摘要：
Glucosinolates are amino acid-derived secondary metabolites that act as chemical defense agents against pests. However, the presence of high levels of glucosinolates severely diminishes the nutritional value of seed meals made from rapeseed (Brassica napus L.). To identify the loci affecting seed glucosinolate content (SGC), we conducted genome-wide resequencing in a population of 307 diverse B. napus accessions from the three B. napus ecotype groups, namely, spring, winter, and semi-winter. These resequencing data were used for a genome-wide association study (GWAS) to identify the loci affecting SGC. In the three ecotype groups, four common and four ecotype-specific haplotype blocks (HBs) were significantly associated with SGC. To identify candidate genes controlling SGC, transcriptome analysis was carried out in 36 accessions showing extreme SGC values. Analyses of haplotypes, genomic variation, and candidate gene expression pointed to five and three candidate genes in the common and spring group-specific HBs, respectively. Our expression analyses demonstrated that additive effects of the three candidate genes in the spring group-specific HB play important roles in the SGC of B. napus.
关键词：
captation du plomb;croissance racinaire;endophytes;lead uptake;root growth
摘要：
Endophytic bacteria are generally helpful for plant growth and protection. We isolated from tobacco seeds three Pseudomonas strains (K03, Y04, and N05) that could produce siderophores, indole-3-acetic acid, and 1-aminocyclopropane-1-carboxylate deaminase, fix nitrogen, dissolve phosphorus and potassium, and tolerate heavy metals. In pot experiments, the three isolated strains significantly promoted root growth and increased the root enzyme activity in Nicotiana tobacum K326. Furthermore, bacterial inoculations increased the proportion of residual lead (Pb) by 8.36%-51.63% and decreased the total Pb content by 3.28%-6.38% in the contaminated soil during tobacco planting, compared with uninoculated soils. An effective decrease in Pb content was also found in tobacco leaves with bacterial inoculations. K03 inoculation decreased the Pb content in the upper leaves by 49.80%, and Y04 inoculation had the best effect, decreasing the Pb content in the middle leaves by 70.12%. Additionally, soil pH and root activity had significant effects on transformation and translocation of Pb. The study suggested that in response to Pb pollution in soil, a reasonable application of endophytes (e.g., Pseudomonas) might be a promising approach in promoting tobacco growth and reducing Pb content in tobacco, while simultaneously enhancing Pb stabilization in soils.
通讯作者：
Shouwen Chen<&wdkj&>Jizhong Zhou<&wdkj&>Zhili He
作者机构：
[Wu, Bo; He, Zhili] Sun Yat Sen Univ, Environm Microbi Res Ctr & Guangdong Prov Key Lab, Guangzhou, Peoples R China.;[Deng, Ye; Wu, Bo; Wu, Liyou; Ning, Daliang; He, Zhili; Zhou, Jizhong; Liu, Feifei; Shen, Lina] Univ Oklahoma, Inst Environm Genom & Dept Microbiol & Plant Biol, Norman, OK USA.;[Wu, Bo; He, Zhili; Chen, Shouwen] Huazhong Agr Univ, State Key Lab Agr Microbiol, Wuhan, Peoples R China.;[Liu, Feifei] Guangdong Inst Microbiol & State Key Lab Appl Mic, Guangdong Prov Key Lab Microbial Culture Collect, Guangzhou, Peoples R China.;[Weiser, Michael D.] Univ Oklahoma, Dept Biol, Norman, OK USA.
通讯机构：
[Shouwen Chen] S;[Jizhong Zhou] I;[Zhili He] E;State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China<&wdkj&>Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, College of Life Sciences, Hubei University, Wuhan, China<&wdkj&>Environmental Microbiomics Research Center and Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, China<&wdkj&>Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA<&wdkj&>State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China<&wdkj&>College of Agriculture, Hunan Agricultural University, Changsha, Hunan, China<&wdkj&>Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA<&wdkj&>Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA<&wdkj&>School of Environment, Tsinghua University, Beijing, China
摘要：
<jats:title>Abstract</jats:title><jats:p>
<jats:list>
<jats:list-item><jats:p>Micro‐organisms harbouring the <jats:italic>nosZ</jats:italic> gene convert N<jats:sub>2</jats:sub>O to N<jats:sub>2</jats:sub> and play a critical role in reducing global N<jats:sub>2</jats:sub>O emissions. As higher denitrifier diversity can result in higher denitrification rates, here we aimed to understand the diversity, composition and spatial structure of N<jats:sub>2</jats:sub>O‐reducing microbial assemblages in forest soils across a large latitudinal and temperature gradient.</jats:p></jats:list-item>
<jats:list-item><jats:p>We sequenced <jats:italic>nosZ</jats:italic> gene amplicons of 126 soil samples from six forests with mean annual soil temperatures (<jats:styled-content style="fixed-case">MAST</jats:styled-content>) ranging from 3.7 to 25.3°C and tested predictions of the metabolic theory of ecology (<jats:styled-content style="fixed-case">MTE</jats:styled-content>) and metabolic‐niche theory (<jats:styled-content style="fixed-case">MNT</jats:styled-content>). As predicted, α‐diversity of <jats:italic>nosZ</jats:italic> communities increased with increasing <jats:styled-content style="fixed-case">MAST</jats:styled-content>, within‐site β‐diversity decreased and two (<jats:styled-content style="fixed-case">pH</jats:styled-content> and soil moisture) of the three niche widths examined were larger with increasing <jats:styled-content style="fixed-case">MAST</jats:styled-content>.</jats:p></jats:list-item>
<jats:list-item><jats:p>We calculated β‐nearest taxon distance and Raup–Crick metric to quantify the relative influence of the assembly processes determining <jats:italic>nosZ</jats:italic> assemblage structure. Environmental selection was the primary process driving assemblage structure in all six forests. Homogenizing dispersal was also important at one site, which could be explained by the site's much lower variability in soil chemistry.</jats:p></jats:list-item>
<jats:list-item><jats:p>We used canonical correspondence analysis and multiple regression on matrices to examine relationships between <jats:italic>nosZ</jats:italic> communities and environmental factors, and found that temperature and spatial distance were significant predictors of <jats:italic>nosZ</jats:italic> assemblage structure.</jats:p></jats:list-item>
<jats:list-item><jats:p>Overall our results support both theories (<jats:styled-content style="fixed-case">MTE</jats:styled-content> and <jats:styled-content style="fixed-case">MNT</jats:styled-content>) tested, showing that higher temperatures are correlated with higher local diversity, wider niche breadths and lower within‐site turnover rates.</jats:p></jats:list-item>
</jats:list>
</jats:p><jats:p>A <jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="http://onlinelibrary.wiley.com/doi/10.1111/1365-2435.13091/suppinfo">plain language summary</jats:ext-link> is available for this article.</jats:p>
关键词：
Crop morbidity;Biological control agents;Bacterial interactions;Bacterial diversity;Bacterial community structure
摘要：
Bacterial wilt, caused by Ralstonia solanacearum, occurs occasionally during tobacco planting and potentially brings huge economic losses in affected areas. Soil microbes in different management stages play important roles in influencing bacterial wilt incidence. Studies have focused on the impacts of species diversity and composition during cropping periods on disease morbidity; however, the effects of the soil bacterial biomass, species diversity, species succession, and population interactions on morbidity remain unclear during non-cropping periods. In this study, we explored the soil bacterial communities in the non-cropping winter fallow (WF) and cropping late growing (LG) periods under consecutive monoculture systems using 16S ribosomal RNA gene sequencing and qPCR and further analyzed their effects on tobacco bacterial wilt incidence. We found that the bacterial communities in the WF period were significantly different from those in the LG period based on detrended correspondence analysis and dissimilarity tests. Crop morbidity was significantly related to bacterial community structure and to the presence of some genera during WF and LG periods. These genera, such as Arthrobacter, Pseudomonas, Acidobacteria GP6, and Pasteuria, may be potential biological control agents for bacterial wilt. Further analysis indicated that low soil bacterial diversity during the WF period, decrease of bacterial interactions from the WF to LG periods, and low soil biomass during the LG period all have the potential to increase morbidity. In conclusion, an increase of soil bacterial diversity and control of some bacterial abundances in the WF period might be an effective approach in controlling bacterial wilt incidence.
通讯机构：
[Yan, Mingli] H;Hunan Univ Sci & Technol, Sch Life Sci, Xiangtan 411201, Hunan, Peoples R China.
关键词：
Microbial community;Molecular ecological networks;Heavy metal contamination;Microbial interactions
摘要：
Due to the persistence of metals in the ecosystem and their threat to all living organisms, effects of heavy metal on soil microbial communities were widely studied. However, little was known about the interactions among microorganisms in heavy metal-contaminated soils. In the present study, microbial communities in Non (CON), moderately (CL) and severely (CH) contaminated soils were investigated through high-throughput Illumina sequencing of 16s rRNA gene amplicons, and networks were constructed to show the interactions among microbes. Results showed that the microbial community composition was significantly, while the microbial diversity was not significantly affected by heavy metal contamination. Bacteria showed various response to heavy metals. Bacteria that positively correlated with Cd, e.g. Acidobacteria_Gp and Proteobacteria_thiobacillus, had more links between nodes and more positive interactions among microbes in CL- and CH-networks, while bacteria that negatively correlated with Cd, e.g. Longilinea, Gp2 and Gp4 had fewer network links and more negative interactions in CL and CH-networks. Unlike bacteria, members of the archaeal domain, i.e. phyla Crenarchaeota and Euryarchaeota, class Thermoprotei and order Thermoplasmatales showed only positive correlation with Cd and had more network interactions in CH-networks. The present study indicated that (i) the microbial community composition, as well as network interactions was shift to strengthen adaptability of microorganisms to heavy metal contamination, (ii) archaea were resistant to heavy metal contamination and may contribute to the adaption to heavy metals. It was proposed that the contribution might be achieved either by improving environment conditions or by cooperative interactions. (C) 2017 Elsevier Ltd. All rights reserved.
通讯机构：
[Boulos Chalhoub] I;[Wei Hua; Hanzhong Wang] T;Institut National de Recherche Agronomique (INRA), Unité de Recherche en Génomique Végétale (URGV), UMR1165, Organization and Evolution of Plant Genomes (OEPG), 2 rue Gaston Crémieux, 91057 Evry, France<&wdkj&>The Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture of the PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062 China
摘要：
<jats:title>Summary</jats:title><jats:p>Allotetraploid oilseed rape (<jats:italic>Brassica napus</jats:italic> L.) is an agriculturally important crop. Cultivation and breeding of <jats:italic>B</jats:italic>. <jats:italic>napus</jats:italic> by humans has resulted in numerous genetically diverse morphotypes with optimized agronomic traits and ecophysiological adaptation. To further understand the genetic basis of diversification and adaptation, we report a draft genome of an Asian semi‐winter oilseed rape cultivar ‘<jats:styled-content style="fixed-case">ZS</jats:styled-content>11’ and its comprehensive genomic comparison with the genomes of the winter‐type cultivar ‘Darmor‐<jats:italic>bzh</jats:italic>’ as well as two progenitors. The integrated <jats:styled-content style="fixed-case">BAC</jats:styled-content>‐to‐<jats:styled-content style="fixed-case">BAC</jats:styled-content> and whole‐genome shotgun sequencing strategies were effective in the assembly of repetitive regions (especially young long terminal repeats) and resulted in a high‐quality genome assembly of <jats:italic>B</jats:italic>. <jats:italic>napus</jats:italic> ‘<jats:styled-content style="fixed-case">ZS</jats:styled-content>11’. Within a short evolutionary period (~6700years ago), semi‐winter‐type ‘<jats:styled-content style="fixed-case">ZS</jats:styled-content>11’ and the winter‐type ‘Darmor‐<jats:italic>bzh</jats:italic>’ maintained highly genomic collinearity. Even so, certain genetic differences were also detected in two morphotypes. Relative to ‘Darmor‐<jats:italic>bzh</jats:italic>’, both two subgenomes of ‘<jats:styled-content style="fixed-case">ZS</jats:styled-content>11’ are closely related to its progenitors, and the ‘<jats:styled-content style="fixed-case">ZS</jats:styled-content>11’ genome harbored several specific segmental homoeologous exchanges (<jats:styled-content style="fixed-case">HE</jats:styled-content>s). Furthermore, the semi‐winter‐type ‘<jats:styled-content style="fixed-case">ZS</jats:styled-content>11’ underwent potential genomic introgressions with <jats:italic>B</jats:italic>. <jats:italic>rapa</jats:italic> (A<jats:sub>r</jats:sub>). Some of these genetic differences were associated with key agronomic traits. A key gene of A03.<jats:italic><jats:styled-content style="fixed-case">FLC</jats:styled-content>3</jats:italic> regulating vernalization‐responsive flowering time in ‘<jats:styled-content style="fixed-case">ZS</jats:styled-content>11’ was first experienced <jats:styled-content style="fixed-case">HE</jats:styled-content>, and then underwent genomic introgression event with A<jats:sub>r</jats:sub>, which potentially has led to genetic differences in controlling vernalization in the semi‐winter types. Our observations improved our understanding of the genetic diversity of different <jats:italic>B</jats:italic>. <jats:italic>napus</jats:italic> morphotypes and the cultivation history of semi‐winter oilseed rape in Asia.</jats:p>
关键词：
auxins;cytokinins;gibberellins;Gossypium hirsutum;iTRAQ;near-isogenic line
摘要：
Identifying important regulative elements and pathways related to dwarfism in cotton is a major challenge in cotton breeding. An isobaric tags for relative and absolute quantitation (iTRAQ)-based proteomics of the stem terminal buds from the upland cotton (Gossypium hirsutum L.) dwarf line LA-1 and high near-isogenic line LH-1 was performed. Moreover, the transcriptional expression of differentially-expressed proteins (DEPs) belonging to the phytohormone signal transduction, hormone biosynthesis, and ubiquitin system were analysed using the quantitative real-time polymerase chain reaction.. A total of 4 849 proteins were identified from LA-1 and LH-1, 697 of which showed differential accumulations. Most of the DEPs have catalytic, binding, and transporter activity and are involved in metabolism- and protein processing-related pathways. In particular, seven DEPs, including two gibberellin (GA) receptors, three cytokinin (CK) receptors, CK oxidase and CK-N-glucosyltransferase were up-regulated in LA-1, and gibberellin 20-oxidase was down-regulated in LA-1. Our results suggest that the DELLA-independent GA signalling pathway is the primary cause of dwarfism in LA-1 and indicate that cytokinin response element CRE1-2, gibberellininsensitive dwarf, cytokinin oxidase,and gibberellin 3-β-dioxygenase are potential indicators of dwarf cotton. The profiling of DEPs may offer a valuable resource for cotton breeding.
摘要：
With the massive data generated by the Human Microbiome Project, how to transform such data into useful information and knowledge remains challenging. Here, with currently available sequencing information (reference genomes and metagenomes), we have developed a comprehensive microarray, HuMiChip2, for strain-level identification and functional characterization of human microbiomes. HuMiChip2 was composed of 29,467 strain-specific probes targeting 2063 microbial strains/species and 133,924 sequence- and group-specific probes targeting 157 key functional gene families involved in various metabolic pathways and host-microbiome interaction processes. Computational evaluation of strain-specific probes suggested that they were not only specific to mock communities of sequenced microorganisms and metagenomes from different human body sites but also to non-sequenced microbial strains. Experimental evaluation of strain-specific probes using single strains/species and mock communities suggested a high specificity of these probes with their corresponding targets. Application of HuMiChip2 to human gut microbiome samples showed the patient microbiomes of alcoholic liver cirrhosis significantly (p < 0.05) shifted their functional structure from the healthy individuals, and the relative abundance of 21 gene families significantly (p < 0.1) differed between the liver cirrhosis patients and healthy individuals. At the strain level, five Bacteroides strains were significantly (p < 0.1) and more frequently detected in liver cirrhosis patients. These results suggest that the developed HuMiChip2 is a useful microbial ecological microarray for both strain-level identification and functional profiling of human microbiomes.
摘要：
<jats:title>Abstract</jats:title><jats:p><jats:italic>Sinapis alba</jats:italic> possesses a number of desirable traits that can be employed to broaden genetic variability in <jats:italic>Brassica oleracea</jats:italic> or <jats:italic>B. napus</jats:italic>. Using transgenic <jats:italic>B. oleracea</jats:italic> (CC, 2n=18) as paternal plants and non-transgenic <jats:italic>S. alba</jats:italic> (SS, 2n=24) as maternal plants, 11 hybrid plants were successfully obtained by using a combination of ovary culture and embryo rescue, while 2 seedlings of the reciprocal cross were generated but lost during the propagation. The hybridity of these plants was confirmed by flower color and other agronomic characteristics, chromosome counting, and pollen viability. Most of the intergeneric F<jats:sub>1</jats:sub> plants showed only one set each of S and C chromosome (SC, 2n=21) and were male sterile, while a few plants were semi-fertile and had one set of S chromosomes but two sets of C chromosomes (CCS, 2n=30). PCR, genomic Southern blotting and qRT-PCR for <jats:italic>bar</jats:italic> gene revealed that among the F<jats:sub>1</jats:sub> hybrid plants only 9.1% was <jats:italic>bar</jats:italic> positive and could be forwarded to F<jats:sub>2</jats:sub> and F<jats:sub>3</jats:sub> generation. The majority of F<jats:sub>3</jats:sub> plants obtained sufficient resistance to <jats:italic>Alternaria brassicae</jats:italic>. Thus, the generation of disease (<jats:italic>A. brassicae</jats:italic>) and herbicide (Bastar) resistant intergeneric hybrids was of importance for breeding program. The existence of <jats:italic>bar</jats:italic> gene in these intermediate materials will facilitate the identification of hybridity and transfer of <jats:italic>S.alba</jats:italic> traits into target genetic background.</jats:p>
期刊：
Agricultural Water Management,2016年170:20-25 ISSN：0378-3774
通讯作者：
Huang, Huang;Zhang, Canming
作者机构：
[Zheng, Huabin; Li, Jingyi; Huang, Huang] Hunan Agr Univ, Coll Agron, Changsha 410128, Hunan, Peoples R China.;[Zheng, Huabin; Li, Jingyi; Huang, Huang] Collaborat Innovat Ctr Grain & Oil Crop Southern, Changsha 410128, Hunan, Peoples R China.;[Zhang, Canming] Asia Europe Meeting ASEM Water Resources Res & De, Changsha 410013, Hunan, Peoples R China.
通讯机构：
[Huang, Huang] H;[Zhang, Canming] A;Hunan Agr Univ, Coll Agron, Changsha 410128, Hunan, Peoples R China.;Asia Europe Meeting ASEM Water Resources Res & De, Changsha 410013, Hunan, Peoples R China.
摘要：
As China requires more cultivated land to feed its increasing population, the sustainable development of cultivated land in its intensive agricultural production system has become a major issue for government and society. We firstly reviewed the progress of paddy-upland rotation (PUR) and conservation tillage, found that PUR was improve significantly soil properties, including redox potential of soil, the mineralization of soil organic matter, and the abundance of beneficial microorganisms, suggested that conservation tillage was an effective measurement for remedying the deficiency under the PUR. Meanwhile, we also systemically reviewed the statues of water resource infrastructure and policy level. Consequently, with current agriculture technology and the increasing capacity of adjusted artificial water resources, our results highlight the development of national-scale PUR as an effective adaptation strategy to protect and improve soil fertility and ensure agricultural security under climate change. In other words, from national strategy scale, national-scale PUR was a good choice in the major grain-producing areas of northern China in the coming 50-100 years. Lastly, further research in the few aspects was needed to better provide theoretical and technical support for promoting effectively the PUR. (C) 2016 Elsevier B.V. All rights reserved.
摘要：
<jats:title>Abstract</jats:title><jats:sec><jats:label /><jats:p>To introgress the good fiber quality and yield from <jats:italic>Gossypium barbadense</jats:italic> into a commercial Upland cotton variety, a high‐density simple sequence repeat (SSR) genetic linkage map was developed from a BC<jats:sub>1</jats:sub>F<jats:sub>1</jats:sub> population of <jats:italic>Gossypium hirsutum</jats:italic> × <jats:italic>Gossypium barbadense</jats:italic>. The map comprised 2,292 loci and covered 5115.16 centiMorgan (cM) of the cotton AD genome, with an average marker interval of 2.23 cM. Of the marker order for 1,577 common loci on this new map, 90.36% agrees well with the marker order on the D genome sequence genetic map. Compared with five published high‐density SSR genetic maps, 53.14% of marker loci were newly discovered in this map. Twenty‐six quantitative trait loci (QTLs) for lint percentage (LP) were identified on nine chromosomes. Nine stable or common QTLs could be used for marker‐assisted selection. Fifty percent of the QTLs were from <jats:italic>G</jats:italic>. <jats:italic>barbadense</jats:italic> and increased LP by 1.07%–2.41%. These results indicated that the map could be used for screening chromosome substitution segments from <jats:italic>G</jats:italic>. <jats:italic>barbadense</jats:italic> in the Upland cotton background, identifying QTLs or genes from <jats:italic>G</jats:italic>. <jats:italic>barbadense</jats:italic>, and further developing the gene pyramiding effect for improving fiber yield and quality.</jats:p></jats:sec>
