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Identification of QTLs and candidate genes for physiological traits associated with drought tolerance in cotton

Journal of Cotton Research 2020年第1期3卷 13-45页

作者： MAGwangA Richard Odongo LU Pu KIRUNGU Joy Nyangasi CAI Xiaoyan ZHOU Zhongli AGONG Stephen Gaya wang kunbo LIU Fang State Key Laboratory of Cotton Biology/Institute of Cotton Research Chinese Academy of Agricultural SciencesAnyang 455000HenanChina Jaramogi Oginga Odinga University of Science and Technology P.O Box 210-40601BondoKenya

Background:Cotton is mainly grown for its natural fiber and edible *** fiber obtained from cotton is the indispensable raw material for the textile *** ever changing climatic condition,threatens cotton production due to a lack of sufficient water for its *** of drought stress are estimated to affect more than 50%of the cotton growing *** elucidate the drought tolerance phenomenon in cotton,a backcross population was developed from ***,a drought tolerant donor parent and *** which is highly susceptible to drought ***:A genetic map of 10888 SNP markers was developed from 200 BC_2F_2 *** map spanned 4191.3 centi-Morgan(c M),with an average distance of 0.1047 c M,covering 51%and 49%of At and Dt sub genomes,*** stable Quantitative trait loci(QTLs)were detected,in which more than a half were detected in the At ***-nine candidate genes were mined within the QTL regions for three traits:cell membrane stability(CMS),saturated leaf weight(SLW)and chlorophyll *** genes had varied physiochemical properties.A majority of the genes were interrupted by introns,and only 15 genes were intronless,accounting for 17%of the mined *** genes were found to be involved molecular function(MF),cellular component(CC)and biological process(BP),which are the main gene ontological(GO)functions.A number of mi RNAs were detected,such as mi R164,which is associated with NAC and MYB genes,with a profound role in enhancing drought tolerance in *** RT-q PCR analysis,5 genes were found to be the key genes involved in enhancing drought tolerance in *** cotton harbors a number of favorable alleles,which can be exploited to aid in improving the narrow genetic base of the elite cotton *** detection of 30 stable QTLs and 89 candidate genes found to be contributed by the donor parent,***,showed the significant genes harbored by the wild progenitors which

关键词： Cotton spp. Quantitative trait loci Genetic map Drought tolerance mi RNAs Gene ontology

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Widespread incomplete lineage sorting and introgression shaped adaptive radiation in the Gossypium genus

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Plant Communications 2024年第2期5卷 185-197页

作者： Yanchao Xu Yangyang Wei Zhongli Zhou Xiaoyan Cai Scott ABoden Muhammad Jawad Umer Luqman BSafdar Yuling Liu Dingsha Jin Yuqing Hou Yuhong wang Sarah Brooke Wall kunbo wang Shuxun Yu Baohong Zhang Renhai Peng Fang Liu National Key Laboratory of Cotton Bio-breeding and Integrated Utilization Institute of Cotton ResearchChinese Academy of Agricultural SciencesAnyang 455000China College of Plant Science and Technology Huazhong Agricultural UniversityWuhan 40070China College of Biology and Food Engineering Anyang Institute of TechnologyAnyang 455000China National Nanfan Research Institute(Sanya) Chinese Academy of Agricultural SciencesSanya 572024China School of Agriculture Food and WineUniversity of AdelaideAdelaideSA 5005Australia Sanya Institute Hainan Academy of Agricultural SciencesSanya 572000China Department of Biology East Carolina UniversityGreenvilleNC 27858USA School of Agricultural Sciences Zhengzhou UniversityZhengzhou 450001China

Cotton(Gossypium)stands as a crucial economic crop,serving as the primary source of naturalfiber for the textile ***,the evolutionary mechanisms driving speciation within the Gossypium genus remain *** this investigation,we leveraged 25 Gossypium genomes and introduced four novel assem-blies—***,***,***,and ***(Gklo)—to delve into the speciation history of this ***,we encountered intricate phylogenies potentially stemming from *** complexities are further compounded by incomplete lineage sorting(ILS),a factor likely to have been instrumental in shaping the swift diversification of *** focus subsequently shifted to the rapid radiation episode during a concise period in Gossypium *** a recently diverged lineage comprising ***,Gklo,and ***,we constructed afinely detailed ILS ***,this analysis revealed the non-random distribution of ILS regions across the reference Gklo ***,we identified signs of robust natural selection influencing specific ILS *** variations per-taining to speciation emerged between the closely related sister species Gklo and ***-mately 15.74%of speciation structural variation genes and 12.04%of speciation-associated genes were esti-mated to intersect with ILS *** enrich our understanding of the role of ILS in adaptive radiation,shedding fresh light on the intricate speciation history of the Gossypium genus.

关键词： cotton speciation Gossypium genus incomplete lineage sorting ILS phylogenetic analysis gene tree resolution

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Design of Quasi-planar Ridge SOI Waveguide Resonator for Integrated Optical Gyro

Design of Quasi-planar Ridge SOI Waveguide Resonator for Int...

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中国材料大会2012

作者： kunbo wang Lishuang Feng Zhengfang Dong Laboratory on Inertial Science and Technology Beihang University Key Laboratory of Micro-nano Measurement-Manipulation and Physics (Ministry of Education) Beihang University

ISBN: (纸本)9783037856079

In order to realize the opto-electronic integration of optic gyro, the quasi-planar ridge SOI waveguide resonator is proposed due to its low loss and small bend radius. First, the single mode condition and smallest bend radius were simulated by using the 3-dimension finite difference beam propagation method （3-D BPM）. Then the relationship between the sensitivity of gyro and the resonator characteristics, such as radius and coupling coefficient, was analyzed by applying the model of the integrated optical gyro. Based on these simulations, the ridge height and width of the waveguide were 220 nm and 1.2 μmrespectively and the smallest bend radius was 600μm. It is shown that the theoretical detection limit of the gyro was 0.031 °/s when the resonator diameter was 5cm and the coupler’s splitting ratio was 46.7:53.3. This gyro system is suitable for tactical and civil applications.

关键词： Integrated optics Waveguide Resonator Gyroscope SOI Quasi-planar

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Genome wide identification and characterization of light-harvesting Chloro a/b binding(LHC)genes reveals their potential role in enhancing drought tolerance in Gossypium hirsutum

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Journal of Cotton Research 2021年第2期4卷 147-159页

作者： MEHARI Teame Gereziher XU Yanchao MAGwangA Richard Odongo UMER Muhammad Jawad KIRUNGU Joy Nyangasi CAI Xiaoyan HOU Yuqing wang Yuhong YU Shuxun wang kunbo ZHOU Zhongli LIU Fang State Key Laboratory of Cotton Biology/Institute of Cotton Research Chinese Academy of Agricultural Sciences(ICRCAAS)Anyang455000HenanChina Ethiopian Institute of Agricultural Research Mekhoni Agricultural Research CenterP.O.Box 47MekhoniTigrayEthiopia School of Biological and Physical Sciences(SBPS) Main CampusJaramogi Oginga Odinga University of Science and Technology(JOOUST)Main CampusP.O.Box 210-40601BondoKenya School of Agricultural Sciences Zhengzhou UniversityZhengzhouHenan450001China

Background: Cotton is an important commercial crop for being a valuable source of natural *** production has undergone a sharp decline because of abiotic stresses,*** is one of the major abiotic stress causing significant yield losses in ***,plants have evolved self-defense mechanisms to cope abiotic factors like drought,salt,cold,*** evolution of stress responsive transcription factors such as the trihelix,a nodule-inception-like protein(NLP),and the late embryogenesis abundant proteins have shown positive response in the resistance improvement to several abiotic ***: Genome wide identification and characterization of the effects of Light-Harvesting Chloro a/b binding(LHC)genes were carried out in cotton under drought stress conditions.A hundred and nine proteins encoded by the LHC genes were found in the cotton genome,with 55,27,and 27 genes found to be distributed in Gossypium hirsutum,***,and ***,*** proteins encoded by the genes were unevenly distributed on various *** Ka/Ks(Non-synonymous substitution rate/Synonymous substitution rate)values were less than one,an indication of negative selection of the gene *** expressions of genes showed that majority of the genes are being highly upregulated in the roots as compared with leaves and stem *** genes were found to be highly expressed in MR-85,a relative drought tolerant ***: The results provide proofs of the possible role of the LHC genes in improving drought stress tolerance,and can be explored by cotton breeders in releasing a more drought tolerant cotton varieties.

关键词： Cotton G hirsutum LHC genes Gene expression Drought tolerance

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Knockdown of 60S ribosomal protein L14‑2 reveals their potential regulatory roles to enhance drought and salt tolerance in cotton

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Journal of Cotton Research 2021年第4期4卷 308-321页

作者： SHIRAKU Margaret Linyerera MAGwangA Richard Odongo CAI Xiaoyan KIRUNGU Joy Nyangasi XU Yanchao MEHARI Teame Gereziher HOU Yuqing wang Yuhong wang kunbo PENG Renhai ZHOU Zhongli LIU Fang State Key Laboratory of Cotton Biology/Institute of Cotton Research Chinese Academy of Agricultural Science(ICRCAAS)Anyang 455000HenanChina School of Biological and Physical Sciences(SBPS) Main CampusJaramogi Oginga Odinga University of Science and Technology(JOOUST)Main CampusP.O.Box 210‑40601BondoKenya Anyang Institute of Technology Anyang 455000HenanChina School of Agricultural Sciences Zhengzhou UniversityZhengzhou 450001HenanChina

Background:Cotton is a valuable economic crop and the main significant source of natural fiber for textile industries *** effects of drought and salt stress pose a challenge to strong fiber and large-scale production due to the ever-changing climatic ***,plants have evolved a number of survival strategies,among them is the induction of various stress-responsive genes such as the ribosomal protein large(RPL)*** RPL gene families encode critical proteins,which alleviate the effects of drought and salt stress in *** this study,comprehensive and functional analysis of the cotton RPL genes was carried out under drought and salt ***:Based on the genome-wide evaluation,26,8,and 5 proteins containing the RPL14B domain were identified in Gossypium hirsutum,***,and ***,***,through bioinformatics analysis,key cis-regulatory elements related to RPL14B genes were *** Myb binding sites(MBS),abscisic acid-responsive element(ABRE),CAAT-box,TATA box,TGACG-motif,and CGTCA-motif responsive to methyl jasmonate,as well as the TCA-motif responsive to salicylic acid,were *** analysis revealed a key gene,Gh_D01G0234(RPL14B),with significantly higher induction levels was further evaluated through a reverse genetic *** knockdown of Gh_D01G0234(RPL14B)significantly affected the performance of cotton seedlings under drought/salt stress conditions,as evidenced by a substantial reduction in various morphological and physiological ***,the level of the antioxidant enzyme was significantly reduced in VIGS-plants,while oxidant enzyme levels increased significantly,as demonstrated by the higher malondialdehyde concentration ***:The results revealed the potential role of the RPL14B gene in promoting the induction of antioxidant enzymes,which are key in oxidizing the various *** key pathways need to be investigated and even as we exploit these genes

关键词： Abiotic stress Cotton Ribosomal protein large Transcription factor Virus-induced gene silencing

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Genome-wide identification and analysis of the CNGC gene family in upland cotton under multiple stress conditions

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Journal of Cotton Research 2023年第3期6卷 195-208页

作者： KIRUNGU Joy Nyangasi MAGwangA Richard Odongo SHIRAKU Margaret Linyerera OKUTO Erick CAI Xiaoyan XU Yanchao HOU Yuqing AGONG' Stephen Gaya wang kunbo wang Yuhong ZHOU Zhongli LIU Fang State Key Laboratory of Cotton Biology/Institute of Cotton Research Chinese Academy of Agricultural Science(ICR-CAAS)AnyangHenan 455000China School of Biological PhysicalMathematics and Actuarial Sciences(SBPMAS)Jaramogi Oginga Odinga University of Science and Technology(JOOUST)Bondo210‑40601Kenya School of Agricultural Sciences Zhengzhou UniversityZhengzhouHenan 450001China

Background The cyclic nucleotide-gated channel(CNGC)gene family plays a significant role in the uptake of both essential and toxic cations,and has a role in enhancing tolerance to various forms of abiotic stresses as well as the modulation of the heavy metal toxicity to plant through the absorption of heavy *** A complete genome-wide identification and functional characterization of the cotton CNGC genes was carried out,in which 55,28,and 29 CNGC genes were identified in Gossypium hirsutum,***,and ***,*** protein encoded by the CNGC genes exhibited GRAVY value below zero,indicating their hydrophilic *** genes were unevenly distributed in 19 out of 26 chromosomes,in which the highest density were observed on Ah05,with 8 *** gene coverage was observed among the diploid cotton species,with CNGC genes mapped on all A chromosomes and on 11 out of 13 of D *** majority of CNGC proteins were localized in the endoplasmic reticulum,nucleus,and plasma *** expression analysis revealed the up-regulation of Gh_A01G0520(CNGC4)and Gh_D13G1974(CNGC5)across various forms of abiotic ***,down-regulation of Gh_A01G0520(CNGC4)and Gh_D13G1974(CNGC5)in CNGCs silenced plants caused the significantly reduced ability to tolerate drought and salt *** CNGCs silenced plants were recorded to have significantly low content of antioxidants but relatively higher content of oxidant,including MDA and H_(2)O_(2).Furthermore,SPAD,CMS(cell membrane stability),ELWL(excised leaf water loss),SDW(shoot dry matter weight),and RDW(root dry matter weight)were all lower in CNGCs silenced plants compared with the wild type *** Significant reduction in antioxidant content and negative effects of physiological and morphological characters in CNGCs silenced plants has revealed the novel role of CNGC genes in enhancing cell integrity under abiotic stress *** results provide vital information

关键词： Cyclic nucleotide-gated channel Abiotic stress Differential expression VIGS-plants Chromosome Tetraploid cotton

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Constructing a high-density linkage map for Gossypium hirsutum × Gossypium barbadense and identifying QTLs for lint percentage

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Journal of Integrative Plant Biology 2015年第5期57卷 450-467页

作者： 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 State Key Laboratory of Cotton Biology Key Laboratory of Biological and Genetic Breeding of Cottonthe Ministry of AgricultureInstitute of Cotton Researchthe Chinese Academy of Agricultural Sciences Agricultural College of Jiangxi Agricultural University Academy of Agricultural Sciences of Luohe City of Henan Province College of Bioscience and Biotechnology Hunan Agricultural University College of Agronomy Hunan Agricultural University Agricultural College of Southwest University

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 com-prised 2,292 loci and covered 5115.16 centiMorgan （cM） of the cotton AD genome, with an average marker interval of 2.23 cM. 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 pub-lished 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.

关键词： Cotton (Gossypium spp.) genetic linkage map Gossypiumbarbadense lint percentage simple sequence repeat

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Transcriptional landscape of cotton roots in response to salt stress at single-cell resolution

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Plant Communications 2024年第2期5卷 46-66页

作者： Pengtao Li Qiankun Liu Yangyang Wei Chaozhu Xing Zhongping Xu Fang Ding Yuling Liu Quanwei Lu Nan Hu Tao wang Xiangqian Zhu Shuang Cheng Zhaoguo Li Zilin Zhao Yanfang Li Jiangping Han Xiaoyan Cai Zhongli Zhou kunbo wang Baohong Zhang Fang Liu Shuangxia Jin Renhai Peng College of Biology and Food Engineering Anyang Institute of TechnologyAnyangHenan 455000China State Key Laboratory of Cotton Biology Institute of Cotton ResearchChinese Academy of Agricultural SciencesAnyangHenan 455000China Research Base Anyang Institute of TechnologyState Key Laboratory of Cotton BiologyAnyang 455000HenanChina School of Life Sciences Zhengzhou UniversityZhengzhouHenan 450001China Hubei Hongshan Laboratory National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubeiChina Hubei Key Laboratory of Plant Pathology Huazhong Agricultural UniversityWuhanHubei 430070China Department of Biology East Carolina UniversityGreenvilleNC 27858USA

Increasing soil salinization has led to severe reductions in plant yield and quality,and investigating the mo-lecular mechanism of salt stress response is therefore an urgent *** this study,we systematically analyzed the response of cotton roots to salt stress using single-cell transcriptomics technology;56281 high-quality cells were obtained from 5-day-old lateral root tips of Gossypium arboreum under natural growth conditions and different salt *** cell types with an array of novel marker genes were identified and confirmed by in situ RNA hybridization,and pseudotime analysis of some specific cell types revealed their potential differentiation *** changes in cell numbers under salt stress were observed for outer epidermal and inner endodermal cells,which were significantly enriched in response to stress,amide biosynthetic process,glutathione metabolism,and glycolysis/*** of differentially expressed genes identified in multiple comparisons revealed other functional ag-gregations concentrated on plant-type primary cell wall biogenesis,defense response,phenylpropanoid biosynthesis,and metabolic *** candidate differentially expressed genes encoding transcrip-tion factors or associated with plant hormones also responsive to salt stress were identified,and the func-tion of Ga03G2153,annotated as auxin-responsive GH3.6,was confirmed by virus-induced gene *** GaGH3.6-silenced plants showed a severe stress-susceptible phenotype,and physiological and biochemical measurements indicated that they suffered more significant oxidative *** results suggest that GaGH3.6 might participate in cotton salt tolerance by regulating redox *** thus construct a transcriptional atlas of salt-stressed cotton roots at single-cell resolution,enabling us to explore cellular heterogeneity and differentiation trajectories and providing valuable insights into the mo-lecular mechanisms that underlie plan

关键词： cotton salt stress scRNA-seq root cell types virus-induced gene silencing

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Genetic map construction and functional characterization of genes within the segregation distortion regions(SDRs)in the F_(2:3) populations derived from wild cotton species of the D genome

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Journal of Cotton Research 2020年第4期3卷 278-296页

作者： KIRUNGU Joy Nyangasi MAGwangA Richard Odongo SHIRAKU Margaret Linyerera LU Pu MEHARI Teame Gereziher XU Yuanchao HOU Yuqing AGONG Stephen Gaya ZHOU Yun CAI Xiaoyan ZHOU Zhongli wang kunbo LIU Fang State Key Laboratory of Cotton Biology/Institute of Cotton Research Chinese Academy of Agricultural ScienceAnyang 455000HenanChina School of Biological PhysicalMathematics and Actuarial Sciences(SBPMAS)Jaramogi Oginga Odinga University of Science and Technology(JOOUST)210-40601BondoKenya School of Life Science Henan University/State Key Laboratory of Cotton Biology/Henan Key Laboratory of Plant Stress BiologyKeifang 475004HenanChina School of Agricultural Sciences Zhengzhou UniversityZhengzhou 450001HenanChina.

Background:Segregation distortion(SD)is a common phenomenon among stable or segregating populations,and the principle behind it still puzzles many *** F2:3 progenies developed from the wild cotton species of the D genomes were used to investigate the possible plant transcription factors within the segregation distortion regions(SDRs).A consensus map was developed between two maps from the four D genomes,map A derived from F2:3 progenies of Gossypium klotzschianum and *** while Map B from *** and *** F2:3 *** each map,188 individual plants were ***:The consensus linkage map had 1492 markers across the 13 linkage groups with a map size of 1467.445 cM and an average marker distance of 1.0370 *** D502 had the highest percentage of SD with 58.6%,followed by Chromosome D507 with 47.9%.Six thousand and thirty-eight genes were mined within the SDRs on chromosome D502 and D507 of the consensus *** chromosome D502 and D507,2308 and 3730 genes were mined,respectively,and were found to belong to 1117 gourp out of which 622 groups were common across the two ***,genes within the top 9 groups related to plant resistance genes(R genes),whereas 188 genes encoding protein kinase domain(PF00069)comprised the largest *** analysis of the dominant gene group revealed that 287 miRNAs were found to target various genes,such as the gra-miR398,gramiR5207,miR164a,miR164b,miR164c among others,which have been found to target top-ranked stress-responsive transcription factors such as NAC ***,some of the stress-responsive cis-regulatory elements were also ***,RNA profiling of the genes from the dominant family showed that higher numbers of genes were highly upregulated under salt and osmotic stress conditions,and also they were highly expressed at different stages of fiber ***:The results indicated the critical role of the SDRs in the evolution of the k

关键词： Genetic map Segregation distortion region Cis-regulatory elements Genes miRNA

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基于微机电系统波纹振膜的高灵敏度光纤传声器

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光学学报 2021年第18期41卷 27-34页

作者：王坤博周瑜刘超魏晓村中国电子科技集团公司第三研究所北京100015

提出了一种基于微机电系统(MEMS)波纹振膜的高灵敏度光纤传声器,通过波纹振膜研制法布里-珀罗干涉腔,可进一步提升光纤传声器的灵敏度。在理论分析中,应用有限元分析软件COMSOL对振膜进行建模,仿真分析了波纹宽度、波纹深度和波纹间距... 详细信息

提出了一种基于微机电系统(MEMS)波纹振膜的高灵敏度光纤传声器,通过波纹振膜研制法布里-珀罗干涉腔,可进一步提升光纤传声器的灵敏度。在理论分析中,应用有限元分析软件COMSOL对振膜进行建模,仿真分析了波纹宽度、波纹深度和波纹间距等参数对振膜灵敏度和工作频率的影响。实验结果表明,基于MEMS波纹振膜研制的光纤传声器样机灵敏度为630 mV/Pa,频率响应范围为50 Hz~8 kHz;且该光纤传声器的结构简单,能很好地应用于远场语音拾取等领域。

关键词：光纤光学传声器波纹振膜远场语音拾取

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