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  • Hosted by:Chinese Academy of Sciences
    Sponsored by:Institute of Botany, Chinese Academy of Sciences, Botanical Society of China
    Co-hosted by:Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences
    Institute of Biotechnology and Germplasm Resources, Yunnan AgriculturalAcademy
    Fujian Agriculture and Forestry University
    Hunan Provincial Key Laboratory of Phytohormones and Growth Development, Hunan Agricultural University
    State Key Laboratory of Crops Biology, Shandong Agricultural University

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Current Issue
Editor-in-Chief:Kang Zhong
ISSN 1674-3466 CN 11-5705/Q
Post Code:2-967
Volume 55 Issue 4
01 July 2020
  
COMMENTARIES
New Insight into Strigolactone Signaling
Ruifeng Yao,Daoxin Xie
Chinese Bulletin of Botany. 2020, 55(4):  397-402.  doi:10.11983/CBB20099
Abstract ( 383 )   HTML ( 13 )   PDF (1426KB) ( 313 )   Save
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It is well-known that DELLA, AUX/IAA, JAZ and D53/SMXL act as repressor proteins that bind and repress transcription factors to suppress expression of hormone-responsive genes, while hormone molecules trigger signal transduction to induce degradation of these repressor proteins and eventually activate expression of hormone-responsive genes essential for various biological processes. The research team led by Dr. Jiayang Li recently reported that SMXL6, SMXL7 and SMXL8 (SMXL6,7,8) in strigolactone (SL) signaling pathway serve as dual-function repressor proteins which act as both repressors and transcription factors. They found that SMXL6,7,8 can function as transcription factors by directly binding to the promoters of SMXL6,7,8 genes and repressing their expression. In addition, they identified a large number of novel SL-responsive genes, and revealed molecular mechanisms underlying how SL regulates shoot branching, leaf elongation and anthocyanin biosynthesis. These important findings provide new insights into our understanding of plant hormone action, which are scientifically significant and agriculturally important.

A 360-degree Scanning of Population Genetic Variations—a Pan-genome Study of Soybean
Guangtao Zhu,Sanwen Huang
Chinese Bulletin of Botany. 2020, 55(4):  403-406.  doi:10.11983/CBB20096
Abstract ( 169 )   HTML ( 3 )   PDF (735KB) ( 152 )   Save
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Soybean (Glycine max) is an important oil and protein crop. The abundancy of genetic diversity within the species provides an essential resource for traits exploration and breeding improvement. However, one reference genome is inadequate for discovering all genetic diversity of a species. Pan-genome provides a new solution to overcome this limitation. Recently, Prof. Zhixi Tian’ Group and Prof. Chengzhi Liang’ Group from the Institute of Genetics and Develop- mental Biology, Chinese Academy of Sciences, selected 26 representative soybeans from 2 898 sequenced accessions. Together with three previously published genomes, they constructed a pan-genome and a graph-based genome of wild and cultivated soybean germplasm. The core, dispensable, and private genes as well as all the vast majority of genetic variations within this species were identified and characterized. These data comprehensively revealed allelic variations and gene fusion event of maturity gene E3, the haploid types of seed coat color gene I and their evolutionary relationship, and structural variations affecting gene expression and regional adaptation selection of ferric ion transporters. This study provide a new mode for crop genomics, and will facilitate genetic variations identification, traits exploration and germplasm innovation of soybean.

EXPERIMENTAL COMMUNICATIONS
Response of Arabidopsis Cohesin RAD21 to Cell Division after Enhanced UV-B Radiation
Fangfang He,Huize Chen,Jinlin Feng,Lin Gao,Jiao Niu,Rong Han
Chinese Bulletin of Botany. 2020, 55(4):  407-420.  doi:10.11983/CBB20009
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The effect of UV-B radiation on plants is reflected in multiple levels. DNA damage is caused by UV-B radiation, which leads to abnormal mitosis and ultimately affects plant growth and physiological and biochemical processes. RAD21.3 is a subunit of cohesin complex, which is involved in chromosome separation during mitosis. In this paper, Columbia-0 Arabidopsis thaliana and atrad21.3 were used as materials, and the control and UV-B treatment group were set up to analyze the root length, plant height, bolting time, physiological and biochemical parameters of WT, atrad21.3 and overexpressed transgenic plants. The mitosis of Arabidopsis root tip cells was observed by basic fuchsin staining, and the aberration rate was counted. After UV-B treatment of the WT and atrad21.3 mutants, it was found that the UV-B treated-WT and atrad21.3 had similar bolting time, plant height and various physiological and biochemical indexes. Through the construction of expression vector, the results showed that RAD21.3 was located in the nucleus. Further observation of mitosis revealed abnormal phenomena such as lagging chromosomes, chromosomes bridge, fragments chromosomes, etc. Statistics show that the aberration rate of the UV-B treated-WT is similar to atrad21.3, and the aberration rate of the UV-B treated-atrad21.3 increases. The above results indicate that RAD21.3 may respond to abnormal mitosis induced by UV-B radiation.

Response of AtR8 lncRNA to Salt Stress and Its Regulation on Seed Germination in Arabidopsis
Nan Zhang,Ziguang Liu,Shichen Sun,Shengyi Liu,Jianhui Lin,Yifang Peng,Xiaoxu Zhang,He Yang,Xi Cen,Juan Wu
Chinese Bulletin of Botany. 2020, 55(4):  421-429.  doi:10.11983/CBB19244
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Long non-coding RNA (lncRNA) is a type of non-coding RNA that is longer than 200 nucleotides and does not encode proteins. lncRNAs are mainly produced by the transcription of RNA polymerase II and are abundant in the organism and have various biological functions. AtR8 lncRNA is transcribed by RNA polymerase III in Arabidopsis thaliana. Previous studies revealed that Salicylic acid (SA) induces AtR8 lncRNA expression in germinated seeds and that the deletion of AtR8 lncRNA decreases seed germination under SA stress. In this study, we found a conserved salt-stress-responsive element (TCTTCTTCTTTA) in the transcriptional region of AtR8 lncRNA. NaCl treatment inhibited AtR8 lncRNA expression in the germinated seeds. High concentration of NaCl significantly inhibited seed germination of atr8, which had partial deletion of AtR8 lncRNA, compared to that of the wild type, indicating that AtR8 lncRNA plays an important role in regulating seed germination in response to salt stress.

Proteome Analysis of Different Resistant Apple Cultivars in Response to the Stress of Ring Rot Disease
Caixia Zhang,Gaopeng Yuan,Xiaolei Han,Wuxing Li,Peihua Cong
Chinese Bulletin of Botany. 2020, 55(4):  430-441.  doi:10.11983/CBB19204
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The aim of this study was to investigate the differential expression of resistance related proteins in resistant and susceptible apple leaves in response to ring rot disease. The resistant and susceptible apple cultivars Huayue and Golden Delicious were analyzed by high-throughput isobaric tag (IBT) marker quantitative analysis combined with liquid chromatography-tandem mass spectrometry (LC-MS), proteome differential expression of resistant and susceptible apple leaves before and after pathogen treatment was analyzed, and 171 differential expression proteins (DEPs) were identified. GO enrichment and KEGG pathway analysis showed that 686 GO entries were annotated in cell components, molecular functions, and biological processes, of which 52 DEPs were annotated in 18 distinct pathways of KEGG pathway (P<0.05). Subcellular localization prediction analysis showed that 170 DEPs in 171 DEPs were located in 8 organelles. Functional annotation analysis showed that 46 DEPs were annotated in 7 classes of resistance-related proteins, including the thaumatin-like proteins, peroxidases, polyphenol oxidases, Mal d1 proteins, chitinases, endo-1,3-beta-glucosidases and MLP-like proteins. In addition, the expression characteristics and gene quantitative results of resistance-related proteins were analyzed. The results of this study provided a technical reference for further understanding the resistance mechanism of resistant and susceptible apples to the stress of ring rot disease.

Identification and Evolution of LRR VIII-2 Subfamily Genes in Four Model Plant Species
Chenyang Yan,Yingnan Chen
Chinese Bulletin of Botany. 2020, 55(4):  442-456.  doi:10.11983/CBB19157
Abstract ( 241 )   HTML ( 5 )   PDF (1184KB) ( 129 )   Save
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Whole-genome duplication and tandem duplication are two important mechanisms for gene duplication, which play important roles in promoting the genomic and genetic diversity. In Arabidopsis, AtLRR-RLK encodes receptor-like kinases rich in leucine repeats, which is a multi-gene family arising from large-scale gene expansion during angiosperm evolution. It is composed of 15 subfamilies, among which, AtLRR VIII-2 is the subfamily with the highest proportion of tandem repeats. In this study, we use the genes in LRR VIII-2 as an example to analyze the gene expansion and differential retention in four model plants (Arabidopsis thaliana, Populus trichocarpa, Vitis vinifera and Carica papaya). Results showed that paralogous gene pairs were identified in the LRR VIII-2 subfamily in Arabidopsis, poplar and grape, while no such pair was found in papaya. The LRR VIII-2 subfamily expanded the most significantly in poplar and moderately expanded in Arabidopsis and grape, but some genes of the LRR VIII-2 subfamily in papaya have been lost. In addition, the paralogous and orthologous genes in the LRR VIII-2 subfamily were under strong purifying selection in the four investigated plant species, except for a pair of paralogous genes in poplar. An in-depth phylogenetic analysis of the LRR VIII-2 subfamily helps to understand the role and significance of gene duplication in plant evolution, and provides useful information for predicting the function of homologous gene among different species. This analytical pipeline is also applicable for deciphering the evolution history of other gene families.

Phylogenetic Study of Amaranthaceae sensu lato Based on Multiple Plastid DNA Fragments
Jiuxiang Huang,Wenna Chen,Yuling Li,Gang Yao
Chinese Bulletin of Botany. 2020, 55(4):  457-467.  doi:10.11983/CBB19228
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Amaranthaceae sensu lato, including Amaranthaceae sensu stricto and Chenopodiaceae, is the second largest family in Caryophyllales. However, the family status of Chenopodiaceae is disputable and phylogenetic relationships among all of the subfamilies circumscribed within Amaranthaceae s.l. have not been well resolved to date. In the present study, phylogeny of Amaranthaceae s.l. was reconstructed based on a comprehensive taxonomic sampling of all 13 subfamilies (59 species) circumscribed using eight plastid DNA fragments, and a molecular dating analysis of the family was also conducted. Results revealed that, the monophyly of Amaranthaceae both in broad and narrow sense was strongly supported, but the monophyly of Chenopodiaceae was rejected. Thus the concept of Amaranthaceae s.l. is accepted here. Phylogenetic positions of all subfamilies were all resolved with strong support values, except that the position of the subfamily Polycnemoideae was weakly supported. Additionally, the crown age of Amaranthaceae s.l. was estimated at ca. 69.9 million years ago (Ma) in the late Cretaceous, and a period of rapid divergence may have occurred near the Cretaceous-Paleogene (K-Pg) boundary (ca. 66.0 Ma).

INVITED PROTOCOLS
Methods for Examining Transcription Factor-DNA Interaction in Plants
Liwen Yang,Shuangrong Liu,Yuhong Li,Rongcheng Lin
Chinese Bulletin of Botany. 2020, 55(4):  468-474.  doi:10.11983/CBB20057
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Transcription affects the growth and development of plants through regulating the spatio-temporal expression of downstream genes. The interaction between transcription factors and DNA is a key section in the process of exploring transcriptional regulatory networks. In the past few years, researchers utilize yeast one hybrid (Y1H) and electrophoresis mobility shift assay (EMSA) to examine whether a transcription factor directly interacts with target DNA. In addition, transient luciferase activity assay provides a convenient method for researchers to test the regulation of transcription factors on downstream gene expression. In this paper, we elaborate the principles, methods, and advantages and limitations of Y1H, EMSA and transient luciferase activity assay, to provide technical references for exploring the transcription factor-DNA interactions.

Protocols for Chromatin Immunoprecipitation
Hongli Wang,Yuling Jiao
Chinese Bulletin of Botany. 2020, 55(4):  475-480.  doi:10.11983/CBB20076
Abstract ( 163 )   HTML ( 4 )   PDF (851KB) ( 106 )   Save
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Chromatin immunoprecipitation (ChIP) is a teschnique used to investigate protein-DNA interaction. Briefly, protein and associated DNA are crosslinked, which is optional. Then the DNA-protein complexes are fragmented. By using an appropriate antibody, cross-linked DNA fragments associated with the protein of interest are selectively immunoprecipitated. ChIP is commonly used to identify binding regions of DNA-binding proteins, such as transcription factors. ChIP is also used to analyze histone modification profiles in combination with antibodies against specific histone modifications. Here we describe protocols and related tips for cross-linked ChIP and ultra-low-input micrococcal nuclease-based native ChIP (ULI-NChIP), which can be applied to rare cell populations at the 103 cell level.

SPECIAL TOPICS
NLR and Its Regulation on Plant Disease Resistance
Chenghuizi Yang,Xianyu Tang,Wei Li,Shitou Xia
Chinese Bulletin of Botany. 2020, 55(4):  497-504.  doi:10.11983/CBB19207
Abstract ( 426 )   HTML ( 5 )   PDF (914KB) ( 240 )   Save
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In order to adapt to various living environments, plants have gradually evolved a complex immune system against the infections caused by pathogens. The nucleotide-bounding leucine-rich repeat proteins (NLRs) act as typical resistance (R) proteins which commonly exist in plants and play an important role in regulating plant disease resistance. In this paper, the research progress of NLRs is reviewed from the aspects of NLR protein structures, signal transductions and regulations of plant disease resistance.

Research Advances in AP2/ERF Transcription Factors in Regulating Plant Responses to Abiotic Stress
Lin Hong,Lei Yang,Haijian Yang,Wu Wang
Chinese Bulletin of Botany. 2020, 55(4):  481-496.  doi:10.11983/CBB19243
Abstract ( 316 )   HTML ( 12 )   PDF (1076KB) ( 313 )   Save
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Low temperature, drought, high salt, hypoxia and other adverse environmental changes affect plant growth and development. Plants adapt to these adverse conditions through the development of complex regulatory mechanisms during long-term evolution. APETALA2/ethylene responsive factor (AP2/ERF) is a plant-specific transcription factor that plays a key regulatory role in various stress responses. In recent years, more and more studies have shown that plant hormone-mediated signaling is closely related to stress responses, and AP2/ERF transcription factor and hormone signal transduction form a cross-regulatory network. Many AP2/ERF transcription factors respond to plant hormones abscisic acid (ABA) and ethylene (ET), activating the expression of stress response genes that are dependent on and independent of ABA and ET. In addition, AP2/ERF transcription factors are also involved in gibberellin (GA), cytokinin (CTK) and brassinsteroid (BR) mediated growth and developmental processes and stress responses. This paper briefly reviews the research progress of AP2/ERF transcription factors in term of structure, transcriptional regulation, posttranslational modifications, binding sites and interacting proteins as well as its transduction pathways involved in hormone dependent- or independent- regulation of the abiotic stress responses, which will provide the basis for further understanding the roles of different AP2/ERF transcription factors in the regulation of hormone and stress response network in plants.

Stepping out of the Shadow of Goethe: for a More Scientific Plant Systematics
Xin Wang,Zhongjian Liu,Wenzhe Liu,Wenbo Liao,Xin Zhang,Zhong Liu,Guangwan Hu,Xuemin Guo,Yaling Wang
Chinese Bulletin of Botany. 2020, 55(4):  505-512.  doi:10.11983/CBB19093
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According to the Traditional Theory, a carpel (basic unit of angiosperm gynoecium) is derived from a modified leaf or megasporophyll through longitudinal folding and inward enrolling. Unfortunately, this theory introduces an unnegotiable gap between angiosperms and gymnosperms. Different from the Traditional Theory, the Unifying Theory provides a link bridging the gap mentioned above—an angiosperm carpel is derived from the synorganization between an ovule-bearing branch and an enclosing leaf. Recently two papers authored by leading botanists, Peter R. Crane and Peter K. Endress, respectively, expressed their opinions different from the Traditional Theory of angiosperm evolution. Endress stated that a carpel is result of synorganization between foliar part(s) plus ovule(s); and Crane stated that ovules/seeds are borne on the termini of branches. Combining the two, it is easy to infer that a carpel is equivalent to a foliar part plus an ovuliferous branch, a conclusion in line with the core conception of the Unifying Theory. The subtle changes in perspectives of these two leading botanists imply that there will be a major paradigm shift in botany soon. In order to make our botanists aware of the coming-soon changes in plant evolution theory, we summarize the latest progresses in relevant areas.

Research Progress on Uptake and Transport of Nanopesticides in Plants
Jing Li,Liang Guo,Haixin Cui,Bo Cui,Guoqiang Liu
Chinese Bulletin of Botany. 2020, 55(4):  513-528.  doi:10.11983/CBB20008
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Pesticide is a kind of chemicals to control crop diseases, pests and weeds for ensuring crop yields and food safety. Large particles, low effective utilization rate and large dosage are the major defects of the traditional pesticide formulations, leading to the destruction of the ecological environment. Pesticide nanoformulations can improve the dispersibility, stability and biological activity of traditional formulations. This is an important scientific approach to overcome the defects of traditional formulations, enhance the effective utilization rate of pesticides, and reduce environmental pollution. Elucidating the uptake and transport behavior of nanopesticides in plants is useful for understanding the interaction between nanopesticides and plants, revealing their uptake mechanism and bioaccumulation effect, and clarifying their biological safety. This article reviews the uptake and transport studies of nanopesticides in plants in four aspects: factors affecting the uptake and transport of nanopesticides in plants, mechanisms of uptake and transport, related analysis methods and their biological safety. This article also elaborates the modes and research methods of the uptake and transport of inorganic and organic nanopesticides in plants, and further proposes their potential applications. This piece will provide theoretical and technical basis for the design, construction and reasonable application of nanopesticides.

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