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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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Genetic dissection and origin of pleiotropic loci underlying multilevel fiber quality traits in upland cotton(Gossypium hirsutum L.)

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Journal of Integrative Agriculture 2024年第10期23卷 3250-3263页

作者： Hongge Li Shurong Tang Zhen Peng Guoyong Fu Yinhua Jia Shoujun Wei Baojun Chen Muhammad Shahid Iqbal Shoupu He Xiongming Du Zhengzhou research Base State Key Laboratory of Cotton Bio-breeding and Integrated Utilization/School of Agricultural SciencesZhengzhou UniversityZhengzhou 450001China state key laboratory of cotton Bio-breeding and Integrated Utilization/institute of cotton research Chinese Academy of Agricultural SciencesAnyang 455000China

cotton fiber quality is a persistent concern that determines planting benefits and the quality of finished textile ***,the limitations of measurement instruments have hindered the accurate evaluation of some important fiber characteristics such as fiber maturity,fineness,and neps,which in turn has impeded the genetic improvement and industrial utilization of cotton ***,12 single fiber quality traits were measured using Advanced Fiber Information System(AFIS)equipment among 383 accessions of upland cotton(Gossypium hirsutum L.).In addition,eight conventional fiber quality traits were assessed by the High Volume Instrument(HVI)***-wide association study(GWAS),linkage disequilibrium(LD)block genotyping and functional identification were conducted sequentially to uncover the associated elite loci and candidate genes of fiber quality *** a result,the previously reported pleiotropic locus FL_D11 regulating fiber length-related traits was identified in this *** importantly,three novel pleiotropic loci(FM_A03,FF_A05,and FN_A07)regulating fiber maturity,fineness and neps,respectively,were detected based on AFIS *** highly promising candidate genes were screened out by integrating RNA-seq and qRT-PCR analyses,including the reported GhKRP6 for fiber length,the newly identified GhMAP8 for maturity and GhDFR for *** origin and evolutionary analysis of pleiotropic loci indicated that the selection pressure on FL_D11,FM_A03 and FF_A05 increased as the breeding period approached the present and the origins of FM_A03 and FF_A05 were traced back to cotton *** findings reveal the genetic basis underlying fiber quality and provide insight into the genetic improvement and textile utilization of fiber in ***.

关键词： upland cotton single fiber quality pleiotropic loci candidate genes locus origin

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Identification of an Aux/IAA regulator for flesh firmness using combined GWAS and bulked segregant RNA-Seq analysis in watermelon

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Horticultural Plant Journal 2024年第5期10卷 1198-1213页

作者： Muhammad Anees Hongju Zhu Muhammad Jawad Umer Chengsheng Gong Pingli Yuan Xuqiang Lu Nan He Mohamed Omar Kaseb Dongdong Yang Yong Zhao Wenge Liu Henan Joint International research laboratory of South Asian Fruits and Cucurbits Zhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouHenan 450009China Henan key laboratory of Fruit and Cucurbit biology Zhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouHenan 450009China state key laboratory of cotton biology Institute of Cotton ResearchChinese Academy of Agricultural Science(ICRCAAS)AnyangHenan 455000China National key laboratory for Germplasm Innovation&Utilization of Horticultural Crops Zhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouHenan 450009China

Watermelon is a highly cultivated fruit crop renowned for its quality properties of fruit *** various quality factors,fruit flesh firmness is a crucial quality parameter influencing the fruit texture,shelf life and its commercial *** auxin/indole-3-acetic acid(Aux/IAA)plays a significant role in fruit development and ripening of non-climacteric ***,the regulatory mechanism of Aux/IAA in controlling fruit flesh firmness and ripening in watermelon remains *** this study,we employed an integrative approach combining genome-wide association study(GWAS)and bulked segregant RNA-Seq analysis(BSR-Seq)to identify an overlapping candidate region between 12776310 and 12968331 bp on chromosome 6,underlying an auxin-responsive gene(Aux/IAA)associated with flesh firmness in *** analysis,followed by real-time quantitative reverse transcription PCR(qRT-PCR),confirmed that the expression of Aux/IAA was consistently higher in fruits with high flesh *** sequence alignment revealed a single base mutation in the coding region of Aux/***,the concomitant Kompetitive/Competitive allele-specific PCR(KASP)genotyping data sets for F2 population and germplasm accessions identified Aux/IAA as a strong candidate gene associated with flesh ***/IAA was enriched in the plant hormone signal transduction pathway,involving cell enlargement and leading to low flesh *** determined the higher accumulation of abscisic acid(ABA)in fruits with low flesh firmness than hard ***,overexpression of Aux/IAA induced higher flesh firmness with an increased number of fruit flesh cells while reducing ABA content and flesh cell ***,the allelic variation in Aux/IAA for soft flesh firmness was found to exist in Citrullus mucosospermus and gradually fixed into Citrullus lanatus during domestication,indicating that soft flesh firmness was a domesticated *** findings significantly enhanced our unders

关键词： Watermelon Flesh firmness GWAS BSR-Seq KASP marker analysis Transient overexpression

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EPSPS regulates cell elongation by disrupting the balance of lignin and flavonoid biosynthesis in cotton

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Journal of Integrative Agriculture 2024年第10期23卷 3437-3456页

作者： Qingdi Yan Wei Hu Chenxu Gao Lan Yang Jiaxian Yang Renju Liu Masum Billah Yongjun Lin Ji Liu Pengfei Miao Zhaoen Yang Fuguang Li Wenqiang Qin state key laboratory of cotton Bio‑breeding and Integrated Utilization/institute of cotton research Chinese Academy ofAgricultural SciencesAnyang 455000China National key laboratory of Crop Genetic Improvement and National Center of Plant Gene research Huazhong AgriculturalUniversityWuhan 430070China state key laboratory of cotton Bio-breeding and Integrated Utilization/Zhengzhou University Zhengzhou 450066China National Nanfan research institute(Sanya) Chinese Academy of Agricultural SciencesSanya 572025China

EPSPS is a key gene in the shikimic acid synthesis pathway that has been widely used in breeding crops with herbicide ***,its role in regulating cell elongation is poorly *** the overexpression of EPSPS genes,we generated lines resistant to glyphosate that exhibit an unexpected dwarf phenotype.A representative line,DHR1,exhibits a stable dwarf phenotype throughout its entire growth *** for plant height,the other agronomic traits of DHR1 are similar to its transgenic explants *** section observations showed that DHR1 internodes are shortened due to reduced elongation and division of the internode *** hormones confirmed that DHR1 is not a classical brassinolide(BR)-or gibberellin(GA)-related dwarfing *** analysis and fine mapping confirmed that the EPSPS gene is the causal gene for dwarfism,and the phenotype can be inherited in different *** and metabolome analyses showed that genes associated with the phenylpropanoid synthesis pathway are enriched in DHR1 compared with *** metabolites are enriched in DHR1,whereas lignin metabolites are *** enhancement of flavonoids likely results in differential expression of auxin signal pathway genes and alters the auxin response,subsequently affecting cell *** study provides a new strategy for generating dwarfs and will accelerate advancements in light simplification in the cultivation and mechanized harvesting of cotton.

关键词： EPSPS cotton T-DNA dwarfism herbicide resistance

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Pectin methylesterase inhibitors GhPMEI53 and AtPMEI19 improve seed germination by modulating cell wall plasticity in cotton and Arabidopsis

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Journal of Integrative Agriculture 2024年第10期23卷 3487-3505页

作者： Yayue Pei Yakong Wang Zhenzhen Wei Ji Liu Yonghui Li Shuya Ma Ye Wang Fuguang Li Jun Peng Zhi Wang Zhengzhou research Base State Key Laboratory of Cotton Bio-breeding and Integrated UtilizationZhengzhou UniversityZhengzhou 450001China National Nanfan research institute(Sanya) Chinese Academy of Agricultural SciencesSanya 572024China National key laboratory of cotton Bio-breeding and Integrated Utilization/institute of cotton research Chinese Academy ofAgricultural SciencesAnyang 455000China

The germination process of seeds is influenced by the interplay between two opposing factors,pectin methylesterase(PME)and pectin methylesterase inhibitor(PMEI),which collectively regulate patterns of pectin *** the recognized importance of pectin methylesterification in seed germination,the specific mechanisms that govern this process remain *** this study,we demonstrated that the overexpression of GhPMEI53is associated with a decrease in PME activity and an increase in pectin *** leads to seed cell wall softening,which positively regulates cotton seed ***19,the homologue in Arabidopsis thaliana,plays a similar role in seed germination to GhPMEI53,indicating a conserved function and mechanism of PMEI in seed germination *** studies revealed that GhPMEI53 and AtPMEI19 directly contribute to promoting radicle protrusion and seed germination by inducing cell wall softening and reducing mechanical ***,the pathways of abscicic acid(ABA)and gibberellin(GA)in the transgenic materials showed significant changes,suggesting that GhPMEI53/AtPMEI19-mediated pectin methylesterification serves as a regulatory signal for the related phytohormones involved in seed *** summary,GhPMEI53 and its homologs alter the mechanical properties of cell walls,which influence the mechanical resistance of the endosperm or ***,they impact cellular phytohormone pathways(e.g.,ABA and GA)to regulate seed *** findings enhance our understanding of pectin methylesterification in cellular morphological dynamics and signaling transduction,and contribute to a more comprehensive understanding of the PME/PMEI gene superfamily in plants.

关键词： cotton seed germination cell wall pectin demethylesterification PMEI ABA

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ORPA:a fast and efficient phylogenetic analysis method for constructing genome-wide alignments of organelle genomes

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Journal of Genetics and Genomics 2024年第3期51卷 352-358页

作者： Guiqi Bi Xinxin Luan Jianbin Yan Shenzhen Branch Guangdong Laboratory of Lingnan Modern AgricultureKey Laboratory of Synthetic BiologyMinistry of Agriculture and Rural AffairsAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenGuangdong 518124China Zhengzhou research Base State Key Laboratory of Cotton BiologySchool of Agricultural SciencesZhengzhou UniversityZhengzhouHenan 450001China

Creating a multi-gene alignment matrix for phylogenetic analysis using organelle genomes involves aligning single-gene datasets manually,a process that can be time-consuming and prone to *** HomBlocks pipeline has been created to eliminate the inaccuracies arising from manual *** processing of a large number of sequences,however,remains a time-consuming *** conquer this challenge,we develop a speedy and efficient method called Organelle Genomes for Phylogenetic Analysis(ORPA).ORPA can quickly generate multiple sequence alignments for whole-genome comparisons by parsing the result files of NCBI BLAST,completing the task just in 1 *** increasing data volume,the efficiency of ORPA is even more pronounced,over 300 times faster than HomBlocks in aligning 60 high-plant chloroplast *** phylogenetic tree outputs from ORPA are equivalent to HomBlocks,indicating its outstanding *** to its speed and accuracy,ORPA can identify species-level evolutionary conflicts,providing valuable insights into evolutionary cognition.

关键词： Ultrafast alignment Organelle phylogenomics Phylogenomic conflict Efficient pipeline Multiple sequence alignment pipeline

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Small particles,big effects:How nanoparticles can enhance plant growth in favorable and harsh conditions

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Journal of Integrative Plant biology 2024年第7期66卷 1274-1294页

作者： Jie Wang Honghong Wu Yichao Wang Wuwei Ye Xiangpei Kong Zujun Yin Zhengzhou research Base State Key Laboratory of Cotton Bio‐breeding and Integrated UtilizationSchool of Agricultural SciencesZhengzhou UniversityZhengzhou 450001China state key laboratory of cotton Bio‐breeding and Integrated Utilization Institute of Cotton ResearchChinese Academy of Agricultural SciencesAnyang 455000China National key laboratory of Crop Genetic Improvement Huazhong Agricultural UniversityWuhan 430070China School of Engineering Design and Built EnvironmentWestern Sydney UniversityPenrith NSW 2751Australia Western Agricultural research Center Chinese Academy of Agricultural SciencesChangji 831100China The key laboratory of Plant Development and Environmental Adaptation biology Ministry of EducationCollege of Life SciencesShandong UniversityQingdao 266237China

By 2050,the global population is projected to reach 9 billion,underscoring the imperative for innovative solutions to increase grain yield and enhance food *** has emerged as a powerful tool,providing unique solutions to this ***(NPs)can improve plant growth and nutrition under normal conditions through their high surface-to-volume ratio and unique physical and chemical ***,they can be used to monitor crop health status and augment plant resilience against abiotic stresses(such as salinity,drought,heavy metals,and extreme temperatures)that endanger global *** of NPs can enhance stress tolerance mechanisms in plants,minimizing potential yield losses and underscoring the potential of NPs to raise crop yield and *** review highlights the need for a comprehensive exploration of the environmental implications and safety of nanomaterials and provides valuable guidelines for researchers,policymakers,and agricultural *** thoughtful stewardship,nanotechnology holds immense promise in shaping environmentally sustainable agriculture amid escalating environmental challenges.

关键词： abiotic stress agricultural defense system nano-particles nanotechnology oxidative stress reactive oxygen species toxicity

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Identification of candidate genes for early-maturity traits by combining BSA-seq and QTL mapping in upland cotton(Gossypium hirsutum L.)

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Journal of Integrative Agriculture 2024年第10期23卷 3472-3486页

作者： Liang Ma Tingli Hu Meng Kang Xiaokang Fu Pengyun Chen Fei Wei Hongliang Jian Xiaoyan Lü Meng Zhang Yonglin Yang state key laboratory of cotton Bio-breeding and Integrated Utilization/institute of cotton research Chinese Academy ofAgricultural SciencesAnyang 455000China School of Agriculture Henan Institute of Science and TechnologyXinxiang 453003China Shihezi Academy of Agricultural Sciences Shihezi 832099China

cotton breeding for the development of early-maturing varieties is an effective way to improve multiple cropping indexes and alleviate the conflict between grains and cotton in the cultivated fields in *** the present study,we aimed to identify upland cotton quantitative trait loci(QTLs)and candidate genes related to early-maturity traits,including whole growth period(WGP),flowering timing(FT),node of the first fruiting branch(NFFB),height of the node of the first fruiting branch(HNFFB),and plant height(PH).An early-maturing variety,CCRI50,and a latematuring variety,Guoxinmian 11,were crossed to obtain biparental *** populations were used to map QTLs for the early-maturity traits for two years(2020 and 2021).With BSA-seq analysis based on the data of population 2020,the candidate regions related to early maturity were found to be located on chromosome *** then developed 22 polymorphic insertions or deletions(InDel)markers to further narrow down the candidate regions,resulting in the detection of five and four QTLs in the 2020 and 2021 populations,*** to the results of QTL mapping,two candidate regions(InDel_G286-InDel_G144 and InDel_G24-InDel_G43)were *** these regions,three genes(GH_D03G0451,GH_D03G0649,and GH_D03G1180)have nonsynonymous mutations in their exons and one gene(GH_D03G0450)has SNP variations in the upstream sequence between CCRI50 and Guoxinmian *** four genes also showed dominant expression in the floral *** expression levels of GH_D03G0451,GH_D03G0649 and GH_D03G1180 were significantly higher in CCRI50 than in Guoxinmian 11 during the bud differentiation stages,while GH_D03G0450 showed the opposite *** functional verification of GH_D03G0451 indicated that the GH_D03G0451-silenced plants showed a delay in the flowering *** results suggest that these are the candidate genes for cotton early maturity,and they may be used for breeding early-maturity cotton varieties.

关键词： cotton genomics early-maturity traits BSA-seq QTL mapping molecular breeding

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Straw return increases crop production by improving soil organic carbon sequestration and soil aggregation in a long-term wheat-cotton cropping system

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Journal of Integrative Agriculture 2024年第2期23卷 669-679页

作者： Changqin Yang Xiaojing Wang Jianan Li Guowei Zhang Hongmei Shu Wei Hu Huanyong Han Ruixian Liu Zichun Guo institute of Industrial Crops Jiangsu Academy of Agricultural Sciences/Key Laboratory of Cotton and RapeseedMinistry of Agriculture and Rural AffairsNanjing 210014China College of Life Sciences and Food Engineering Huaiyin Institute of TechnologyHuai’an 223003China College of Agriculture Nanjing Agricultural UniversityNanjing 210095China cotton research institute Xinjiang Academy of Agricultural and Reclamation ScienceShihezi 832000China institute of Soil Science Chinese Academy of Sciences/State Key Laboratory of Soil and Sustainable AgricultureNanjing 210008China

Straw return is a promising strategy for managing soil organic carbon(SOC)and improving yield ***,the optimal straw return strategy for sustainable crop production in the wheat(Triticum aestivum L.)-cotton(Gossypium hirsutum L.)cropping system remains *** objective of this study was to quantify the long-term(10 years)impact of carbon(C)input on SOC sequestration,soil aggregation and crop yields in a wheat-cotton cropping system in the Yangtze River Valley,*** treatments were arranged with a single-factor randomized design as follows:no straw return(Control),return of wheat straw only(Wt),return of cotton straw only(Ct),return of 50%wheat and 50%cotton straw(Wh-Ch)and return of 100%wheat and 100%cotton straw(Wt-Ct).In comparison to the Control,the SOC content increased by 8.4 to 20.2%under straw return.A significant linear positive correlation between SOC sequestration and C input(1.42-7.19 Mg ha^(−1)yr^(−1))(P2 and 1-2 mm at the 0-20 cm soil depth were also significantly elevated under straw return,with the greatest increase of the aggregate stability in the Wt-Ct treatment(28.1%).The average wheat yields increased by 12.4-36.0%and cotton yields increased by 29.4-73.7%,and significantly linear positive correlations were also detected between C input and the yields of wheat and *** average sustainable yield index(SYI)reached a maximum value of 0.69 when the C input was 7.08 Mg ha^(−1)yr^(−1),which was close to the maximum value(SYI of 0.69,C input of 7.19 Mg ha^(−1)yr^(-1))in the Wt-Ct ***,the return of both wheat and cotton straw was the best strategy for improving SOC sequestration,soil aggregation,yields and their sustainability in the wheat-cotton rotation system.

关键词： straw return crop yields SOC soil aggregates wheat-cotton cropping system

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Mining elite loci and candidate genes for root morphology-related traits at the seedling stage by genome-wide association studies in upland cotton(Gossypium hirsutum L.)

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Journal of Integrative Agriculture 2024年第10期23卷 3406-3418页

作者： Huaxiang Wu Xiaohui Song Muhammad Waqas-Amjid Chuan Chen Dayong Zhang Wangzhen Guo state key laboratory of Crop Genetics&Germplasm Enhancement and Utilization/Engineering research Center of cotton Germplasm Enhancement and Application Ministry of Education/Nanjing Agricultural UniversityNanjing 210095China

Root system architecture plays an essential role in water and nutrient acquisition in plants,and it is significantly involved in plant adaptations to various environmental *** this study,a panel of 242 cotton accessions was collected to investigate six root morphological traits at the seedling stage,including main root length(MRL),root fresh weight(RFW),total root length(TRL),root surface area(RSA),root volume(RV),and root average diameter(AvgD).The correlation analysis of the six root morphological traits revealed strong positive correlations of TRL with RSA,as well as RV with RSA and AvgD,whereas a significant negative correlation was found between TRL and ***,a genome-wide association study(GWAS)was performed using the root phenotypic and genotypic data reported previously for the 242 accessions using 56,010 single nucleotide polymorphisms(SNPs)from the cottonSNP80K array.A total of 41 quantitative trait loci(QTLs)were identified,including nine for MRL,six for RFW,nine for TRL,12 for RSA,12 for RV and two for *** them,eight QTLs were repeatedly detected in two or more *** these results with a transcriptome analysis,we identified 17 candidate genes with high transcript values of transcripts per million(TPM)≥30 in the ***,we functionally verified the candidate gene GH_D05G2106,which encodes a WPP domain protein 2in root development.A virus-induced gene silencing(VIGS)assay showed that knocking down GH_D05G2106significantly inhibited root development in cotton,indicating its positive role in root system architecture ***,these results provide a theoretical basis and candidate genes for future studies on cotton root developmental biology and root-related cotton breeding.

关键词： cotton root-morphology traits quantitative trait loci candidate genes GWAS

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