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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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Suppressing a mitochondrial calcium uniporter activates the calcium signaling pathway and promotes cell elongation in cotton

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The Crop Journal 2024年第2期12卷 411-421页

作者： Yujia Duan Xiaoguang Shang Ruiping Tian Weixi Li Xiaohui Song Dayong Zhang Wangzhen Guo State Key Laboratory of Crop Genetics&germplasm Enhancement and Utilization Nanjing Agricultural UniversityNanjing 210095JiangsuChina Engineering Research Center of Ministry of Education for Cotton germplasm Enhancement and Application Nanjing Agricultural UniversityNanjing 210095JiangsuChina

Mitochondrial calcium uniporter(MCU)is a conserved calcium ion(Ca^(2+))transporter in the mitochondrial inner membrane of eukaryotic *** MCU proteins regulate Ca^(2+)flow and modulate plant cell development remain largely ***,we identified the gene GhMCU4 encoding a MCU protein that negatively regulates plant development and fiber elongation in cotton(Gossypium hirsutum).GhMCU4expressed constitutively in various tissues with the higher transcripts in elongating fiber *** of GhMCU4 in cotton significantly elevated the plant height and root *** calcium signaling pathway was significantly activated and calcium sensor genes,including Ca^(2+)dependent modulator of interactor of constitutively active ROP(GhCMI1),calmodulin like protein(GhCML46),calciumdependent protein kinases(GhCPKs),calcineurin B-like protein(GhCBLs),and CBL-interacting protein kinases(GhCIPKs),were dramatically upregulated in GhMCU4-silenced *** processes were preferentially enriched,and genes related to regulation of transcription were upregulated in GhMCU4-silenced *** contents of Ca^(2+)and H_(2)O_(2)were significantly increased in roots and leaves of GhMCU4-silenced *** length and Ca^(2+)and H_(2)O_(2)contents in fibers were significantly increased in GhMCU4-silenced *** study indicated that GhMCU4 plays a negative role in regulating cell elongation in cotton,thus expanding understanding in the role of MCU proteins in plant growth and development.

关键词： Calcium signaling Hydrogen peroxide Metabolic processed Gossypium hirsutum

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Gut microbiota affects the estrus return of sows by regulating the metabolism of sex steroid hormones

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Journal of Animal Science and Biotechnology 2024年第2期15卷 578-599页

作者： Min Liu Jia Zhang Yunyan Zhou Shuqi Xiong Mengqing Zhou Lin Wu Qin Liu Zhe Chen Hui Jiang Jiawen Yang Yuxin Liu Yaxiang Wang Congying Chen Lusheng Huang National Key Laboratory of Swine Genetic Improvement and germplasm Innovation Jiangxi Agricultural UniversityNanchang 330045China

Background Sex hormones play important roles in the estrus return of post-weaning *** studies have demonstrated a complex and bi-directional regulation between sex hormones and gut ***,the extent to which the gut microbiota affects estrus return of post-weaning sows is largely *** In this study,we first screened 207 fecal samples from well-phenotyped sows by 16S rRNA gene sequencing and identified significant associations between microbes and estrus return of post-weaning *** metagenomic sequencing data from 85 fecal samples,we identified 37 bacterial species that were significantly associated with estrus *** returning sows were characterized by increased abundances of *** and *** and decreased abundances of ***,***,and *** changes in gut microbial composition significantly altered the functional capacity of steroid hormone biosynthesis in the gut *** results were confirmed in a validation *** changes in sex steroid hormones and related compounds were found between normal and non-return sows via metabolome *** integrated analysis of differential bacterial species,metagenome,and fecal metabolome provided evidence that normal return-associated bacterial species *** and Prevotella *** in the degradation of pregnenolone,progesterone,and testosterone,thereby promoting estrogen ***,the microbial metabolites related to sow energy and nutrient supply or metabolic disorders also showed relationships with sow estrus *** An integrated analysis of differentially abundant bacterial species,metagenome,and fecal metabolome revealed the involvement of *** and Prevotella *** sow estrus *** findings provide deep insight into the role of gut microbiota in the estrus return of post-weaning sows and the complex cross-talk between gut microbiota and sex hormones,suggesting that the manipulatio

关键词： Estrus return Fecal metabolome Gut microbiota Metagenomics Sex steroid hormones Sow

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Telomere-to-telomere genome assemblies of cultivated and wild soybean provide insights into evolution and domestication under structural variation

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Plant Communications 2024年第8期5卷 92-95页

作者： Kai-Hua Jia Xiaoyan Zhang Lei-Lei Li Tian-Le Shi Dan Liu Yongyi Yang Yunzhe Cong Runfang Li Yanyan Pu Yongchao Gong Xue Chen Yu-Jun Si Rumei Tian Zhenya Qian Hanfeng Ding Nana Li National Saline-Alkali Tolerant Crop germplasm Resources Nursery(Dongying) Shandong International Joint Laboratory of Agricultural Germplasm Resources InnovationInstitute of Crop Germplasm ResourcesShandong Academy of Agricultural SciencesJinan 250100China College of Biological Sciences and Technology Beijing Forestry UniversityBeijing 100083China Shandong Provincial Center of Forest and Grass germplasm Resources Jinan 250102China Weifang Academy of Agricultural Sciences Weifang 261017China Shandong Huaya Agricultural Technology Co. Ltd.Jining 272400China

Dear Editor,Soybean(Glycine max)is a critical crop worldwide,renowned as a major source of edible oil and *** was domesticated approximately 5000-9000 years ago in China,between latitudes 32°N and 40°N,from its wild progenitor,Glycine *** recent years,numerous genome assemblies for both cultivated and wild soybeans have been published,with cultivated soybean genomes even achieving telomere-to-telomere(T2T)completeness(Zhang et al.,2023a,2023b;Wang et al.,2023;Huang et al.,2024).

关键词： soybean insight evolution

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Pig H3K4me3,H3K27ac,and gene expression profiles reveal reproductive tissue-specific activity of transposable elements

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Zoological Research 2024年第1期45卷 138-151页

作者： Tao Jiang Zhi-Min Zhou Zi-Qi Ling Qing Zhang Zhong-Zi Wu Jia-Wen Yang Si-Yu Yang Bin Yang Lu-Sheng Huang National Key Laboratory of Pig Genetic Improvement and germplasm Innovation Jiangxi Agricultural UniversityNanchangJiangxi 330045China

Regulatory sequences and transposable elements(TEs)account for a large proportion of the genomic sequences of species;however,their roles in gene transcription,especially tissue-specific expression,remain largely *** serve as an excellent animal model for studying genomic sequence biology due to the extensive diversity among their wild and domesticated ***,we conducted an integrated analysis using H3K27ac ChIP-seq,H3K4me3 ChIP-seq,and RNA-seq data from 10 different tissues of seven fetuses and eight closely related adult *** aimed to annotate the regulatory elements and TEs to elucidate their associations with histone modifications and mRNA expression across different tissues and developmental *** on correlation analysis between mRNA expression and H3K27ac and H3K4me3 peak activity,results indicated that H3K27ac exhibited stronger associations with gene expression than ***,1.45%of TEs overlapped with either the H3K27ac or H3K4me3 peaks,with the majority displaying tissue-specific ***,a TE subfamily(LTR4C_SS),containing binding motifs for SIX1 and SIX4,showed specific enrichment in the H3K27ac peaks of the adult and fetal ***-seq analysis also revealed widespread expression of TEs in the exons or promoters of genes,including 4688 TE-containing transcripts with distinct development stage-specific and tissue-specific *** note,1967 TE-containing transcripts were enriched in the *** identified a long terminal repeat(LTR),MLT1F1,acting as a testis-specific alternative promoter in SRPK2(a cell cycle-related protein kinase)in our pig *** element was also conserved in humans and mice,suggesting either an ancient integration of TEs in genes specifically expressed in the testes or parallel evolutionary ***,our findings demonstrate that TEs are deeply embedded in the genome and exhibit important tissue-specific biological functions,particularly in the reproductive

关键词： Transposable elements Porcine Histone modification Alternative promoter TE-containing transcript

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E3 ubiquitin ligase PbrATL18 is a positive factor in pear resistance to drought and Colletotrichum fructicola infection

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Horticultural Plant Journal 2024年第3期10卷 698-712页

作者： Likun Lin Qiming Chen Kaili Yuan Caihua Xing Qinghai Qiao Xiaosan Huang Shaoling Zhang State Key Laboratory of Crop Genetics and germplasm Enhancement/College of Horticulture Nanjing Agricultural UniversityNanjingJiangsu210095China

The Arabidopsis Toxicos en Levadura(ATL)protein is a subfamily of the E3 ubiquitin ligases,which exists widely in plants and is extensively involved in plant growth and *** the ATL family has been identified in other species,such as Arabidopsis,Oryza sativa,and grapevine,few reports on pear ATL gene families have been *** this study,92 PbrATL genes were identified and analyzed from the Pyrus breschneideri *** analysis and phylogenetic tree generation divided them into nine subgroups,and chromosome localization analysis showed that the 92 PbrATL genes were distributed in 16 of 17 pear *** data and quantitative real-time polymerase chain reaction(qRT-PCR)experiments demonstrated that PbrATL18,PbrATL41,and PbrATL88 were involved in both pear drought resistance and Colletotrichum fructicola *** addition,Arabidopsis thaliana overexpressing PbrATL18 showed greater resistance to drought stress than the wild type(WT),and PbrATL18-silenced pear seedlings showed greater sensitivity to drought and *** infection than the ***18 regulated plant resistance by regulating chitinase(CHI),phenylalanine ammonia-lyase(PAL),polyphenol oxidase(PPO),catalase(CAT),peroxidase(POD),and superoxide dismutase(SOD)*** study provided a reference for further exploring the functions of the PbrATL gene in drought resistance and *** infection.

关键词： Pear Colletotrichum fructicola Arabidopsis Toxicos en Levadura(ATL) Drought stress

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Identification of key genes regulating the synthesis of quercetin derivatives in Rosa roxburghii through integrated transcriptomics and metabolomics

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Journal of Integrative Agriculture 2024年第3期23卷 876-887页

作者： Liyao Su Min Wu Tian Zhang Yan Zhong Zongming(Max) Cheng State Key Laboratory of Crop Genetics and germplasm Enhancement College of HorticultureNanjing Agricultural UniversityNanjing210095China

Rosa roxburghii fruit is rich in flavonoids, but little is known about their biosynthetic pathways. In this study, we employed transcriptomics and metabolomics to study changes related to the flavonoids at five different stages of R. roxburghii fruit development. Flavonoids and the genes related to their biosynthesis were found to undergo significant changes in abundance across different developmental stages, and numerous quercetin derivatives were identified. We found three gene expression modules that were significantly associated with the abundances of the different flavonoids in R. roxburghii and identified three structural UDP-glycosyltransferase genes directly involved in the synthesis of quercetin derivatives within these modules. In addition, we found that RrBEH4, RrLBD1 and RrPIF8could significantly increase the expression of downstream quercetin derivative biosynthesis genes. Taken together,these results provide new insights into the metabolism of flavonoids and the accumulation of quercetin derivatives in R. roxburghii.

关键词： Rosa roxburghii quercetin derivatives weighted gene co-expression network analysis transcription factor transcriptome metabolome

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Abiotic stress treatment reveals expansin like A gene OfEXLA1 improving salt and drought tolerance of Osmanthus fragrans by responding to abscisic acid

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Horticultural Plant Journal 2024年第2期10卷 573-585页

作者： Bin Dong Qianqian Wang Dan Zhou Yiguang Wang Yunfeng Miao Shiwei Zhong Qiu Fang Liyuan Yang Zhen Xiao Hongbo Zhao School of Landscape Architecture Zhejiang Agriculture and Forestry UniversityHangzhouZhejiang 311300China Zhejiang Provincial Key Laboratory of germplasm Innovation and Utilization for Garden Plants HangzhouZhejiang 311300China Key Laboratory of National Forestry and Grassland Administration on germplasm Innovation and Utilization for Southern Garden Plants HangzhouZhejiang 311300China

Sweet osmanthus(Osmanthus fragrans) is a having general approval aromatic tree in China that is widely applied to landscaping and gardening. However, the evergreen tree adaptability is limited by many environmental stresses. Currently, limited information is available regarding the genetic analysis and functional identification of expansin genes in response to abiotic stress in sweet osmanthus. In this study, a total of 29 expansin genes were identified and divided into four groups by genome-wide analysis from the sweet osmanthus genome. Transcriptome and quantitative Real-time PCR analysis showed that the cell wall-localized protein expansin-like A(OfEXLA1) gene was significantly induced by salt and drought treatment. Histochemical GUS staining of transgenic Arabidopsis lines in which GUS activity was driven with the OfEXLA1 promoter, GUS activity was significantly induced by salt, drought, and exogenous abscisic acid(ABA). In yeast, we found OfEXLA1overexpression significantly improved the population of cells compared with wild-type strains after NaCl and polyethylene glycol(PEG)treatment. Additionally, OfEXLA1 overexpression not only promoted plant growth, but also improved the salt and drought tolerance in Arabidopsis. To gain insight into the role of ABA signaling in the regulation of OfEXLA1 improving abiotic tolerance in sweet osmanthus, four differentially expressed ABA Insensitive 5(ABI5)-like genes(OfABL4, OfABL5, OfABL7, and OfABL8) were identified from transcriptome, and dualluciferase(dual-LUC) and yeast one hybrid(Y1H) assay showed that OfABL4 and OfABL5 might bind to OfEXLA1 promoter to accumulate the OfEXLA1 expression by responding to ABA signaling to improve abiotic tolerance in sweet osmanthus. These results provide the information for understanding the molecular functions of expansin-like A gene and molecular breeding of sweet osmanthus in future.

关键词： Osmanthus fragrans Abiotic tolerance Expansin Abscisic acid

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Single-cell profiling of the pig cecum at various developmental stages

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Zoological Research 2024年第1期45卷 55-68页

作者： Yan-Yuan Xiao Qing Zhang Fei Huang Lin Rao Tian-Xiong Yao Si-Yu Yang Lei Xie Xiao-Xiao Zou Li-Ping Cai Jia-Wen Yang Bin Yang Lu-Sheng Huang National Key Laboratory for Swine Genetic Improvement and germplasm Innovation Ministry of Science and Technology of ChinaJiangxi Agricultural UniversityNanchangJiangxi 330045China

The gastrointestinal tract is essential for food digestion,nutrient absorption,waste elimination,and microbial ***-cell transcriptome profiling of the intestinal tract has greatly enriched our understanding of cellular diversity,functional heterogeneity,and their importance in intestinal tract development and *** such profiling has been extensively conducted in humans and mice,the single-cell gene expression landscape of the pig cecum remains ***,single-cell RNA sequencing was performed on 45572 cells obtained from seven cecal samples in pigs at four different developmental stages(days(D)30,42,150,and 730).Analysis revealed 12 major cell types and 38 subtypes,as well as their distinctive genes,transcription factors,and regulons,many of which were conserved in *** increase in the relative proportions of CD8^(+)T and Granzyme A(low expression)natural killer T cells(GZMA^(low)NKT)cells and a decrease in the relative proportions of epithelial stem cells,Tregs,RHEX^(+)T cells,and plasmacytoid dendritic cells(pDCs)were noted across the developmental ***,the post-weaning period exhibited an up-regulation in mitochondrial genes,COX2 and ND2,as well as genes involved in immune activation in multiple cell ***-cell crosstalk analysis indicated that IBP6^(+)fibroblasts were the main signal senders at D30,whereas IBP6^(−)fibroblasts assumed this role at the other *** cells established interactions with epithelial cells and IBP6^(+)fibroblasts in the D730 cecum through mediation of GZMA-F2RL1/F2RL2 *** study provides valuable insights into cellular heterogeneity and function in the pig cecum at different development stages.

关键词： Single-cell RNA-seq Cecum Bama Xiang pigs Various developmental stages Cellular heterogeneity

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Identification of S-RNase genotype and analysis of its origin and evolutionary patterns in Malus plants

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Journal of Integrative Agriculture 2024年第4期23卷 1205-1221页

作者： Zhao Liu Yuan Gao Kun Wang Jianrong Feng Simiao Sun Xiang Lu Lin Wang Wen Tian Guangyi Wang Zichen Li Qingshan Li Lianwen Li Dajiang Wang Research Institute of Pomology Chinese Academy of Agricultural Sciences/Key Laboratory of Horticultural Crops Germplasm Resources UtilizationMinistry of Agriculture and Rural AffairsXingcheng 125100China College of Agriculture Shihezi University/Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization of Xinjiang Production and Construction CorpsShihezi 832000China

Identification of the S genotype of Malus plants will greatly promote the discovery of new genes,the cultivation and production of apple,the breeding of new varieties,and the origin and evolution of self-incompatibility in Malus *** this experiment,88 Malus germplasm resources,such as Aihuahong,Xishuhaitang,and Reguanzi,were used as *** gene-specific primer combinations were used in the genotype *** amplification using leaf DNA produced a single S-RNase gene fragment in all *** results revealed that 70 of the identified materials obtained a complete S-RNase genotype,while only one S-RNase gene was found in 18 of *** homology comparison and analysis,13 S-RNase genotypes were obtained:S_(1)S_(2)(Aihuahong,etc.),S_(1)S_(28)(Xixian Haitang,etc.),S_(1)S_(51)(Hebei Pingdinghaitang),S_(1)S_(3)(Xiangyangcun Daguo,etc.),S_(2)S_(3)(Zhaiyehaitang,etc.),S_(3)S_(51)(Xishan 1),S_(3)S_(28)(Huangselihaerde,etc.),S_(2)S_(28)(Honghaitang,etc.),S_(4)S_(28)(Bo 11),S_(7)S_(28)(Jiuquan Shaguo),S_(10)S_e(Dongchengguan 13),S_(10)S_(21)(Dongxiangjiao)and S_(3)S_(51)(Xiongyue Haitang).Simultaneously,the frequency of the S gene in the tested materials was *** findings revealed that different S genes had varying frequencies in Malus resources,as well as varying frequencies between intraspecific and interspecific.S_(3) had the highest frequency of 68.18%,followed by S_(1)(42.04%).In addition,the phylogenetic tree and origin evolution analysis revealed that the S gene differentiation was completed prior to the formation of various apple species,that cultivated species also evolved new S genes,and that the S_(50) gene is the oldest S allele in Malus *** S_(1),S_(29),and S_(33) genes in apple-cultivated species,on the other hand,may have originated in ***,***,and ***,*** addition to ***,*** and *** may have also played a role in the origin and evolution of some Chine

关键词： Malus S-RNase genotype self-incompatibility origin and evolution

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