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| 1 | Expression patterns and functional divergence of homologous genes accompanied by polyploidization in cotton(Gossypium hirsutum L.)显示文摘Naturally allotetraploid cotton has been widely used as an ideal model to investigate gene expression remodeling as a consequence of polyploidization.However,the global gene pattern variation during early fiber development was unknown.In this study,through RNA-seq technology,we comprehensively investigated the expression patterns of homologous genes between allotetraploid cotton(G.hirsutum)and its diploid progenitors(G.arboreum and G.raimondii)at the fiber early development stage.In tetraploid cotton,genes showed expression level dominance(ELD)bias toward the A genome.This phenomenon was explained by the up-/downregulation of the homologs from the nondominant progenitor(D genome).Gene ontology(GO)enrichment results indicated that the ELD-A genes might be a prominent cause responsible for fiber property change through regulating the fatty acid biosynthesis/metabolism and microtubule procession,and the ELD-D genes might be involved in transcription regulation and stress inducement.In addition,the number and proportion of completely A-and D-subfunctionalized gene were similar at different fiber development stages.However,for neofunctionalization,the number and proportion of reactivated D-derived genes were greater than those of A at 3 and 5 DPA.Eventually,we found that some homologous genes belonging to several specific pathways might create novel asymmetric transcripts between two subgenomes during polyploidization and domestication process,further making the fiber property meet the human demands.Our study identified determinate pathways and their involved genes between allotetraploid cotton and their progenitors at early fiber development stages,providing new insights into the mechanism of cotton fiber evolution. | Zhen Peng Hua Cheng Gaofei Sun Zhaoe Pan Xiao Wang Xiaoli Geng Shoupu He Xiongming Du | 2020 | Science China(Life Sciences)2020，63，10： | 2 |
| 2 | Comparative effect of allopolyploidy on transposable element composition and gene expression between Gossypium hirsutum and its two diploid progenitors显示文摘An allopolyploidization event formed allotetraploid Gossypium species from an A-genome diploid species and a D-genome diploid species. To explore the responses of transposable elements(TEs) to allopolyploidy, we assembled parallel TE datasets from G. hirsutum, G. arboreum and G. raimondii and analyzed the TE types and the effects of TEs on orthologous gene expression in the three Gossypium genomes.Gypsy was the most abundant TE type and most TEs were located $500 bp from genes in all three genomes. In G. hirsutum, 35.6% of genes harbored TE insertions, whereas insertions were more frequent in G. arboreum and G. raimondii. G. hirsutum had the highest proportion of uniquely matching 24-nt small interfering RNAs(siRNAs) that targeted TEs. TEs,particularly those targeted by 24-nt siRNAs, were associated with reduced gene expression, but the effect of TEs on orthologous gene expression varied substantially among species. Orthologous gene expression levels in G. hirsutum were intermediate between those of G. arboreum and G. raimondii, which did not experience TE expansion or reduction resulting from allopolyploidization. This study underscores the diversity of TEs co-opted by host genes and provides insights into the roles of TEs in regulating gene expression in Gossypium. | Hua Cheng Gaofei Sun Shoupu He Wenfang Gong Zhen Peng Ruiping Wang Zhongxu Lin Xiongming Du | 2019 | Journal of Integrative Plant Biology2019，61，1： | 2 |
| 3 | QTL mapping of agronomic and economic traits for four F_(2)populations of upland cotton显示文摘Background:Upland cotton(Gossypium hirsutum)accounts for more than 90%of the annual world cotton output because of its high yield potential.However,yield and fiber quality traits often show negative correlations.We constructed four F_(2)populations of upland cotton,using two normal lines(4133B and SGK9708)with high yield potential but moderate fiber quality and two introgression lines(Suyuan04–3 and J02–247)with superior fiber quality,and used them to investigate the genetic basis underlying complex traits such as yield and fiber quality in upland cotton.We also phenotyped eight agronomic and economic traits and mapped quantitative trait loci(QTLs).Results:Extensive phenotype variations and transgressive segregation were found across the segregation populations.We constructed four genetic maps of 585.97 centiMorgan(cM),752.45 cM,752.45 cM,and 1163.66 cM,one for each of the four F_(2)populations.Fifty QTLs were identified across the four populations(7 for plant height,27 for fiber quality and 16 for yield).The same QTLs were identified in different populations,including qBW4 and qBW2,which were linked to a common simple sequence repeat(SSR)marker,NAU1255.A QTL cluster containing eight QTLs for six different traits was characterized on linkage group 9 of the 4133B×Suyuan04–3 population.Conclusions:These findings will provide insights into the genetic basis of simultaneous improvement of yield and fiber quality in upland cotton breeding. | LI Hongge PAN Zhaoe HE Shoupu JIA Yinhua GENG Xiaoli CHEN Baojun WANG Liru PANG Baoyin DU Xiongming | 2021 | Journal of Cotton Research2021，4，1： | 2 |
| 4 | A comprehensive overview of cotton genomics,biotechnology and molecular biological studies显示文摘Cotton is an irreplaceable economic crop currently domesticated in the human world for its extremely elongated fiber cells specialized in seed epidermis,which makes it of high research and application value.To date,numerous research on cotton has navigated various aspects,from multi-genome assembly,genome editing,mechanism of fiber development,metabolite biosynthesis,and analysis to genetic breeding.Genomic and 3D genomic studies reveal the origin of cotton species and the spatiotemporal asymmetric chromatin structure in fibers.Mature multiple genome editing systems,such as CRISPR/Cas9,Cas12(Cpf1)and cytidine base editing(CBE),have been widely used in the study of candidate genes affecting fiber development.Based on this,the cotton fiber cell development network has been preliminarily drawn.Among them,the MYB-b HLH-WDR(MBW)transcription factor complex and IAA and BR signaling pathway regulate the initiation;various plant hormones,including ethylene,mediated regulatory network and membrane protein overlap fine-regulate elongation.Multistage transcription factors targeting Ces A 4,7,and 8 specifically dominate the whole process of secondary cell wall thickening.And fluorescently labeled cytoskeletal proteins can observe real-time dynamic changes in fiber development.Furthermore,research on the synthesis of cotton secondary metabolite gossypol,resistance to diseases and insect pests,plant architecture regulation,and seed oil utilization are all conducive to finding more high-quality breeding-related genes and subsequently facilitating the cultivation of better cotton varieties.This review summarizes the paramount research achievements in cotton molecular biology over the last few decades from the above aspects,thereby enabling us to conduct a status review on the current studies of cotton and provide strong theoretical support for the future direction. | Xingpeng Wen Zhiwen Chen Zuoren Yang Maojun Wang Shuangxia Jin Guangda Wang Li Zhang Lingjian Wang Jianying Li Sumbul Saeed Shoupu He Zhi Wang Kun Wang Zhaosheng Kong Fuguang Li Xianlong Zhang Xiaoya Chen Yuxian Zhu | 2023 | Science China(Life Sciences)2023，66，10： | 2 |
| 5 | Identification and expression analysis of Tubulin gene family in upland cotton显示文摘Background:Cott on fibers are single-celled exte nsions of the seed epidermis,a model tissue for studying cytoskeleton.Tubulin genes play a critical role in synthesizing the microtubules(MT)as a core element of the cytoskeleton.However,there is a lack of studies concerning the systematic characterization of the tubulin gene family in cotton.Therefore,the identification and portrayal of G.hirsutum tubulin genes can provide key targets for molecular manipulation in cotton breeding.Result:In this study,we investigated all tubulin genes from different plant species and identified 98 tubulin genes in G.hirsutum.Phylogenetic an a lysis showed that tubulin family genes were classified into three subfamilies.The protein motifs and gene structure ofβ-tubulin genes are more conserved compared withγ-tubulin genes.Most tubulin genes are located at the proximate ends of the chromosomes.Spatiotemporal expression pattern by transcriptome and qRT-PCR analysis revealed that 12α-tubulin andβ-tubulin genes are specifically expressed during different fiber development stages.However,Gh.A03G027200,Gh.D03G 169300,and Gh.A1lG258900 had differential expression patterns at distinct stages of fiber development in varieties JO2508 and ZRI015.Conclusion:In this study,the evol ut io nary an alysis showed that the tubulin genes were divided into three clades.The genetic structures and molecular functions were highly con served in different plants.Three candidate genes,Gh.A03G027200f Gh.D03G169300,and Gh.A11G258900 may play a key role during fiber development complementing fiber length and strength. | CHEN Baojun ZHAO Junjie FU Guoyong PEI Xinxin PAN Zhao'e LI Hongge AHMED Haris HE Shoupu DU Xiongming | 2021 | Journal of Cotton Research2021，4，3： | 1 |
| 6 | GhWDL3 is involved in the formation and development of fiber cell morphology in upland cotton(Gossypium hirsutum L.)显示文摘Background Cotton fiber is a model tissue for studying microtubule-associated proteins(MAPs).The Xklp2(TPX2)proteins that belong to the novel MAPs member mainly participate in the formation and development of microtubule(MT).However,there is a lack of studies concerning the systematic characterization of the TPX2 genes family in cotton.Therefore,the identification and portrayal of G.hirsutum TPX2 genes can provide key targets for molecular manipula-tion in the breeding of cotton fiber improvement.Result In this study,TPX2 family genes were classified into two distinct subclasses TPXLs and MAP genes WAVE DAMP-ENED2-LIKE(WDLs)and quite conservative in quantity.GhWDL3 was significantly up-regulated in 15 days post anthe-sis fibers of ZRI-015(an upland cotton with longer and stronger fiber).GhWDL3 promotes all stem hairs to become straight when overexpressed in Arabidopsis,which may indirectly regulate cotton fiber cell morphology during fiber development.Virus induced gene silencing(VIGS)results showed that GhWDL3 inhibited fiber cell elongation at fiber development periods through regulating the expression of cell wall related genes.Conclusion These results reveal that GhWDL3 regulated cotton fiber cell elongation and provide crucial information for the further investigation in the regulatory mechanisms/networks of cotton fiber length. | CHEN Baojun TIAN Zailong FU Guoyong ZHANG Ai SUN Yaru WANG Jingjing PAN Zhaoe LI Hongge HU Daowu XIA Yingying HE Shoupu DU Xiongming | 2024 | Journal of Cotton Research2024，7，1： | 0 |
| 7 | Genomic insight into the divergence and adaptive potential of a forgotten landrace G.hirsutum L.purpurascens显示文摘Wild progenitors are an excellent source for strengthening the genetic basis and accumulation of desirable variation lost because of directional selection and adaptation in modern cultivars.Here,we re-evaluate a landrace of Gossypium hirsutum,formerly known as Gossypium purpurascens.Our study seeks to understand the genomic structure,variation,and breeding potential of this landrace,providing potential insights into the biogeographic history and genomic changes likely associated with domestication.A core set of accessions,including current varieties,obsolete accessions,G.purpurascens,and other geographical landraces,are subjected to genotyping along with multilocation phenotyping.Population fixation statistics suggests a marked differentiation between G.purpurascens and three other groups,emphasizing the divergent genomic behavior of G.purpurascens.Phylogenetic analysis establishes the primitive nature of G.purpurascens,identifying it as a vital source of functional variation,the inclusion of which in the upland cotton(cultivated G.hirsutum)gene pool may broaden the genetic basis of modern cultivars.Genome-wide association results indicate multiple loci associated with domestication regions corresponding to flowering and fiber quality.Moreover,the conserved nature of G.purpurascens can also provide insights into the evolutionary process of G.hirsutum. | Mian Faisal Nazir Shoupu He Haris Ahmed Zareen Sarfraz Yinhua Jia Hongge Li Gaofei Sun Muhammad Shahid Iqbal Zhaoe Pan Xiongming Du | 2021 | Journal of Genetics and Genomics2021，48，6： | 0 |
| 8 | A genome-wide association study of lateral root number for Asian cotton(Gossypium arboreum L.)显示文摘Background:The lateral root is one of the most important organs that constitute the root architecture system in plants.It can directly affect the contact area between plants and soil and plays an important role in plant structural support and nutrient absorption.Optimizing root architecture systems can greatly increase crop yields.This study was designed to identify the molecular markers and candidate genes associated with lateral root development in cotton and to evaluate correlations with yield and disease traits.Result:The number of lateral roots for 14-day old seedlings was recorded for 215 Gossypium arboreum accessions.A correlation analysis showed that the number of lateral roots positively correlates with the sympodial branch node and seed index traits,but negatively correlates with lint percentage.A Genome-wide association study(GWAS)identified 18 significant SNPs with 19 candidate genes associated with the lateral root number.Expression analysis identified three genes(FLA 12,WRKY29,and RBOHA)associated with lateral root development.Conclusion:GWAS an alysis identified key SNPs and candidate gen esfor lateral root number,a nd gen es of FLA 12,WRKY29,and RBOHA may play a pivotal role in lateral root development in Asian cotton. | HU Daowu HE Shoupu SUN Gaofei JIA Yinhua GENG Xiaoli WANG Liru PAN Zhaoe CHEN Baojun LI Hongge ZUBAIR Iqbal WANG Xiaoyang ZHAO Zibo GE Yuting PANG Baoyin DU Xiongming | 2022 | Journal of Cotton Research2022，5，2： | 0 |
| 9 | Genomic divergence in cotton germplasm related to maturity and heterosis显示文摘Commercial varieties of upland cotton(Gossypium hirsutum)have undergone extensive breeding for agronomic traits,such as fiber quality,disease resistance,and yield.Cotton breeding programs have widely used Chinese upland cotton source germplasm(CUCSG)with excellent agronomic traits.A better understanding of the genetic diversity and genomic characteristics of these accessions could accelerate the identification of desirable alleles.Here,we analyzed 10,522 high-quality singlenucleotide polymorphisms(SNP)with the CottonSNP63 K microarray in 137 cotton accessions(including 12 hybrids of upland cotton).These data were used to investigate the genetic diversity,population structure,and genomic characteristics of each population and the contribution of these loci to heterosis.Three subgroups were identified,in agreement with their knownpedigrees,geographical distributions,and times since introduction.For each group,we identified lineagespecific genomic divergence regions,which potentially harbor key alleles that determine the characteristics of each group,such as early maturity-related loci.Investigation of the distribution of heterozygous loci,among 12 commercial cotton hybrids,revealed a potential role for these regions in heterosis.Our study provides insight into the population structure of upland cotton germplasm.Furthermore,the overlap between lineagespecific regions and heterozygous loci,in the high-yield hybrids,suggests a role for these regions in cotton heterosis. | Shoupu He Gaofei Sun Longyu Huang Daigang Yang Panhong Dai Dayun Zhou Yuzhen Wu Xiongfeng Ma Xiongming Du Shoujun Wei Jun Peng Meng Kuang | 2019 | Journal of Integrative Plant Biology2019，61，8： | 0 |
| 10 | Genetic diversity and population structure of Gossypium arboreum L. collected in China显示文摘Background: Gossypium arboreum is a diploid species cultivated in the Old World. It possesses favorable characters that are valuable for developing superior cotton cultivars.Method: A set of 197 Gossypium arboreum accessions were genotyped using 80 genome-wide SSR markers to establish patterns of the genetic diversity and population structure. These accessions were collected from three major G. arboreum growing areas in China. A total of 255 alleles across 80 markers were identified in the genetic diversity analysis.Results: Three subgroups were found using the population structure analysis, corresponding to the Yangtze River Valley, North China, and Southwest China zones of G.arboreum growing areas in China. Average genetic distance and Polymorphic information content value of G. arboreum population were 0.34 and 0.47, respectively, indicating high genetic diversity in the G. arboreum germplasm pool. The Phylogenetic analysis results concurred with the subgroups identified by Structure analysis with a few exceptions. Variations among and within three groups were observed to be 13.61% and 86.39%, respectively.Conclusion: The information regarding genetic diversity and population structure from this study is useful for genetic and genomic analysis and systematic utilization of economically important traits in G. arboreum. | JIA Yinhua PAN Zhaoe HE Shoupu GONG Wenfang GENG Xiaoli PANG Baoyin WANG Liru DU Xiongming | 2018 | Journal of Cotton Research2018，1，3： | 0 |
| 11 | Validating field regeneration capacity for selected accessions of Gossypium hirsutum using callus induction and regeneration capacity显示文摘Background Gossypium hirsutum undergoes rapid clonal propagation to regenerate a mature plant through tissue culture.However,the correlation between cotton leaf regeneration,callus induction,and regeneration ability was still obscure.In this research,cotton leaf regeneration level for 21 accessions in the field(new leaves)was observed after the first harvest,and a comparison between field regeneration level and callus induction with its regeneration capacity(new shoots and roots)for the same 21 accessions was carried out.Agronomic traits,including plant height,leaf area,fresh leaf weight,dry leaf weight,the number of flowers and bolls,and biochemical(proline content)and physiological(chlorophyll and carotenoid content)traits during the flowering stage of 21 upland cotton accessions,were investigated.Result A significant correlation between physiological parameters and callus induction was discovered.Callus induction and regeneration capacity of roots and shoots for hypocotyl,cotyledons,and shoot tip tissues were used to validate field leaf regeneration level after the first harvest.CCRI 24 showed significant leaf regeneration in the field and callus induction capacity through callus induction and regeneration.Conclusion We found a substantial relationship between field regeneration capability and callus induction with its regeneration capacity for the hypocotyl,cotyledons,and shoot tip.The results showed that ZS061,Lumian 378,Jimian 863,and ZS065 have the highest moisture retention capacity,while CCRI 24,Liaoyang Duomaomian,and Beizhe Gongshemian have the lowest moisture retention capacity.CCRI 24 has the highest leaf regeneration capacity in the field,while Beizhe Gongshemian has the lowest leaf regeneration capacity.All our result provides a clue for checking the regeneration capacity through leaf regeneration level in the field. | TAJO Sani Muhammad PAN Zhaoe HE Shoupu JIA Yinhua MAHMOOD Tahir NAZIR Mian Fasil HU Daowu WANG Liru SADAU Salisu Bello IBRAHIM Sani AUTA Umar GENG Xiaoli DU Xiongming | 2023 | Journal of Cotton Research2023，6，2： | 0 |
| 12 | Correlation analysis of stem hardness traits with fiber and yield-related traits in core collections of Gossypium hirsutum显示文摘Background:Stem hardness is one of the major influencing factors for plant architecture in upland cotton(Gossypium hirsutum L.).Evaluating hardness phenotypic traits is very important for the selection of elite lines for resistance to lodging in Gossypium hirsutum L.Cotton breeders are interested in using diverse genotypes to enhance fiber quality and high-yield.Few pieces of research for hardness and its relationship with fiber quality and yield were found.This study was designed to find the relationship of stem hardness traits with fiber quality and yield contributing traits of upland cotton.Results:Experiments were carried out to measure the bending,acupuncture,and compression properties of the stem from a collection of upland cotton genotypes,comprising 237 accessions.The results showed that the genotypic difference in stem hardness was highly significant among the genotypes,and the stem hardness traits(BL,BU,AL,AU,CL,and CU)have a positive association with fiber quality traits and yield-related traits.Statistical analyses of the results showed that in descriptive statistics result bending(BL,BU)has a maximum coefficient of variance,but fiber length and fiber strength have less coefficient of variance among the genotypes.Principal component analysis(PCA)trimmed quantitative characters into nine principal components.The first nine principal components(PC)with Eigenvalues>1 explained 86%of the variation among 237 accessions of cotton.Both 2017 and 2018,PCA results indicated that BL,BU,FL,FE,and LI contributed to their variability in PC1,and BU,AU,CU,FD,LP,and FWPB have shown their variability in PC2.Conclusion:We describe here the systematic study of the mechanism involved in the regulation of enhancing fiber quality and yield by stem bending strength,acupuncture,and compression properties of G.hirsutum. | RAZA Irum HU Daowu AHMAD Adeel LI Hongge HE Shoupu NAZIR Mian Faisal WANG Xiaoyang JIA Yinhua PAN Zhaoe ZHANG Peng YASIR Muhammad IQBAL Muhammad Shahid GENG Xiaoli WANG Liru PANG Baoyin DU Xiongming | 2021 | Journal of Cotton Research2021，4，1： | 0 |
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