作者机构：
[Vinh Ha Dinh Thi; Mestiri, Imen; Chalabi, Smahane; Jabbari, Kamel; Just, Jeremy; Lu, Yunhai; Arnaud, Dominique; Canaguier, Aurelie; Le Clainche, Isabelle; Chalhoub, Boulos; Chelaifa, Houda; Belcram, Harry] Univ Evry Val dEssone, Inst Natl Rech Agron INRA, Unite Rech Genom Vegetale, UMR1165, F-91057 Evry, France.;[Da Silva, Corinne; Denoeud, France; Bento, Pascal; Wincker, Patrick; Labadie, Karine; Alberti, Adriana; Correa, Margot; Noel, Benjamin; Bernard, Maria; Aury, Jean-Marc; Battail, Christophe] Commissariat Energie Atom CEA, Inst Genom IG, F-91057 Evry, France.;[Denoeud, France; Wincker, Patrick] Univ Evry Val dEssone, UMR 8030, F-91057 Evry, France.;[Denoeud, France; Wincker, Patrick] Ctr Natl Rech Sci CNRS, UMR 8030, Evry, France.;[Hu, Qiong; Wang, Xinfa; Tong, Chaobo; Liu, Shengyi; Hua, Wei] Chinese Acad Agr Sci, Key Lab Biol & Genet Improvement Oil Crops, Minist Agr Peoples Republ China, Oil Crops Res Inst, Wuhan 430062, Peoples R China.
通讯机构：
[Chalhoub, Boulos] Univ Evry Val dEssone, Inst Natl Rech Agron INRA, Unite Rech Genom Vegetale, UMR1165, 2 Rue Gaston Cremieux, F-91057 Evry, France.
摘要：
Oilseed rape (Brassica napus L.) was formed similar to 7500 years ago by hybridization between B. rapa and B. oleracea, followed by chromosome doubling, a process known as allopolyploidy. Together with more ancient polyploidizations, this conferred an aggregate 72x genome multiplication since the origin of angiosperms and high gene content. We examined the B. napus genome and the consequences of its recent duplication. The constituent A(n) and C-n subgenomes are engaged in subtle structural, functional, and epigenetic cross-talk, with abundant homeologous exchanges. Incipient gene loss and expression divergence have begun. Selection in B. napus oilseed types has accelerated the loss of glucosinolate genes, while preserving expansion of oil biosynthesis genes. These processes provide insights into allopolyploid evolution and its relationship with crop domestication and improvement.
作者机构：
[Thi, Vinh Ha Dinh; Mestiri, Imen; Chalabi, Smahane; Jabbari, Kamel; Just, Jeremy; Lu, Yunhai; Arnaud, Dominique; Canaguier, Aurelie; Le Clainche, Isabelle; Chalhoub, Boulos; Chelaifa, Houda; Belcram, Harry] Univ Evry Val dEssone, Inst Natl Rech Agron INRA, Unite Rech Genom Vegetale, UMR1165, F-91057 Evry, France.;[Da Silva, Corinne; Denoeud, France; Bento, Pascal; Wincker, Patrick; Labadie, Karine; Alberti, Adriana; Correa, Margot; Noel, Benjamin; Bernard, Maria; Aury, Jean-Marc; Battail, Christophe] Commissariat Energie Atom CEA, Inst Genom IG, F-91057 Evry, France.;[Denoeud, France; Wincker, Patrick] Univ Evry Val dEssone, UMR 8030, F-91057 Evry, France.;[Denoeud, France; Wincker, Patrick] Ctr Natl Rech Sci CNRS, UMR 8030, Evry, France.;[Hu, Qiong; Wang, Xinfa; Tong, Chaobo; Liu, Shengyi; Hua, Wei] Chinese Acad Agr Sci, Key Lab Biol & Genet Improvement Oil Crops, Minist Agr Peoples Republ China, Oil Crops Res Inst, Wuhan 430062, Peoples R China.
通讯机构：
[Chalhoub, Boulos] Univ Evry Val dEssone, Inst Natl Rech Agron INRA, Unite Rech Genom Vegetale, UMR1165, 2 Rue Gaston Cremieux, F-91057 Evry, France.
摘要：
↵* These authors contributed equally to this work.
通讯机构：
[Liu, Shengyi] Chinese Acad Agr Sci, Oil Crops Res Inst, Key Lab Biol & Genet Improvement Oil Crops, Minist Agr PRC, Wuhan 430062, Peoples R China.
摘要：
Polyploidization has provided much genetic variation for plant adaptive evolution, but the mechanisms by which the molecular evolution of polyploid genomes establishes genetic architecture underlying species differentiation are unclear. Brassica is an ideal model to increase knowledge of polyploid evolution. Here we describe a draft genome sequence of Brassica oleracea, comparing it with that of its sister species B. rapa to reveal numerous chromosome rearrangements and asymmetrical gene loss in duplicated genomic blocks, asymmetrical amplification of transposable elements, differential gene co-retention for specific pathways and variation in gene expression, including alternative splicing, among a large number of paralogous and orthologous genes. Genes related to the production of anticancer phytochemicals and morphological variations illustrate consequences of genome duplication and gene divergence, imparting biochemical and morphological variation to B. oleracea. This study provides insights into Brassica genome evolution and will underpin research into the many important crops in this genus.
作者机构：
[An, Ning; Ma, Lin; Fan, Mingsheng; Wu, Liangquan; Zhang, Fusuo; Wu, Liang; Wang, Guiliang; Chen, Xinping; Cui, Zhenling; Zhang, Weifeng] China Agr Univ, Coll Resources & Environm Sci, Beijing 100193, Peoples R China.;[Vitousek, Peter] Stanford Univ, Dept Biol, Stanford, CA 94305 USA.;[Zhao, Ming; Zhang, Weijian] Chinese Acad Agr Sci, Inst Crop Sci, Beijing 100081, Peoples R China.;[Ma, Wenqi] Agr Univ Hebei, Coll Resources & Environm Sci, Baoding 071001, Peoples R China.;[Zhang, Jiwang; He, Mingrong; Wang, Zhenlin] Shandong Agr Univ, Coll Agron, Tai An 271000, Shandong, Peoples R China.
通讯机构：
[Zhang, Fusuo] China Agr Univ, Coll Resources & Environm Sci, Beijing 100193, Peoples R China.
摘要：
Agriculture faces great challenges to ensure global food security by increasing yields while reducing environmental costs(1,2). Here we address this challenge by conducting a total of 153 site-year field experiments covering the main agro-ecological areas for rice, wheat and maize production in China. A set of integrated soil-crop system management practices based on a modern understanding of crop ecophysiology and soil biogeochemistry increases average yields for rice, wheat and maize from 7.2 million grams per hectare (Mg ha(-1)), 7.2 Mg ha(-1) and 10.5 Mg ha(-1) to 8.5 Mg ha(-1), 8.9 Mg ha(-1) and 14.2 Mg ha(-1), respectively, without any increase in nitrogen fertilizer. Model simulation and life-cycle assessment(3) show that reactive nitrogen losses and greenhouse gas emissions are reduced substantially by integrated soil-crop system management. If farmers in China could achieve average grain yields equivalent to 80% of this treatment by 2030, over the same planting area as in 2012, total production of rice, wheat and maize in China would be more than enough to meet the demand for direct human consumption and a substantially increased demand for animal feed, while decreasing the environmental costs of intensive agriculture.
作者：
Dong-Lei Yang;Jian Yao;Chuan-Sheng Mei;Xiao-Hong Tong;Long-Jun Zeng;Qun Li;Lang-Tao Xiao;Tai-ping Sun;Jigang Li;Xing-Wang Deng;Chin Mei Lee;Michael F. Thomashow;Yinong Yang;Zuhua He;Sheng Yang He
期刊：
Proceedings of the National Academy of Sciences of the United States of America,2012年109(19):E1192-E1200 ISSN：0027-8424
通讯作者：
Yang, Yinong
作者机构：
[Zuhua He; Xiao-Hong Tong; Long-Jun Zeng; Qun Li; Dong-Lei Yang] Chinese Acad Sci, Natl Key Lab Plant Mol Genet, Inst Plant Physiol & Ecol, Shanghai Inst Biol Sci, Shanghai 200032, Peoples R China.;[Yinong Yang; Chuan-Sheng Mei] Univ Arkansas, Dept Plant Pathol, Fayetteville, AR 72701 USA.;[Sheng Yang He; Jian Yao; Michael F. Thomashow; Chin Mei Lee] Michigan State Univ, Dept Energy Plant Res Lab, E Lansing, MI 48824 USA.;[Sheng Yang He; Jian Yao] Howard Hughes Med Inst, Chevy Chase, MD 20815 USA.;[Lang-Tao Xiao] Hunan Agr Univ, Hunan Prov Key Lab Phytohormones, Changsha 410128, Hunan, Peoples R China.
通讯机构：
[Yang, Yinong] Univ Arkansas, Dept Plant Pathol, Fayetteville, AR 72701 USA.
摘要：
Plants must effectively defend against biotic and abiotic stresses to survive in nature. However, this defense is costly and is often accompanied by significant growth inhibition. How plants coordinate the fluctuating growth-defense dynamics is not well understood and remains a fundamental question. Jasmonate (JA) and gibberellic acid (GA) are important plant hormones that mediate defense and growth, respectively. Binding of bioactive JA or GA ligands to cognate receptors leads to proteasome-dependent degradation of specific transcriptional repressors (the JAZ or DELLA family of proteins), which, at the resting state, represses cognate transcription factors involved in defense (e.g., MYCs) or growth [e.g. phytochrome interacting factors (PIFs)]. In this study, we found that the coi1 JA receptor mutants of rice (a domesticated monocot crop) and Arabidopsis (a model dicot plant) both exhibit hallmark phenotypes of GA-hypersensitive mutants. JA delays GA-mediated DELLA protein degradation, and the della mutant is less sensitive to JA for growth inhibition. Overexpression of a selected group of JAZ repressors in Arabidopsis plants partially phenocopies GA-associated phenotypes of the coi1 mutant, and JAZ9 inhibits RGA (a DELLA protein) interaction with transcription factor PIF3. Importantly, the pif quadruple (pifq) mutant no longer responds to JA-induced growth inhibition, and overexpression of PIF3 could partially overcome JA-induced growth inhibition. Thus, a molecular cascade involving the COI1-JAZ-DELLA-PIF signaling module, by which angiosperm plants prioritize JA-mediated defense over growth, has been elucidated.
摘要：
Increasing soil pollution problems have caused world-wide concerns. Large numbers of contaminants such as polycyclic aromatic hydrocarbons (PAHs), petroleum and related products, pesticides, chlorophenols and heavy metals enter the soil, posing a huge threat to human health and natural ecosystem. Chemical and physical technologies for soil remediation are either incompetent or too costly. Composting or compost addition can simultaneously increase soil organic matter content and soil fertility besides bioremediation, and thus is believed to be one of the most cost-effective methods for soil remediation. This paper reviews the application of composting/compost for soil bioremediation, and further provides a critical view on the effects of this technology on microbial aspects in contaminated soils. This review also discusses the future research needs for contaminated soils.
摘要：
Applying biochar to soils may cause a win-win situation resulting in C sequestration and soil fertility improvement. The effect may be more evident in highly weathered and infertile tropical soils, but will be dependent on biochar quality. An Ultisol, typical to southern China, was used to evaluate amendment with biochars produced by a range of temperatures and durations, to investigate its effects on soil properties and plant growth. Rice straw-derived biochars were charred at temperatures from 250 to 450 degrees C for between 2 and 8 h. The increase of temperature caused smaller less structured (as viewed by SEM) fragments to form with less 0, H and aliphatic C functional groups, but more aromatic C as indicated by infrared spectroscopy. The mean residence time of biochars under controlled conditions (25 degrees C, 40% field capacity) was estimated from 244 to 1700 years, generally increasing with charring temperature and duration. Amendment of 1% biochar increased pH by 0.1-0.46 (P < 0.01) and CEC by 3.9-17.3% (P < 0.05), but had no effect on aggregate stability. In pot trials maize biomass was increased by 64% (without NPK) to 146% (with NPK) after biochar amendment. The study emphasizes that amendment with biochar can improve soil fertility at least in the short term. Future studies focusing on the persistence of biochar fertility in the field must explicitly take into account additional factors to transfer this technology. (C) 2011 Elsevier B.V. All rights reserved.
关键词：
Biotic and abiotic stresses;Crop improvement;Crop management;Grain yield;Rice research;Stress tolerance
摘要：
Rice production in China has more than tripled in the past five decades mainly due in increased grain yield rather than increased planting area. This increase has come from the development of high-yielding varieties and improved crop management practices such as nitrogen fertilization and irrigation. However, yield stagnation of rice has been observed in the past ten years in China. As its population rises, China will need to produce about 20% more rice by 2030 in order to meet is domestic needs if rice consumption per capita stays at the current level. This is not an easy task because several trends and problems in the Chinese rice production system constrain the sustainable increase in total rice production. Key trends include a decline in arable land, increasing water scarcity, global climate change, labor shortages, and increasing comsumer demand for high-quality rice (which often comes from low-yielding varieties). The major problems confronting rice production in China are narrow genetic background, overuse of fertilizers and pesticides, breakdown of irrigation infrastructure, oversimplified crop management, and a weak extension system. Despite these challenges, good research strategies call drive increased rice production in China. These include the development of the new rice varieties with high yield potential, improvement of resistances to major diseases and insects, and to major abiotic stresses such as drought and heat, and the establishment of integrated crop management. We believe that a sustainable increase in rice production is achievable in China with the development of new technology through rice research.
摘要：
Precise coordination between stamen and pistil development is essential to make a fertile flower. Mutations impairing stamen filament elongation, pollen maturation, or anther dehiscence will cause male sterility. Deficiency in plant hormone gibberellin (GA) causes male sterility due to accumulation of DELLA proteins, and GA triggers DELLA degradation to promote stamen development. Deficiency in plant hormone jasmonate (JA) also causes male sterility. However, little is known about the relationship between GA and JA in controlling stamen development. Here, we show that MYB21, MYB24, and MYB57 are GA-dependent stamen-enriched genes. Loss-of-function of two DELLAs RGA and RGL2 restores the expression of these three MYB genes together with restoration of stamen filament growth in GA-deficient plants. Genetic analysis showed that the myb21-t1 myb24-t1 myb57-t1 triple mutant confers a short stamen phenotype leading to male sterility. Further genetic and molecular studies demonstrate that GA suppresses DELLAs to mobilize the expression of the key JA biosynthesis gene DAD1, and this is consistent with the observation that the JA content in the young flower buds of the GA-deficient quadruple mutant ga1-3 gai-t6 rga-t2 rgl1-1 is much lower than that in the WT. We conclude that GA promotes JA biosynthesis to control the expression of MYB21, MYB24, and MYB57. Therefore, we have established a hierarchical relationship between GA and JA in that modulation of JA pathway by GA is one of the prerequisites for GA to regulate the normal stamen development in Arabidopsis.
摘要：
Most fruits in our daily diet are the products of domestication and breeding. Here we report a map of genome variation for a major fruit that encompasses ∼3.6 million variants, generated by deep resequencing of 115 cucumber lines sampled from 3,342 accessions worldwide. Comparative analysis suggests that fruit crops underwent narrower bottlenecks during domestication than grain crops. We identified 112 putative domestication sweeps; 1 of these regions contains a gene involved in the loss of bitterness in fruits, an essential domestication trait of cucumber. We also investigated the genomic basis of divergence among the cultivated populations and discovered a natural genetic variant in a β-carotene hydroxylase gene that could be used to breed cucumbers with enhanced nutritional value. The genomic history of cucumber evolution uncovered here provides the basis for future genomics-enabled breeding.
