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BIOCELL 2022年第5期46卷 1347-1356页

作者： QUANWEI LU YUZHEN SHI RUILI CHEN XIANGHUI XIAO pengTAO LI JUWU GONG renhai peng YOULU YUAN College of Biotechnology and Food Engineering Anyang Institute of TechnologyAnyangChina State Key Laboratory of Cotton Biology Institute of Cotton ResearchChinese Academy of Agricultural SciencesAnyangChina Engineering Research Centre of Cotton Ministry of Education/College of AgricultureXinjiang Agricultural UniversityUrumqiChina

Aluminum-activated malate transporters(ALMT)are widely involved in plant growth and metabolic processes,including adaptation to acid soils,guard cell regulation,anion homeostasis,and seed *** ALMT genes have been identified in Arabidopsis,wheat,barley,and Lotus japonicus,little is known about its presence in Gossypium hirsutum *** this study,ALMT gene recognition in diploid and tetraploid cotton were done using bioinformatics analysis that examined correlation between homology and *** regulated ALMT genetic profile in *** was examined,using RNA sequencing and qRT-PCR,during six fiber developmental time-points,namely 5 d,7 d,10 d,15 d,20 d,and 25 *** detected 36 ALMT genes in ***,which were subsequently annotated and divided into seven *** these ALMT genes,34 had uneven distribution across 14/26 *** domains and gene structure analysis indicated that ALMT genes were highly conserved and composed of exons and *** GhALMT gene expression profile at different DPA(days post anthesis)in different varieties of *** is indicative of a crucial role of ALMT genes in fiber development in *** study provides basis for advancements in the cloning and functional enhancements of ALMT genes in enhancing fiber development and augmenting high quality crop production.

关键词： homeostasis analysis characterization

Construction of a bacterial artificial chromosome library for Gossypium herbaceum var. africanum

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Chinese Science Bulletin 2013年第26期58卷 3199-3201页

作者： GAO HaiYan WANG XingFen LIU Fang peng renhai ZHANG Yan CHENG Hua MA ZhiYing WANG KunBo State Key Laboratory of Cotton Biology/Cotton Research Institute Chinese Academy of Agricultural Sciences North China Key Laboratory for Crop Germplasm Resources of Education Ministry Key Laboratory for Crop Germplasm Resources of Hebei Province Agricultural University of Hebei Anyang Institute of Technology

Gossypium herbaceum var. africanum is the only wild cotton species within the cultivated diploid G. herbaceum. As the A sub-genome donor of tetraploid cotton, it is characterized by its resistance to insects, diseases, and other adversities. We have constructed the first bacterial artificial chromosome library (BAC) for G. herbaceum var. africanum. With high quality and broad coverage, this library includes 75000 clones, with an average insert size of about 115 kb and fewer than 4% empty clones. Our library is approximately five-fold the size of the A-genome (1667 Mb) and it provides 99.3% probability for isolating genes of interest or their sequences. Using nine SSR markers that are located on five different chromosomes and linked with resistance to Verticillium wilt, seven of nine could amplify the 40 superpools and got 1-14 hits. Because of its moderate wide coverage and relative large insert size, this library will be an important genomic resource for classifying and analyzing the evolution of cotton species, as well as for isolating disease-resistance genes and control elements.

关键词：细菌人工染色体文库草棉变种非洲 A基因组棉花品种 SSR标记基因序列

Single‑cell RNA sequencing opens a new era for cotton genomic research and gene functional analysis

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Journal of Cotton Research 2024年第2期7卷 215-218页

作者： PAN Xiaoping peng renhai ZHANG Baohong Department of Biology East Carolina UniversityGreenvilleNC 27858USA College of Biology and Food Engineering Anyang Institute of TechnologyAnyangHenan 455000China

Single-cell RNA sequencing(scRNA-seq)is one of the most advanced sequencing technologies for studying transcriptome landscape at the single-cell *** provides numerous advantages over traditional *** it was first used to profile single-cell transcriptome in plants in 2019,it has been extensively employed to perform different research in ***,scRNA-seq was also quickly adopted by the cotton research community to solve lots of scientific questions which have been never *** this comment,we highlighted the significant progress in employing scRNA-seq to cotton genetic and genomic study and its future potential applications.

关键词： Cotton Single-cell RNA sequencing Transcriptome

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

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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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

荧光原位杂交技术的发展及其在植物基因组研究中的应用

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分子植物育种 2018年第17期16卷 5696-5703页

作者：刘玉玲刘林杰彭仁海安阳工学院安阳455000

荧光原位杂交(FISH)技术能够实现DNA序列在染色体上的物理定位,已经广泛应用于植物基因组研究中。本综述基于FISH技术分辨率和灵敏度的提高,从探针类型和靶标染色体类型两个方面总结了FISH技术的发展进程及不同FISH技术的应用优势和不... 详细信息

荧光原位杂交(FISH)技术能够实现DNA序列在染色体上的物理定位,已经广泛应用于植物基因组研究中。本综述基于FISH技术分辨率和灵敏度的提高,从探针类型和靶标染色体类型两个方面总结了FISH技术的发展进程及不同FISH技术的应用优势和不足之处。在技术应用方面,总结了FISH技术在植物染色体识别、核型分析、系统进化及亲缘关系分析、异源染色质及转基因鉴定、基因定位和物理图谱构建等研究中的应用进展,并对其应用前景进行了展望,以期为植物基因组研究提供更多的研究思路。

关键词：荧光原位杂交(FISH)技术染色体识别核型分析物理图谱

陆地棉LTR反转录转座子的数量分布与功能分析

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河南师范大学学报（自然科学版） 2017年第6期45卷 72-78页

作者：刘震卢全伟张国强彭仁海安阳工学院生物与食品工程学院河南安阳455000 中国农业科学院棉花研究所河南安阳455000

LTR(Long terminal repeat)反转录转座子是真核生物基因组中普遍存在的一类遗传因子,它们以RNA为媒介在基因组中不断自我复制.在高等植物中,LTR反转录转座子是基因组的重要成分之一.本研究通过多种方法挖掘并注释了陆地棉基因组中的LTR... 详细信息

LTR(Long terminal repeat)反转录转座子是真核生物基因组中普遍存在的一类遗传因子,它们以RNA为媒介在基因组中不断自我复制.在高等植物中,LTR反转录转座子是基因组的重要成分之一.本研究通过多种方法挖掘并注释了陆地棉基因组中的LTR反转录转座子,结果表明陆地棉基因组LTR反转录转座子的Gypsy超家族与基因的分布呈近似的反比关系,而Copia超家族在各染色体的起始端有较多的分布.通过皮尔森相关系数发现陆地棉LTR反转录转座子的拷贝数与染色体大小之间有强相关性.在LTR反转录转座子上游和下游分布的基因具有类似的富集特征,其分子功能主要集中在结合和催化活性等方面.本研究结果加深了对陆地棉LTR反转录转座子的认识,为深入研究棉花基因组提供了重要数据支撑.

关键词：陆地棉 LTR反转录转座子分布功能

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瑟伯氏棉着丝粒重复序列鉴定

河南师范大学学报（自然科学版） 2019年第6期47卷 103-109页

作者：陈晔刘玉玲韦洋洋杨太有彭仁海河南师范大学生命科学学院河南新乡453007 安阳工学院生物与食品工程学院河南安阳455000

棉花着丝粒染色质主要由重复序列组成,包括高度重复的着丝粒反转录转座子和卫星重复序列等,但其着丝粒重复序列进化机制尚不清楚.为了深入了解着丝粒重复列的演化,利用染色质免疫共沉淀(ChIP)和中期染色体荧光原位杂交(FISH)技术对瑟伯... 详细信息

棉花着丝粒染色质主要由重复序列组成,包括高度重复的着丝粒反转录转座子和卫星重复序列等,但其着丝粒重复序列进化机制尚不清楚.为了深入了解着丝粒重复列的演化,利用染色质免疫共沉淀(ChIP)和中期染色体荧光原位杂交(FISH)技术对瑟伯氏棉(Gossypium thurberi,D 1)着丝粒序列进行了分析.结果表明,相应的ChIP-DNA序列属于着丝粒功能区域,发现了10个较为富集的着丝粒重复序列.中期染色体FISH定位发现,CL179和CL234在四倍体陆地棉中的A和D染色体组中都有杂交信号,在二倍体A组亚洲棉中没有检测到信号,由此可推断在形成四倍体后一些着丝粒特异的重复序列进行了扩增.重复序列CL95在瑟伯氏棉以及陆地棉部分染色体的着丝粒区域出现杂交信号,而在二倍体D组雷蒙德氏棉和A组亚洲棉的着丝粒区域并没有出现信号,可认为该序列是瑟伯氏棉特异的且在四倍体形成后被保留了下来.通过对瑟伯氏棉着丝粒序列及演化的分析能够为揭示棉属植物着丝粒重复序列及染色体组的演化关系提供重要的理论依据.

关键词：瑟伯氏棉着丝粒重复序列染色质免疫沉淀荧光原位杂交

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不同小麦新品系萌发期抗旱性的筛选与鉴定

分子植物育种 2018年第21期16卷 7138-7147页

作者：张树林刘玉玲田丽宋卓恒郭瑞林彭仁海安阳工学院生物与食品工程学院安阳455000

为筛选和鉴定出抗旱小麦新品系,并研究不同小麦品系(种)在萌发期对于干旱胁迫下做出的响应,望能为小麦抗旱品系(种)的筛选研究提供更多的依据,有助于了解小麦抗旱机制。本研究选取52个小麦新品系为供试材料,并用周麦18作为对照;采用人... 详细信息

为筛选和鉴定出抗旱小麦新品系,并研究不同小麦品系(种)在萌发期对于干旱胁迫下做出的响应,望能为小麦抗旱品系(种)的筛选研究提供更多的依据,有助于了解小麦抗旱机制。本研究选取52个小麦新品系为供试材料,并用周麦18作为对照;采用人工气候箱培养,以200 g/L PEG-6000水溶液模拟干旱胁迫环境,萌发8 d后测定发芽势、发芽率、根长等8个萌发性状;依据主成分分析的综合因子得分函数和聚类分析对萌发期小麦新品系的抗旱性进行综合评定。结果发现52份小麦品系按萌发期抗旱性的强弱分为3大类:AG1218和AG1513为抗旱性极强的品系;AG1301、AG1306、AG1312等47个品系为干旱敏感品系;AG1271、AG1322、AG0822和蓝麦4个品系为高度干旱敏感品系。本研究发现的AG1218和AG1513为抗旱性极强的品系,可以作为新品种或者育种材料进行应用和推广;主成分结果表明小麦品系的芽长、发芽势、根鲜重等萌发指标可用于萌发期抗旱性鉴定的筛选依据。

关键词：小麦新品系萌发抗旱性主成分分析聚类分析