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| 1 | Analyses of the NAC Transcription Factor Gene Family in Gossypium raimondii Ulbr.:Chromosomal Location,Structure,Phylogeny,and Expression Patterns显示文摘NAC 域蛋白质是知道在各种各样的植物起多样的作用的植物特定的抄写因素发展进程。在现在的学习,我们在 Gossypium raimondii Ulbr 执行了 NAC 基因家庭的第一全面研究,合并种系发生,介绍的 chromosomal 地点,基因结构,保存主题,和表示分析。我们识别了种系发生地被聚类进 18 个不同亚科的 145 NAC 抄写因素(NAC-TF ) 基因。这些, 127 NAC-TF 基因越过 13 个染色体被散布,(55%) 80 优先地被保留位于两个的副本复制了区域,六位于 triplicated chromosomal 区域。NAC-TF 基因的多数出现了时间 -- ,空间 -- ,并且织物特定的表示模式基于 transcriptomic 和 qRT-PCR 分析。然而,几副本基因的表示模式部分是冗余的,建议在他们的进化期间的 sub-functionalization 的出现。基于他们的 genomic 组织,我们结束了复制在 G 显著地贡献了到 NAC-TF 基因家庭的扩大的那 genomic。raimondii。他们的表示侧面的全面分析能在 G 在 NAC 基因家庭的成员之中提供新奇卓见进功能的分叉。raimondii。 | Haihong Shang Wei Li Changsong Zou Youlu Yuan | 2013 | Journal of Integrative Plant Biology2013，55，7： | 25 |
| 2 | Comprehensive analysis of NAC transcription factors in diploid Gossypium: sequence conservation and expression analysis uncover their roles during fiber development显示文摘Determining how function evolves following gene duplication is necessary for understanding gene expansion.Transcription factors(TFs)are a class of proteins that regulate gene expression by binding to specific cis-acting elements in the promoters of target genes,subsequently activating or repressing their transcription.In the present study,we systematically examined the functional diversification of the NAC transcription factor(NAC-TFs)family by analyzing their chromosomal location,structure,phylogeny,and expression pattern in Gossypium raimondii(Gr)and G.arboreum(Ga).The 145 and 141 NAC genes identified in the Gr and Ga genomes,respectively,were annotated and divided into 18 subfamilies,which showed distinct divergence in gene structure and expression patterns during fiber development.In addition,when the functional parameters were examined,clear divergence was observed within tandem clusters,which suggested that subfunctionalization had occurred among duplicate genes.The expression patterns of homologous gene pairs also changed,suggestive of the diversification of gene function during the evolution of diploid cotton.These findings provide insights into the mechanisms underlying the functional differentiation of duplicated NAC-TFs genes in two diploid cotton species. | Haihong Shang Zhongna Wang Changsong Zou Zhen Zhang Weijie Li Junwen Li Yuzhen Shi Wankui Gong Tingting Chen Aiying Liu Juwu Gong Qun Ge Youlu Yuan | 2016 | Science China(Life Sciences)2016，59，2： | 12 |
| 3 | Genome-Wide Analysis of the Sus Gene Family in Cotton显示文摘蔗糖 synthase (怀疑) 是在植物蔗糖新陈代谢的关键酶。在棉花,怀疑(EC 2.4.1.13 ) 是降级的主要的酶从种子上衣的韧皮部进口进棉花纤维的蔗糖。这研究示威了 Gossypium arboreum L. 的染色体, G。raimondii Ulbr,和 G。hirsutum L. ,包含了 8, 8,和 15 分别地怀疑基因。他们的结构的组织,种系发生的关系,和表示侧面被描绘。genomic 和编码序列的比较识别了哪个高度被保存在之间的多重 introns,数字和位置双并且 allotetraploid 棉花种类。大多数种系发生的 clades 从所有三种包含了序列,建议 tetraploid G 的 Sus 基因。hirsutum 它的双祖先源于那些。一个人怀疑组(怀疑我) 在棉花期间经历了扩大进化。表示分析显示大多数怀疑基因差别在各种各样的纸巾被表示并且在棉花纤维房间有发展依赖者表示侧面。一样的 orthologous 组的成员在所有三种有很类似的表示模式。这些结果提供新卓见进棉花的进化在纤维生长和开发期间怀疑基因家庭,和卓见进它的成员的生理的功能。 | Changsong Zou Cairui Lu Haihong Shang Xinrui Jing Hailiang Cheng Youping Zhang Guoli Song | 2013 | Journal of Integrative Plant Biology2013，55，7： | 10 |
| 4 | Constructing a high-density linkage map for Gossypium hirsutum × Gossypium barbadense and identifying QTLs for lint percentage显示文摘To introgress the good fiber quality and yield from Gossypium barbadense into a commercial Upland cotton variety, a high-density simple sequence repeat(SSR) genetic linkage map was developed from a BC1F1 population of Gossypium hirsutum×Gossypium barbadense. The map comprised 2,292 loci and covered 5115.16 centi Morgan(c M) of the cotton AD genome, with an average marker interval of 2.23 c M. 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 G. barbadense and increased LP by 1.07%–2.41%. These results indicated that the map could be used for screening chromosome substitution segments from G. barbadense in the Upland cotton background, identifying QTLs or genes from G. barbadense, and further developing the gene pyramiding effect for improving fiber yield and quality. | Yuzhen Shi Wentan Li Aiguo Li Ruihua Ge Baocai Zhang Junzhi Li Guangping Liu Junwen Li Aiying Liu Haihong Shang Juwu Gong Wankui Gong Zemao Yang Feiyü Tang Zhi Liu Weiping Zhu Jianxiong Jiang Xiaonan Yu Tao Wang Wei Wang Tingting Chen Kunbo Wang Zhengsheng Zhang Youlu Yuan | 2015 | Journal of Integrative Plant Biology2015，57，5： | 7 |
| 5 | Cloning and expression analysis of a dirigent protein gene from the resurrection plant Boea hygrometrica显示文摘Resurrection plants are tolerant to extreme dehydration and are useful model systems to study genes that play a role in drought tolerance. A gene fragment encoding a dirigent protein that is predicted to function in lignin biosynthesis was identified from leaves of the resurrection plant Boea hygrometrica via cDNA microarray screening. A cDNA, designated BhDIR1, containing the complete predicted open reading frame, was obtained by 50-RACE. BhDIR1 transcripts were found to be accumulated in response to changes in plant dehydration status, exogenously applied phytohormones and signaling molecules, and temperature stresses. BhDIR1 encodes a protein of 199 amino acids, which shows 20-40% similarity to dirigent proteins reported from other plants. BhDIR1 is predicted to contain a cleavable signal peptide at the N-terminal, and its plasma membrane/cell wall localization was confirmed using a GFP fusion protein assay. Consistent with this discovery, the acid-soluble lignin content decreased in dehydrated B. hygrometrica leaves. Taken together, our results indicate a protective role for a dirigent protein in response to drought stress by changing the physical characters of lignin which in turn is predicted to affect the mechanical strength and flexibility of the plant cell wall. | Renhua Wu, Lili Wang, Zhi Wang, Haihong Shang, Xia Liu, Yan Zhu, Dongdong Qi, Xin Deng * Key Laboratory of Photosynthesis and Environmental Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China | 2009 | Progress in Natural Science:Materials International2009，19，3： | 6 |
| 6 | QTL mapping for fiber quality and yieldrelated traits across multiple generations in segregating population of CCRI 70显示文摘Background:Cotton is a significant economic crop that plays an indispensable role in many domains.Gossypium hirsutum L.is the most important fiber crop worldwide and contributes to more than 95%of global cotto n production.Identifying stable quantitative trait locus(QTLs)controlling fiber quality and yield related traits are necessary prerequisites for marker-assisted selection(MAS).Results:A genetic linkage map was constructed with 312 simple sequence repeat(SSR)loci and 35 linkage groups using JoinMap 4.0;the map spanned 1 929.9 cM,with an average interval between two markers of 6.19 cM,and covered approximately 43.37%of the cotton genome.A total of 74 QTLs controlling fiber quality and 41 QTLs controlling yield-related traits were identified in 4 segregating generations.These QTLs were distributed across 20 chromosomes and collectively explained 1.01%?27.80%of the observed phenotypic variations.In particular,35 stable QTLs could be identified in multiple generations,25 common QTLs were con sistent with those in previous studies,and 15 QTL clusters were found in 11 chromosome segments.Conclusion:These studies provide a theoretical basis for improving cotton yield and fiber quality for molecular marker-assisted selection. | DENG Xiaoying GONG Juwu LIU Aiying SHI Yuzhen GONG Wankui GE Qun LI Junwen SHANG Haihong WU Yuxiang YUAN Youlu | 2019 | Journal of Cotton Research2019，2，2： | 3 |
| 7 | The draftgenome of a diploid cotton gossypium raimondii 显示文摘 | Kunbo Wang Zhiwen Wang Fuguang Li Wuwei Ye Junyi Wang Guoli Song Zhen Yue Lin Cong Haihong Shang Shilin Zhu Changsong Zou Qin Li Youlu Yuan Cairui Lu Hengling Wei Caiyun Gou Zequn Zheng Ye Yin Xueyan Zhang Kun Liu Bo Wang Chi Song Nan Shi Russell J Kohel Richard G Percy John Z Yu Yu-xian Zhu Jun Wang Shuxun Yu | 2012 | Nat Genet2012，，44： | 1 |
| 8 | A genome-wide identification of the BLH gene family reveals BLH1 involved in cotton fiber development显示文摘Background:Cotton is the world’s largest and most important source of renewable natural fiber.BEL1-like homeodomain(BLH)genes are ubiquitous in plants and have been reported to contribute to plant development.However,there is no comprehensive characterization of this gene family in cotton.In this study,32,16,and 18 BLH genes were identified from the G.hirsutum,G.arboreum,and G.raimondii genome,respectively.In addition,we also studied the phylogenetic relationships,chromosomal location,gene structure,and gene expression patterns of the BLH genes.Results:The results indicated that these BLH proteins were divided into seven distinct groups by phylogenetic analysis.Among them,25 members were assigned to 15 chromosomes.Furthermore,gene structure,chromosomal location,conserved motifs,and expression level of BLH genes were investigated in G.hirsutum.Expression profiles analysis showed that four genes(GhBLH1_3,GhBLH1_4,GhBLH1_5,and GhBLH1_6)from BLH1 subfamily were highly expressed during the fiber cell elongation period.The expression levels of these genes were significantly induced by gibberellic acid and brassinosteroid,but not auxin.Exogenous application of gibberellic acid significantly enhanced GhBLH1_3,GhBLH1_4,and GhBLH1_5 transcripts.Expression levels of GhBLH1_3 and GhBLH1_4 genes were significantly increased under brassinosteroid treatment.Conclusions:The BLH gene family plays a very important role in many biological processes during plant growth and development.This study deepens our understanding of the role of the GhBLH1 gene involved in fiber development and will help us in breeding better cotton varieties in the future. | LIU Cuixia LI Zhifang DOU Lingling YUAN Yi ZOU Changsong SHANG Haihong CUI Langjun XIAO Guanghui | 2020 | Journal of Cotton Research2020，3，3： | 1 |
| 9 | QTL mapping for plant height and fruit branch number based on RIL population of upland cotton显示文摘Background:Plant height(PH)and fruit branch number(FBN)are important traits for improving yield and mechanical harvesting of cotton.In order to identify genes of PH and FBN in cotton germplasms to develop superior cultivars,quantitative trait loci(QTLs)for these traits were detected based on the phenotypic evaluation data in nine environments across four locations and 4 years and a previously reported genetic linkage map of an recombinant inbred line(RIL)population of upland cotton.Results:In total,53 QTLs of PH and FBN,were identified on 21 chromosomes of the cotton genome except chromosomes c02,c09-c11,and c22.For PH,27 QTLs explaining 3.81%–8.54%proportions of phenotypic variance were identified on 18 chromosomes except c02,c08-c12,c15,and c22.For FBN,26 QTLs explaining 3.23%–11.00%proportions of phenotypic variance were identified on 16 chromosomes except c02-c03,c06,c09-c11,c17,c22-c23,and c25.Eight QTLs were simultaneously identified in at least two environments.Three QTL clusters containing seven QTLs were identified on three chromosomes(c01,c18 and c21).Eleven QTLs were the same as previously reported ones,while the rest were newly identified.Conclusions:The QTLs and QTL clusters identified in the current study will be helpful to further understand the genetic mechanism of PH and FBN development of cotton and will enhance the development of excellent cultivars for mechanical managements in cotton production. | LIU Ruixian XIAO Xianghui GONG Juwu LI Junwen ZHANG Zhen LIU Aiying LU Quanwei SHANG Haihong SHI Yuzhen GE Qun IQBAL Muhammad Sajid CHEN Quanjia YUAN Youlu GONG Wankui | 2020 | Journal of Cotton Research2020，3，1： | 1 |
| 10 | Evolution of pectin synthesis relevant galacturonosyltransferase gene family and its expression during cotton fiber development显示文摘Background:Pectin is a key substance involved in cell wall development,and the galacturonosyltransferases(GAUTs)gene family is a critical participant in the pectin synthesis pathway.Systematic and comprehensive research on GAUTs has not been performed in cotton.Analysis of the evolution and expression patterns of the GAUT gene family in different cotton species is needed to in crease kno wledge of the functi on of pectin in cotto n fiber development.Results:In this study,we have identified 131 GAUT genes in the genomes of four Gossypium species(G.raimondii,G barbadense,G.hirsutum,and G.arboreum),and classified them as GAUT-A,GAUT-B and GAUT-C,which coding probable galacturonosyltransferases.Among them,the GAUT genes encode proteins GAUT1 to GAUT15.All GAUT proteins except for GAUT7 contai n a con served glycosyl transferase family 8 domain(H-DN-A-SW-S-V-H-T-F).The conserved sequence of GAUT7 is PLN(phospholamban)02769 domain.According to c/s-elemet analysis,GAUT genes transcript levels may be regulated by horm ones such as JA,GA,SA,ABA,Me-JA,and IA A.The evoluti on and transcription patterns of the GAUT gene family in different cotton species and the transcript levels in upland cotton lines with different fiber st「ength were analyzed.Peak transcript level of GhGAUT genes have been observed before 15 DPA.In the six materials with high fiber strength,the transcription of GhGAUT genes were concentrated from 10 to 15 DPA;while the highest transcript levels in low fiber st「ength materials were detected between 5 and 10 DPA.These results lays the foundation for future research on gene function during cotton fiber development.Conclusions:The GAUT gene family may affect cotton fiber development,including fiber elongation and fiber thickening.In the low strength fiber lines,GAUTs mainly participate in fiber elongation,whereas their major effect on cotton with high strength fiber is related to both elongation and thickening. | FAN Senmiao LIU Aiying ZOU Xianyan ZHANG Zhen GE Qun GONG Wankui LI Junwen GONG Juwu SHI Yuzhen DENG Xiaoying JIA Tingting YUAN Youlu SHANG Haihong | 2021 | Journal of Cotton Research2021，4，3： | 0 |
| 11 | Rapid Identification of a Candidate Gene Related to Fiber Strength Using a Superior Chromosome Segment Substitution Line from Gossypium hirsutum × Gossypium barbadense via Bulked Segregant RNA-Sequencing显示文摘Cotton is the most widely cultivated commercial crop producing natural fiber around the world.As a critical trait for fiber quality,fiber strength principally determined during the secondary wall thickening period.Based on the developed BC5F3:5 CSSLs(chromosome segment substitution lines)from Gossypium hirsutum CCRI36×G.barbadense Hai 1,the superior MBI9915 was chosen to construct the secondary segregated population BC7F2 with its recurrent parent CCRI36,which was subsequently subjected to Bulk segregant RNA-sequencing(BSR-seq)for rapid identification of candidate genes related to fiber strength.A total of 4 fiber-transcriptome libraries were separately constructed and sequenced,including two parents(CCRI36 and MBI9915)and two extreme pools at 20 DPA(days post anathesis).Through multiple comparisons,536 DEGs(differentially expressed genes)were overlapped at 20 DPA.Allelic-polymorphism comparison in mRNA sequences revealed 831 highly probable SNPs between two extreme pools related to fiber strength.Linkage analysis was performed between two extreme pools with SNP-index method.Eighteen correlated regions with 1981 annotation genes were obtained between two pools at 20 DPA,of which 12 common DEGs were similarly identified both between two parents and two pools.One gene(Gh_A07G0837)in the candidate region related to fiber strength was differentially expressed in both parents and extreme pools and involved in fiber strength development through reactive oxygen species(ROS)activity.Co-expression analysis of Gh_A07G0837 showed that Gh_A07G0837 may cooperate with other genes to regulate fiber strength.The reliability of BSR-seq results was validated by the quantitative real-time PCR(qRT-PCR)experiments on 5 common DGEs 20 DPA.Co-expressed analysis results indicated that there were some genes expressed especially low in MBI9915,resulting in good fiber strength.Focusing on bulked segregant analysis on the extreme pools derived from superior CSSL population,this study indicates that BSR-seq can be efficiently applied on rapid identification of candidate genes related to fiber strength,which make contributions to our understanding of fiber quality formation in cotton. | Qi Zhang Pengtao Li Aiying Liu Shaoqi Li Quanwei Lu Qun Ge Junwen Li Wankui Gong Xiaoying Deng Haihong Shang Yuzhen Shi Youlu Yuan | 2021 | Phyton-International Journal of Experimental Botany2021，90，3： | 0 |
| 12 | Patterns of presence-absence variants in Upland cotton显示文摘Dear Editor,Sources of genetic variations in genomes include small-scale sources(such as single-nucleotide polymorphisms(SNPs),insertions/deletions(InDels),and simple sequence repeats and larger-scale structural variations(mainly presence-absence variants(PAVs))and copy number variants).PAVs are sequences that are either inserted or missing in genomes in comparison with a reference sequence or genome.PAVs can have a much longer sequence than SNPs and InDels,as illustrated in the human genome(Conrad et al.,2010).PAVs are important genomic structural variations that can directly affect genomic structure and key functional genes in the genome(Kumar et al.,2007).Moreover,the use of PAVs for studying quantitative traits has been valuable(Lam et al.,2010). | Junfang Liu Xianliang Zhang Lingling Dou Wei Li Xiaojian Zhou Yangai Liu Xiaoyu Pei Zhongying Ren Wensheng Zhang Huaizhu Li Wenbo Wang Changsong Zou Kunlun He Fei Zhang Wenyu Ma Haihong Shang Hongbin Li Daigang Yang Guanghui Xiao Xiongfeng Ma | 2020 | Science China(Life Sciences)2020，63，10： | 0 |
| 13 | The plasmodesmata-associated β-1,3-glucanase gene GhPdBG regulates fiber development in cotton显示文摘Trichomes are specialized structures that originate from epidermal cells of organs in higher plants.The cotton fiber is a unique single-celled trichome that elongates from the seed coat epidermis.Cotton(Gossypium hirsutum)fibers and trichomes are models for cell differentiation.In an attempt to elucidate the intercellular factors that regulate fiber and trichome cell development,we identified a plasmodesmal β-1,3-glucanase gene(designated GhPdBG)controlling the opening and closing of plasmodesmata in cotton fibers.Structural and evolutionary analysis showed haplotypic variation in the promoter region of the GhPdBG gene among 352 cotton accessions,but high conservation in the coding region.GhPdBG was expressed predominantly in cotton fibers and localized to plasmodesmata(PD).Expression patterns of PdBG that corresponded to PD permeability were apparent during fiber development in G.hirsutum and G.barbadense.The PdBG-mediated opening-closure of PD appears to be involved in fiber development and may account for the contrasting fiber traits of these two species.Ectopic expression of GhPdBG revealed that it functions in regulating fiber and trichome length and/or density by modulating plasmodesmatal permeability.This finding suggests that plasmodesmal targeting of GhPdBG,as a switch of intercellular channels,regulates single-celled fiber and trichome development in cotton. | Yijie Fan Shuangshuang Lin Yanhui Lyu Haihong Shang Youlu Yuan Zhengmin Tang Chengzhi Jiao Aiyun Chen Piyi Xing Li Zhang Yuxiao Sun Haixia Guo Tongtong Li Zhonghai Ren Fanchang Zeng | 2023 | The Crop Journal2023，11，6： | 0 |
| 14 | Genome-wide identification and expression analysis of the GhIQD gene family in upland cotton(Gossypium hirsutum L.)显示文摘Background:Calmodulin(CaM)is one of the most important Ca^(2+)signaling receptors because it regulates diverse physiological and biochemical reactions in plants.CaM functions by interacting with CaM-binding proteins(CaMBPs)to modulate Ca^(2+)signaling.IQ domain(IQD)proteins are plant-specific CaMBPs that bind to CaM by their specific CaM binding sites.Results:In this study,we identified 102 GhIQD genes in the Gossypium hirsutum L.genome.The GhIQD gene family was classified into four clusters(Ⅰ,Ⅱ,Ⅲ,andⅣ),and we then mapped the GhIQD genes to the G.hirsutum L.chromosomes.Moreover,we found that 100 of the 102 GhIQD genes resulted from segmental duplication events,indicating that segmental duplication is the main force driving GhIQD gene expansion.Gene expression pattern analysis showed that a total of 89 GhIQD genes expressed in the elongation stage and second cell wall biosynthesis stage of the fiber cells,suggesting that GhIQD genes may contribute to fiber cell development in cotton.In addition,we found that 20 selected GhIQD genes were highly expressed in various tissues.Exogenous application of MeJA significantly enhanced the expression levels of GhIQD genes.Conclusions:Our study shows that GhIQD genes are involved in fiber cell development in cotton and are also widely induced by MeJA.Thw results provide bases to systematically characterize the evolution and biological functions of GhIQD genes,as well as clues to breed better cotton varieties in the future. | DOU Lingling LV Limin KANG Yangyang TIAN Ruijie HUANG Deqing LI Jiayin LI Siyi LIU Fengping CAO Lingyan JIN Yuhua LIU Yang LI Huaizhu WANG Wenbo PANG Chaoyou SHANG Haihong ZOU Changsong SONG Guoli XIAO Guanghui | 2021 | Journal of Cotton Research2021，4，1： | 0 |
| 15 | Overexpressed PKM2 promotes macrophage phagocytosis and atherosclerosis显示文摘Background:The expression of pyruvate kinase muscle 2(PKM2)is augmented in macrophages of patients with atherosclerotic coronary artery disease.The role of PKM2 in atherosclerosis is to be determined.Methods:Global and myeloid cell-specific PKM2 knock-in mice with ApoE^(-/-)background(ApoE^(-/-),PKM2^(KI/KI)and Lyz2-cre,ApoE^(-/-),and PKM2^(flox/flox))were produced to evaluate the clinical significance of PKM2 in atherosclerosis development.Wild-type and PKM2 knock-in macrophages were isolated to assess the function of PKM2 in macrophage phagocytosis.Atherosclerotic mice were treated with PKM2 inhibitor shikonin(SKN)to evaluate the therapeutic potential of PKM2 suppression in atherosclerosis.Results:Oxidized low-density lipoprotein(oxLDL)upregulated PKM2 in macrophages.PKM2 in return promoted the uptake of oxLDL by macrophages.Overexpressed PKM2 accelerated atherosclerosis in mice.SKN blocked the progress of mouse atherosclerosis.Conclusions:PKM2 accelerates macrophage phagocytosis and atherosclerosis.Targeting PKM2 is a potential therapy for atherosclerosis. | Xiaochen Gai Fangming Liu Yuting Wu Baohui Zhang Bufu Tang Kezhuo Shang Lianmei Wang Haihong Zhang Yixin Chen Shuhui Yang Weiwei Deng Peng Li Jing Wang Hongbing Zhang | 2023 | Animal Models and Experimental Medicine2023，6，2： | 0 |
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