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| 1 | Allele-aware chromosome-level genome assembly of Artemisia annua reveals the correlation between ADS expansion and artemisinin yield显示文摘Artemisia annua is the major natural source of artemisinin,an anti-malarial medicine commonly used worldwide.Here,we present chromosome-level haploid maps for two A.annua strains with different artemisinin contents to explore the relationships between genomic organization and artemisinin production.High-fidelity sequencing,optical mapping,and chromatin conformation capture sequencing were used to assemble the heterogeneous and repetitive genome and resolve the haplotypes of A.annua.Approximately 5o,ooo genes were annotated for each haplotype genome,and a triplication event that occurred approximately 58.12million years ago was examined for the first time in this species.A total of 3,903,467-5,193,414 variants(SNPs,indels,and structural variants)were identified in the 1.5-Gb genome during pairwise comparison between haplotypes,consistent with the high heterozygosity of this species.Genomic analyses revealed a correlation between artemisinin concents and the copy number of amorpha-4,11-dienes ynthasegenes.This correlation was further confirmed by resequencing of 36A.annua samples with varied artemisinin contents.Circular consensus sequencing of transcripts facilitated the detection of paralog expression.Collectively,our study provides chromosome-level allele-aware genome assemblies for two A.annua strains and new insights into the biosynthesis of artemisinin and its regulation,which will contribute to conquering malaria worldwide. | Baosheng Liao Xiaofeng Shen Li Xiang Shuai Guo Shiyu Chen Ying Meng Yu Liang Dandan Ding Junqi Bai Dong Zhang Tomasz Czechowski Yi Li Hui Yao Tingyu Mai Caroline Howard Chao Sun Haitao Liu Jiushi Liu Jin Pei Jihai Gao Jigang Wang Xiaohui Qiu Zhihai Huang Hongyi Li Ling Yuan Jianhe Wei lan Graham Jiang Xu Boli Zhang Shilin Chen | 2022 | Molecular Plant2022，15，8： | 9 |
| 2 | Development of nutritious rice with high zinc/selenium and low cadmium in grains through QTL pyramiding显示文摘Enriching zinc(Zn) and selenium(Se) levels,while reducing cadmium(Cd) concentration in rice grains is of great benefit for human diet and health.Large natural variations in grain Zn, Se, and Cd concentrations in different rice accessions enable Zn/Sebiofortification and Cd-minimization through molecular breeding. Here, we report the development of new elite varieties by pyramiding major quantitative trait loci(QTLs) that significantly contribute to high Zn/Se and low Cd accumulation in grains. A chromosome segment substitution line CSSLGCC7 with the PA64s-derived GCC7 allele in the 93-11 background, exhibited steadily higher Mn and lower Cd concentrations in grains than those of 93-11. This elite chromosome segment substitution line(CSSL) was used as the core breeding material to cross with CSSLs harboring other major QTLs for essential mineral elements, especially CSSLGZC6 for grain Zn concentration and CSSLGSC5 for grain Se concentration. The CSSLGCC7+GZC6 and CSSLGCC7+GSC5 exhibited lower Cd concentration with higher Zn and Se concentrations in grains, respectively. Our study thus provides elite materials for rice breeding targeting high Zn/Se and low Cd concentrations in grains. | Chaolei Liu Shilin Ding Anpeng Zhang Kai Hong Hongzhen Jiang Shenglong Yang Banpu Ruan Bin Zhang Guojun Dong Longbiao Guo Dali Zeng Qian Qian Zhenyu Gao | 2020 | Journal of Integrative Plant Biology2020，62，3： | 7 |
| 3 | Exploring Seasonal and Circadian Rhythms in Structural Traits of Field Maize from LiDAR Time Series显示文摘Plant growth rhythm in structural traits is important for better understanding plant response to the ever-changing environment.Terrestrial laser scanning(TLS)is a well-suited tool to study structural rhythm under field conditions.Recent studies have used TLS to describe the structural rhythm of trees,but no consistent patterns have been drawn.Meanwhile,whether TLS can capture structural rhythm in crops is unclear.Here,we aim to explore the seasonal and circadian rhythms in maize structural traits at both the plant and leaf levels from time-series TLS.The seasonal rhythm was studied using TLS data collected at four key growth periods,including jointing,bell-mouthed,heading,and maturity periods.Circadian rhythms were explored by using TLS data acquired around every 2 hours in a whole day under standard and cold stress conditions.Results showed that TLS can quantify the seasonal and circadian rhythm in structural traits at both plant and leaf levels.(1)Leaf inclination angle decreased significantly between the jointing stage and bell-mouthed stage.Leaf azimuth was stable after the jointing stage.(2)Some individual-level structural rhythms(e.g.,azimuth and projected leaf area/PLA)were consistent with leaf-level structural rhythms.(3)The circadian rhythms of some traits(e.g.,PLA)were not consistent under standard and cold stress conditions.(4)Environmental factors showed better correlations with leaf traits under cold stress than standard conditions.Temperature was the most important factor that significantly correlated with all leaf traits except leaf azimuth.This study highlights the potential of time-series TLS in studying outdoor agricultural chronobiology. | Shichao Jin Yanjun Su Yongguang Zhang Shilin Song Qing Li Zhonghua Liu Qin Ma Yan Ge LingLi Liu Yanfeng Ding Frédéric Baret Qinghua Guo | 2021 | Plant Phenomics2021，3，1： | 5 |
| 4 | Wushan Arch Bridge, The Worldwide Longest Arch Constructed of Concrete-Filled Steel Tube显示文摘 | Zhang Zuo-an Liu Shilin Ding Daiun | 2006 | Travaux2006，829，： | 1 |
| 5 | Mining physical protein-protein interactions from theliterature显示文摘 | HUANG Minlie DING Shilin WANG Hongning | 2008 | Genome Biology2008，9，2： | 1 |
| 6 | OsRLR4 binds to the OsAUX1 promoter to negatively regulate primary root development in rice显示文摘Root architecture is one of the most important agronomic traits that determines rice crop yield. The primary root(PR) absorbs mineral nutrients and provides mechanical support;however, the molecular mechanisms of PR elongation remain unclear in rice. Here, the two loss-of-function T-DNA insertion mutants of root length regulator 4(Os RLR4), osrlr4-1 and osrlr4-2 with longer PR, and three Os RLR4 overexpression lines, OE-Os RLR4-1/-2/-3 with shorter PR compared to the wild type/Hwayoung(WT/HY), were identified. Os RLR4 isone of five members of the PRAF subfamily of the regulator chromosome condensation1(RCC1) family. Phylogenetic analysis of Os RLR4 from wild and cultivated rice indicated that it is under selective sweeps, suggesting its potential role in domestication. Os RLR4 controls PR development by regulating auxin accumulation in the PR tip and thus the root apical meristem activity. A series of biochemical and genetic analyses demonstrated that Os RLR4 functions directly upstream of the auxin transporter Os AUX1. Moreover, Os RLR4 interacts with the TRITHORAX-like protein Os Trx1 to promote H3 K4 me3 deposition at the Os AUX1 promoter, thus altering its transcription level. This work provides insight into the cooperation of auxin and epigenetic modifications in regulating root architecture and provides a genetic resource for plant architecture breeding. | Chendong Sun Dongming Li Zhenyu Gao Lei Gao Lianguang Shang Mei Wang Jiyue Qiao Shilin Ding Chuanyou Li Markus Geisler Dean Jiang Yanhua Qi Qian Qian | 2022 | Journal of Integrative Plant Biology2022，64，1： | 0 |
| 7 | A Recessive Mutant of argonaute 1b/gsnl4 Leads to Narrow Leaf, Small Grain Size and Low Seed Setting in Rice显示文摘A gsnl4 mutant characterized by small grain size,narrow leaf and low seed-setting rate was obtained by ethyl methane sulfonate(EMS)mutagenesis of a japonica rice variety Wuyunjing 21.Genetic analysis showed that gsnl4 is a loss-of-function mutant.A single-base mutation in gsnl4 resulted in the substitution of Ser to Asn in the Piwi domain of OsAGOlb protein.CRISPR/Cas9-mediated editing of OsAGOlb yielded a mutant phenotypically resembling gsnl4.Furthermore,miRNA-Seq analysis showed that the transcript expression levels of miRNAs in the signal transduction pathways related to pollen development,leaf morphology and honnone activation were significantly different between the gsnl4 mutant and the wild type(WT)plants.Several miRNAs were downregulated,and their target genes were upregulated in gsnl4 mutants.The auxin content in the root tips of the gsnl4 mutant decreased,and the expression of most auxin-related genes was altered.In summary,GSNL4 not only regulates organ development by controlling cell division and expansion,but also plays an important role in regulating auxin transport in rice. | SONG Mengqiu RUAN Shuang PENG Youlin WANG Zhongwei Jahan NOUSHIN ZHANG Yu CUI Yongtao HU Haitao JIANG Hongzhen DING Shilin SHEN Lan GAO Zhenyu HU Xingming QIAN Qian GUO Longbiao | 2021 | Rice science2021，28，6： | 0 |
| 8 | Identification of QTLs for Cadmium Tolerance During Seedling Stage and Validation of qCDSL1 in Rice显示文摘Cadmium(Cd)is a non-essential toxic metal that is harmful to plants.To investigate the genetic mechanism of Cd tolerance in rice,quantitative trait loci(QTLs)associated with Cd tolerance at the seedling stage were analyzed using a recombinant inbred line(RIL)population derived from a cross between PA64s and 93-11.A total of 36 QTLs associated with shoot length,root length,shoot dry weight,root dry weight and total dry weight were detected in Hangzhou and Lingshui of China.Among them,15 QTLs were identified under the control condition and 15 QTLs were identified under the Cd stress condition,and 6 QTLs for Cd tolerant coefficient were detected on chromosomes 1,3,7 and 9.The qCDSL1.1 and qCDSL1.2 were identified in Hangzhou and Lingshui,respectively,and had overlapping intervals on chromosome 1.To further confirm the effects of qCDSL1.1 and qCDSL1.2,we developed a chromosome segment substitution line(CSSL),CSSLqCDSL1,in 93-11 background harboring qCDSL1.1/qCDSL1.2 from PA64s.Compared to 93-11,CSSLqCDSL1 had increased shoot length under the Cd stress condition.These results pave the way for further isolation of those genes controlling Cd tolerance in rice and marker-assistant selection of rice elite varieties with Cd tolerance. | Ding Shilin Liu Chaolei Shang Lianguang Yang Shenglong Zhang Anpeng Jiang Hongzhen Ruan Banpu Fang Guonan Tian Biao Ye Guoyou Guo Longbiao Qian Qian Gao Zhenyu | 2021 | Rice science2021，28，1： | 0 |
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