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1. 小麦DnaJ家族的全基因组鉴定及其对小麦黄花叶病毒侵染的调控分析
LIU Ting-ting, XU Miao-ze, GAO Shi-qi, ZHANG Yang, HU Yang, JIN Peng, CAI Lin-na, CHENG Ye, CHEN Jian-ping, YANG Jian, ZHONG Kai-li
Journal of Integrative Agriculture    2022, 21 (1): 153-169.   DOI: 10.1016/S2095-3119(21)63619-5
摘要258)      PDF    收藏

DnaJ蛋白最初是在大肠杆菌中鉴定的一种大小约为41kDa的热休克蛋白,其蛋白家族是分子伴侣中最多样化的家族,在蛋白质折叠和各种生理活动的调节中扮演了重要角色,且在植物发育和胁迫应答中发挥重要作用。DnaJ家族蛋白已在许多物种中广泛研究,例如人类,果蝇,蘑菇,西红柿和拟南芥等,但在小麦中的作用以及其与植物病毒之间的相互作用机制却鲜少有研究。在这篇文章中,我们鉴定了236TaDnaJs,并对其保守结构域,基因结构蛋白质基序蛋白质结构染色体定位和共线性以及顺式作用元件进行了全基因组分析。根据分析结果,我们将这些TaDnaJs按其结构域分DJADJBDJC三组,并从分组中随机选择了6个基因进行组织特异性分析和激素胁迫下的基因表达谱分析,结果表明TaDnaJ基因在不同组中存在组织差异表达,DJA组的基因表达集中顶部叶片,对ABAGA更为敏感;DJB组的基因表达水平在根和种子中最高,对ABA更为敏感;DJC组中的基因表达在小麦叶片中最高,其次是根和种子,对SAGA最敏感。另外我们随机选择了17个基因分析植物病毒侵染后基因表达水平的变化,结果显示,在测试的17TaDnaJ基因中,有16个基因在小麦黄花叶病毒(WYMV染后呈现上调表达,这表明TaDnaJ家族可能参与了植物防御反应。随后我们通过酵母两杂交实验验证了WYMV NIaNIb7KD蛋白与WYMV染后表达水平变化最显著的TraesCS7A02G506000相互作用。在这篇文章中,我们探究了DnaJ蛋白介导的胁迫耐受性和敏感性的分子机制,DnaJ基因可能参与了植物对非生物和生物胁迫的抗性。本研究提高了对TaDnaJ基因表达谱认识,并且为TaDnaJ家族与植物防御机制之间的研究提供了一定的研究基础。

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2. Effects of rearing system (floor vs. cage) and sex on performance, meat quality and enteric microorganism of yellow feather broilers
WANG Lai-di, ZHANG Yang, KONG Ling-ling, WANG Zhi-xiu, BAI Hao, JIANG Yong, BI Yu-lin, CHANG Guo-bin, CHEN Guo-hong
Journal of Integrative Agriculture    2021, 20 (7): 1907-1920.   DOI: 10.1016/S2095-3119(20)63420-7
摘要189)      PDF    收藏

为了探究黄羽肉鸡的高效饲养模式,本研究以雪山草鸡为研究素材,按照2×2完全随机试验探究2种饲养方式以及性别对雪山草鸡生长性能、肉品质以及肠道微生物的影响。本试验将200只体重相近的雪山草鸡公母各半,按照性别和饲养方式随机分为四组,饲养方式分为笼饲和平养。结果表明,雄性肉鸡和笼养肉鸡比雌性肉鸡和平养肉鸡表现出更好的生产性能(P<0.001)和更高的全净膛率(P<0.001)。饲养模式和性别的交互作用对胸肌率和腿肌率有影响(P<0.05),雌性平养肉鸡胸肌率和腿肌率最高(P<0.02)。无论是雌鸡还是雄鸡,在笼养模式下肉鸡腹脂率均高于平养模式(P<0.01)。相比于其他组,雌性笼养肉鸡的胸肌肉品质较好(P<0.05)。雄性肉鸡的胸肌pH值低于雌性肉鸡,且与腿肌pH值的结果趋势一致,笼养肉鸡胸肌pH值高于平养肉鸡,而腿肌的pH值与此相反。肉品质指标的差异与肉鸡活动量差异有一定的关系。福利指标结果显示,平养模式下肉鸡的羽毛质量优于笼养肉鸡(P<0.01),步态得分无显著影响(P>0.05)。基于16S rRNA扩增测序的肠道菌群结果显示,各组肠道菌群中以厚壁菌门、变形菌门和拟杆菌门为主,盲肠菌群组成相对稳定。平养模式下鸡只肠道菌群的多样性较笼养模式更为丰富,但alpha多样性在各组间无显著差异(P>0.06)。肠道中拟杆菌门与厚壁菌门的比例、幽门螺杆菌和罗姆布茨菌的丰度等可能影响肉鸡的生产性能。综合看来,笼养模式以及雄性雪山鸡的选择可获得高效的生产性能,这可能与相关肠道菌群丰度差异有一定的关系,而平养模式下鸡只羽毛质量更好,肠道微生物群种类更为丰富,生产中可根据具体市场需求进行选择。


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3. Reduction in cadmium accumulation in japonica rice grains by CRISPR/Cas9-mediated editing of OsNRAMP5
YANG Chang-hong, ZHANG Yang, HUANG Chao-feng
Journal of Integrative Agriculture    2019, 18 (3): 688-697.   DOI: 10.1016/S2095-3119(18)61904-5
摘要237)      PDF(pc) (625KB)(195)    收藏
Cadmium (Cd) intake is harmful to human health and Cd contamination in rice grains represents a severe threat to those consuming rice as a staple food.  Knockout of Cd transporters is a promising strategy to reduce Cd accumulation in rice grains.  OsNRAMP5 is the major transporter for Cd and manganese (Mn) uptake in rice.  Nevertheless, it is uncertain whether knockout of OsNRAMP5 is applicable to produce low Cd rice without affecting plant growth and grain yield.  In this study, we adopted CRISPR/Cas9-based gene editing technology to knock out OsNRAMP5 in two japonica varieties.  We generated three independent transgene-free osnramp5 mutants and investigated the effect of osnramp5 mutations on Cd accumulation and plant growth.  Hydroponic experiments showed that plant growth and chlorophyll content were significantly reduced in osnramp5 mutants at low Mn conditions, and this defective growth in the mutants could be fully rescued by supply of high levels of Mn.  Cd and Mn accumulation in both roots and shoots was markedly reduced in the mutants compared to that in wild-type plants.  In paddy field experiments, although Cd in flag leaves and grains was greatly reduced in osnramp5 mutants, some agronomic traits including plant height, seed setting rate, and grain number per panicle were affected in the mutants, which ultimately caused a mild reduction in grain yield.  The reduced plant growth in the mutants can be attributed to a marked decrease in Mn accumulation.  Our results reveal that the manipulation of OsNRAMP5 should be treated with caution: When assessing the applicability of osnramp5 mutants, soil pH and soil water content in paddy fields need to be taken into consideration, since they might affect the levels of available Mn in the soil and consequently determine the effect of the mutation on grain yield.
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4. Nitrogen mobility, ammonia volatilization, and estimated leaching loss from long-term manure incorporation in red soil
HUANG Jing, DUAN Ying-hua, XU Ming-gang, ZHAI Li-mei, ZHANG Xu-bo, WANG Bo-ren, ZHANG Yang-zhu, GAO Su-duan, SUN Nan
Journal of Integrative Agriculture    2017, 16 (09): 2082-2092.   DOI: 10.1016/S2095-3119(16)61498-3
摘要771)      PDF    收藏
Nitrogen (N) loss from fertilization in agricultural fields has an unavoidable negative impact on the environment and a better
understanding of the major pathways can assist in developing the best management practices. The aim of this study was
to evaluate the fate of N fertilizers applied to acidic red soil (Ferralic Cambisol) after 19 years of mineral (synthetic) and
manure fertilizer treatments under a cropping system with wheat-maize rotations. Five field treatments were examined:
control (CK), chemical nitrogen and potash fertilizer (NK), chemical nitrogen and phosphorus fertilizer (NP), chemical nitrogen,
phosphorus and potash fertilizer (NPK) and the NPK with manure (NPKM, 70% N from manure). Based on the soil
total N storage change in 0–100 cm depth, ammonia (NH3) volatilization, nitrous oxide (N2O) emission, N plant uptake, and
the potential N leaching loss were estimated using a mass balance approach. In contrast to the NPKM, all mineral fertilizer
treatments (NK, NP and NPK) showed increased nitrate (NO3-N) concentration with increasing soil depth, indicating higher
leaching potential. However, total NH3 volatilization loss was much higher in the NPKM (19.7%) than other mineral fertilizer
treatments (≤4.2%). The N2O emissions were generally low (0.2–0.9%, the highest from the NPKM). Total gaseous loss
accounted for 1.7, 3.3, 5.1, and 21.9% for NK, NP, NPK, and NPKM treatments, respectively. Estimated N leaching loss
from the NPKM was only about 5% of the losses from mineral fertilizer treatments. All data demonstrated that manure
incorporation improved soil productivity, increased yield, and reduced potential leaching, but with significantly higher NH3
volatilization, which could be reduced by improving the application method. This study confirms that manure incorporation is an essential strategy in N fertilization management in upland red soil cropping system.
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5. Diversity shifts of rumen bacteria induced by dietary forages in dairy cows and quantification of the changed bacteria using a new primer design strategy
JIN Di, ZHAO Sheng-guo, ZHANG Yang-dong, SUN Peng, BU Deng-pan, Yves Beckers, WANG Jia-qi
Journal of Integrative Agriculture    2016, 15 (11): 2596-2603.   DOI: 10.1016/S2095-3119(16)61346-1
摘要1406)      PDF    收藏
    The partial 16S rRNA gene sequences (100 to 500 bp) were widely used to reveal rumen bacterial composition influenced by diets, while quantification of the changed uncultured bacteria was inconvenient due to difficult designing of specific primers based on short sequences. This study evaluated the effect of forage resources on rumen bacterial diversity and developed new strategy for primer design based on short sequences to quantify the changed uncultured bacteria. Denaturing gradient gel electrophoresis (DGGE) analysis and subsequent band sequencing were used to reveal the distinct rumen bacteria composition in cows fed with two forage sources (single corn stover vs. mixed forages including alfalfa hay and corn silage). The bacterial diversity in the rumen of dairy cows fed with corn stover was lower than that with mixed forages (P<0.05). The bacterium named R-UB affiliating to uncultured Succinivibrionaceae was identified, and it was abundant in the rumen of cows fed with mixed forages compared to corn stover. The full length 16S rRNA gene sequences with identity of >97% to the R-UB 16S rRNA gene sequence were obtained from GenBank and used to design specific primers to quantify uncultured bacterium R-UB. All sequences of amplicon from the new primers were of 100% identity to R-UB sequences indicating the high specificity of new primers. Quantitative PCR confirmed that abundance of R-UB in the rumen of cows fed with corn stover was lower than those fed with mixed forages (P<0.01). New strategy for designing primers based on partial 16S rRNA genes to quantify targeted uncultured bacteria was successfully developed. The rumen bacteria descending significantly in the cows fed corn stover compared to those fed mixed forages was identified as uncultured R-UB from Succinivibrionaceae.
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6. Analysis of the Genetic Diversity and Origin of Some Chinese Domestic Duck Breeds
ZHANG Yang, CHEN Yang, ZHEN Ting, HUANG Zheng-yang, CHEN Chang-yi, LI Xin-yu
Journal of Integrative Agriculture    2014, 13 (4): 849-857.   DOI: 10.1016/S2095-3119(13)60447-5
摘要1761)      PDF    收藏
Twelve fluorescence-labeled microsatellite markers were used to analyze the genetic diversity of 12 domestic duck breeds and 2 wild duck breeds to determine the relationship and origin of Chinese domestic duck breeds. Gene frequency, effective number of alleles (Ne), expected heterozygosity (He), polymorphism information contents (PIC), inbreeding coefficient in population (Fis), standard genetic distance (DS), and genetic distance (DA) were calculated by FSTAT and distance and phylogenetic analysis after the dates which were output from the Microsatellite-Toolkit software. Genetic distances between 12 domestic duck breeds and 2 wild duck breeds were analyzed by variance analysis. Unweighted pair group method with arithmetic mean (UPGMA) and phylogenetic trees used for cluster analysis were structured. The results indicated that 11 loci had medium- or high-level genetic diversity among the 12 loci, which could be efficiently used in the detection of the genetic parameters of each population. The values of He were 0.5414 to 0.7343, those of PIC proved similar, and those of Fis were 0.1101 to 0.3381 among all populations. All breeds were clustered into three groups by UPGMA phylogenetic trees. Banzui duck was clustered into a separate group. Differences of the DA were analysed by t-test. The results showed that difference in DA between the 12 domestic duck breeds and Lvtou duck and the Banzui duck were very significant (P<0.01), indicating that these 12 domestic duck breeds originated from Lvtou wild duck, but not Banzui duck.
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7. A Co-Dominant Marker BoE332 Applied to Marker-Assisted Selection of Homozygous Male-Sterile Plants in Cabbage (Brassica oleracea var. capitata L.)
CHEN Chen, ZHUANG Mu, FANG Zhi-yuan, WANG Qing-biao, ZHANG Yang-yong, LIU Yu-mei
Journal of Integrative Agriculture    2013, 12 (4): 596-602.   DOI: 10.1016/S2095-3119(13)60277-4
摘要1193)      PDF    收藏
The dominant genic male sterility (DGMS) gene CDMs399-3 derived from a spontaneous mutation in the line 79-399-3 of spring cabbage (Brassica oleracea var. capitata L.), has been successfully applied in hybrid seed production of several cabbage cultivars in China. During the development of dominant male sterility lines in cabbage, the conventional identification of homozygous male-sterile plants (CDMs399-3/CDMs399-3) is a laborious and time-consuming process. For marker-assisted selection (MAS) of the gene CDMs399-3 transferred into key spring cabbage line 397, expressed sequence tag-simple sequence repeats (EST-SSR) and SSR technology were used to identify markers that were linked to CDMs399-3 based on method of bulked segregant analysis (BSA). By screening a set of 978 EST-SSRs and 395 SSRs, a marker BoE332 linked to the CDMs399-3 at a distance of 3.6 cM in the genetic background of cabbage line 397 were identified. 7 homozygous male-sterile plants in population P1170 with 20 plants were obtained finally via MAS of BoE332. Thus, BoE332 will greatly facilitate the transferring of the gene CDMs399-3 into the key spring cabbage line 397 and improve the application of DGMS in cabbage hybrid breeding.
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8. Research on Development of Agricultural Geographic Information Ontology
HUANG Yong-qi, CUI Wei-hong, ZHANG Yang-jian, DENG Gao-yan
Journal of Integrative Agriculture    2012, 11 (5): 865-877.   DOI: 10.1016/S1671-2927(00)8609
摘要1286)      PDF    收藏
This paper first analyzes the reason that agricultural geographic information gives rise to semantic heterogeneity and solution thereof. Although OWL (web ontology language) is the standard of ontology representation language in semantic web, it is insufficient in representing spatial characteristics, especially spatial relationship. Consequently it is pointed out to build geo-ontology by virtue of three theories such as mereology, location theory and topology in this paper. This paper introduces mereology, location theory and topology, and then discusses how to adopt these three theories to build geo-ontology. The outcome of experiment shows that solution put forward by this paper is feasible.
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9. Resistance Level and Metabolism of Barnyard-Grass (Echinochloa crusgalli (L.) Beauv.) Populations to Quizalofop-p-ethyl in Heilongjiang Province, China
HUAN Zhi-bo, ZHANG Hong-jun, HOU Zhen, ZHANG Shao-yi, ZHANG Yang, LIU Wei-tang, BI Yaling , WANG Jin-xin
Journal of Integrative Agriculture    2011, 10 (12): 1914-1922.   DOI: 10.1016/S1671-2927(11)60192-2
摘要1727)      PDF    收藏
Eleven barnyardgrass populations were assayed. The highest resistant population was Geqiushan R with RI 125.45 resulted from the seed assay and 87.29 resulted from the whole plant bioassay followed by 853 R with RI 2.79 resulted from the seed assay and 6.04 resulted from the whole plant bioassay. The resistance level of other nine populations was low with RI 1.13-2.61 resulted from the seed assay and 1.48-3.63 resulted from the whole plant bioassay. The activity of an important metabolic enzyme glutathione S-transferases (GSTs) and three protective enzymes (SOD, POD, and CAT) were determined in vivo for Geqiushan R, 853 R, and Wudalianchi R. Compared with the S controls, the activities of POD in Geqiushan R, GSTs in 853 R, and Wudalianchi R were increased.
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10. Transformation of Cabbage (Brassica oleracea L. var. capitata) with Bt cry1Ba3 Gene for Control of Diamondback Moth 
YI Deng-xia, CUI Lei, LIU Yu-mei, ZHUANG Mu, ZHANG Yang-yong, FANG Zhi-yuan , YANG Li-mei
Journal of Integrative Agriculture    2011, 10 (11): 1693-1700.   DOI: 10.1016/S1671-2927(11)60167-3
摘要2358)      PDF    收藏
To obtain transgenic cabbage line with broad insect resistance, a new synthetic Bacillus thuringiensis cry1Ba3 gene was introduced into white cabbage via Agrobacterium tumefaciens-mediated transformation and 37 transformants were obtained. Polymerase chain reaction (PCR) and Southern blot analyses confirmed that cry1Ba3 was successfully inserted into the genome of cabbage. Reverse transcription-polymerase chain reaction (RT-PCR) demonstrated that cry1Ba3 was expressed. Western blot results confirmed the production of insecticidal protein encoded by cry1Ba3. Insect bioassays showed that transgenic cabbages effectively controlled both susceptible and Cry1Ac-resistant diamondback moth (DBM) larvae.
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