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Apical meristem transcriptome analysis identifies a role for the blue light receptor gene GhFKF1 in cotton architecture development

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The Crop Journal 2024年第4期12卷 1126-1136页

作者： Xiao Li yuanlong Wu Zhenping Liu Hengling Wei Hantao Wang shuxun yu National Key Laboratory of Crop Genetic Improvement Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhan 430070HubeiChina State Key Laboratory of Cotton Biology Institute of Cotton Research of the Chinese Academy of Agricultural SciencesAnyang 455000HenanChina State Key Laboratory of Subtropical Silviculture Zhejiang A&F UniversityLin’an 311300ZhejiangChina Xianghu Laboratory Hangzhou 311200ZhejiangChina

Cotton architecture is determined by the differentiation fate transition of axillary meristem(AM),and influences cotton yield and the efficiency of mechanized *** observed that the initiation of flowering primordium was earlier in early-maturing than that in late-maturing cultivars during the differentiation and development of *** RNA-Seq and expression level analyses showed that genes FLAVIN BINDING,KELCH REPEAT,F-BOX1(GhFKF1),and GIGANTEA(GhGI)were in response to circadian rhythms,and involved in the regulation of cotton *** gene structure,predicted protein structure,and motif content analyses showed that in Arabidopsis,cotton,rapseed,and soybean,proteins GhFKF1 and GhGI were functionally conserved and share evolutionary *** to the wild type,in GhFKF1 mutants that were created by the CRISPR/Cas9 system,the initiation of branch primordium was ***,the knocking out of GhGI increased the number of AM differentiating into flower primordium,and there were much more lateral branch differentiation and ***,we investigated that proteins GhFKF1 and GhGI can interact with each *** results suggest that GhFKF1 and GhGI are key regulators of cotton architecture development,and may collaborate to regulate the differentiation fate transition of AM,ultimately influencing plant *** describe a strategy for using the CRISPR/Cas9 system to increase cotton adaptation and productivity by optimizing plant architecture.

关键词： Cotton Axillary meristem GhFKF1 GhGI Plant architecture

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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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Identification of genes associated with cotyledon senescence in upland cotton

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Chinese Science Bulletin 2006年第9期51卷 1085-1094页

作者： SHEN Fafu yu shuxun XlE Qingen HAN Xiulan FAN Shuli Key Laboratory of Shangdong Province for Crop Biology College of Agronomy Shandong Agricultural University Taian 271018 China Cotton Research Institute Chinese Agricultural Academy of Sciences Anyang 455112 China

In order to unravel the biochemical pathways and understand the molecular mechanisms involved in leaf senescence, suppression subtractive hybridization (SSH) was used to generate a cDNA library enriched for transcripts differentially expressed in developmental senescence cotyledons of upland cotton. After differential screening by membrane- based hybridization and subsequent confirmation by reverse Northern blot analysis, selected 678 clones were sequenced and analyzed. Sequencing of these cDNA fragments reveals that 216 of expressed se- quence tags (ESTs) represented unique genes. Of these 216 cDNAs, 151 clones (69.9%) show signifi- cant homologies to previously known genes, while the remaining 65 do not match any known sequences. 151 unique ESTs are assigned to twelve different categories based on their putative functions gener- ated by BLAST analysis. These SAG-encoded pro- teins are likely to participate in macromolecule deg- radation, nutrient recycling, detoxification of oxidative metabolites, and signaling and regulatory events. The expression pattern of selection of genes was confirmed using northern hybridization. Northern hybridization confirmed several distinct patterns, from expression at a very early stage to the terminal phase of the senescence syndrome. Clones encod- ing proteases and proteins involved in macromole- cule degradation and gluconeogenesis, as well as stress-related genes, are up regulated in senescence cotyledons.

关键词：棉花衰老 EST 序列分析育种基因工程

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Molecular Cloning and Function Analysis of Two SQUAMOSA-Like MADS-Box Genes From Gossypium hirsutum L.

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Journal of Integrative Plant Biology 2013年第7期55卷 597-607页

作者： Wenxiang Zhang Shuli Fan Chaoyou Pang Hengling Wei Jianhui Ma Meizhen Song shuxun yu State Key Laboratory of Cotton Biology Institute of Cotton Research of Chinese Academy of Agriculture Sciences College of Agronomy Northwest A & F University

The MADS-box genes encode a large family of transcription factors having diverse roles in plant development. The SQUAMOSA （SQUA）/APETALA1 （AP1）/FRUITFULL （FUL） subfamily genes are essential regulators of floral transition and floral organ identity. Here we cloned two MADS-box genes, GhMADS22 and GhMADS23, belonging to the SQUA/AP1/FUL subgroup from Gossypium hirsutum L. Phylogenetic analysis and sequence alignment showed that GhMAD$22 and GhMADS23 belonged to the euFUL and euAP1 subclades, respectively. The two genes both had eight exons and seven introns from the start codon to the stop codon according to the alignment between the obtained cDNA sequence and the Gossypium raimondii L. genome sequence. Expression profile analysis showed that GhMADS22 and GhMADS23 were highly expressed in developing shoot apices, bracts, and sepals. Gibberellic acid promoted GhMADS22 and GhMADS23 expression in the shoot apex. Transgenic Arabidopsis lines overexpressing 35S：：GhMADS22 had abnormal flowers and bolted earlier than wild type under long-day conditions （16 h light/8 h dark）. Moreover, GhMADS22 over- expression delayed floral organ senescence and abscission and it could also respond to abscisic acid. In summary, GhMADS22 may have functions in promoting flowering, improving resistance and delaying senescence for cotton and thus it may be a candidate target for promoting early-maturation in cotton breeding.

关键词： Arabidopsis transformation flowering time MADS-box SQUAMOSA-like overexpression.

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High-density Linkage Map of Cultivated Allotetraploid Cotton Based on SSR, TRAP, SRAP and AFLP Markers

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Journal of Integrative Plant Biology 2007年第5期49卷 716-724页

作者： Jiwen yu shuxun yu Cairui Lu Wu Wang Shuli Fan Meizhen Song Zhongxu Lin Xianlong Zhang Jinfa Zhang National Key Laboratory of Crop Genetic Improvement Huazhong Agricultural University Wuhan 430070 China Key Laboratory for Cotton Genetic Improvement Ministry of Agriculture Anyang 455004 China China Cotton Research Institute Chinese Academy of Agricultural Science Anyang 455004 China Department of Plant and Environmental Sciences New Mexico State University Las Cruces NM 88003 USA

A high-density linkage map was constructed for an F2 population derived from an Interspecific cross of cultivated allotetraploid species between Gossypium hirsutum L. and G. barbadense L. A total of 186 F2 individuals from the Interspecific cross of ＂CRI 36 × Hal 7124＂ were genotyped at I 252 polymorphic loci Including a novel marker system, target region amplification polymorphism （TRAP）. The map consists of 1 097 markers, including 697 simple se- quence repeats （SSRs）, 171 TRAPs, 129 sequence-related amplified polymorphisms, 98 amplified fragment length polymorphisms, and two morphological markers, and spanned 4 536.7 cM with an average genetic distance of 4.1 cM per marker. Using 45 duplicated SSR loci among chromosomes, 11 of the 13 pairs of homologous chromosomes were Identified In tetraploid cotton. This map will provide an essential resource for high resolution mapping of quantitative trait loci and molecular breeding in cotton.

关键词： cotton linkage map target region amplification polymorphism

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A comparative analysis of small RNAs between two Upland cotton backcross inbred lines with different fiber length: Expression and distribution

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The Crop Journal 2019年第2期7卷 198-208页

作者： Guoyuan Liu Man Wu Wenfeng Pei Xihua Li Nuohan Wang Jianjiang Ma Xinshan Zang shuxun yu Jinfa Zhang Jiwen yu State Key Laboratory of Cotton Biology Cotton Institute of the Chinese Academy of Agricultural Sciences Key Laboratory of Cotton Genetic Improvement Ministry of Agriculture Department of Plant and Environmental Sciences New Mexico State University

The cotton fiber is the most important raw material for the textile industry and an ideal model system for studying cell elongation. However, the genetic variation of fiber elongation in relation to miRNA is poorly understood. A high-throughput comparative RNA-seq of two lines differing in fiber length(FL) from a backcross inbred line(BIL)population of G. hirsutum × G. barbadense revealed differentially expressed(DE) miRNAs and their targets in rapidly elongating fibers. A real-time quantitative PCR analysis was further performed to validate the results. A total of 463(including 47 DE) miRNAs were identified,and seven DE miRNAs were co-localized with seven FL quantitative trait loci(QTL)identified in the G. hirsutum × G. barbadense population. Of 82(including 21 DE) targets identified, nine(including one DE) were also co-localized with the seven FL QTL. The relationship between the allopolyploid and its diploid ancestral species with respect to miRNAs and their targets was also characterized. These results will facilitate the understanding of the molecular genetic mechanism of fiber elongation with regards to miRNAs in cotton.

关键词： Allopolyploid Gossypium Fiber elongation miRNA QTL hotspots

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Identification and Profiling of Known and Novel Fiber MicroRNAs during the Secondary Wall Thickening Stage in Cotton(Gossypium hirsutum) via High-Throughput Sequencing

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Journal of Genetics and Genomics 2014年第10期41卷 553-556页

作者： Dingwei yua Yanmei Wang Wei Xue Shuli Fan shuxun yu Jin-yuan Liu Laboratory of Plant Molecular Biology Center for Plant Biology School of Life Sciences Tsinghua University State Key Laboratory of Cotton Biology Institute of Cotton Research Chinese Academy of Agricultural Sciences

Upland cotton （Gossypium hirsutum L.） is an allotetraploid species originated from interspecific hybridization between AA-genome diploid （G. arboretum） and DD-genome diploid （G. raimondii）（Wendel et al., 1992）. Cotton fibers are single-celled trichomes that emerge from the ovule epidermal cells. Indexed by the number of days post-anthesis （dpa）, fiber morphogenesis includes four distinct but overlapping steps： initiation （0-3 dpa）, elongation （3-20 dpa）, secondary cell wall thickening （15-45 dpa） and maturation （40-60 dpa）（Yang et al., 2008, Du et al., 2013）. The efficiency and duration of each morphogenesis stage is important to the quality attributes of the mature fiber. Cell elongation is critical for fiber length, whereas secondary cell wall thickening is important for fiber fineness and strength （Meinert and Delmer, 1977）.

关键词： SWT Gossypium hirsutum via High-Throughput Sequencing Identification and Profiling of Known and Novel Fiber MicroRNAs during the Secondary Wall Thickening Stage in Cotton RNA

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Selection and Characterization of a Novel Photoperiod-Sensitive Male Sterile Line in Upland Cotton

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Journal of Integrative Plant Biology 2013年第7期55卷 608-618页

作者： Jianhui Ma Hengling Wei Ji Liu Meizhen Song Chaoyou Pang Long Wang Wenxiang Zhang Shuli Fan shuxun yu State Key Laboratory of Cotton Biology the Institute of Cotton Researchthe Chinese Academy of Agricultural Sciences College of Life Sciences Henan Normal University College of Agronomy Northwest A & F University

Upland cotton （Gossypium hirsutum L.） shows strong heterosis. However, heterosis is not widely utilized owing to the high cost of hybrid seed production. Creation of a photoperiod-sensitive genetic male sterile line could substantially reduce the cost of hybrid seed production in upland cotton. Such a mutant with virescent marker was found by space mutation in near-earth orbit and its traits had been stable after 4 years of selection in Anyang and Sanya, China. This mutant was fertile with an 11-12.5 h photoperiod when the temperature was higher than 21.5 ℃ and was sterile with a 13-14.5 h photoperiod. Genetic analysis indicated that both traits were controlled by a single recessive gene or two closely linked genes. Also, the cytological observations and transcriptome profiling analysis showed that the degradation of pollen grain cytoplasm should be the primary reason why the mutant line were male sterile under long-day conditions.

关键词： Photoperiod-sensitive genetic male sterile sterility mechanism upland cotton virescent marker.

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A targeted QTL analysis for fiber length using a genetic population between two introgressed backcrossed inbred lines in upland cotton(Gossypium hirsutum)

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The Crop Journal 2019年第3期7卷 273-282页

作者： Guoyuan Liua Wenfeng Pei Dan Li Jianjiang Ma yupeng Cui Nuohan Wang Jikun Song Man Wu Libei Li Xinshan Zang shuxun yu Jinfa Zhang Jiwen yu State Key Laboratory of Cotton Biology Cotton Institute of the Chinese Academy of Agricultural SciencesKey Laboratory of Cotton Genetic ImprovementMinistry of AgricultureAnyang 455000HenanChina Xinjiang Research Base State Key Laboratory of Cotton BiologyXinjiang Agricultural UniversityUrumqi 830001XinjiangChina Department of Plant and Environmental Sciences New Mexico State UniversityLas CrucesNM 88003USA

Cotton fiber is the most important natural raw material for the textile industry, and fiber length(FL) is one of the most important traits in *** trait locus(QTL)mapping based on high-density genetic maps is an efficient approach to identify genetic regions for *** our study, two backcrossed inbred lines(BILs) were chosen as parents to construct a high-density genetic map in F2 which was used to fine map FL QTL in F2:3 *** genetic map had a total size of 3462.8 cM, containing 9182 singlenucleotide polymorphisms(SNPs) based on *** FL related stable QTL were identified on two chromosomes(qFL-A08–1 on A08 and qFL-D03–1 on D03),and qFL-A08–1 was confirmed by a *** previously obtained RNA-seq data for the two BILs and qRT-PCR analysis, two candidate genes annotated as cytochrome b5(CB5, Gh_A08 G1729) and microtubule end-binding 1 C(EB1C, Gh_D03 G0232) that may regulate FL during the fiber elongation stage were *** addition, nine recombination hotspots in this population were *** results of this study will provide an important foundation for further studies on the molecular and genetic regulation of fiber elongation.

关键词： Gossypium Single-nucleotide polymorphism Fiber length Quantitative trait locus

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A new approach to dissecting complex traits by combining quantitative trait transcript (QTT) mapping and diallel cross analysis

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Chinese Science Bulletin 2012年第21期57卷 2695-2700页

作者： YANG DaiGang YE ChengYin MA XiongFeng ZHU ZhiHong ZHOU XiaoJian WANG HaiFeng MENG QingQin PEI Xiaoyu yu shuxun ZHU Jun Cotton Research Institute Chinese Academy of Agricultural SciencesState Key Laboratory of Cotton BiologyAnyang 455000China Department of Agronomy Zhejiang UniversityHangzhou 310058China

A promising way to uncover the genetic architectures underlying complex traits may lie in the ability to recognize the genetic variants and expression transcripts that are responsible for the traits' ***,statistical methods capable of investigating the association between the inheritance of a quantitative trait and expression transcripts are still *** this study,we described a two-step approach that we developed to evaluate the contribution of expression transcripts to the inheritance of a complex ***,a mixed linear model approach was applied to detect significant trait-associated differentially expressed ***,conditional analysis were used to predict the contribution of the differentially expressed genes to a target *** cross data of cotton was used to test the application of the *** proposed that the detected differentially expressed transcripts with a strong impact on the target trait could be used as intermediates for screening lines to improve the traits in plant and animal breeding *** can benefit the discovery of the genetic mechanisms underlying complex traits.

关键词：双列杂交分析数量性状成绩差异表达基因映射解剖混合线性模型遗传变异

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