillus strains were well adapted to peanut production in the field as biological control agent with plant growth promoting rhizobacteria (PGPR) features.
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