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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 56 Issue 1
01 January 2021
  
COMMENTARIES
Genomic Basis of Rice Adaptation to Soil Nitrogen Status
Wei Xuan, Guohua Xu
Chinese Bulletin of Botany. 2021, 56(1):  1-5.  doi:10.11983/CBB20208
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Crop productivity relies heavily on inorganic nitrogen (N) fertilization, while excess application of N fertilizers results in detrimental effects on ecosystem and plant developmental process. Thus, the improvement of crop N use efficiency (NUE) is critical for the development of sustainable agriculture. Thus far, significant advances in understanding the regulation of NUE have been achieved in rice (Oryza sativa), one of the most important food crops. Several key transporter and regulatory genes involved in N uptake, translocation, and metabolism have been cloned and characterized in rice. However, the genetic mechanisms underlying the geographic adaptation of rice to the change of local soil N status remain elusive. Recently, a team led by Prof. Chengcai Chu, in Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, evaluated the responses to N supplies of rice germplasm resources collected from different eco-geographical regions worldwide. By performing genome-wide association study on rice tillering response to N (TRN), OsTCP19 is identified as a repressor of TRN, and a 29 bp InDel polymorphism in its promoter determines TRN variations among the rice varieties. OsTCP19 regulates TRN by inhibiting the transcription of DLT, a tiller-promoting gene, whilst the transcription of OsTCP19 itself is controlled by a N responsive suppressor LATERAL ORGAN BOUNDARIES DOMAIN (LBD) protein. Notably, OsTCP19 haplotypes were selected among rice germplasms and correlated with local soil N content. This study not only reveals the genetic basis of geographic adaptation of cultivated rice to the changes of soil N environment, but also provides novel genetic candidates for effective breeding of higher NUE rice cultivars.

Auxin Regulates the Lateral Root Development Through MAPK-mediated VLCFAs Biosynthesis
Rongfeng Huang, Tongda Xu
Chinese Bulletin of Botany. 2021, 56(1):  6-9.  doi:10.11983/CBB20190
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Mitogen-activated protein kinase (MAPK) cascade is an important and highly conserved cellular signal transduction pathway by delivery and amplification of upstream signals through protein kinase cascade phosphorylation in eukaryotes. In plants, MAPK signaling pathways not only mediate plant responses to environment, but also play crucial roles in regulating plant growth and development. A recent study from the Zhaojun Ding’s group of Shandong University uncovered a novel molecular mechanism of MPK14-mediated auxin signaling in lateral root development via ERF13- regulated very-long-chain fatty acids (VLCFAs) biosynthesis. This study reveals the molecular mechanism of the lateral root development from a new perspective, and further confirms the coupling between the vital phytohormone auxin and the ancient MAPKs module. Since lateral roots act as essential organs for plants in response to environment, deciphering the MAPK signaling pathway in regulation of lateral root development will provide a new strategy for how plants integrate development signals and environmental cues.

EXPERIMENTAL COMMUNICATIONS
Quantitative Definition and Classification of Leaves in Large- flowered Chinese Chrysanthemum Based on the Morphological Traits
Xuebin Song, Kang Gao, He Huang, Zhilan Liu, Silan Dai, Yu Ji
Chinese Bulletin of Botany. 2021, 56(1):  10-24.  doi:10.11983/CBB20014
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The leaf morphology of Chinese traditional chrysanthemum varieties is very variable, but it has not been scientifically defined and classified, so it is impossible to make effective use of these morphological traits for variety identification and genetic analysis. The definition and classification of plant morphology by quantitative analysis is the premise of genetic analysis of plant traits. In this study, 24 leaf traits of 436 chrysanthemum varieties were re-defined and measured. The correlation analysis identified 8 relatively independent traits, and principal component analysis further focused on 5 key traits, including the leaf blade length/leaf blade width, widest part length/leaf blade length, right lower leaf lobe length/leaf vein length of right lower lobe, right lower leaf lobe length/right lower leaf lobe width, leaf petiole length/leaf blade length. The leaf shapes were classified into 16 types by Q clustering analysis. This study established a quantitative definition and classification system for the leaves of Chinese traditional chrysanthemum varieties. It provided an effective leaf evaluation standard for the identification of chrysanthemum varieties, and a new method for the analysis of complex traits of ornamental plants.

QTL Mapping of Candidate Genes Involved in Cd Accumulation in Rice Grain
Chenyang Pan, Hanfei Ye, Weiyong Zhou, Sheng Wang, Mengjia Li, Mei Lu, Sanfeng Li, Xudong Zhu, Yuexing Wang, Yuchun Rao, Gaoxing Dai
Chinese Bulletin of Botany. 2021, 56(1):  25-32.  doi:10.11983/CBB20148
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Rice is one of the world’s most important crops, but cadmium (Cd) pollution and Cd accumulation in rice fields pose a serious threat to its yield and quality as well as to human health. How to reduce Cd accumulation in rice has become a major concern. In this study, a japonica rice variety Nekken2 was used as the maternal parent, and an indica rice variety HZ was used as the paternal parent. After F1 generation was obtained by cross-breeding, successive selfings were performed for 120 recombinant inbred lines (RILs) population as the QTL mapping populations. We measured the Cd content in rice grains of each line at the maturity stage. Meanwhile, QTL mapping was performed using genetic map. As a result, a total of 7 QTLs were detected, which were located on chromosome 2, 3, 9, and 12 of rice, with the highest LOD score of 4.97. The qRT-PCR analysis on the candidate genes involved in metal ion stress resistance in these QTL regions showed that the expression level of LOC_Os02g50240, LOC_Os02g52780, LOC_Os09g31200, LOC_Os09g35030 and LOC_Os09g37949 was significantly different from the parents. Combined with the data of concentration of different metal ions in the parents, we speculated that the high expression of LOC_Os02g50240, LOC_Os09g31200 and LOC_Os09g35030 might greatly improve the absorption and tolerance of rice to Cd ion stress. And these genes may be related to the accumulation of Cd in rice grains, and may affect the ability of rice to tolerate Cd stress, which could help for further breeding and screening for rice varieties to tolerate Cd stress, and exploring the molecular regulation mechanism of Cd accumulation in rice.

Genome-wide Identification and Analysis of CONSTANS-like Gene Family in Nicotiana tabacum
Yawen Zhang, Shan Liang, Guoyun Xu, Wuxia Guo, Shulin Deng
Chinese Bulletin of Botany. 2021, 56(1):  33-43.  doi:10.11983/CBB20147
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Nicotiana tabacum (tobacco) is one of the model plants for molecular biology research as well as an important economic crop in the world. A suitable living environment is essential for the growth and reproduction of tobacco. CONSTANS-like (COL) family proteins are not only key regulators for flowering time, but also play important roles in stress response of plants. Our aim was to identify the COL family members, analyze their gene structure, evolutionary relationship, transcriptional regulatory elements and expression patterns, and explore their possible functions in response to cold stress in tobacco. We identified a total of 15 COL genes with similar physiochemical properties in tobacco. Evolutionary analysis divided all COL genes into three categories, and similar intron structure and motif distribution were observed among genes within each category. The promoter regions of tobacco COL genes contain a large number of cis-acting elements related to responses to light, low temperature, drought and phyto hormone. Gene expression analysis showed that low temperature significantly affected the expression of COL genes in tobacco, but the effects on different genes were different. Our study showed different parental (N. sylvestris (maternal) and N. tomentosiformis (paternal)) expression bias between different COL genes in tobacco, and most of the bias patterns were maintained from 6-7 leaf stage to budding stage.

INVITED PROTOCOLS
CRISPR-based DNA Fragment Deletion in Plants
Xianrong Xie, Dongchang Zeng, Jiantao Tan, Qinlong Zhu, Yaoguang Liu
Chinese Bulletin of Botany. 2021, 56(1):  44-49.  doi:10.11983/CBB20203
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CRISPR/Cas9-based genome editing technology has been an important tool to study the gene function and genomic modification. Directed by a guide RNA, Cas9 protein can cleavage the genomic DNA at the target site, and produce mutations, including deletion, insertion, substitution and fragment deletion, by DNA double strand break (DSB) repair mechanism. In this protocol, we introduce the method to use CRISPR/Cas9 system to increase the efficiency of genomic DNA fragment deletion with microhomology-mediated end joining, especially the details in target design and detection of mutant plants.

Saturation Mutagenesis Using Dual Cytosine and Adenine Base Editors
Rui Zhang, Caixia Gao
Chinese Bulletin of Botany. 2021, 56(1):  50-55.  doi:10.11983/CBB21009
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Because the genome of an organism determines its primary phenotype, evolutionary principles suggest that genetic variations enhance phenotypic diversity towards increased fitness. Targeted saturation mutagenesis of crop genes could be used to screen for genetic variants with improved agronomic traits. Compared to traditional mutational breeding or directed evolution in heterologous organisms, targeted mutagenesis via dual cytosine and adenine base editors effectively generates endogenous mutagenesis and facilitates in vivo directed evolution of plant genes. In this protocol, we detail the process towards using saturated targeted endogenous mutagenesis editors (STEMEs) to generate targeted, random mutagenesis of plant genes. In particular, we focus on the process of designing targets, screening and genotyping the resulting evolved variants.

TECHNIQUES AND METHODS
A Rapid, Non-destructive and Continuous Sampling Technique and DNA Extraction for Soybean Seed
Zhengjun Xia, Yuzhuo Li, Jinlong Zhu, Hongyan Wu, Kun Xu, Hong Zhai
Chinese Bulletin of Botany. 2021, 56(1):  56-61.  doi:10.11983/CBB20095
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Establishment of a simple, quick, non-destructive, and continuous sampling procedure, can save planting cost and accelerate gene functional analysis and breeding procedures. In this study, we created a rapid, non-destructive, and continuous sampling technique using micro electric driller and air pump. We also optimized the high throughput DNA extraction method for the 384 deep-well plate and genotyping method. Furthermore, this technique could be applied in rice, maize and other crops for seed sampling and high throughput genotyping.

Establishment of Biolistic Mediated Transformation System for Elymus sibiricus
Pengfei Du, Yu Wang, Yingping Cao, Song Yang, Zhichao Sun, Decai Mao, Jiajun Yan, Daxu Li, Meizhen Sun, Chunxiang Fu, Shiqie Bai
Chinese Bulletin of Botany. 2021, 56(1):  62-70.  doi:10.11983/CBB20174
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Elymus sibiricus cv. ‘Chuancao No.2’ is the main cultivated grass species for desertification control and construction of high-yield and high-quality pasture in northwest Sichuan Plateau. In this study, we tested five explants of E. sibiricus cv. ‘Chuancao No.2’ for callus induction, and found that only inflorescence calli were able to differentiate and regenerate. The calli of inflorescence with dense and hard structure cultured for 25 d and 35 d were used for Agrobacterium and biolistic mediated transformation respectively. The results showed that only biolistic-mediated transformation could produce positive transgenic calli of ‘Chuancao No.2’. In the process of biolistic-mediated transformation, the calli was pretreated in two ways: hyperosmotic culture and filter paper drying. The results revealed that the transformation efficiency of filter paper drying was higher than that of hyperosmotic treatment. For the inflorescence callus after 25 d induction, the transformation efficiency under the condition of 2 h drying of filter paper was highest which reached about 40%. In short, we applied the biolistic technology in ‘Chuancao No.2’ for the first time and successfully obtained the positive transgenic inflorescence calli. This work will lead to establishment of the robust transformation system for E. sibiricus in future.

Establishment and Optimization of a Shoot Tip-based Genetic Transformation System for Foxtail Millet
Lan Yang, Ya Liu, Yang Xiang, Xiujuan Sun, Jingwei Yan, Aying Zhang
Chinese Bulletin of Botany. 2021, 56(1):  71-79.  doi:10.11983/CBB20119
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In this study, a simple and stable genetic transformation system of foxtail millet (Seteria italica) was established and optimized, in which shoot tips were used as the explant. We transformed Yugu 1, an elite millet cultivar, by Agrobacterium-mediated transformation, and tested different treatments to boost transformation efficiency. We used a PCR-based assay to screen transformants in third-leaf stage seedlings. We determined an optimal lethal concentration of glufosinate (Basta) when sprayed to millet seedlings, and tested the different PCR-based genotyping methods with or without Basta spary. Using the newly established pipeline, we further optimized various crucial factors that affect genetic transformation efficiency. We found that an optimal concentration of bacterial culture was OD600=1.4, an optimal concentration of acetolsyringone was 800 μmol∙L -1. We also obtained high transformation efficiency with an infecting pressure at 0.05 MPa, and an infecting time of 40 min. We used the above-mentioned transformation method to transform a Seteria italica calcineurin B-like protein 4 (SiCBL4) overexpression construct. Genetic stability analysis on T2 generation transformed plants was performed by the combination assay of Basta resistance and real-time quantitative fluorescence RT-PCR, which can save the time of genotyping. Altogether, this study establishes a shoot tip-based stable genetic transformation system for foxtail millets, and also develops a robust pipeline to detect transgenic offsprings.

SPECIAL TOPICS
Advances in the Molecular Mechanism and Genetic Regulation of Grain-filling Rate in Rice
Sunlu Chen, Chengfang Zhan, Hong Jiang, Linhan Li, Hongsheng Zhang
Chinese Bulletin of Botany. 2021, 56(1):  80-89.  doi:10.11983/CBB20157
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High yield and good quality of rice are important guarantees for food security in China, as well as the objective which breeders are pursuing. Grain-filling rate (GFR) is an important and complex agronomic trait in rice, directly affecting grain plumpness, weight, and quality. To date, elite rice germplasm with rapid GFR is rare, and valuable gene resources for breeding remain limited, which has become a bottleneck for further improvement of yield and quality in rice breeding. Comparing with other rice agronomic traits, GFR is highly complex for its spatio-temporal dynamics and environment- dependent variability, the research of which has long been concentrated on the physiological and biochemical characteristics and cultivation measure control of grain-filling period. The study on the molecular mechanism and genetic regulation of GFR has arisen relatively recently. Here, focusing on the GFR-related genes in rice identified recently, we reviewed the preliminarily known molecular mechanism and genetic regulation of GFR, including the influence of sugar metabolism and transport-related genes on GFR, the transcriptional and translational regulatory genes in GFR, the function of grain size and weight-related quantitative trait loci (QTLs) of GFR, and the analysis of GFR-related QTLs; we also discussed the future perspective of the research strategies for GFR, especially the application potential of phenomics-related technologies for GFR research, in order to promote the foundational research and application in rice breeding.

Research Progress on Sex Determination Genes of Woody Plants
Jing Lu, Yingnan Chen, Tongming Yin
Chinese Bulletin of Botany. 2021, 56(1):  90-103.  doi:10.11983/CBB20123
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Dioecious plants provide ideal materials for studying the sex determination mechanisms and the origin and evolution of sex chromosomes. Cloning of sex determination genes is crucial for revealing the sex-determination mechanism. There are many woody dioecious plant species, which contain two opposite sex determination systems: XY (females are homogametic XX and males are heterogametic XY) and ZW (females are heterogametic ZW and males are homogametic ZZ). Besides, trees of different sexes may have different economic values. Studies on the sex determination of woody plants not only have theoretical significances, but also have potential practical applications. With the development of large-scale sequencing technology, more and more sex determination genes of woody plants have been identified and cloned, which provides strong experimental evidence for the evolutionary history of dioecious plants and sex chromosomes. In this review, we summarized the important research progress on sex determination genes of woody plants, and discussed some future perspectives in this area.

Advances in Molecular Mechanisms of Stress Tolerance in Wild Soybean
Yan Wang, Bowei Jia, Mingzhe Sun, Xiaoli Sun
Chinese Bulletin of Botany. 2021, 56(1):  104-115.  doi:10.11983/CBB20144
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Wild soybeans (Glycine soja) originated in China, which was the closest ancestor of soybean. Because of the remarkable adaptability to adverse conditions, wild soybean has become an ideal material for the study of key genes in regulating stress tolerance. In this review, we provided an overview on the genome, transcriptome and proteome of wild soybean in stress tolerance. Meanwhile, we summarized current research progress on the protein kinases, transcription factors, ion channels and redox regulation in response to stress, which will provide new ideas for the cultivation of stress- tolerant crops in the future.

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